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60c74c6f337d6ce608e27c56 | 10.26434/chemrxiv.12479321.v1 | A Simple Approach to Achieve Organic Radicals with Unusual Solid-State Emission and Extraordinary Stability | Herein, we report a simple approach to generate stable<br />luminescent radicals in the presence of gentle UV irradiation. The newly generated radical<br />species are capable of emitting unusual red light with a maximum fluorescence quantum<br />efficiency of 4.6% at ambient conditions in the solid state. Additionally, the luminescent<br />radicals show extraordinary stability with more than one-year life-span at ambient conditions.<br />X-ray diffraction study combined with photophysical and computational analyses reveal that<br />the unique molecular symmetry breaking in the crystalline state lead to the unusual formation<br />and stabilization of radical ion pairs via the photo-induced electron transfer (PET) process. Such<br />results represent the first time to achieve stable emissive radicals in the solid state at ambient<br />conditions via in-situ PET process.
<br /> | Xueqian ZHAO; zheng zhao; Junyi Gong; Chao Ma,; Parvej Alam; Yanpei wang; Jing Guo; Zebing Zeng; Zikai He; Herman H.-Y. Sung; ian duncan williams; Kam Sing Wong; Jacky W. Y. Lam; Ben Zhong Tang | Magnetic Materials; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c6f337d6ce608e27c56/original/a-simple-approach-to-achieve-organic-radicals-with-unusual-solid-state-emission-and-extraordinary-stability.pdf |
657889d97acf130c32132a94 | 10.26434/chemrxiv-2023-rql38 | A New Nonreactive Force Field for Accurate Molecular Dynamics Simulations of TATB at Extreme Conditions | Insensitive high explosives based on TATB (1,3,5-triamino-2,4,6-trinitrobenzene) are needed in applications when safety is of paramount importance, but the basic material properties that give rise to its insensitivity are not fully understood. Molecular dynamics (MD) modeling using empirical force fields (FFs) has been the main route to characterize many complicated dynamical properties of the single crystal, but these FFs have not been comprehensively tested at extreme conditions typical of detonation. We collect a benchmark data set of (quasi)static TATB physical properties as determined by experiments and electronic structure calculations and apply this data set to validate four existing TATB FFs along with a new TATB FF that we develop here and denote as the CEA-LLNL-Missouri (CLM) FF. Benchmark data include vibrational spectra, the TATB crystal temperature-pressure-dependent equation of state and lattice parameters, properties of TATB crystal polymorphs and transitions to the gaseous and liquid states, dimer energy landscapes, the pressure-dependent elastic tensor, and the energy landscape for inelastic deformation via sliding of TATB crystal layers. As a general assessment, we find that the existing nonreactive FFs are more accurate in describing TATB's physical properties than the ReaxFF-based variants. The new CLM FF is found to consistently yield similar or better agreement with experiments and electronic structure theory than any of the existing FF models, and it presents a distinct improvement in accurately modeling TATB elasticity and equation of state. This work is expected to help improve the accuracy of FF-based modeling of complicated dynamic responses that ultimately govern the safety and performance characteristics of this material. | Matthew Kroonblawd; Paul Lafourcade; Laurence Fried; Jean-Bernard Maillet; Tommy Sewell | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657889d97acf130c32132a94/original/a-new-nonreactive-force-field-for-accurate-molecular-dynamics-simulations-of-tatb-at-extreme-conditions.pdf |
629bd3054f43d62bd8301bf4 | 10.26434/chemrxiv-2022-40z5x-v2 | TMAO: Protecting Proteins from Feeling the Heat | Osmolytes are ubiquitous in the cell and play an important role in controlling protein stability under stress. The natural osmolyte trimethylamine N-oxide (TMAO) is used by marine animals to counteract the effect of pressure denaturation at large depths. The molecular mechanism of TMAO stabilization against pressure and urea denaturation has been extensively studied, but unlike the case of other osmolytes the ability of TMAO to protect proteins from high temperature has not been quantified. To reveal the effect of TMAO on folded and unfolded protein ensembles and the hydration shell at different temperatures, we study a mutant of the well-characterized, fast-folding model protein B (PRB). We carried out >190 µs in total all-atom simulations of thermal folding/unfolding of PRB at multiple temperatures and concentrations of TMAO. The simulations show increased thermal stability of PRB in presence of TMAO. Partly structured, compact ensembles are favored over the unfolded state. TMAO forms two shells near the protein: an outer shell away from the protein surface alters hydrogen bond lifetimes of water molecules and increases hydration of the protein to help stabilize it; a less-populated inner shell with opposite TMAO orientation closer to the protein surface binds exclusively to basic side chains. The cooperative co-solute effect of the inner and outer shell TMAO has a small number of TMAO molecules ‘herding’ water molecules into two hydration shells at or near the protein surface. The stabilizing effect of TMAO on our protein saturates at 1 M despite higher TMAO solubility, so there may be little evolutionary pressure for extremophiles to produce higher intracellular TMAO concentrations if true in general. | Mayank Boob; Shahar Sukenik; Martin Gruebele; Taras Pogorelov | Theoretical and Computational Chemistry; Physical Chemistry; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629bd3054f43d62bd8301bf4/original/tmao-protecting-proteins-from-feeling-the-heat.pdf |
67182177d433919392e2111d | 10.26434/chemrxiv-2024-4fxh7 | Ultrathin Catalytic Condensers with engineered Pt/HfO2 interfaces for charge modulation | Catalytic condensers offer a flexible platform for programmable catalysis by modulating the electronic properties of active sites through applied voltage. Constructed as metal-oxide-semiconductor (MOS) stacks, these devices feature a high-k dielectric separating two conductive films, with the top electrode serving as both a catalytic layer and charge distributor. Here, we enhanced the architecture of the catalytic condensers to improve charge distribution and localization. By reducing the hafnia dielectric thickness from 70 nm to sub-5 nm using an optimized Atomic Layer Deposition (ALD) process and integrating single-layer graphene as a charge distributor, we achieved a charge density of 4.6 x 10¹³ charges cm-2 without exceeding a leak current of 100 μA cm-2. Systematic ALD studies revealed that purge time affects the dielectric constant and resulting leak current, enabling the fabrication of a more electrically insulating and thin dielectric layer. These optimized condensers demonstrated leak currents as low as 1 nA cm-2 at 1.0 x 10¹³ charges cm-2. The ultrathin catalytic condensers were then used to explore several new geometries aimed at maximizing charge accumulation per platinum atom. The most effective design, the "blanket condenser," featured small platinum nanoislands at the interface of the top electrode and hafnia dielectric, covered by either single-layer graphene or porous carbon nanotubes. This configuration effectively blanketed the nanoislands, closing the electrical circuit while minimizing the distance between the dielectric and the active nanoislands. Compared to a continuous platinum electrode, the blanket condenser enabled accumulation of significantly more charge per platinum atom, opening new opportunities for catalytic applications. | Mostapha Dakhchoune; Katelyn Groenhout; Rachita Rana; Yuriy Román-Leshkov | Materials Science; Catalysis; Chemical Engineering and Industrial Chemistry; Thin Films; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67182177d433919392e2111d/original/ultrathin-catalytic-condensers-with-engineered-pt-hf-o2-interfaces-for-charge-modulation.pdf |
6344b4020e3c6a2df43c42f0 | 10.26434/chemrxiv-2022-g3qng | A Syn Outer-Sphere Oxidative Addition: The Reaction Mechanism in Pd/Senphos-Catalyzed Carboboration of 1,3-Enynes | We report a combined experimental and computational study of Pd/Senphos catalyzed carboboration of 1,3-enynes utilizing DFT calculations, 31P NMR study, kinetic study, Hammett analysis and Arrhenius/Eyring analysis. Our mechanistic study provides evidence against the conventional inner-sphere β-migratory insertion mechanism. Instead, a syn outer-sphere oxidative addition mechanism featuring a Pd-π-allyl intermediate followed by coordination-assisted rearrangements is consistent with all the experimental observations.
| Ziyong Wang; Walid Lamine; Karinne Miqueu; Shih-Yuan Liu | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Physical Organic Chemistry; Computational Chemistry and Modeling; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6344b4020e3c6a2df43c42f0/original/a-syn-outer-sphere-oxidative-addition-the-reaction-mechanism-in-pd-senphos-catalyzed-carboboration-of-1-3-enynes.pdf |
650db98360c37f4f76420623 | 10.26434/chemrxiv-2023-glls8-v2 | Catalyst Engineering for the Selective Reduction of CO2 to CH4; A First-Principles Study on X-MOF-74 (X = Mg, Mn, Fe, Co, Ni, Cu, Zn) | The conversion of carbon dioxide (CO2) into more valuable chemical compounds represents a critical objective for addressing environmental challenges and advancing sustainable energy sources. The CO2 reduction reaction (CO2RR) holds promise for transforming CO2 into versatile feedstock materials and fuels. Leveraging first-principles methodologies provides a robust approach to evaluate catalysts and steer experimental efforts. In this study, we examine the CO2RR process using a diverse array of representative cluster models derived from X-MOF-74 (where X encompasses Mg, Mn, Fe, Co, Ni, Cu, or Zn) through first-principles methods. Notably, our investigation highlights the Fe-MOF-74 cluster's unique attributes, including favorable CO2 binding and the lowest limiting potential of the studied clusters for converting CO2 to methane (CH4) at 0.32 eV. Our analysis identified critical factors driving the selective CO2RR pathway, enabling the formation CH4 on the Fe-MOF-74 cluster. These factors involve less favorable reduction of hydrogen to H2 and strong binding affinities between the Fe open-metal site and reduction intermediates, effectively curtailing desorption processes of closed-shell intermediates such as formic acid (HCOOH), formaldehyde (CH2O), and methanol (CH3OH), to lead to selective CH4 formation. | Gavin McCarver; Taner Yildirim; Wei Zhou | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650db98360c37f4f76420623/original/catalyst-engineering-for-the-selective-reduction-of-co2-to-ch4-a-first-principles-study-on-x-mof-74-x-mg-mn-fe-co-ni-cu-zn.pdf |
628c187743d1f0ae4736f2e9 | 10.26434/chemrxiv-2021-mdjf6-v2 | Nickel-Catalyzed Reductive Alkylation of Heteroaryl Imines | A Ni-catalyzed reductive cross-coupling of heteroaryl imines with C(sp3) electrophiles for the preparation of heterobenzylic amines is reported. This umpolung-type alkylation proceeds under mild conditions, avoids the pre-generation of organometallic reagents, and exhibits good functional group tolerance. Mechanistic studies are consistent with the imine substrate acting as a redox-active ligand upon coordination to a low-valent Ni center. The resulting bis(2-imino)heterocycle·Ni complexes can engage in alkylation reactions with a variety of C(sp3) electrophiles, giving heterobenzylic amine products in good yields. | Marco Brandstätter; Raymond F. Turro; Sarah Reisman | Organic Chemistry; Inorganic Chemistry; Organometallic Chemistry; Organic Synthesis and Reactions; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628c187743d1f0ae4736f2e9/original/nickel-catalyzed-reductive-alkylation-of-heteroaryl-imines.pdf |
67a493ac81d2151a025cf210 | 10.26434/chemrxiv-2025-bh7sc | Nanoconfined Photopolymerization in Self-Assembled Glycerol Monooleate, Hydroxyethyl Acrylate and Water Suprastructures | The nanoconfinement of lipid self-assembled structures offers a dynamic environment for chemical reactions. It enables the integration of regents of various polarities, their alignment at the lipid/water interface for regio-specific reactions, and tailored reaction dimensions from restricted diffusion in the nanoconfinement. However, the effects of monomer integration and polymerization on the self-assembly structure and reaction products remain to be fully understood. Here, we report the photo-initiated polymerization of hydroxyethyl acrylate (HEA) within the inverse bicontinuous cubic structure of glycerol monooleate (GMO), yielding biocompatible hybrid materials. The initial structures are formed in bulk and as thin films on silicon wafers through the self-assembly of the GMO molecules with water. Using small-angle X-ray scattering (SAXS) and grazing incidence (GI)SAXS, we find that HEA actively integrates into the lipid/water interface, modifying the self-assembled packing geometries. Photo-polymerization triggered structural transformations and changes in orientation relative to the substrate surface. Nuclear magnetic resonance spectroscopy (NMR) and gel permeation chromatography reveal larger polymer sizes and smaller polydispersity under nanoconfined conditions compared to polymerization in water. These findings enhance the understanding of self-assembled structures as reaction nanoconfinements and establish a foundation for advanced material design. | Meron Debas; Dinh Phuong Trinh Nguyen; Andreas F. M. Kilbinger; Artur G. Glavic; Heinz Amenitsch; Stefan Salentinig | Physical Chemistry; Polymer Science; Polymerization (Polymers); Self-Assembly; Structure; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a493ac81d2151a025cf210/original/nanoconfined-photopolymerization-in-self-assembled-glycerol-monooleate-hydroxyethyl-acrylate-and-water-suprastructures.pdf |
6771386581d2151a0246e2cf | 10.26434/chemrxiv-2024-ft169 | Electric double layer structure of water-in-salt electrolyte in a porous carbon electrode elaborated with Raman spectroscopy and electrochemical methods | Understanding the interplay between ion association, desolvation, and electric double layer (EDL) structure is crucial for designing high-performance energy storage devices with concentrated electrolytes. However, these dynamics in water-in-salt electrolytes within the nanopores of carbon electrodes are not fully understood. This study explores the ion association in water-in-salt LiTFSI electrolyte in more detail, classifying various ion pairs as a function of concentration. Based on Raman spectroscopy data of electrolyte and electrochemical investigations on non-porous electrodes, modification in the classical Gouy-Chapman-Stern (GCS) model has been proposed by incorporating ionicity to estimate Debye length. The modified model shows a sharp Debye length decrease as the concentration rises from 1 to 10 mol∙kg⁻¹ but an increase beyond 10 mol∙kg⁻¹ due to ion pairing. The modified model accurately reflects differential and experimental EDL capacitance values obtained from cyclic voltammetry and electrochemical impedance spectroscopy. The data obtained for non-porous electrodes was adjusted by dividing it with the MacMullin number of the carbon electrode to estimate the Debye length in pores. Further, introducing the MacMullin number into the Stokes-Einstein equation enabled the estimation of ionic radii within pores, which was subsequently utilized to calculate extent of ion desolvation/dehydration in micro- and mesopores. The concentration-dependent ionic association governs the Debye length trends in pores, which correlate with confined ionic radii, ion desolvation, and resulting EDL charging dynamics. Our findings highlight 5 mol∙kg⁻¹ LiTFSI as optimal for faster charging rates and 10 mol∙kg⁻¹ for higher energy density, providing critical insights for developing efficient electrolytes and porous carbon electrodes. | Tauhidul Islam; Harald Fitzek; Bernhard Gollas; Qamar Abbas | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study; Interfaces; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6771386581d2151a0246e2cf/original/electric-double-layer-structure-of-water-in-salt-electrolyte-in-a-porous-carbon-electrode-elaborated-with-raman-spectroscopy-and-electrochemical-methods.pdf |
613b21fe27d906d4c183cfc1 | 10.26434/chemrxiv-2021-pp88m | Benchmarking molecular feature attribution methods with activity cliffs | Feature attribution techniques are popular choices within the explainable artificial intelligence toolbox, as they can help elucidate which parts of the provided inputs used by an underlying supervised-learning method are considered relevant for a specific prediction. In the context of molecular design, these approaches typically involve the coloring of molecular graphs, whose presentation to medicinal chemists can be useful for making a decision of which compounds to synthesize or prioritize. The consistency of the highlighted moieties alongside expert background knowledge is expected to contribute to the understanding of machine-learning models in drug design. Quantitative evaluation of such coloring approaches, however, has so far been limited to substructure identification tasks. We here present an approach that is based on maximum common substructure algorithms applied to experimentally-determined activity cliffs. Using the proposed benchmark, we found that molecule coloring approaches in conjunction with classical machine-learning models tend to outperform more modern, deep-learning-based alternatives. However, none of the tested feature attribution methods sufficiently and consistently generalized when confronted with unseen examples. | José Jiménez Luna; Miha Skalic; Nils Weskamp | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613b21fe27d906d4c183cfc1/original/benchmarking-molecular-feature-attribution-methods-with-activity-cliffs.pdf |
656e44b6cf8b3c3cd7c95502 | 10.26434/chemrxiv-2023-j1tc1 | Porphyrins in Photodynamic Therapy: A Review | Porphyrins have emerged as versatile and highly effective photosensitizers in the field of photodynamic therapy (PDT). This promising therapeutic approach relies on the light-induced generation of reactive oxygen species (ROS) by photosensitizing agents. This comprehensive review explores the multifaceted role of porphyrins across various PDT applications, encompassing anticancer PDT, immuno-PDT, antimicrobial PDT, and antiviral PDT. Porphyrins exhibit the potential to serve as organic supramolecular platforms for developing various photosensitizers (PSs) tailored for specific PDT modalities. The exceptional capacity of porphyrins to specifically accumulate in target cancer cells or microorganisms, their proficiency in generating ROS upon exposure to light, and their capability to amass within cell mitochondria to facilitate apoptosis establish porphyrins as invaluable assets in a wide array of therapeutic applications. Ongoing research endeavours and clinical investigations continually unveil the vast potential of porphyrin-based PDT in combatting a wide range of diseases, spanning from cancer and infections to viral ailments. Furthermore, porphyrins hold promise in addressing drug-resistant cancers and antimicrobial resistance through non-invasive PDT, offering efficient alternatives to commercially available PDT drugs. In the context of advanced cancer management, porphyrin-based PDT offers the prospect of combinatorial therapy, enabling a sequence of immunogenic post-PDT actions that can effectively overcome anticancer resistance and tackle metastatic cancers. The future of PDT appears promising, with porphyrin scaffolds expected to play pivotal roles in advancing this field. | Debdulal Sharma; Devashish Sengupta | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656e44b6cf8b3c3cd7c95502/original/porphyrins-in-photodynamic-therapy-a-review.pdf |
65ae49d966c138172900a26f | 10.26434/chemrxiv-2024-qzjwj | Dynamic Interchange Between Two Protonation States is Characteristic of Active Sites of Cholinesterases | Cholinesterases are well-known and widely studied enzymes crucial to human health and involved in neurology, Alzheimer, and lipid metabolism. The protonation pattern of cholinesterases’ active sites influences all the chemical processes within, including reaction, covalent inhibition by nerve agents, and reactivation. Our understanding of it is, however, limited. In this study, we used enhanced-sampling quantum-mechanical/molecular-mechanical calculations to show that cholinesterases mostly function as dynamical mixtures of two protonation states. Proton transfer between two non-catalytic glutamate residues occurs by Grotthuss mechanism via a mediator water molecule. We show that this uncovered complexity of active sites presents a challenge for classical molecular dynamics simulations that calls for special treatment. The proton transfer barrier of 1.65 kcal/mol opens the discussion on potential existence of two conjugated low barrier hydrogen bonds in the inhibited form of butyrylcholinesterase. These findings expand our understanding of structural features expressed by highly evolved enzymes and guide future advances in cholinesterase-related protein- and drug design studies. | Alexander Zlobin; Ivan Smirnov; Andrey Golovin | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Bioinformatics and Computational Biology; Computational Chemistry and Modeling; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2024-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ae49d966c138172900a26f/original/dynamic-interchange-between-two-protonation-states-is-characteristic-of-active-sites-of-cholinesterases.pdf |
60c74914567dfe558bec4b13 | 10.26434/chemrxiv.11913393.v2 | New theoretical insight into high coordination number complexes in actinides-centered borane | <p>The coordination number of a given element behaving
to understand its chemistry shows a great interest, which greatly promotes the
extension and development of new materials, but remains challenging. Herein we report a
new record high coordination number (CN) for actinide established in the
cage-like An(BH)<sub>24</sub> (An = Th to Cm) via using relativistic quantum
chemistry methods. Analysis of U(BH)<sub>n</sub> (n = 1 to 24) confirms these series
of systems being as geometric minima, with the BH as a ligand located in the first
shell around the uranium. Contrast, global searches reveal the low CN half-cage
structure for UB<sub>24</sub>, which is extended to the series of AnB<sub>24</sub>
and prevails over the competing structural isomers such as cage. The intrinsic geometric
difference for AnB<sub>24 </sub>and An(BH)<sub>24</sub> mainly arise from the B
sp<sup>3</sup> hybridization in borane inducing strong interactions between An
5f6d7s hybrid orbitals and B 2p<sub>z</sub> orbitals in An(BH)<sub>24</sub> comparing
to that of AnB<sub>24</sub>. The fundamental trend presents a valuable insight
for future experimental endeavor searching for isolable complexes with high-coordination
actinide and provides a new structural motif of boron clusters and
nanostructures.<br /></p> | Shuxian Hu; Peng Zhang; wenli zou; ping zhang | Bonding; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Theory - Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74914567dfe558bec4b13/original/new-theoretical-insight-into-high-coordination-number-complexes-in-actinides-centered-borane.pdf |
60c741ea469df45bcdf42efc | 10.26434/chemrxiv.8174783.v1 | An Efficient Computational Assay for β-Lactam Antibiotic Breakdown by Class A β-Lactamases | <div>Breakdown of β-lactam antibiotics by β-lactamases is one of the most common resistance mechanisms against these drugs. Here, we present a computationally efficient combined quantum mechanics/molecular mechanics simulation protocol for hydrolysis of the β-lactamase acylenzyme with meropenem, a carbapenem antibiotic. Starting from the previously published computational assay, we have successfully reduced both the conformational space and the sampling time, which leads to a more than 99% reduction on computer resources needed for this assay (less than 24 CPU hours per reaction). This simplified <i>in silico</i> protocol distinguishes accurately between class A β-lactamases that are able or unable to break down carbapenems. We further demonstrate that these protocols can be used to elucidate mechanistic details of β-lactam breakdown. The new efficient computational assay</div><div>may be used to predict carbapenem hydrolytic activity of new β-lactamase variants as they arise, and in identifying routes to development of new, more resilient β-lactam antibiotics or new generations of mechanism-based β-lactamase inhibitors.</div> | Viivi H. A. Hirvonen; Katharine Hammond; Ewa I. Chudyk; Michael A. L. Limb; James Spencer; Adrian Mulholland; Marc W. van der Kamp | Biochemistry; Microbiology; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741ea469df45bcdf42efc/original/an-efficient-computational-assay-for-lactam-antibiotic-breakdown-by-class-a-lactamases.pdf |
61856fe4d828a4f4e76cb125 | 10.26434/chemrxiv-2021-r7k5v | Cold Denaturation of Proteins in the Absence of Solvent | The effect of temperature on the stability of proteins is well explored for high temperatures, but harder to track below the freezing point of water. This challenge is met with the use of variable temperature ion mobility mass spectrometry (VT IM-MS), which allows the structure of isolated, solvent free molecules to be measured at sub ambient temperatures in the form of their collision cross section (CCS). Here we monitor conformational changes that occur to two isotypes of monoclonal antibodies over a temperature range from 295 to 165 K. For each we observe a large increase in the magnitude of the CCS at 250K (-20 °C) substantially above that predicted. This loss of structure in the absence of bulk solvent is attributed to a change in the strength of stabilizing intermolecular interactions, causing rearrangement. At 190 K (-80 °C) the CCS distribution narrows which we attribute to better resolution. These findings indicate that in vacuo deep-freezing minimizes denaturation and maintains the gas phase native fold supporting this practice in vitro. Comparing the data for each isotype suggests that the disulfide bridging influences thermal structural rearrangement and taken together we show that this method provides unique insights to the phenomenon of cold denaturation. | Emma Norgate; Rosie Upton; Bruno Bellina; Kjetil Hansen; Catherine Brookes; Argyris Politis; Perdita Barran | Physical Chemistry; Analytical Chemistry; Mass Spectrometry; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61856fe4d828a4f4e76cb125/original/cold-denaturation-of-proteins-in-the-absence-of-solvent.pdf |
615c034e8b620da36145038b | 10.26434/chemrxiv-2021-kvtmv | The transfer and persistence of metals in latent fingermarks | In forensic science, knowledge and understanding of material transfer and persistence is inherent to the interpretation of trace evidence and can provide vital information on the activity level surrounding a crime. Detecting metal ions in fingermark residue has long been of interest in the field of forensic science, due to the possibility of linking trace metal ion profiles to prior activity with specific metal objects (e.g. gun or explosive handling). Unfortunately, the imaging capability to visualise trace metal ions at sufficient spatial resolution to determine their distribution within a fingermark (micron level) was not previously available. Here, we demonstrate for the first time transfer and persistence of metals in fingermarks, at micron spatial resolution, using synchrotron sourced x-ray fluorescence microscopy. Fingermarks were taken before and after brief handling of a gun barrel, ammunition cartridge case and party sparkler to demonstrate the transfer of metals. The results reveal increased metal content after contact with these objects, and critically, a differential pattern of metal ion increase was observed after handling different objects. Persistence studies indicate that these metals are removed as easily as they are transferred, with a brief period of hand washing appearing to successfully remove metallic residue from subsequent fingermarks. Preliminary work using x-ray absorption near edge structure spectroscopic mapping highlighted the potential use of this technique to differentiate between different chemical forms of metals and metal ions in latent fingermarks. It is anticipated that these findings can now be used to assist future work for the advancement of trace metal detection tests and fingermark development procedures | Rhiannon Boseley; Daryl Howard; Mark Hackett; Simon Lewis | Analytical Chemistry; Imaging; Microscopy; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615c034e8b620da36145038b/original/the-transfer-and-persistence-of-metals-in-latent-fingermarks.pdf |
60c74fb2842e6547eedb38d1 | 10.26434/chemrxiv.12919367.v1 | Using Purely Sinusoidal Voltammetry for Rapid Parameterization of Surface-Confined Electrochemistry | The paper includes a thorough charac-terisation of a technique called Purely Sinusoidal Voltammetry (PSV). This technique is usedto infer reaction parameters about a surface-linked redox process, and the characterisationeffort involves both computational and experimental methods. | Henry Lloyd-Laney; Martin Robinson; Alice R. Hewson; Jack Firth; Jie Zhang; Alan Bond; Alison Parkin; David Gavaghan; Nick Yates; Darell Elton | Electrochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fb2842e6547eedb38d1/original/using-purely-sinusoidal-voltammetry-for-rapid-parameterization-of-surface-confined-electrochemistry.pdf |
6400b9a29789de3dd9cb6312 | 10.26434/chemrxiv-2023-698w9 | Skeletal Transformation of Unactivated Arenes Enabled by a Low-Temperature Dearomative (3+2) Cycloaddition | Simple aromatic compounds like benzene are abundant feedstocks, for which the preparation of derivatives chiefly begins with electrophilic substitution reactions, or less frequently reductions. Their high stability makes them particularly reluctant to participate in cycloadditions under ordinary reaction conditions. Here we demonstrate the exceptional ability of 1,3-diaza-2-azoniaallene cations to undergo formal (3+2) cycloadditions with unactivated benzene derivatives, below room temperature, to provide thermally stable dearomatized adducts on a multi-gram scale. The cycloaddition, which tolerates polar functional groups, activates the ring toward further elaboration. On treatment with dienophiles the cycloadducts undergo a (4+2) cycloaddition-cycloreversion cascade to yield substituted or fused arenes, including naphthalene derivatives. The overall sequence results in the transmutation of arenes through an exchange of the ring's carbons: a two-carbon fragment from the original aromatic ring is replaced with another from the incoming dienophile, introducing an unconventional disconnection for the synthesis of ubiquitous aromatic building blocks. Applications of this two-step sequence to the preparation of substituted acenes, isotopically labeled molecules, and medicinally relevant compounds are demonstrated. | Sajan Pradhan; Fahimeh Mohammadi; Jean Bouffard | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6400b9a29789de3dd9cb6312/original/skeletal-transformation-of-unactivated-arenes-enabled-by-a-low-temperature-dearomative-3-2-cycloaddition.pdf |
60c74034842e65668adb1c67 | 10.26434/chemrxiv.7087538.v2 | A New Approach to Enhancing the CO2 Capture Performance of Defective UiO-66 via Post-Synthetic Defect Exchange | Zirconium-based metal-organic frameworks (Zr-MOFs) are a subclass of MOFs known for their remarkable stability, especially in the presence of water. This makes them extremely attractive for practical applications, including CO<sub>2</sub> capture from industrial emission sources; however, the CO<sub>2</sub> adsorption capacity of Zr-MOFs is moderate compared to that of the best performing MOFs reported to date. Functionalization of Zr-MOFs with amino groups has been demonstrated to increase their affinity for CO<sub>2</sub>. In this work, we assessed the potential of post-synthetic defect exchange (PSDE) as an alternative approach to introduce amino functionalities at missing-cluster defective sites in formic acid modulated UiO-66. Both pyridine-containing (picolinic acid and nicotinic acid) and aniline-containing (3-aminobenzoic acid and anthranilic acid) monocarboxylates were integrated within defective UiO-66 with this method. Non-defective UiO-66 modified with linkers bearing the same amino groups (2,5-pyridinedicarboxylic acid and 2-aminoterephthalic acid) were prepared by classical post-synthetic ligand exchange (PSE), in order to compare the effect of introducing functionalities at defective sites versus installing them on the backbone. PSDE reduces the porosity of defective UiO-66, but improves both the CO<sub>2</sub> uptake and the CO<sub>2</sub>/N<sub>2</sub> selectivity, whereas PSE has no effect on the porosity of non-defective UiO-66, improving the CO<sub>2</sub> uptake but leaving selectivity unchanged. Modification of defective UiO-66 with benzoic acid reveals that pore size reduction is the main factor responsible for the observed uptake improvement, whereas the presence of nitrogen atoms in the pores seems to be beneficial for increasing selectivity. <br /> | Athanasios Koutsianos; Ewa Kazimierska; Andrew R. Barron; Marco Taddei; Enrico Andreoli | Coordination Chemistry (Inorg.); Solid State Chemistry; Ligands (Organomet.); Clusters | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74034842e65668adb1c67/original/a-new-approach-to-enhancing-the-co2-capture-performance-of-defective-ui-o-66-via-post-synthetic-defect-exchange.pdf |
65b8a0b09138d23161060392 | 10.26434/chemrxiv-2024-0k5mt | In-situ reduction of graphene oxide for electrochemical supercapacitor application | Reduced graphene oxide (rGO) is a widely studied electrode material for energy storage, however, its strong re-stacking tendency during chemical reduction always leads to a degraded specific surface area and thus limits its performance. Therefore, it is necessary to control the morphology of rGO during the reduction process. Here, we develop a novel in-situ membrane-based method for the reduction of graphene oxide (GO) using a green and efficient vitamin C (VC) aqueous solution as reductant. The obtained electrode material (vitamin C reduced GO via membrane-based method, VG-M) exhibits a specific capacitance of 174 F/g at 1 A/g and 75.9% of retention at 40 A/g, which is about 9 times better than the highly self-stacked material from conventional methods (vitamin C reduced GO via stirring method, VG-S). This designed method successfully achieves the maintenance of rGO sheet morphology through laminar confinement in GO membrane and presents a simple approach towards two-dimensional (2D) material morphology control. | Tongxi Lin ; Xiaojun Ren; Xinyue Wen; Amir Karton ; Vanesa Quintano; Rakesh Joshi | Materials Science; Nanoscience; Carbon-based Materials; Nanostructured Materials - Nanoscience | CC BY 4.0 | CHEMRXIV | 2024-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b8a0b09138d23161060392/original/in-situ-reduction-of-graphene-oxide-for-electrochemical-supercapacitor-application.pdf |
64ae55fd6e1c4c986b3fa63a | 10.26434/chemrxiv-2023-7c5g6 | Peptide Bispecifics Inhibiting HIV-1 Infection by an Orthogonal Chemical and Supramolecular Strategy | Viral infections pose a significant threat to human health and effective antiviral strategies are urgently needed. Antiviral peptides have emerged as a promising class of therapeutic agents due to their unique properties and mechanisms of action. While effective on their own, combining antiviral peptides may allow to enhance antiviral activity, broaden the antiviral spectrum, and prevent viral resistance. Here, we developed an orthogonal chemical strategy to prepare a heterodimeric peptide conjugate assembled on a protein-based nanoplatform. Specifically, we combined optimized version of two peptides inhibiting HIV-1 by distinct mechanisms. Virus-inhibitory peptide (VIRIP) is a 20 amino acid fragment of α1-antitrypsin that inhibits HIV-1 by targeting the gp41 fusion peptide. Endogenous Peptide Inhibitor of CXCR4 (EPI-X4) is a 16-residue fragment of human serum albumin that prevents HIV-1 entry by binding to the viral CXCR4 coreceptor. We assembled supramolecular nanoplatforms carrying biotinylated optimized forms of both peptides. We show that the tetravalent, bispecific assemblies show increased activity against CXCR4-tropic HIV-1variants. Our results are proof-of-concept that antiviral peptides with different modes of action can be assembled on nanoplatforms without loss of activity. | Dominik Schauenburg; Fabian Zech ; Astrid Johanna Heck ; Pascal von Maltitz ; Mirja Harms ; Siska Führer ; Nico Alleva; Jan Münch ; Seah Ling Kuan ; Frank Kirchhoff ; Tanja Weil | Biological and Medicinal Chemistry; Biochemistry; Cell and Molecular Biology; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2023-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ae55fd6e1c4c986b3fa63a/original/peptide-bispecifics-inhibiting-hiv-1-infection-by-an-orthogonal-chemical-and-supramolecular-strategy.pdf |
63f125139da0bc6b332681a0 | 10.26434/chemrxiv-2023-nwvl2 | First principles search for novel ultrahard high-density carbon allotropes: hexagonal C6, C9 and C12 | Hexagonal carbon allotropes C6, C9 and C12 with qtz, sta and lon topologies, respectively, were predicted on the basis of crystal chemistry and first principles (DFT) calculations. The new allotropes are mechanically (elastic properties) and dynamically (phonons) stable phases and are characterized by ultra-high Vickers hardness, exceptionally high for qtz C6 and C12, close to the previously studied qtz C3. The electronic band structures of all new allotropes show semi-conducting to insulating behavior. lon C12 can be considered as novel superlonsdaleite. | Samir F. Matar; Vladimir L. Solozhenko | Materials Science; Carbon-based Materials; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f125139da0bc6b332681a0/original/first-principles-search-for-novel-ultrahard-high-density-carbon-allotropes-hexagonal-c6-c9-and-c12.pdf |
60c7481b567dfe60a5ec4965 | 10.26434/chemrxiv.10039943.v2 | A Thermal Imaging Methodology To Study Evaporation Kinetics in Mine Tailings | <p>Predicting why, how, and when mine
tailings disposal sites become prone to dust scattering events is often hampered
by our limited understanding of the factors that affect the drying rates from their
surface layers. As a case study, thermal
imaging is demonstrated here to be a valuable tool to study the evaporation
mechanisms and rates from bauxite residues as a function of their thickness and
physicochemical properties, as well as environmental conditions. These investigations reveal their that late
stage drying rates are limited by gas phase diffusion through the interstitial
air within their internal microporosity. The smallness of the effective
diffusion coefficient indicates that water adsorption on bauxite residues surfaces
is the dominant phenomenon responsible for their slow water vapour transport
kinetics, a phenomenon that ultimately controls their late stage drying rates,
that is when dust scattering is most likely to occur. As such, application of this
thermal imaging methodology in the field may also contribute to improve the accuracy
of risk assessment protocols, support intervention and mitigation strategies,
underpin optimization efforts for mining residues management, and improve
forecasting of fugitive dust emissions from mine tailings by enabling more
accurate predictions of the evolution in their surface drying state.</p> | Josée Maurais; Étienne Beaumont; Joanick Bourret; Emrik Dauphinais; Nicolas-Alexandre Bouchard; Patrick Ayotte | Hydrology and Water Chemistry; Wastes | CC BY NC 4.0 | CHEMRXIV | 2020-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7481b567dfe60a5ec4965/original/a-thermal-imaging-methodology-to-study-evaporation-kinetics-in-mine-tailings.pdf |
60c742409abda2660cf8bf91 | 10.26434/chemrxiv.7673129.v2 | A Chemical Probe For Tudor Domain Protein Spindlin1 to Investigate Chromatin Functions | Modifications of histone tails, including
lysine/arginine methylation, provide the basis of a 'chromatin or histone
code'. Proteins that contain 'reader' domains can bind to these modifications
and form specific effector complexes, which ultimately mediate chromatin
function. The spindlin1 (SPIN1) protein contains three Tudor
methyllysine/arginine reader domains and was identified as a putative oncogene
and transcriptional co-activator. Here we report a SPIN1 chemical probe
inhibitor with low nanomolar in vitro activity, exquisite selectivity on a
panel of methyl reader and writer proteins, and with submicromolar cellular
activity. X-ray crystallography showed that this Tudor domain chemical probe
simultaneously engages Tudor domains 1 and 2 via a bidentate binding mode.
Small molecule inhibition and siRNA knockdown of SPIN1, as well as
chemoproteomic studies, identified genes which are transcriptionally regulated
by SPIN1 in squamous cell carcinoma and suggest that SPIN1 may have a roll in
cancer related inflammation and/or cancer metastasis.<br /> | Vincent Fagan; Catrine Johansson; Carina Gileadi; Octovia P. Monteiro; James E. Dunford; Reshma Nibhani; Martin Philpott; Jessica Malzahn; Graham Wells; Ruth Farham; Adam Cribbs; Nadia Halidi; Fengling Li; Irene Chau; Holger Greschik; Srikannathasan Velupillai; Abdellalh Allali- Hassani; James Bennett; Thomas Christott; Charline Giroud; Andrew M Lewis; Kilian Huber; Nick Athanasou; Chas Bountra; Manfred Jung; Roland Schüle; Masoud Vedadi; Cheryl Arrowsmith; Yan Xiong; Jian Jin; Oleg Fedorov; Gillian Farnie; Paul Brennan; Udo Oppermann | Biochemistry; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742409abda2660cf8bf91/original/a-chemical-probe-for-tudor-domain-protein-spindlin1-to-investigate-chromatin-functions.pdf |
60c754e7bdbb8954dea3a71e | 10.26434/chemrxiv.13849442.v1 | Terphenyl-based Small-Molecule Inhibitors of Programmed Cell Death-1/Programmed Death-Ligand 1 Protein−Protein Interaction | <p>Here, we
report a novel class of potent PD-L1/PD-1 inhibitors based on the rigidified
biphenyl-inspired structure – terphenyls. Using in-silico docking, we designed
and later experimentally shown the efficacy of terphenyl-based scaffolds to
inhibit the PD-1/PD-L1 complex formation using various biophysical and
biochemical techniques. We also report a high-resolution structure of the PD-L1
complex with our most potent inhibitors allowing the identification of key
interactions with PD-L1 at the molecular level. Moreover, we show the efficacy
of our most potent inhibitors at activating the antitumor response using
primary T-cells derived from healthy donors. This effect was not observed even
for the therapeutic antibodies. This makes our compounds prominent candidates for further optimization for
anti-PD-L1 cancer treatments.</p> | Damian Muszak; Ewa Surmiak; Jacek Plewka; Katarzyna Magiera-Mularz; Justyna Kocik; Bogdan Musielak; Dominik Sala; Radosław Kitel; Małgorzata Stec; Maciej Siedlar; Alexander Domling; Łukasz Skalniak; Tad Holak | Biochemistry; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754e7bdbb8954dea3a71e/original/terphenyl-based-small-molecule-inhibitors-of-programmed-cell-death-1-programmed-death-ligand-1-protein-protein-interaction.pdf |
65fc234c9138d23161efde62 | 10.26434/chemrxiv-2024-b92s3 | Machine Learning in Chemistry | Machine Learning (ML) can be defined as a class of Artificial Intelligence for automated data analysis, which is capable of detecting patterns in data. The extracted patterns can be used to predict un-known data or to assist in decision-making processes under uncertainty. Recent advances in experimental and computational methods are increasing the quantity and complexity of generated data. Within the field of computational materials science, such an abundance of data is possible mainly due to the success of density functional theory (DFT) and High throughput (HT) methods. This article aims to show how Machine Learning approaches to modern computational chemistry are being used to uncover complexities in different fields. | Muhammad Hanzla; Abdul Rehman Shinwari | Biological and Medicinal Chemistry; Agriculture and Food Chemistry; Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2024-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fc234c9138d23161efde62/original/machine-learning-in-chemistry.pdf |
60c73e154c891960e5ad1ced | 10.26434/chemrxiv.6427643.v1 | Fe-N-C Artificial Enzyme: Activation of Oxygen for Dehydrogenation and Monoxygenation of Organic Substrates under Mild Condition and Cancer Therapeutic Application | Developing highly efficient artificial enzymes that directly employ O<sub>2</sub> as terminal oxidant has long been pursued but has rarely achieved
yet. We report Fe-N-C has unusual enzyme-like activity in both dehydrogenation and monoxygenation of organic
substrates with ~100% selectivity by direct using O<sub>2</sub>. | Fei He; Li Mi; Yanfei Shen; Toshiyuki Mori; Songqin Liu; Yuanjian Zhang | Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems; Heterogeneous Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e154c891960e5ad1ced/original/fe-n-c-artificial-enzyme-activation-of-oxygen-for-dehydrogenation-and-monoxygenation-of-organic-substrates-under-mild-condition-and-cancer-therapeutic-application.pdf |
677ffabbfa469535b958ba9a | 10.26434/chemrxiv-2024-8tqvn-v2 | Stabilization of the Ferryl=oxoheme Form of Staphylococcus aureus IsdG by Electron Transfer from a Second-Sphere Tryptophan | The ferryl heme forms of Staphylococcus aureus IsdG and IsdI have novel UV/Vis absorption spectra that are distinct from those of the three forms of ferryl heme typically found in biological systems: compound I, compound II, and com-pound ES. In this work, the ferryl heme form of IsdG was characterized because it is an analogue for the immediate product of enzyme-catalyzed heme hydroxylation. The ferryl heme form of IsdG generated following the addition of meta-chloroperoxybenzoic acid to the ferric heme form of IsdG has a half-life of 4.0 ± 0.2 min, which is more than 100 times longer than the half-life for the ferryl heme form of human heme oxygenase (hHO). Magnetic circular dichroism characterization of the IsdG species yielded spectral data and zero-field splitting parameters consistent with either a compound II- or compound ES-like ferryl heme. Further characterization of isotopically-enriched samples with elec-tron paramagnetic resonance spectroscopy revealed the presence of a protein-based organic radical, as would be ex-pected for compound ES. Finally, multi-scale quantum mechanics / molecular mechanics and time-dependent density functional theory strongly suggest that the ferryl heme form of IsdG has a ruffled porphyrin ligand and an oxo ligand. Thus, the ferryl heme form of IsdG is assigned to a compound ES-like species with a Trp67-based radical. Electron transfer from Trp67 to porphyrin will stabilize the immediate product of heme hydroxylation and provide a thermodynamic driving force for the reaction. Furthermore, the ability to transfer an electron between Trp67 and the substrate may explain the differential reactivity of meso-hydroxyheme in IsdG and hHO. | Aarzoo Grover; Matthew A Conger; Matthew D Liptak | Biological and Medicinal Chemistry; Inorganic Chemistry; Bioinorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677ffabbfa469535b958ba9a/original/stabilization-of-the-ferryl-oxoheme-form-of-staphylococcus-aureus-isd-g-by-electron-transfer-from-a-second-sphere-tryptophan.pdf |
60c74e3b567dfe5660ec54b5 | 10.26434/chemrxiv.12727649.v1 | Thermally Activated Delayed Fluorescence from Locally Excited State: Theoretical Prediction and Experimental Validation | <div>As is well known, the thermally activated delayed fluorescence (TADF) is always generated from charge-transfer (CT) excited states in electron-donor (D) – electron-acceptor (A) systems. Here, a novel design strategy is proposed for realizing TADF from a locally excited (LE) state through controlling the intersystem crossing (ISC) and reverse intersystem crossing (RISC) processes between the LE singlet and higher triplet CT states. Based on the strategy, a boron difluoride derivative is theoretically predicted to emit TADF from the LE state, whose radiative decay rate constant is much larger kr (S<sub>1</sub> →S<sub>0</sub> )=1.12 * 10<sup>8</sup> s <sup>-1</sup> , two orders of magnitude larger than those of common TADF systems. And its lifetimes of the prompt and delayed fluorescence are experimentally validated to be 0.44 ns and 0.7 μs, respectively. This work is a breakthrough in the understanding of TADF and opens a new avenue for extending the TADF materials.</div> | Xiaoxiao Xiao; Shuai Li; Hua Geng; Yuai Duan; Guo Wang; Qian Peng; Zhigang Shuai; Hongbing Fu; Yi Liao | Photochemistry (Org.); Photochemistry (Physical Chem.); Physical and Chemical Properties; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e3b567dfe5660ec54b5/original/thermally-activated-delayed-fluorescence-from-locally-excited-state-theoretical-prediction-and-experimental-validation.pdf |
60c74edb0f50dbe4303972dd | 10.26434/chemrxiv.12813923.v1 | Decoding the Kinetic Limitations of Plasmon Catalysis: The Case of 4-Nitrothiophenol Dimerization | Plasmon-mediated chemistry presents an intriguing new approach to photocatalysis. However, the reaction enhancement<br />mechanism is not well understood. In particular, the relative importance of plasmon-generated hot charges and<br />photoheating are strongly debated. In this article, we evaluate the influence of microscopic photoheating on the kinetics of<br />a model plasmon-catalyzed reaction: the light-induced 4-nitrothiophenol (4NTP) to 4,4’-dimercaptoazobenzene (DMAB)<br />dimerization. Direct measurement of the reaction temperature by nanoparticle Raman-thermometry demonstrated that<br />the thermal effect plays a dominant role in the kinetic limitations of this multistep reaction. On the same time, no reaction<br />is possible by dark heating to the same temperature. This shows that plasmon nanoparticles have the unique ability to<br />enhance several steps of complex tandem reactions simultaneously. These results provide insight into the role of hot<br />electron and thermal effects in plasmonic catalysis of complex organic reactions, which highly important for the ongoing<br />development of plasmon based photosynthesis.
<br /> | Wouter Koopman; Radwan M. Sarhan; Felix Stete; Clemens N. Z. Schmitt; Matias Bargheer | Nanocatalysis - Reactions & Mechanisms; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74edb0f50dbe4303972dd/original/decoding-the-kinetic-limitations-of-plasmon-catalysis-the-case-of-4-nitrothiophenol-dimerization.pdf |
67059d0451558a15ef8973a1 | 10.26434/chemrxiv-2024-63t4k-v2 | Assessing the Partial Hessian Approximation in QM/MM-based Vibrational Analysis | The partial Hessian approximation is often used in vibrational analysis of QM/MM (quantum mechanics/molecular mechanics) systems because calculating the full Hessian matrix is computationally impractical. This approach aligns with the core concept of QM/MM, which focuses on the QM subsystem. Thus, using the partial Hessian approximation implies that the main interest is in the local vibrational modes of the QM subsystem. Here, we investigate the accuracy and applicability of the partial Hessian vibrational analysis (PHVA) approach as it is typically used within QM/MM, i.e., only the Hessian belonging to the QM subsystem is computed. We focus on solute–solvent systems with small, rigid solutes. To separate two of the major sources of errors, we perform two separate analyses. First, we study the effects of the partial Hessian approximation on local normal modes, harmonic frequencies, and harmonic IR and Raman intensities by comparing them to those obtained using full Hessians, where both partial and full Hessians are calculated at the QM level. Then, we quantify the errors introduced by QM/MM used with the PHVA by comparing normal modes, frequencies, and intensities obtained using partial Hessians calculated using a QM/MM-type embedding approach to those obtained using partial Hessians calculated at the QM level. Another aspect of the PHVA is the appearance of normal modes resembling the translation and rotation of the QM subsystem. These pseudo-translational and pseudo-rotational modes should be removed as they are collective vibrations of the atoms in the QM subsystem relative to a frozen MM subsystem and, thus, not well-described. We show that projecting out translation and rotation, usually done for systems in isolation, can adversely affect other normal modes. Instead, the pseudo-translational and pseudo-rotational modes can be identified and removed. | Jonas Vester; Jógvan Magnus Haugaard Olsen | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67059d0451558a15ef8973a1/original/assessing-the-partial-hessian-approximation-in-qm-mm-based-vibrational-analysis.pdf |
62ebefdcd131b71fc70c4ef2 | 10.26434/chemrxiv-2022-456nv | Atomic structural changes in the formation of transition metal tungstates: The role of polyoxometalate structures in material crystallization | Nucleation processes in wet-chemical synthesis methods are poorly understood, nevertheless an atomistic understanding of material formation would aid in the design of synthesis methods for tailor-made functional materials. Here, in situ X-ray total scattering experiments were performed during the hydrothermal synthesis of wolframite-type MWO4 (M: Mn, Fe, Co, Ni), enabling pair distribution function (PDF) analysis of the process. Upon mixing of the aqueous precursors, a crystalline precursor formed for the MnWO4 synthesis, while amorphous pastes formed for the FeWO4, CoWO4 and NiWO4 syntheses. Upon heating, the crystalline MnWO4 precursor converted directly to a crystalline wolframite-type MnWO4 phase, while the amorphous precursor led to the formation of an intermediate phase before the crystalline tungstates. The structure of the amorphous precursors was studied in detail using PDF analysis. Database mining was initially used to extract chemically relevant cluster structures, with the conclusion that the structure of the precursor contains Keggin fragments, well known from polyoxometalate chemistry. Such fragments are present in the Tourné ‘sandwich’ cluster, which has previously been found to be involved in the formation of some tungstates. We then used our recently developed ML-MotEx algorithm to identify which structural motifs in the sandwich structure are important to obtain a good fit of the data throughout the reaction. This analysis led to the identification of a skewed sandwich cluster to best describe the amorphous precursor structures. For the intermediate phase, ML-MotEx favoured motifs found both in the precursor and product phases, and the PDF of the intermediate phase could be described up to 20 Å by a disordered MWO4 structure. We found that the more disordered the precursor phase is, the longer reaction time is required to form crystalline products. More generally, we see that polyoxometalate chemistry is useful when describing the initial wet-chemical formation of mixed metal oxides. | Susanne Linn Skjærvø; Andy S. Anker; Magnus C. Wied; Emil T. S. Kjær; Mikkel Juelsholt; Troels Lindahl Christiansen; Kirsten Marie Ørnsbjerg Jensen | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ebefdcd131b71fc70c4ef2/original/atomic-structural-changes-in-the-formation-of-transition-metal-tungstates-the-role-of-polyoxometalate-structures-in-material-crystallization.pdf |
6342aa8a2984c94e797ea89d | 10.26434/chemrxiv-2022-jrpdx | A spin-flip variant of the second-order approximate coupled-cluster singles and doubles method | We report an implementation of a spin-flip variant of the second-order approximate coupled-cluster singles and doubles (CC2) method. The resolution-of-the-identity approximation or, alternatively, Cholesky decomposition of the two-electron integrals are used to reduce the memory requirements. We illustrate the performance of the new method by constructing potential energy curves of H2 and HF and by computing singlet-triplet splittings for various diradicals including some binuclear copper complexes that are of interest as molecular magnets. We find that spin-flip CC2 performs very similarly to the spin-flip variant of the algebraic diagrammatic construction scheme for the polarization propagator of second order (ADC(2)). Application to ozone shows that spin-flip CC2 predicts a barrierless symmetric dissociation of this molecule similar to spin-conserving CC2 and in contrast to spin-flip ADC(2) and coupled-cluster singles and doubles. | Garrette Pauley Paran; Cansu Utku; Thomas-Christian Jagau | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6342aa8a2984c94e797ea89d/original/a-spin-flip-variant-of-the-second-order-approximate-coupled-cluster-singles-and-doubles-method.pdf |
67879a9c81d2151a023de436 | 10.26434/chemrxiv-2025-xsxgn | Affordable Arsenic Detection Device Using Handmade Lokta Paper for Decentralized and Sustainable Manufacturing | The reliance on centralized manufacturing systems often shows vulnerability of global supply chains, as evidenced by disruptions during the COVID-19 pandemic and geopolitical conflicts. This study reports an affordable and portable paper strip sensor for arsenic detection in groundwater, developed using distributed manufacturing and sustainability principles. Handmade Lokta Paper (HLP), produced in the laboratory from bark of a native Lokta plant, Daphne, through eco-friendly methods, served as the sensor substrate. The HLP strip employed the Gutzeit reaction and integrated smartphone imaging for qualitative, semi-quantitative, and quantitative arsenic analysis. The assay optimization was achieved with 1% (w/v) HgBr₂ impregnation, 5-minute dipping time, 15-minute arsine exposure, and imaging within minutes. Testing of 21 groundwater samples from Nepal revealed strong agreement between the HLP strip and a commercial kit (Cohen’s kappa = 0.811). The HLP strip demonstrated a lower limit of detection (18 μg/L vs. 20 μg/L) and limit of quantification (54 μg/L vs. 61 μg/L). Most samples had arsenic concentrations below 10 μg/L, with few reaching Nepal’s regulatory limit of 50 μg/L. In addition to robust analytical performance, the HLP strip exemplifies the scalability and cost-effectiveness of arsenic sensors, with a production cost of USD 0.37 per test—significantly lower than commercial alternatives. This innovation may foster local economic growth, minimize supply chain dependency, and reduce environmental impact through the sustainable utilization of Lokta paper. The study highlights the potential of integrating traditional materials with advanced analytical techniques to address global health and environmental challenges while promoting regional resilience and sustainability. | Ramdeep Shrestha; Bhanu Bhakta Neupane; Basant Giri | Analytical Chemistry; Environmental Analysis; Imaging | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67879a9c81d2151a023de436/original/affordable-arsenic-detection-device-using-handmade-lokta-paper-for-decentralized-and-sustainable-manufacturing.pdf |
60c755eb0f50db344b397fc9 | 10.26434/chemrxiv.14182454.v1 | Mechanistic Insights into the Conversion of Dimethyl Ether over ZSM-5 Catalysts: A Combined Temperature Programmed Surface Reaction and Microkinetic Modelling Study | Rates of adsorption, desorption, and surface reaction of dimethyl ether (DME) to olefins over fresh and working ZSM-5 catalysts of different Si/Al ratios (36 and 135) have been decoupled using a combination of temperature programmed surface reaction experiments and microkinetic modelling. Transient reactor performance was simulated by solving coupled 1D non-linear partial differential equations accounting for elementary steps occurring during the induction period based on the methoxymethyl mechanism on the zeolite catalyst, and axial dispersion and convection in the reactor. Propylene is the major olefin formed and scaling relations between activation energies of DME desorption and barriers of formation of methoxymethyl and methyl propenyl ether are observed. Six ensembles of sites are observed with a maximum of three adsorption/desorption sites and three adsorption/desorption/reaction sites. Barriers are generally higher over working catalysts than fresh catalysts. Activation energies of propylene formation of ca. 200 kJ mol<sup>-1</sup> are obtained corroborating direct mechanistic proposals. | Toyin Omojola; Andre van Veen | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755eb0f50db344b397fc9/original/mechanistic-insights-into-the-conversion-of-dimethyl-ether-over-zsm-5-catalysts-a-combined-temperature-programmed-surface-reaction-and-microkinetic-modelling-study.pdf |
60c75322842e6551cedb3ebb | 10.26434/chemrxiv.11401347.v10 | Synthesis and styrene copolymerization of novel fluoro-iodo, trifluoromethyl, and trifluoromethoxy ring-substituted isobutyl phenylcyanoacrylates | <p>Novel fluoro-iodo, trifluoromethyl, and trifluoromethoxy ring-substituted isobutyl phenylcyanoacrylates, RPhCH=C(CN)CO<sub>2</sub>CH<sub>2</sub>CH(CH<sub>3</sub>)<sub>2</sub> (where R is 2-fluoro-5-iodo, 2-fluoro-6-iodo, 2-trifluoromethyl, 3-trifluoromethyl,
4-trifluoromethyl, 2-trifluoromethoxy, 3-trifluoromethoxy, 4-trifluoromethoxy) were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-substituted benzaldehydes and isobutyl cyanoacetate and characterized by CHN analysis, IR, <sup>1</sup>H and <sup>13</sup>C NMR. The acrylates were copolymerized with styrene in solution with radical initiation (ABCN) at 70C. The compositions of the copolymers were calculated from nitrogen analysis.</p> | Alessandra Cimino; Amaan M. Azeemullah; Danielle E. Comp; Sydney C. Hunt; Madison M. Janakis; Sonia S. Khan; Patryk Labedz; Christopher Lee; Sara M. Rocus; William S. Schjerven; Gregory Kharas | Organic Synthesis and Reactions; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75322842e6551cedb3ebb/original/synthesis-and-styrene-copolymerization-of-novel-fluoro-iodo-trifluoromethyl-and-trifluoromethoxy-ring-substituted-isobutyl-phenylcyanoacrylates.pdf |
60ccda7de21133ccc7df9bcc | 10.26434/chemrxiv-2021-d94vz-v2 | Docking Ligands into Flexible and Solvated Macromolecules. 8. Forming New Bonds – Challenges and Opportunities. | Over the years, structure-based design programs and specifically docking small molecules to
proteins have become prominent in drug discovery. However, many of these computational tools have
been developed to primarily dock enzyme inhibitors (and ligand to other protein classes) relying heavily
on hydrogen bonds, electrostatic and hydrophobic interactions. In reality, many drug targets either feature
metal ions, can be targeted covalently, or are simply not even proteins (e.g., nucleic acids). Herein, we
describe several new features that we have implemented into FITTED to broaden its applicability to a wide
range of covalent enzyme inhibitors, and to metalloenzymes, where metal coordination is essential for
drug binding. We also report new datasets that were essential demonstrate areas of success and those
where additional efforts are required. This resource could be used by other program developers to assess
their own | Nicolas Moitessier; Anne Labarre; Julia Stille; Mihai Burai Patrascu; Andrew Martins; Joshua Pottel | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60ccda7de21133ccc7df9bcc/original/docking-ligands-into-flexible-and-solvated-macromolecules-8-forming-new-bonds-challenges-and-opportunities.pdf |
60c74706842e65c4a8db28f2 | 10.26434/chemrxiv.11477895.v1 | Excited-State Electronic Structure of Molecules Using Many-Body Green's Functions: Quasiparticles and Electron-Hole Excitations with VOTCA-XTP | <div>We present the open-source VOTCA-XTP software for the calculation of the excited-state electronic structure of molecules using many-body Green’s functions theory in the GW approximation with the Bethe–Salpeter Equation (BSE). This work provides a summary of the underlying theory and discusses details of its implementation based on Gaussian orbitals, including, i.a., resolution-of-identity techniques, different approaches to the frequency integration of the self-energy or acceleration by offloading compute-intensive matrix operations using GPUs in a hybrid OpenMP/Cuda scheme. A distinctive feature of VOTCA-XTP is the capability to couple the calculation of electronic excitations to a classical polarizable environment on atomistic level in a coupled quantum- and molecular-mechanics (QM/MM) scheme, where a complex morphology can be imported from Molecular Dynamics simulations. The capabilities and limitations of the GW -BSE implementation are illustrated with two examples. First, we study the dependence of optically active electron-hole excitations in a series of diketopyrrolopyrrole-based oligomers on molecular-architecture modifications and the number of repeat units. Second, we use the GW -BSE/MM setup to investigate the effect of polarization on localized and intermolecular charge-transfer excited states in morphologies of low-donor content rubrene-fullerene mixtures. These showcases demonstrate that our implementation currently allows to treat systems with up to 2500 basis functions on regular shared-memory workstations, providing accurate descriptions of quasiparticle and coupled electron-hole excited states of various character on an equal footing.</div> | Gianluca Tirimbò; Vivek Sundaram; Onur Çaylak; Wouter Scharpach; Javier Sijen; Christoph Junghans; Joshua Brown; Felipe Zapata Ruiz; Nicolas Renaud; Jens Wehner; Björn Baumeier | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74706842e65c4a8db28f2/original/excited-state-electronic-structure-of-molecules-using-many-body-green-s-functions-quasiparticles-and-electron-hole-excitations-with-votca-xtp.pdf |
60c743989abda25ab3f8c205 | 10.26434/chemrxiv.9275441.v1 | Manganese-Catalyzed Electrochemical Deconstructive Chlorination of Cycloalkanols via Alkoxy Radicals | <div>
<div>
<div>
<p>A manganese-catalyzed electrochemical deconstructive chlorination of cycloalkanols has been developed. This
electrochemical method provides access to alkoxy radicals from
alcohols and exhibits a broad substrate scope, with various cyclopropanols and cyclobutanols converted into synthetically
useful β- and γ-chlorinated ketones (40 examples). Furthermore,
the combination of recirculating flow electrochemistry and continuous inline purification was employed to access products on
gram scale.
</p>
</div>
</div>
</div> | Benjamin D. W. Allen; Mishra Deepak Hareram; Alex C. Seastram; Tom McBride; Thomas Wirth; Duncan L. Browne; Louis C. Morrill | Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2019-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743989abda25ab3f8c205/original/manganese-catalyzed-electrochemical-deconstructive-chlorination-of-cycloalkanols-via-alkoxy-radicals.pdf |
63f8e711897b18336f101817 | 10.26434/chemrxiv-2023-4m5mk | Pericyclic or Pseudopericyclic? Deep Mechanism Insight into The Mi-gration Selectivity of Cb-Substituted-4aH-Carbazoles: Competition between Orbital Interaction and Electrostatic Interaction | The migration selectivity of Cb-substituted-4aH-carbazoles has been studied by DFT methods. For n-Bu and Ph substituted sub-strates, C4 migration and Ca-C1 migration are all pericyclic. C4 migration is favorable for more aromatic transition states. For halo-gen substituted substrates, C4 migration locates in the junction zone of pericyclic reactions and pseudopericyclic reactions while Ca-C1 migration is pseudopericyclic. Ca-C1 migration is favorable due to more positive NPA charges and LUMO distributions on Ca than C4. The acid catalysts with large steric hindrance can adjust the reaction selectivity through to some extent. | Jingyang Zhang; Yaqiu Zhao; Liansuo Zu | Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f8e711897b18336f101817/original/pericyclic-or-pseudopericyclic-deep-mechanism-insight-into-the-mi-gration-selectivity-of-cb-substituted-4a-h-carbazoles-competition-between-orbital-interaction-and-electrostatic-interaction.pdf |
60c751fdbb8c1a4d683dbde4 | 10.26434/chemrxiv.13238402.v1 | Population-level Membrane Diversity Triggers Growth and Division of Protocells | <div><p>To date, multiple mechanisms have been described for the growth and division of model protocells, all of which exploit the cumulative, unidirectional movement of lipids. The aggregate that is more complex grows at the expense of the smaller or less complex aggregate. Imbalances between surface area and volume during growth can generate filamentous vesicles which are typically divided by shear forces. Here we describe another pathway for growth and division that depends simply on differences in composition of fatty acid membranes. Growth is driven by the entropically-favored mixing of lipids between two populations. Division is the result of growth-induced curvature. Importantly, growth and division are cyclic and bidirectional, meaning that vesicles made from one type of lipid, e.g. short-chain fatty acids, grow and divide when fed with vesicles consisting of another type of lipid, e.g. long-chain fatty acids, and vice versa. After equilibration, additional rounds of growth and division are possible through the addition of compositionally distinct vesicles. Since prebiotic synthesis likely gave rise to mixtures of lipids, the data are consistent with the presence of growing and dividing protocells on the prebiotic Earth.</p></div> | Ö. Duhan Toparlak; Anna Wang; Sheref Mansy | Supramolecular Chemistry (Org.); Chemical Biology; Biophysical Chemistry; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751fdbb8c1a4d683dbde4/original/population-level-membrane-diversity-triggers-growth-and-division-of-protocells.pdf |
60c748e3702a9b182d18b081 | 10.26434/chemrxiv.11994489.v1 | Iron Catalyzed Synthesis and Chemical Recycling of Telechelic, 1,3-Enchained Oligocyclobutanes | Closed-loop recycling offers the opportunity to help mitigate plastic waste through reversible polymer construction and deconstruction. While examples of the chemical recycling polymers are known, few have been applied to materials derived from abundant commodity olefinic monomers that are the building blocks of ubiquitous plastic resins. Here we describe a [2+2] cycloaddition oligomerization of 1,3-butadiene to yield a previously unrealized telechelic microstructure of (1,n’-divinyl)oligocyclobutane. This material is thermally stable, has stereoregular segments arising from chain-end control, and exhibits high crystallinity even at low molecular weight. Exposure of the oligocyclobutane to vacuum in the presence of the pyridine(diimine) iron precatalyst used to synthesize it resulted in deoligomerization to generate pristine butadiene, demonstrating a rare example of closed-loop chemical recycling of an oligomeric material derived from a commodity hydrocarbon feedstock. | Megan Mohadjer Beromi; C. Rose Kennedy; Jarod M. Younker; Alex E. Carpenter; Sarah J. Mattler; Joseph A. Throckmorton; Paul J. Chirik | Oligomers; Organic Polymers; Polymer chains; Polymerization (Polymers); Polymerization catalysts; Catalysis; Polymerization (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748e3702a9b182d18b081/original/iron-catalyzed-synthesis-and-chemical-recycling-of-telechelic-1-3-enchained-oligocyclobutanes.pdf |
60c74aa0842e659164db2f8e | 10.26434/chemrxiv.8217221.v2 | DFT Benchmark Study of the O--O Bond Dissociation Energy in Peroxides Validated with High-Level Ab-Initio Calculations | <div><div><div><p>Peroxides play a central role in many chemical and biological pro- cesses such as the Fenton reaction. The relevance of these compounds lies in the low stability of the O–O bond which upon dissociation results in radical species able to initiate various chemical or biological processes. In this work, a set of 64 DFT functional-basis set combinations has been validated in terms of their capability to describe bond dissociation energies (BDE) for the O–O bond in a database of 14 ROOH peroxides for which experimental values ofBDE are available. Moreover, the electronic contributions to the BDE were obtained for four of the peroxides and the anion H2O2− at the CBS limit at CCSD(T) level with Dunning’s basis sets up to triple–ζ quality provid- ing a reference value for the hydrogen peroxide anion as a model. Almost all the functionals considered here yielded mean absolute deviations around 5.0 kcal mol−1. The smallest values were observed for the ωB97 family and the Minnesota M11 functional with a marked basis set dependence. Despite the mean deviation, order relations among BDE experimental values of peroxides were also considered. The ωB97 family was able to reproduce the relations correctly whereas other functionals presented a marked dependence on the chemical nature of the R group. Interestingly, M11 functional did not show a very good agreement with the established order despite its good performance in the mean error. The obtained results support the use of similar validation strategies for proper prediction of BDE or other molecular properties by DF Tmethods in subsequent related studies.</p></div></div></div> | Danilo Carmona; Pablo Jaque; Esteban Vöhringer-Martinez | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74aa0842e659164db2f8e/original/dft-benchmark-study-of-the-o-o-bond-dissociation-energy-in-peroxides-validated-with-high-level-ab-initio-calculations.pdf |
60c74a14337d6c1826e277ec | 10.26434/chemrxiv.12142275.v1 | Evaluation of Reaction Between 2,4-Thiazolidinedione and P-Methoxybenzaldehyde in Microreactors for Production of Drugs for Treatment of Diabetes Mellitus Type 2 | The
use of microreactors in chemical and pharmaceutical industries allow a series
of advantages due to their reduced sizes regarding conventional batch reactors.
In the present paper the transposition of the reaction between 2,4-Thiazolidinedione
with p-Methoxybenzaldehyde, generating the compound with potential biological
action against diabetes mellitus type II, from batch to a continuous capillary microreactor
was carried out. The microdevice performance was evaluated experimentally and
numerically by Computational Fluid Dynamics. The efficiency and viability of microreactors usage for
the intermediate pharmaceutical active production was assessed. The optimized
operating conditions were obtained for the batch reactor (processing time) and
microreactor (residence time), the promoter base selection and optimal
concentration was also performed, in order to maximize reactants conversion and
reaction yield. Considering the acquired data, computational fluid dynamic simulations were carried out, allowing obtaining a computational methodology to be used for a fast increment of production from microreactor to industrial demand. | Rodrigo Vieira; Harrson Santana; João Silva Jr.; Paula Meira; Gabriel Bressan; Osvaldir Pereira Taranto; Paulo Calvo; Mauri Palma | Organic Synthesis and Reactions; Pharmaceutical Industry | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a14337d6c1826e277ec/original/evaluation-of-reaction-between-2-4-thiazolidinedione-and-p-methoxybenzaldehyde-in-microreactors-for-production-of-drugs-for-treatment-of-diabetes-mellitus-type-2.pdf |
60c73db8337d6cb644e261d7 | 10.26434/chemrxiv.5827758.v2 | Diazonium-functionalized thin films from the spontaneous reaction of p-phenylenebis(diazonium) salts | Salts of the diazonium coupling agent <i>p</i>-phenylenebis(diazonium) form diazonium-terminated conjugated thin films on a variety of conductive and nonconductive surfaces by spontaneous reaction of the coupling agent with the surface. The resulting diazonium-bearing surface can be reacted with various organic and inorganic nucleophiles to form a functionalized surface. These surfaces have been characterized with voltammetry, XPS, infrared and Raman spectroscopy, and atomic force microscopy. Substrates that can be conveniently and quickly modified with this process include ordinary glass, gold, and an intact, fully assembled commercial screen-printed carbon electrode. The scope and convenience of this process makes it promising for practical surface modification. | Nicholas Marshall; Andres Rodriguez; Scott Crittenden | Coating Materials; Multilayers; Thin Films | CC BY 4.0 | CHEMRXIV | 2018-01-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73db8337d6cb644e261d7/original/diazonium-functionalized-thin-films-from-the-spontaneous-reaction-of-p-phenylenebis-diazonium-salts.pdf |
60c74fc9bb8c1a092e3dba05 | 10.26434/chemrxiv.12366776.v2 | Natural Contaminants in Infant Food: The Case of Regulated and Emerging Mycotoxins | Breast milk substitutes, e.g. infant formulae, are commonly introduced to the diet within the first months of life. As the infants detoxifying capability is not fully developed, it is of vital importance to minimize their exposure to food contaminants. Here, we present a comprehensive multi-mycotoxin assessment in infant food. Samples from the Austrian and Czech market (n=59) were screened for 46 mycotoxins and key metabolites using two complementary LC-MS/MS methods. Trace levels of 17 mycotoxins, including aflatoxin B<sub>1</sub> (0.4 µg/kg), zearalenone (<2.3 µg/kg), deoxynivalenol (<131 µg/kg) and fumonisin B<sub>1</sub> (<39 µg/kg) were detect-ed. Infant formulae were contaminated at lower levels compared to cereal-based products. Overall, the concentrations of most toxins were near or below their respective LOQ value. However, two raw flour samples exceeded the regulatory limit of aflatoxin B<sub>1</sub> for infant foods. Interestingly, two toxins not reported previously, namely aflatoxicol and sterigmatocystin, were identified in 3 and 17% of infant foods, respectively.<br /> | Dominik Braun; Maximilian Eiser; Hannes Puntscher; Doris Marko; Benedikt Warth | Environmental Science; Analytical Chemistry - General; Mass Spectrometry; Food | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fc9bb8c1a092e3dba05/original/natural-contaminants-in-infant-food-the-case-of-regulated-and-emerging-mycotoxins.pdf |
60c74e244c8919e889ad395d | 10.26434/chemrxiv.12643430.v2 | Evidence of Unique Stacking and Related Topological Defects in the Honeycomb Layered Oxide: K2Ni2TeO6 | <div><b>Endowed with a multitude of exquisite properties such as rich electrochemistry, superb topology and eccentric electromagnetic phenomena, honeycomb layered oxides have risen to the top echelons of science with applications in diverse fields ranging from condensed matter physics, solid-state chemistry, materials science, solid-state ionics to electrochemistry. Although these features are known to stem from the utilitarian structure innate in these oxides, their functionalities are vastly underutilised as their underlying atomistic mechanisms remain unknown. Therefore in this study, atomic resolution imaging on pristine K<sub>2</sub>Ni<sub>2</sub>TeO<sub>6 </sub>along multiple zone axes were conducted using spherical aberration-corrected scanning transmission electron microscopy (Cs-corrected STEM) to reveal hitherto unreported topological defects and curvature which can be associated with various phase transitions. Furthermore we discover, <i>for the first time</i>, the occurrence of a new stacking variant with P3-type sequence alongside the well-reported P2-type stacking domains. Through this work, we provide insights into the connection between these unique structural disorders to the electrochemical properties of honeycomb layered oxides. The mechanism of the phase transitions reported herein is bound to become apparent upon high alkali-ion mobility, providing invaluable clues to potentially improve their functional performance in, for instance, energy storage applications. Our findings have the potential to inspire further experimental and theoretical studies into the role of stacking and topology in honeycomb layered oxides.</b></div> | Titus Masese; Yoshinobu Miyazaki; Godwill Mbiti Kanyolo; Teruo Takahashi; Miyu Ito; Hiroshi Senoh; Tomohiro Saito | Ceramics; Composites; Multilayers; Nanostructured Materials - Materials; Imaging; Microscopy; Spectroscopy (Anal. Chem.); Nanostructured Materials - Nanoscience; Coordination Chemistry (Inorg.); Electrochemistry; Solid State Chemistry; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Physical and Chemical Properties; Structure; Crystallography; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e244c8919e889ad395d/original/evidence-of-unique-stacking-and-related-topological-defects-in-the-honeycomb-layered-oxide-k2ni2te-o6.pdf |
62468f9358f7af2f0eae6081 | 10.26434/chemrxiv-2022-8r5v9 | How Good is the Density-Corrected SCAN Functional for Neutral and Ionic Aqueous Systems, and What is so Right about the Hartree-Fock Density? | Density functional theory (DFT) is the most widely used electronic structure method, due to its simplicity and cost effectiveness. The accuracy of a DFT calculation de- pends not only on the choice of the density functional approximation (DFA) adopted but also on the electron density produced by the DFA. SCAN is a modern functional that satisfies all known constraints for meta-GGA functionals. The density-driven errors, defined as energy errors arising from errors of the self-consistent DFA electron density, can hinder SCAN from achieving chemical accuracy in some systems, including water. Density-corrected DFT (DC-DFT) can alleviate this shortcoming by adopting a more accurate electron density which, in most applications, is the electron density obtained at the Hartree-Fock level of theory due to its relatively low computational cost. In this work, we present extensive calculations aimed at determining the accuracy of the DC-SCAN functional for various aqueous systems. DC-SCAN (SCAN@HF) shows remarkable consistency in reproducing reference data obtained at the coupled cluster level of theory, with minimal loss of accuracy. Density-driven errors in the description of ionic aqueous clusters are thoroughly investigated. By comparison with the orbital-optimized CCSD density in the water dimer, we find that the self-consistent SCAN density transfers a spurious fraction of an electron across the hydrogen bond to the hydrogen atom (H⋆, covalently bound to the donor oxygen atom) from the acceptor (OA) and donor (OD) oxygen atoms, while HF makes a much smaller spurious transfer in the opposite direction, consistent with DC-SCAN (SCAN@HF) reduction of SCAN over-binding due to delocalization error. While LDA seems to be the conventional extreme of density delocalization error, and HF the conventional extreme of (usually much smaller) density localization error, these two densities do not quite yield the conventional range of density-driven error in energy differences. Finally, comparisons of the DC-SCAN results with those obtained with the Fermi-Lowdin orbital self-interaction correction (FLOSIC) method show that DC-SCAN represents a more accurate approach to reducing density-driven errors in SCAN calculations of ionic aqueous clusters. | Saswata Dasgupta; Chandra Shahi; Pradeep Bhetwal; John P. Perdew; Francesco Paesani | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Physical and Chemical Properties; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62468f9358f7af2f0eae6081/original/how-good-is-the-density-corrected-scan-functional-for-neutral-and-ionic-aqueous-systems-and-what-is-so-right-about-the-hartree-fock-density.pdf |
65536f12dbd7c8b54b3e7de4 | 10.26434/chemrxiv-2023-pp9p5 | Kinetic Asymmetry and Directionallity of Nonequilibrium Molecular Systems | Scientists have long been fascinated by the biomolecular machines in living systems that process energy and information to sustain life. The first synthetic molecular rotor capable of performing repeated 360o rotations due to a combination of photo- and thermally activated processes was reported in 1999. The progress in designing different molecular machines in the intervening years has been remarkable, with several outstanding examples appearing in the last few years. Despite the synthetic accomplishments, there remains confusion regarding the fundamental design principles by which the motions of molecules can be controlled, with significant intellectual tension between mechanical and chemical ways of thinking about and describing molecular machines. A thermodynamically consistent analysis of the kinetics of several molecular rotors and pumps shows that while light driven rotors operate by a power-stroke mechanism, kinetic asymmetry – the relative heights of energy barriers – is the sole determinant of the directionality of catalysis driven machines. Power-strokes – the relative depths of energy wells – play no role whatsoever in determining the sign of the directionality. These results, elaborated using trajectory thermodynamics and the nonequilibrium pump equality, show that kinetic asymmetry governs the response of many non-equilibrium chemical phenomena. | Raymond Dean Astumian | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Biophysical Chemistry; Chemical Kinetics; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65536f12dbd7c8b54b3e7de4/original/kinetic-asymmetry-and-directionallity-of-nonequilibrium-molecular-systems.pdf |
6787d2be81d2151a0244e927 | 10.26434/chemrxiv-2025-5brgq | Environmental Control of Spin State Through Solution Aggregation | Direct environmental control of the spin state is observed in alkyl sulfate Fe(III) complexes of 5-OMeSal2trien. High spin, low spin and mixed spin state responses are controlled by the aggregation properties of the dodecyl and octadecyl sulfate anions. Smaller particles favour the LS state due to size constraints, while larger aggregate formation favours the HS state allowing it to take up more space in a larger, relaxed particle. | Francesca Robertson; Glenieliz Dizon; Anthony Fitzpatrick | Inorganic Chemistry; Coordination Chemistry (Inorg.); Magnetism; Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6787d2be81d2151a0244e927/original/environmental-control-of-spin-state-through-solution-aggregation.pdf |
6228badb57a9d22b467929bc | 10.26434/chemrxiv-2022-4rkf5 | Controlling One- or Two-Electron Oxidation for Selective Amine Functionalization by Alternating Current Frequency | Here, we report a unique electrosynthetic method that enables selective one-electron oxidation of tertiary amines to generate α-amino radical intermediates over the two-electron oxidation to iminium cations, providing easy access to arylation products by simply applying an optimal alternating current (AC) frequency. More importantly, we have discovered an electrochemical descriptor from cyclic voltammetry studies to predict the optimal AC frequency for various amine substrates, circumventing the time-consuming trial-and-error methods for optimizing reaction conditions. This new development in AC electrolysis provides an alternative strategy to solving challenging chemoselectivity problems in synthetic organic chemistry. | Disni Gunasekera,; Jyoti Mahajan; Yanick Wanzi; Sachini Rodrigo; Wei Liu; Ting Tan; LONG LUO | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6228badb57a9d22b467929bc/original/controlling-one-or-two-electron-oxidation-for-selective-amine-functionalization-by-alternating-current-frequency.pdf |
62e692fb5be0413e00a384ab | 10.26434/chemrxiv-2022-sqg7v | Modeling coarse-grained van der Waals interactions using dipole-coupled anisotropic quantum Drude oscillators | The Quantum Drude Oscillator (QDO) model is a promising candidate for accurately calculating the van der Waals (vdW) energies. Anisotropic QDO models have recently been used to represent molecular fragments rather than single atoms. While this model promises accurate calculation of vdW energies, there is significant room for improvements such as incorporating a proper fragmentation method, higher-order dispersion corrections, etc. The present work attempts to gauge dipole-dipole interactions’ ability without
fragmentation. A suitable anisotropic damping function is also introduced to work with anisotropic QDO. This revised model accurately predicts the vdW complex for the majority of the systems considered. This work indicates the limit of dipole approximation for an anisotropic QDO-based model. | Prasanta Bandyopadhyay; Mainak Sadhukhan | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e692fb5be0413e00a384ab/original/modeling-coarse-grained-van-der-waals-interactions-using-dipole-coupled-anisotropic-quantum-drude-oscillators.pdf |
63bd1ab7a68d7b3f623290d3 | 10.26434/chemrxiv-2023-64n4r | Tracking C-H activation with orbital resolution | The reactivity towards C-H bond activation of alkanes with transition metals is determined by the ability of the metal to donate and withdraw electron density in due proportion. Manipulating this reactivity in a controlled way is difficult, because the hypothesized metal-alkane charge-transfer interactions are challenging to access experimentally. Using time-resolved X-ray spectroscopy, we track the charge-transfer interactions in a C-H activating Rh complex and reveal changes in oxidation state as well as valence-orbital energies and character from femtosecond Rh-alkane bond formation to nanosecond C-H bond cleavage. Our X-ray spectroscopic signatures reflect how alkane-to- metal donation determines metal-alkane bond stability and how metal-to-alkane back-donation facilitates C-H bond cleavage by oxidative addition. The ability to dissect charge-transfer interactions on an orbital-level provides new opportunities for manipulating reactivity for C-H activation with transition metals. | Raphael Jay; Ambar Banerjee; Torsten Leitner; Ru-Pan Wang; Jessica Harich; Robert Stefanuik; Hampus Wikmark; Michael Coates; Emma Beale; Victoria Kabanova; Abdullah Kahraman; Anna Wach; Dmitry Ozerov; Christopher Arrell; Philip Johnson; Camelia Borca; Claudio Cirelli; Camila Bacellar; Christopher Milne; Nils Huse; Grigory Smolentsev; Thomas Huthwelker; Michael Odelius; Philippe Wernet | Physical Chemistry; Inorganic Chemistry; Organometallic Chemistry; Spectroscopy (Inorg.); Bond Activation; Photochemistry (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2023-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bd1ab7a68d7b3f623290d3/original/tracking-c-h-activation-with-orbital-resolution.pdf |
6707796d12ff75c3a106db48 | 10.26434/chemrxiv-2024-fn51v-v2 | Structure-switching DNA templates for the rational and predictable control of cell-free transcription | We report here a strategy to control cell-free in vitro transcription of RNA by the rational design of synthetic structure-switching DNA templates. These templates are programmed to undergo a conformational change between an open (OFF) and a closed (ON) state. By controlling the switching equilibrium constant (KS) of such structure-switching templates, we can finely program their transcription efficiency. We have derived a simplified kinetic model that describes our experimental data with high accuracy, supporting the predictability of our approach. Similarly, we have also performed different molecular dynamic simulations that provide an atomistic description of our results. Finally, the introduction of such a conformational change mechanism in target-responsive templates allows rational control of their dynamic range (i.e., the range of target concentration to which they respond) and of their input-output behavior. The structure-switching templates demonstrated in this work are particularly easy to design and provide a highly programmable approach to control cell-free transcription, a feature that can be of great utility in fields like sensing and RNA therapeutics. | Ana Urosevic; Iacovelli Federico; Gianfranco Ercolani; Andrea Idili; Francesco Ricci | Physical Chemistry; Analytical Chemistry; Nanoscience; Nanodevices; Thermodynamics (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6707796d12ff75c3a106db48/original/structure-switching-dna-templates-for-the-rational-and-predictable-control-of-cell-free-transcription.pdf |
6189298a92abe0059639a51c | 10.26434/chemrxiv-2021-86w18 | Embedding non-rigid solutes in an averaged environment: a case study on rhodopsins | Many simulation methods concerning solvated molecules are based on the assumption that the solvated species and the solvent can be characterized by some representative structure of the solute and some embedding potential corresponding to this structure.
This assumption is re-examined and generalized for conformationally flexible solutes. In the proposed and investigated generalization, the solute is characterized by a set of representative structures and the corresponding embedding potentials. The representative structures are identified by means of subdividing the statistical ensemble, which in this work is generated by a constant-temperature molecular dynamics simulation. The embedding potential defined in Frozen-Density Embedding Theory is used to characterize the average effect of the solvent in each subensemble.
The numerical examples concern vertical excitation energies of protonated retinal Schiff bases in protein environments. It is comprehensively shown that subensemble averaging leads to huge computational savings compared to explicit averaging of the excitation energies in the whole ensemble while introducing only minor errors. | Niccolò Ricardi; Cristina Elizabeth González-Espinoza; Suliman Adam; Jonathan Church; Igor Schapiro; Tomasz Adam Wesolowski | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2021-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6189298a92abe0059639a51c/original/embedding-non-rigid-solutes-in-an-averaged-environment-a-case-study-on-rhodopsins.pdf |
670033ebcec5d6c1422a679e | 10.26434/chemrxiv-2023-33r87-v2 | Disorder-mediated ionic conductivity in irreducible solid electrolytes | Solid state batteries currently receive extensive attention due to their potential to outperform lithium ion batteries in terms of energy density when featuring next generation anodes such as lithium metal or silicon. However, most highly conducting solid electrolytes decompose at the low operating voltages of next-generation anodes leading to irreversible lithium loss and increased cell resistance. Such performance losses may be prevented by designing electrolytes which are thermodynamically stable at low operating voltages (anolytes). Here, we report on the discovery a new family of irreducible (i.e. fully reduced) electrolytes by mechanochemically dissolving lithium nitride into the Li2S antifluorite structure, yielding highly conducting crystalline Li2+xS1-xNx phases reaching > 0.2 mS cm-1 at ambient temperatures. Combining impedance spectroscopy experiments and ab initio density functional theory calculations we clarify the mechanism by which the disordering of the sulfide and nitride ions in the anion sublattice boosts ionic conductivity in Li2+xS1-xNx phases by a factor 10^5 compared to the Li2S host structure. This advance is achieved through a novel theoretical framework, leveraging percolation analysis with local-environment-specific activation energies and is widely applicable to disordered ion conductors. The same methodology allows us to rationalize how increasing nitrogen content in Li2+xS1-xNx antifluorite-like samples leads to both increased ionic conductivity and lower conductivity-activation energy. These findings pave the way to understanding disordered solid electrolytes and eliminating decomposition-induced performance losses on the anode side in solid-state batteries. | Victor Landgraf; Mengfu Tu; Wenxuan Zhao; Anastasiia Lavrinenko; Zhu Cheng; Jef Canals; Joris de Leeuw; Swapna Ganapathy; Alexandros Vasileiadis; Marnix Wagemaker; Theodosios Famprikis | Theoretical and Computational Chemistry; Materials Science; Inorganic Chemistry; Electrochemistry; Solid State Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670033ebcec5d6c1422a679e/original/disorder-mediated-ionic-conductivity-in-irreducible-solid-electrolytes.pdf |
63874df0e474bf261056bcdb | 10.26434/chemrxiv-2022-zgg8s-v2 | MORTAR – A Rich Client Application for in silico Molecule Fragmentation | Developing and implementing computational algorithms for the extraction of specific substructures from molecular graphs (in silico molecule fragmentation) is an iterative process. It involves repeated sequences of implementing a rule set, applying it to relevant structural data, checking the results, and adjusting the rules. This requires a computational workflow with data import, fragmentation algorithm integration, and result visualisation. The described workflow is normally unavailable for a new algorithm and must be set up individually. This work presents an open Java rich client Graphical User Interface (GUI) application to support the development of new in silico molecule fragmentation algorithms and make them readily available upon release. The MORTAR (MOlecule fRagmenTAtion fRamework) application visualises fragmentation results of a set of molecules in various ways and provides basic analysis features. Fragmentation algorithms can be integrated and developed within MORTAR by using a specific wrapper class. In addition, fragmentation pipelines with any combination of the available fragmentation methods can be executed. Upon release, three fragmentation algorithms are already integrated: ErtlFunctionalGroupsFinder, Sugar Removal Utility, and Scaffold Generator. These algorithms, as well as all cheminformatics functionalities in MORTAR, are implemented based on the Chemistry Development Kit (CDK). | Felix Bänsch; Jonas Schaub; Betül Sevindik; Samuel Behr; Julian Zander; Christoph Steinbeck; Achim Zielesny | Theoretical and Computational Chemistry; Organic Chemistry; Natural Products; Organic Compounds and Functional Groups; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63874df0e474bf261056bcdb/original/mortar-a-rich-client-application-for-in-silico-molecule-fragmentation.pdf |
621fbd0191a2e6eb78e27cd1 | 10.26434/chemrxiv-2022-lddzf | Transformer Oil Nanofluids by Two Dimensional hexagonal Boron Nitride Nanofillers | This paper explores the fascinating properties of two-dimensional (2D) nanofillers based transformer oil (TO) nanofluids. Nanofluids of 2D hexagonal boron nitride (h-BN) nanosheets in TO demonstrate stable dispersion with improved dielectric breakdown strength and superior thermo physical properties like thermal conductivity, viscosity and stability. An appreciable augmentation in AC breakdown voltage (BDV) is observed compared to the state-of-the-art boron nitride (BN) particles. This enhancement in BDV is elucidated by the role of the greater surface area of Maxwell-Garnet ‘oil-sheet’ interfacial region of the 2D morphology in charge trapping perspective. The faster rate of heating and cooling along with noteworthy enhancement in thermal conductivity is due to the interfacial heat transfer via 2D nanoadditives prompting good phonon transport which agrees with Maxwell's forecasts. Addition of 2D nanofiller at diluted concentration exhibits better stability and high thermal efficiency compared to its particle counterpart. Hence, 2D nanofillers are better choices for next generation transformer oil nanofluids, due to their high surface area, lower filler fraction and better stability. | Mississippi Missouri Bhunia; Paramita Chattopadhyay; Kalyan Kumar Chattopadhyay | Materials Science; Nanoscience; Materials Processing; Nanofluidics | CC BY NC 4.0 | CHEMRXIV | 2022-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621fbd0191a2e6eb78e27cd1/original/transformer-oil-nanofluids-by-two-dimensional-hexagonal-boron-nitride-nanofillers.pdf |
60c74854bdbb89b1a0a38f76 | 10.26434/chemrxiv.11845272.v2 | Visible-Light Photoswitching of G-Quadruplex Ligand Binding Mode Allows Reversible Control of G-Tetrad Structure | <div><p>Photoresponsive ligands for G-quadruplex oligonucleotides (G4) offer exciting opportunities for the reversible regulation of these assemblies with potential applications in biological chemistry and responsive nanotechnology. However, achieving the robust regulation of G4 ligand activity with low-energy visible light sources that are easily accessible and compatible with biological systems remains a significant challenge to realizing these applications. Herein, we report the G4-binding properties of a photoresponsive dithienylethene (DTE). We demonstrate the first example of G4-specific acceleration of the photoswitching kinetics of a small molecule and the visible-light mediated switching of the G4 ligand binding mode in physiologically-relevant conditions, which in turn allows control over the G4 tetrad structure of telomeric G4 in potassium buffer. The process is fully reversible and avoids the need for high-energy UV light. This affords an efficient, practical and biologically-relevant means of control that may be applied in the generation of new responsive G4/ligand supramolecular systems.</p></div><br /> | Michael O'Hagan; Javier Ramos Soriano; Susanta Haldar; Juan Carlos Morales; Adrian Mulholland; M. Carmen Galan | Bioorganic Chemistry; Organic Compounds and Functional Groups; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74854bdbb89b1a0a38f76/original/visible-light-photoswitching-of-g-quadruplex-ligand-binding-mode-allows-reversible-control-of-g-tetrad-structure.pdf |
650ef9e4ed7d0eccc313249a | 10.26434/chemrxiv-2023-nblfv-v2 | Predicting Poisson's Ratio: A Study of Semi-supervised Anomaly Detection and Supervised Approaches | Auxetics are a rare class of materials that exhibit a negative Poisson's ratio. The existence of these auxetic materials is rare but has a large number of applications in designing exotic materials. We build a complete machine learning framework to detect Auxetic materials as well as Poisson’s ratio of non-auxetic materials. A semi-supervised anomaly detection model is presented which is capable of separating out the auxetics materials (treated as an anomaly) from an unknown database with an average precision of 0.64. Another regression model (supervised) is also created to predict the Poisson’s ratio of non-auxetic materials with an R² ≈ 0.82. Additionally, this regression model helps in finding the optimal features for the anomaly detection model. This methodology can be generalized and used to discover materials with rare physical properties. | Raheel Hammad; Sownyak Mondal | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Elastic Materials; Theory - Computational; Machine Learning | CC BY 4.0 | CHEMRXIV | 2023-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650ef9e4ed7d0eccc313249a/original/predicting-poisson-s-ratio-a-study-of-semi-supervised-anomaly-detection-and-supervised-approaches.pdf |
61fbf76dbd05a0008dfa5325 | 10.26434/chemrxiv-2022-j6nwl | Chemical Synthesis of Human Selenoprotein F and Elucidation of Its Thiol-Disulfide Oxidoreductase Activity | Selenoprotein F (SelF) is an endoplasmic reticulum-residing eukaryotic protein that contains a selenocysteine (Sec) residue. It has been suggested to be involved in a number of physiological processes by acting as a thiol-disulfide oxidoreductase, but the exact role has remained unclear due to the lack of a reliable production method. We document herein a robust synthesis of the human SelF through a three-segment two-ligation semisynthesis strategy. Highlighted in this synthetic route are the use of a mild desulfurization process to protect the side-chain of the Sec residue from being affected and the simultaneous removal of acetamidomethyl and p-methoxybenzyl protection groups by PdCl2, thus facilitating the synthesis of multi-milligram of homogenous SelF. The reduction potential of SelF was determined and the thiol-disulfide oxidoreductase activity was further supported by its ability to catalyze the reduction and isomerization of disulfide bonds. | Peisi Liao; Hongmei Liu; Chunmao He | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61fbf76dbd05a0008dfa5325/original/chemical-synthesis-of-human-selenoprotein-f-and-elucidation-of-its-thiol-disulfide-oxidoreductase-activity.pdf |
63aaa05804902ab2ef110b73 | 10.26434/chemrxiv-2022-8gc2q-v2 | The state of the art in core-shell type lipid polymer hybrid nanocarriers and beyond | The need to enhance the therapeutic effect of drugs and thus reduce their side effects is the reason for the emergence of today's drug delivery systems. With the advent of nanotechnology, numerous molecular structures - from carbon nanotubes to polymeric materials - have been developed, and significant progress has been made. However, all these promising results do not mean that drug delivery systems are a solution to all problems in pharmaceutical technology. This is because any drug delivery system, while having its advantages, also suffers from certain limitations. Therefore, new and hybrid structures are created by combining different materials. In this respect, lipid-polymer hybrid particles emerged as a core-shell structure, where the polymer core is covered with a layer of phospholipids, and have attracted attention in the academic community.
This manuscript, which provides an overview of the fundamentals of these molecular architectures, begins with a description of lipid-polymer hybrid particles. Conventional and unconventional production methods for fabricating these structures are then described. This is followed by a section discussing how the physical properties of these particles are characterized and how the physical properties affect pharmaceutical activity. The final section discusses prominent examples from the literature.
| Ceyda Tuba Sengel-Turk; Onur ALPTÜRK | Biological and Medicinal Chemistry; Polymer Science | CC BY 4.0 | CHEMRXIV | 2022-12-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63aaa05804902ab2ef110b73/original/the-state-of-the-art-in-core-shell-type-lipid-polymer-hybrid-nanocarriers-and-beyond.pdf |
67382f0a5a82cea2fa44c83d | 10.26434/chemrxiv-2024-9l3f2 | Comment on ”Exploring potential energy surfaces to reach saddle points above convex regions” [J. Chem. Phys. 160, 232501 (2024)] by M.Gunde et al. | We comment on the work on convex regions of the potential energy surface (PES) of a molecule by M. Gunde; A. Jay; M. Poberˇznik; N. Salles; N. Richard; G. Landa; N. Mousseau; L. Martin-Samos and A. Hemeryck [J. Chem. Phys. 160, 232501 (2024)]. In contrast to the activation-relaxation technique nouveau (ARTn), in the present work we apply the theory of Newton trajectories (NTs) to the 2D PES. NTs have no problem traversing convex or concave regions of the PES. The ARTn is compared with NTs. | Wolfgang Quapp; Josep Maria Bofill | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67382f0a5a82cea2fa44c83d/original/comment-on-exploring-potential-energy-surfaces-to-reach-saddle-points-above-convex-regions-j-chem-phys-160-232501-2024-by-m-gunde-et-al.pdf |
62e450bdcc34e529406b646b | 10.26434/chemrxiv-2022-v0fbc | Design of workflows for cross-talk detection and lifetime deviation onset in Li-ion batteries
| Developing advanced electrolytes or electrode materials for Li-ion batteries heavily relies on the use of performance metrics, among which capacity retention and coulombic efficiency remains the gold standards. While powerful at predicting initial degradation rates, these metrics fall short to predict knee points that can abruptly lead to the sudden death of battery cells. Indeed, knee points often originate from complex interplays between electrodes, through a cascade of parasitic reactions or modification of cell balancing. In this work, we analyze and demonstrate how combining adequate electrochemical testing protocols, coupled with analysis such as differential voltage analysis or capacity marching analysis, allows disentangling effects as complex as cross talking events for selected graphite/Ni-rich cell chemistries. We believe that, using this set of workflows, comprehensive analysis of capacity retention curves can be accurately carried out, and should become the new standard for screening novel electrolytes and materials for high performance battery chemistries. | Valentin Meunier; Matheus Leal de Souza; Mathieu Morcrette; Alexis Grimaud | Materials Science; Energy; Energy Storage | CC BY NC 4.0 | CHEMRXIV | 2022-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e450bdcc34e529406b646b/original/design-of-workflows-for-cross-talk-detection-and-lifetime-deviation-onset-in-li-ion-batteries.pdf |
6541fa6d48dad23120d390be | 10.26434/chemrxiv-2023-wbpxb | Photoswitchable Imines: Aryliminopyrazoles Quantitatively Convert to Long-Lived Z-Isomers with Visible Light | Arylimines offer promise in dynamic-covalent materials due to their recyclability and ease of synthesis. However, their light-triggered E/Z isomerism has received little attention. This is attributed to challenges that include low thermal stability of their metastable state (<60 s at 20 °C), incomplete photoswitching (<50% to the metastable state), and the need for UV light (≤365 nm). We overcome these limitations with a novel class of imine photoswitch, the aryliminopyrazoles (AIPs). These AIPs can be switched using visible light (470 nm), attain photostationary states with over 95% of the Z-isomer, exhibit great resistance to fatigue, and have thermal half-lives up to 19.2 hours at room temperature. Additionally, they display T-type and negative photochromism under visible light irradiation—a useful property. The quantitative assembly, accessibility of precursors, and recyclability set these photoswitches apart from their azo-based analogues. These findings open avenues for next-generation photoresponsive dynamic-covalent materials driven solely by these new photochromic linkages and further exploration of photocontrolled dynamic combinatorial chemistry. | Jiarong Wu; Lasse Kreimendahl; Suyuan Tao; Olga Anhalt; Jake Greenfield | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Combinatorial Chemistry; Photochemistry (Org.); Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6541fa6d48dad23120d390be/original/photoswitchable-imines-aryliminopyrazoles-quantitatively-convert-to-long-lived-z-isomers-with-visible-light.pdf |
62594a66d048ed914c43d19a | 10.26434/chemrxiv-2022-82s0k | Peptidomimetic small-molecule inhibitors of 3CLPro activity and Spike-ACE2 interaction: towards dual-action molecules against Coronavirus infections | The development of molecules able to target protein-protein interactions (PPIs) is of interest for the development of nov-el therapeutic agents. Since a high percentage of PPIs are mediated by α-helical structure at the interacting surface, pep-tidomimetics that reproduce the essential conformational components of helices are useful templates for the develop-ment of PPIs inhibitors. In this work, the synthesis of a constrained dipeptide isostere and insertion in the short peptide epitope EDLFYQ of the ACE2 α-helix 1 domain resulted in the identification of a molecule capable of inhibiting the SARS-CoV-2 ACE-2/Spike interaction in the micromolar range. Moreover, inhibition of SARS-CoV-2 3CLPro main protease activi-ty was assessed as an additional inhibitory property of the synthesized peptidomimetics, taking advantage of the C-terminal Q amino acid present in both the ACE2 epitope and the Mpro recognising motif (APSTVxLQ), thus paving the way to the development of multitarget therapeutics towards Coronavirus infections. | Filomena Tedesco; Lorenzo Calugi; Elena Lenci; Andrea Trabocchi | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Biochemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62594a66d048ed914c43d19a/original/peptidomimetic-small-molecule-inhibitors-of-3cl-pro-activity-and-spike-ace2-interaction-towards-dual-action-molecules-against-coronavirus-infections.pdf |
63cfd07711259630b878823a | 10.26434/chemrxiv-2023-4l9tl | Enhanced liposomal drug delivery via membrane fusion triggered by dimeric coiled-coil peptides | An ideal nanomedicine system improves the therapeutic efficacy of a drug. However, most nanomedicines enter the cell via endosomal/lysosomal pathways and typically only a small fraction of the cargo enters the cytosol inducing a therapeutic effect. To circumvent these inefficient drug delivery pathways, alternative approaches are desired. Inspired by fusion machinery found in nature, various synthetic fusogens have been developed to mediate the fusion of vesicles. Previously we used lipidated versions of the heterodimeric peptide pair E4/K4 to induce membrane fusion and applied this approach to deliver drugs in vitro and in vivo. Peptide K4 was designed to interact specifically with peptide E, but it was also shown to have an affinity for lipid membranes resulting in membrane remodeling. As the next step towards efficient in vivo membrane fusion for potential therapeutic applications, our rationale was to design efficient fusogen variants that could have multiple interactions simultaneously. To achieve this goal, we synthesized dimeric coiled-coil peptide variants of peptide K to facilitate improved fusion with peptide E-modified liposomes and mammalian cells. The secondary structure and self-assembly of various dimers were studied; the parallel PK4 dimer forms temperature-dependent higher-order assemblies, while linear K4 dimers form tetramer-like homodimers. The findings regarding the structures and membrane interactions of the PK4 dimer were supported by molecular dynamics simulations. Upon addition of the complementary peptide E4, the parallel PK4 dimer induced the strongest coiled-coil interaction resulting in a higher cellular uptake of the liposome-encapsulated cargo, as compared to the linear dimer and monomeric designs. Using a wide spectrum of endocytosis inhibitors, it was shown that membrane fusion was the main cellular uptake pathway. Delivery of the antitumor drug doxorubicin (DOX) resulted in efficient cellular delivery and concomitant antitumor efficacy. These findings not only offer important mechanistic insights into the design of coiled-coil driven membrane fusion systems but also provide novel strategies for developing peptide-based biomaterials. | Ye Zeng; MengJie Shen; Ankush Singhal; Geert Jan Sevink; Niek Crone; Aimee Boyle; alexander kros | Biological and Medicinal Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Biophysics; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63cfd07711259630b878823a/original/enhanced-liposomal-drug-delivery-via-membrane-fusion-triggered-by-dimeric-coiled-coil-peptides.pdf |
60c7514a702a9b6b5a18bf0d | 10.26434/chemrxiv.13146248.v1 | Catalytic Asymmetric and Stereodivergent Oligonucleotide Synthesis | <p>We report the catalytic stereocontrolled synthesis of dinucleotides. Chiral phosphoric
acid (CPA) catalysts are demonstrated to control the formation of stereogenic phosphorous centers
during phosphoramidite transfer for the first time. Unprecedented levels of diastereodivergence
are also demonstrated, enabling access to either phosphite diastereomer. Notably, two different CPA scaffolds prove essential for achieving stereodivergence: peptide-embedded
phosphothreonine-derived CPAs, which reinforce and amplify the inherent substrate preference,
and C2-symmetric BINOL-derived CPAs, which completely overturn this stereochemical
preference. The presently reported catalytic method does not require stoichiometric activators or
chiral auxiliaries and enables asymmetric catalysis with readily available phosphoramidites. The method was applied to the stereocontrolled synthesis of diastereomeric dinucleotides as well as
cyclic dinucleotides (CDNs) which are of broad interest in immono-oncology as agonists of the
STING pathway.</p> | Aaron L. Featherston; Yongseok Kwon; Matthew Pompeo; Oliver Engl; David K. Leahy; Scott Miller | Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7514a702a9b6b5a18bf0d/original/catalytic-asymmetric-and-stereodivergent-oligonucleotide-synthesis.pdf |
63da47f4d1632f652bee4dd5 | 10.26434/chemrxiv-2023-nm4rh | Olefin Hydroboration catalyzed by an iron-borane complex | The well-defined iron(0) complex [(iPrDPBPh)Fe2-(mu-1,2-N2)] (A) reacts with HBPin affords the complex [iPrDBPPh](-H)Fe(H)(BPin)2 via oxidative addition of the H-B bond. Complex A is an effective pre-catalyst for the hydroboration of a range of olefins in synthetically useful yields (typically >80%). | Laura Grose; Darren Willcox | Inorganic Chemistry; Catalysis | CC BY NC 4.0 | CHEMRXIV | 2023-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63da47f4d1632f652bee4dd5/original/olefin-hydroboration-catalyzed-by-an-iron-borane-complex.pdf |
66378eb591aefa6ce1372270 | 10.26434/chemrxiv-2024-kfdkg | Ion-Pair Proximity in Cyclic Voltammetry and DFT studies of Aqueous Transition-Metal-Substituted Polyoxotungstates | Polyoxometalates (POMs), also known as molecular metal oxides, have attracted continuous interest since 1980s due to their unique properties and structural diversity. In general, POMs are redox active, stable in solution, and functional at the nanoscale. Computational chemistry calculations using density functional theory (DFT) to reproduce redox potentials have often been reported without accounting for the electrolyte environment and counterions. These calculations typically use implicit solvation models and compare theoretical results with previously published experimental data, which may not be synchronous. Herein, we employed DFT calculations to assess the accuracy of various exchange-correlation (x-c) functionals in reproducing experimental redox potentials for X5[M(H2O)PW11O39] salts; where X= Li, Na or K, and M = Mn(III/II), Fe(III/II) or Co(III/II). Our aim was to ensure that the experimental conditions and theoretical results are closely fit enabling a higher accuracy when reproducing experimental redox processes. Optimal accuracy was accomplished with PBE/TZP demonstrated by the lowest score for mean absolute error (MAE) of 0.55 V across all compounds in our work. Further analysis of MAE revealed increasing contributions to HF-exchange coincided with larger discrepancies from experimental potentials, U0Exp. The challenge in attaining accurate potentials is effectively controlling the proximity of the ion-pairing. To address this, we have explicitly specified the heteroatom-counterion, dP-X, geometries at discrete intervals (6-10 Å). Our proposed method permits an economical route for attaining accurate potentials, as opposed to necessitating CPU-expensive optimisations with hybrid x-c functionals. | Jake Thompson; Fiona Todman ; Mark Symes ; Laia Vilà-Nadal | Theoretical and Computational Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Electrochemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66378eb591aefa6ce1372270/original/ion-pair-proximity-in-cyclic-voltammetry-and-dft-studies-of-aqueous-transition-metal-substituted-polyoxotungstates.pdf |
6287faa759f0d625fb97c293 | 10.26434/chemrxiv-2022-vt2n9 | Robotic cell assembly to accelerate battery research | Manual cell assembly confounds with research digitalization and reproducibility. Both are however needed for data-driven optimization of cell chemistries and charging protocols. Therefore, we present herein an automatic battery assembly system (AutoBASS) that is capable of assembling batches of up to 64 CR2023 cells. AutoBASS allows us to acquire large datasets on in-house developed chemistries and is herein demonstrated with NMC811 and Si@Graphite electrodes with a focus on formation and manufacturing data. The large dataset enables us to gain insights into the formation process through dQ/dV analysis and assess cell to cell variability. Exact robotic electrode placement provides a baseline for laboratory-scale manufacturing and reproducibility towards the accelerated translation of findings from the laboratory to the pilot plant scale. | Bojing Zhang; Leon Fischer; Alexey Sanin; Helge Sören Stein | Physical Chemistry; Materials Science; Energy; Materials Processing; Robotics | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6287faa759f0d625fb97c293/original/robotic-cell-assembly-to-accelerate-battery-research.pdf |
60c754130f50db5bfd397c8e | 10.26434/chemrxiv.13604777.v1 | (DMP)DAB–Pd–MAH: A Versatile Pd(0) Source for Precatalyst Formation, Reaction Screening, and Preparative-Scale Synthesis | We report an easily prepared and bench-stable
mononuclear Pd(0) source stabilized by a chelating <i>N</i>,<i>N</i>’-diaryldiazabutadiene
ligand and maleic anhydride: <sup>DMP</sup>DAB–Pd–MAH. Phosphine ligands of all
types, including bidentate phosphines and large cone angle biarylphosphines,
rapidly and completely displace the diazabutadiene ligand at room temperature
to give air-stable Pd(0) phosphine complexes. <sup>DMP</sup>DAB–Pd–MAH itself
is readily soluble and stable in several organic solvents, making it an ideal
Pd source for <i>in situ</i> catalyst
preparation during reaction screening, as well as solution-dispensing to
plate-based reaction arrays for high-throughput experimentation. Evaluation of <sup>DMP</sup>DAB–Pd–MAH
alongside other common Pd(0) and Pd(II) sources in microscale reaction screens
reveals that <sup>DMP</sup>DAB–Pd–MAH is superior at identifying hits across
six different C–N, C–C, and C–O coupling reactions. <sup>DMP</sup>DAB–Pd–MAH,
and the phosphine precatalysts derived therefrom, are also effective in
preparative-scale cross couplings at low Pd loadings. | Jingjun Huang; Matthew Isaac; Ryan Watt; Joseph Becica; Emma Dennis; Makhsud I. Saidaminov; William A. Sabbers; David Leitch | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754130f50db5bfd397c8e/original/dmp-dab-pd-mah-a-versatile-pd-0-source-for-precatalyst-formation-reaction-screening-and-preparative-scale-synthesis.pdf |
64cbe3af4a3f7d0c0d89e15a | 10.26434/chemrxiv-2023-jc1bw | Proton-responsive ligands promote atmospheric CO2 capture and accelerate catalytic CO2/HCO2‒ interconversion | The synthesis and investigation of [Rh(DHMPE)2][BF4] (1) is reported. 1 features proton-responsive 1,2-bis(di(hydroxymethyl)phosphino)ethane (DHMPE) ligands, which readily capture CO2 from atmospheric sources upon deprotonation. The protonation state of the DHMPE ligand was observed to have a significant impact on the catalytic reactivity of 1 with CO2. Deprotonation and CO2 binding to 1 results in a ~10-fold rate enhancement in catalytic degenerate CO2 reduction with formate, monitored by 12C/13C isotope exchange between H12CO2- and 13CO2. Studies performed using a similar complex lacking hydroxyl ligand functionality ([Rh(DEPE)2][BF4] where DEPE = 1,2-bis(diethylphosphino)ethane) do not show the same rate enhancements when base is added. CO2 binding to 1 is proposed to facilitate pre-organization of formate/ CO2 in the transition state to lower the activation energy and increase the observed catalytic rate. Incorporation of proton-responsive DHMPE ligands not only permits CO2 capture from air, but also provides a unique approach to accelerate the kinetics of catalytic CO2 reduction to formate. | Jeffery M. Barlow; Nikita Gupta; Ksenija Glusac; David M. Tiede; David M. Kaphan | Inorganic Chemistry; Catalysis; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64cbe3af4a3f7d0c0d89e15a/original/proton-responsive-ligands-promote-atmospheric-co2-capture-and-accelerate-catalytic-co2-hco2-interconversion.pdf |
60c74cc7bb8c1a0dc63db4a6 | 10.26434/chemrxiv.12543518.v1 | Reactivity Studies of Cationic Au(III) Difluorides Supported by N-Ligands | The reactivity of difluoro Au(III) cations supported by pyridine or imidazole ligands is
reported. The Au(III)-F bond is found to be susceptible to metathesis by TMS reagents and
reagents bearing acidic protons such as H-CC-Ph and HOAc. In the latter case the reactions
are slower than analogous reactions reported by other groups where strong -trans donors are
present opposite the Au-F bond. This, coupled with the inability to effect metathesis on only
one Au-F bond in our system indicates the -trans effect is a key consideration in Au-F
chemistry | Lachlan Sharp-Bucknall; Lachlan Barwise; Jason Bennetts; Mohammad Albayer; Jason Dutton | Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cc7bb8c1a0dc63db4a6/original/reactivity-studies-of-cationic-au-iii-difluorides-supported-by-n-ligands.pdf |
61c623dbd1f66255e3448630 | 10.26434/chemrxiv-2021-kmlk8 | Organophotoredox/Ni-Cocatalyzed Allylation of Allenes: Regio-, and Diastereoselective Access to Homoallylic Alcohols | A dual organophotoredox/nickel-catalyzed reductive coupling of allenes with aldehydes has been developed for the rapid assembly of anti-homoallylic alcohols with high levels of regioselectivities (>20:1), and diastereoselectivities (up to >20:1) and yields (up to 91%). The allylation was realized through a crucial π-allylnickel intermediate which was obtained via insertion of allenes with a Ni−H intermediate. Moreover, γ,γ-disubstituted homoallylic alcohols with a quaternary stereocenter can also be prepared by this protocol. | Hui Xie; Bernhard Breit | Organic Chemistry; Catalysis; Stereochemistry; Photocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c623dbd1f66255e3448630/original/organophotoredox-ni-cocatalyzed-allylation-of-allenes-regio-and-diastereoselective-access-to-homoallylic-alcohols.pdf |
66afa2e65101a2ffa814f470 | 10.26434/chemrxiv-2023-0qf21-v2 | Dual-Regime Reaction Kinetics of the Autocatalytic Hydrolyses of Aqueous Alkyl Lactates | Kinetic description of the hydrolysis of alkyl lactates has been limited to acid-catalyzed conditions despite the spontaneous hydrolysis of methyl lactate and ethyl lactate in aqueous solution. As the reaction pro-gresses, generated lactic acid further catalyzes ester hydrolysis, while the rate of the reverse esterification reaction also increases with the accumulation of acid product. The reaction sequence of lactate hydrolysis is described in three kinetic stages: initiation/neutral hydrolysis, autocatalytic hydrolysis, and equilibrium. The evolution of lactate hydrolysis was measured for varying temperatures (1.5 °C to 40 °C) and initial concentrations of methyl or ethyl lactate (1 to 40 mol%) to quantify the kinetic transitions between reac-tion stages. Lower temperatures resulted in a distinct induction period where negligible hydrolysis was observed. The effect of initial concentration on the length of the induction period was non-monotonic and was divided into dilute (below about 6 mol% lactate) and concentrated (above about 6 mol%) regimes. Solutions of either lower or higher lactate concentration corresponded to longer induction periods and slower reactions. A dual kinetic regime best describes the observed hydrolysis behavior. For hydrolysis of alkyl lactates below 10 mol%, a rate law derived from the conventional ester hydrolysis mechanism effec-tively modeled behavior, while at higher lactate concentrations, an additional water molecule must be in-cluded in the rate-determining step to appropriately capture the hydrolysis behavior. | Sophie Brauer; Isaac Mastalski; Madeline Murphy; Benjamin Hoekstra; Lyle Monson; Paul Dauenhauer; Christopher Nicholas | Catalysis; Chemical Engineering and Industrial Chemistry; Thermodynamics (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66afa2e65101a2ffa814f470/original/dual-regime-reaction-kinetics-of-the-autocatalytic-hydrolyses-of-aqueous-alkyl-lactates.pdf |
6490a927853d501c00255675 | 10.26434/chemrxiv-2023-tdhwj | Total Synthesis of (+)-Discorhabdin V | The discorhabdin natural products are a large subset of pyrroloiminoquinone alkaloids with a myriad of biological activities. Despite garnering much synthetic attention, few members have thus far been completed, with none featuring a bridging carbon–nitrogen bond that is found in numerous discorhabdins, including discorhabdin V. Here we report the first total synthesis and full stereochemical assignment of (+)-discorhabdin V in 13 linear steps. To access the pyrroloiminoquinone we developed a convergent N-alkylation/oxidative aminocyclization/bromination cascade that joins two key components, which are both made on multigram scale. An intramolecular Heck reaction then forms the quaternary carbon center in an intermediate containing the carbon–nitrogen bridge, and a reductive N,O-acetal cyclization sequence introduces the final piperidine ring. Furthermore, we have established the relative stereochemistry of (+)-discorhabdin V through experimental NOESY data and DP4 NMR probability calculations. The absolute configuration of the natural product has also been determined via circular dichroism and the use of an amino acid-derived chiral starting material. Our work represents the first report of a total synthesis of a nitrogen-bridged discorhabdin and paves the way for future biological evaluation of such compounds. | Brandon Derstine; Alina Cook; James Collings; Joseph Gair; Josep Saurí; Eugene Kwan; Noah Burns | Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6490a927853d501c00255675/original/total-synthesis-of-discorhabdin-v.pdf |
60c752aa842e656276db3de4 | 10.26434/chemrxiv.13333475.v1 | Identifying the Trade-off between Intramolecular Singlet Fission Requirements in Donor-Acceptor Copolymers | Intramolecular singlet fission (iSF) has shown potential to improve the power conversion efficiency in photovoltaic devices by promoting the splitting of a photon-absorbing singlet exciton into two triplet excitons within a single molecule. Among different possibilities, the donor-acceptor modular strategy of copolymers has shown great promise in its ability to undergo iSF under certain conditions. However, the number of iSF donor-acceptor copolymers reported in the literature remains remarkably narrow and clear trends for the molecular design of better candidates have not yet been established. In this work, we identify the trade-off between the main iSF requirements of the donor-acceptor strategy and formulate design rules that allow them to be tuned simultaneously in a fragment-based approach. Based on a library of 2944 donor-acceptor copolymers, we establish simple guidelines to build promising novel materials for iSF. These consist in (1st) selecting an acceptor core with high intrinsic singlet-triplet splitting, (2nd) locating a donor with a larger monomer frontier molecular orbital (FMO) gap than that of the acceptor, and (3rd) tuning the relative energy of donor and/or acceptor FMOs through functionalization to promote photoinduced charge transfer in the resulting polymer. Remarkably, systems containing benzothiadiazole and thiophehe-1,1-dioxide acceptors, which have been shown to undergo iSF, fulfill all criteria simultaneously when paired with appropriate donors. This is due to their particular electronic features, which make them highly promising candidates in the quest for iSF materials.<br /> | Jacob Terence Blaskovits; Maria Fumanal; Sergi Vela; Raimon Fabregat; Clemence Corminboeuf | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752aa842e656276db3de4/original/identifying-the-trade-off-between-intramolecular-singlet-fission-requirements-in-donor-acceptor-copolymers.pdf |
648bc706be16ad5c57ff7073 | 10.26434/chemrxiv-2023-1524p | Total synthesis N–H (+)-tetrahydro deoxycytisine and application in Pd-catalyzed hydroarylation of ketimine | We have recently reported the synthesis of NH-(+)-tetrahydro deoxycytisine from readily available piperidine. The synthesis mainly involved decarboxylative addition, chiral resolution, Dieckmann condensation, Mannich reaction and Wolff-Kishner reduction reactions. The chiral diamine was obtained in 7 steps with 3.1% overall yield. This chiral ligand has proved to be an efficient inducing agent for the Pd-catalyzed addition reaction of aryl boronic acid onto the cyclic sulfonyl imines in water. | Jianhui Huang; Guotao Lin; Yuting Yan; Omer Yasin; Yuhan Lu; Shihao Huang | Catalysis | CC BY 4.0 | CHEMRXIV | 2023-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648bc706be16ad5c57ff7073/original/total-synthesis-n-h-tetrahydro-deoxycytisine-and-application-in-pd-catalyzed-hydroarylation-of-ketimine.pdf |
671c126c98c8527d9e64a76f | 10.26434/chemrxiv-2024-4sz8x-v3 | Sustainable Triacetic Acid Lactone Production from Sugarcane by Fermentation and Crystallization | There is a pressing need to replace crude oil with renewable feedstocks such as sugarcane to manufacture fuels and chemicals. Triacetic acid lactone (TAL) is a bioproduct of particular interest as a platform chemical with the potential to produce commercially important chemicals including sorbic acid and polydiketoenamine plastics. In this study, we leveraged BioSTEAM−an open-source platform−to design, simulate, and evaluate under uncertainty (via techno-economic analysis, TEA, and life cycle assessment, LCA) biorefineries producing TAL from sugarcane by microbial conversion of sugars. We experimentally characterized TAL solubility, calibrated solubility models, and designed a process to separate TAL from fermentation broths by crystallization. The biorefinery could produce TAL (≥94.0 dry-wt%) at a minimum product selling price (MPSP) of $4.87·kg-1 (baseline) with a range of $4.03−6.08·kg-1 (5th−95th percentiles). The MPSP was below the maximum viable TAL price range for sorbic acid production ($5.99−7.74·kg-1) in ≥93% of simulations and consistently below the benchmark price to produce polydiketoenamines ($10·kg-1). We used a quantitative sustainable design framework to explore the theoretical fermentation space (titer, yield, and productivity combinations), potential separation improvements (mitigating TAL ring-opening decarboxylation through pH control), and operation scheduling and capacity expansion strategies (e.g., through integrated sweet sorghum processing). Advancements in key design and technological parameters could greatly improve the biorefinery’s financial viability (MPSP of $2.60·kg-1 [$2.31−3.16·kg-1], consistently below the maximum viable price range for sorbic acid and polydiketoenamines production) and environmental benefits (carbon intensity of 3.65 [1.90−5.43] kg CO2-eq·kg-1, with net displacement of fossil energy consumption in 70% of simulations). This research highlights the ability of agile TEA-LCA to screen promising designs, navigate sustainability tradeoffs, prioritize research needs, and chart quantitative roadmaps for the continued development of bioproducts and biofuels. | Sarang Bhagwat; Marco Dell'Anna; Yalin Li; Mingfeng Cao; Emma Brace; Sunil Bhagwat; George Huber; Huimin Zhao; Jeremy Guest | Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671c126c98c8527d9e64a76f/original/sustainable-triacetic-acid-lactone-production-from-sugarcane-by-fermentation-and-crystallization.pdf |
60c73f1b469df433f8f42a0c | 10.26434/chemrxiv.7240823.v1 | Activation of Water on MnOx-Modified Rutile (110) and Anatase (101) TiO2 and the Role of Cation Reduction | Surface modification of titania surfaces with dispersed metal oxide
nanoclusters has the potential to enhance photocatalytic activity. These
modifications can induce visible light absorption and suppress charge carrier
recombination which are vital in improving the efficiency. We have studied heterostructures
of Mn<sub>4</sub>O<sub>6</sub> nanoclusters modifying the TiO<sub>2</sub>
rutile (110) and anatase (101) surfaces using density functional theory
corrected for on-site Coulomb interactions (DFT + U). Such studies typically
focus on the pristine surface, free of the point defects and surface hydroxyls
present in real surfaces. In our study we have considered partial hydroxylation
of the rutile and anatase surfaces and the role of cation reduction, via oxygen
vacancy formation, and how this impacts on a variety of properties governing
the photocatalytic performance such as nanocluster adsorption, light
absorption, charge separation and reducibility. Our results indicate that the
modifiers adsorb strongly at the surface and that modification extends light
absorption into the visible range. MnO<sub>x</sub>-modified anatase can show an
off-stoichiometric ground state, through oxygen vacancy formation and cation reduction
spontaneously, and both modified rutile and anatase are highly reducible with
moderate energy costs. Manganese ions are therefore present in a mixture of
oxidation states. Photoexcited electrons and holes localize at cluster metal
and oxygen sites, respectively. The interaction of water at the modified
surfaces depends on the stoichiometry and spontaneous dissociation to surface
bound hydroxyls is favoured in the presence of oxygen vacancies and reduced
metal cations. Comparisons with bare TiO<sub>2</sub> and other TiO<sub>2</sub>-based
photocatalyst materials are presented throughout. | Michael Nolan; Stephen Rhatigan | Catalysts; Computational Chemistry and Modeling; Theory - Computational; Heterogeneous Catalysis; Photocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1b469df433f8f42a0c/original/activation-of-water-on-mn-ox-modified-rutile-110-and-anatase-101-ti-o2-and-the-role-of-cation-reduction.pdf |
672c59775a82cea2fa58daa7 | 10.26434/chemrxiv-2024-nt6g8 | Computational Analysis of IL-13Rα2 Specific CAR T-Cells in Glioblastoma Multiforme (GBM)
| Glioblastoma Multiforme (GBM) is the most aggressive malignancy in the brain or spinal cord astrocytes. GBM makes up nearly all malignant primary brain tumors. Interleukin-13 receptor subunit alpha-2 (IL-13Rα2) is a monomeric receptor overexpressed in most GBM cases. Chimeric Antigen Receptor (CAR) T-cells have exhibited excellent anti-tumoral activity against GBM and other cancer types. Recently, GBM-specific monoclonal antibodies containing CAR T-cell targeting IL-13Rα2 have been created. We hypothesize that to be a GBM-specific CAR T-cell, the CAR should bind to a specific binding region of the IL-13Rα2 receptor. In the current research, we have studied the interactions between antibodies (located on the CAR's surface) and IL-13Rα2 by performing molecular docking simulations. AlphaFold 3 was used to predict the structure of the receptor, and molecular docking simulations using HDOCK2.4 were performed. The GrASP web server suggests that the druggable/binding site on the receptor is on domain 2, and the antibody also binds to this spot. A total of 15 antibodies were evaluated using the following criteria to determine the most suitable binding antibodies: Initially, a visual inspection of IL-13Rα2-antibody complexes was conducted. Subsequently, the binding energy of each IL-13Rα2-antibody interaction was calculated. Finally, the number of hydrogen bonds was analyzed. Based on the above analysis, antibody 1F8T showed the most promising properties and could be used for CAR development. This study will significantly contribute to developing novel antibody-based CAR T therapy for GBM by providing a deeper understanding of the receptor-antibody binding mechanism via computational simulations. | Kaavya Vemuri; Gaurav Sharma | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672c59775a82cea2fa58daa7/original/computational-analysis-of-il-13r-2-specific-car-t-cells-in-glioblastoma-multiforme-gbm.pdf |
60c74b94702a9bc30f18b478 | 10.26434/chemrxiv.12355847.v1 | Oxygen Redox Activity in Cathodes – a Common Phenomenon Calling for Density-Based Descriptors | Lithium-excess transition metal oxide materials are
promising cathode candidates for future secondary batteries due to their
relatively high energy density, which is commonly related to redox-active
oxygen centers. First-principle computations are crucial for the understanding
of the underlying redox mechanism in these compounds, with plane-wave density
functional theory being the most frequently used setup. An important tool for
the assignment of the redox-active species is the projected density of states,
although the atomic contributions postulated this way do not strictly
correspond to any observable physical quantity. By directly analyzing the computed
real-space charge density changes, on the other hand, oxygen redox activity can
be found to be substantial in most transition metal oxide compounds, although a
projection onto atomic states would suggest otherwise. This can be linked to
the shortcomings of the commonly employed spherical approximation for ions in
crystalline compounds used to compute the projected density of states, which
fails to describe the charge density topology in covalent transition metal
oxides and leads to a qualitatively different picture from a charge
density-based approach, specifically, the underrepresentation of oxygen
contributions and exaggeration of transition metal contributions to the density
of states The density based approach,
due to the non-spherical nature of Bader domains, is more apt to properly
describe oxygen redox contributions. This raises the question how meaningful
the descriptors of oxygen redox activity are and how it should be acknowledged
for transition metal oxide compounds in general. | Daniel Koch; Sergei Manzhos | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b94702a9bc30f18b478/original/oxygen-redox-activity-in-cathodes-a-common-phenomenon-calling-for-density-based-descriptors.pdf |
60c74984bb8c1a03413dae4d | 10.26434/chemrxiv.11980119.v2 | Computational Investigation of the Spin-Density Asymmetry in Photosynthetic Reaction Center Models from First Principles | We present a computational analysis of the spin-density asymmetry in cation radical states of reaction center models from photosystem I, photosystem II, and bacteria from Synechococcus elongatus, Thermococcus vulcanus, and Rhodobacter sphaeroides, respectively. The recently developed FDE-diab methodology [J. Chem. Phys., 148 (2018), 214104] allowed us to effectively avoid the spin-density overdelocalization error characteristic for standard Kohn–Sham Density Functional Theory and to reliably calculate spin-density distributions and electronic couplings for a number of molecular systems ranging from inner pairs of (bacterio)chlorophyll a molecules in vacuum to large protein including up to about 2000 atoms. The calculated spin densities show a good agreement with available experimental results and were used to validate reaction center models reported in the literature. Here we demonstrate that the applied theoretical approach is very sensitive to changes in molecular structures and relative orientation of molecules. This makes FDE-diab a valuable tool for electronic structure calculations of large photosynthetic models effectively complementing the existing experimental techniques.<br /> | Denis Artiukhin; Patrick Eschenbach; Johannes Neugebauer | Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2020-03-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74984bb8c1a03413dae4d/original/computational-investigation-of-the-spin-density-asymmetry-in-photosynthetic-reaction-center-models-from-first-principles.pdf |
60c74957bb8c1a65cc3dae18 | 10.26434/chemrxiv.12053037.v1 | Biodegradable Poly(ester) Urethane Acrylate Resins for Digital Light Processing: From Polymer Synthesis to 3D Printed Tissue Engineering Constructs | <div>Digital light processing (DLP) is one of the most accurate and fastest additive manufacturing</div><div>technologies to produce a variety of products, from patient-customized biomedical implants to</div><div>consumer goods; however, DLP’s use in tissue engineering is limited largely due to a lack of</div><div>biodegradable resins. Herein, a library of biodegradable urethane acrylate-capped poly(esters)</div><div>(with variations in molecular weight) is investigated as the basis for a DLP printable ink for</div><div>tissue engineering. The synthesized oligomers show good printability in a DLP resin, capable</div><div>of creating complex structures with mechanical properties matching those of medium-soft</div><div>tissues (1–3 MPa). While fabricated films from different molecular weight resins showed few</div><div>differences in surface topology, wettability, and protein adsorption, the adhesion and metabolic</div><div>activity of L929 and human dermal fibroblasts (HDFs) were significantly different: resins from</div><div>higher molecular weight oligomers provided greater cell adhesion and metabolic activity. These</div><div>printable and biodegradable resins show the importance of oligomer molecular weight on</div><div>scaffold properties, and facilitate the printing of elastomeric customizable scaffolds for a variety</div><div>of tissue engineering applications.</div> | Matthew Baker; Rong Wang; Febriyani Damanik; Tobias Kuhnt; Hans Ippel; Piet Dijkstra; Tessa ten Cate; Aylvin Dias; Lorenzo Moroni | Biocompatible Materials; Biodegradable Materials; Materials Processing; Organic Polymers; Polymer scaffolds; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74957bb8c1a65cc3dae18/original/biodegradable-poly-ester-urethane-acrylate-resins-for-digital-light-processing-from-polymer-synthesis-to-3d-printed-tissue-engineering-constructs.pdf |
6413a3232bfb3dc251e44840 | 10.26434/chemrxiv-2023-x76sp | Halide Non-Innocence and Direct Photo-Reduction of Ni(II) Enables Coupling of Aryl Chlorides in Dual Catalytic, Carbon-Heteroatom Bond Forming Reactions | Recent mechanistic studies of dual photoredox/Ni-catalyzed, light-driven cross-coupling reactions have found that the photocatalyst (PC) operates through either reductive quenching or energy transfer cycles. To date, reports invoking oxidative quenching cycles are comparatively rare and direct observation of such a quenching event has not been reported. However, when PCs with highly reducing excited states are used (e.g. Ir(ppy)3), photo-reduction of Ni(II) to Ni(I) is thermodynamically feasible. Recently, a unified reaction system using Ir(ppy)3 was developed for forming C–O, C–N, and C–S bonds under the same conditions, a prospect that is challenging with PCs that can photo-oxidize these nucleophiles. Herein, in a detailed mechanistic study of this system, we observe oxidative quenching of the PC (Ir(ppy)3 or a phenoxazine) via nanosecond transient absorption spectroscopy. Speciation studies support that a mixture of Ni-bipyridine complexes form under the reaction conditions, and the rate constant for photoreduction increases when more than one ligand is bound. Oxidative addition of an aryl iodide was observed indirectly via oxidation of the resulting iodide by Ir(IV)(ppy)3. Intriguingly, persistence of the Ir(IV)/Ni(I) ion pair formed in the oxidative quenching step was found to be necessary to simulate the observed kinetics. Both bromide and iodide anions were found to reduce the oxidized form of the PC back to its neutral state. These mechanistic insights inspired the addition of a chloride salt additive, which was found to alter Ni speciation, leading to a 36-fold increase in the initial turnover frequency, enabling the coupling of aryl chlorides. | Cameron Chrisman; Max Kudisch; Katherine Puffer; Trevor Stewart; Yisrael Lamb; Chern-Hooi Lim; Randolph Escobar; Pall Thordarson; Jeffrey Johannes; Garret Miyake | Organic Chemistry; Catalysis | CC BY 4.0 | CHEMRXIV | 2023-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6413a3232bfb3dc251e44840/original/halide-non-innocence-and-direct-photo-reduction-of-ni-ii-enables-coupling-of-aryl-chlorides-in-dual-catalytic-carbon-heteroatom-bond-forming-reactions.pdf |
67482ae8f9980725cf4e9126 | 10.26434/chemrxiv-2024-z4g91 | Aminopeptidase N-activated self-immolative hydrogen sulfide donor for inflammatory response-specific wound healing | Hydrogen sulfide (H2S) plays crucial inflammatory modulating roles, representing a promising candidate for anti-inflammatory therapies. However, current H2S delivery approaches lack sufficient specificity against inflammatory response. Herein, regarding the overexpressed aminopeptidase N (APN) at the inflammation sites, an APN-activated self-immolative carbonyl sulfide (COS)/H2S donor (AlaCOS) was developed for inflammatory response-specific H2S delivery. The compound showed sustained H2S generation upon APN activation in the presence of carbonic anhydrase (CA), and the responsiveness could be well regulated by modulating the amino acid sequence. Due to the inflammatory response-specific sustained H2S delivery, AlaCOS provided potent anti-inflammatory capability, which was further validated by RNA sequencing. In vivo experiments on a full-thickness cutaneous wound murine model also showed the strong promoting effect on wound healing, mainly due to the regulation of the inflammatory response by AlaCOS. By introducing a caged coumarin fluorophore to the molecular architecture, self-reporting fluorescence could be generated accompanied with APN-mediated COS/H2S release, which achieved the visualization of H2S delivery in vitro and in vivo. This work not only offers a useful tool for studying the bioactivity of H2S on inflammation, but also provides new insights for developing novel therapies to cope with inflammation-associated diseases. | Fan Rong; Wenxin Bao; Guanyi Li; Yuxuan Ge; Wangyang Zhu; Bin Hao; Yaxue Zhao; Yunsheng Yuan; Yin Wang | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67482ae8f9980725cf4e9126/original/aminopeptidase-n-activated-self-immolative-hydrogen-sulfide-donor-for-inflammatory-response-specific-wound-healing.pdf |
60c742ec469df4536af4308b | 10.26434/chemrxiv.8832425.v1 | Energy Conservation via Thioesters in a Non-Enzymatic Metabolism-like Reaction Network | <p><b>Life’s catabolic processes capture chemical energy from the oxidative breakdown of metabolites. In the catabolic pathways at the core of biochemistry, the oxidation of </b>α-<b>ketoacids or aldehydes is coupled to the synthesis of thioesters, whose energy-releasing hydrolysis is in turn coupled to the production of adenosine 5’-triphosphate (ATP). How these processes became linked before life emerged, and thus how the framework for modern bioenergetics was established, is a major problem for understanding the origins of biochemistry. The structure of biochemical networks suggests that the intermediary role of thioesters in biological energy flows, and their central role in biosynthesis, is a consequence of their entry into metabolism at the earliest stage of biochemical evolution. However, how thioesters could have become embedded within a metabolic network before the advent of enzymes remains unclear. Here we demonstrate non-enzymatic oxidant- or light-driven thioester synthesis from biological </b>α-<b>ketoacids and show it can be integrated within an iron-promoted metabolism-like reaction network. The thioesters obtained are those predicted to be pivotal in computational reconstructions of primitive biochemical networks (acetyl, malonyl, malyl and succinyl thioesters), demonstrating a rare convergence between top-down and bottom-up approaches to the origins of metabolism. The diversity and simplicity of conditions that form thioesters from core metabolites suggests the energetic link between thioester synthesis and catabolism was in place at the earliest stage of prebiotic chemistry, constraining the path for the later evolution of life’s phosphorus-based energy currencies.</b></p> | Elodie Chevallot-Beroux; Jan Gorges; Joseph Moran | Bioorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742ec469df4536af4308b/original/energy-conservation-via-thioesters-in-a-non-enzymatic-metabolism-like-reaction-network.pdf |
60c758280f50db69973983d0 | 10.26434/chemrxiv.14510718.v1 | Ring Expansion to 8-Membered Silacycles via Formal Cross-Dimerization of 5-Membered Palladacycles with Silacyclobutanes | Investigations of the sila-8-membered
ring fused biaryls are of important significance for the discovery of new drug lead compounds. However, such
compounds are still unknown due to the synthetic challenge. Herein we describe the chemo- and regio-selective cross-dimerization of 5-membered palladacycles with silacyclobutanes enabled by Pd-catalytic
conditions, which constitutes an expedient ring
expansion route to the sila-8-membered ring fused biaryl skeletons. | Xi-Chao Wang; Hao-Ran Wang; Xiufang Xu; Dongbing Zhao | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758280f50db69973983d0/original/ring-expansion-to-8-membered-silacycles-via-formal-cross-dimerization-of-5-membered-palladacycles-with-silacyclobutanes.pdf |
67a11f0ffa469535b9f4648c | 10.26434/chemrxiv-2025-21zvt | Higher-level Strategies for Computer-Aided Retrosynthesis | Retrosynthesis is a core technique in organic chemistry that involves simplifying target molecules into more readily available components. Computer-aided synthesis planning (CASP) tools automate this process by recursively proposing immediate precursors of molecules to identify multistep synthetic pathways. However, the application of CASP tools becomes particularly challenging for complex molecules due to the increased length of synthetic pathways and the increased number of possible disconnections. We introduce a novel framework for computer-aided retrosynthesis, higher-level retrosynthesis, that focuses on the broader retrosynthetic strategy. We abstract the detailed substructures in the intermediates of a synthetic pathway that do not appear in the target product, allowing our algorithm to emphasize the general, higher-level strategies instead of considering the specifics of chemically-equivalent functional groups. We demonstrate the empirical effectiveness of our approach with higher success rates in single- and multi-step retrosynthetic planning. We further underscore the practical utility of our framework through case studies involving complex drugs and natural products, illustrating how proposed retrosynthetic strategies can be effectively mapped to complete retrosynthetic plans. Ultimately, focusing on higher-level strategies in computer-aided retrosynthesis enhances its effectiveness and enables chemists to leverage their expertise to improve the synthesis design process. | Jihye Roh; Joonyoung F. Joung; Kevin Yu; Zhengkai Tu; G. Logan Bartholomew; Omar A. Santiago-Reyes; Mun Hong Fong; Richmond Sarpong; Sarah E. Reisman; Connor W. Coley | Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Computational Chemistry and Modeling; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a11f0ffa469535b9f4648c/original/higher-level-strategies-for-computer-aided-retrosynthesis.pdf |
60c748c7ee301c97ccc7993d | 10.26434/chemrxiv.11464968.v2 | Cross-Linker Control of Vitrimer Flow | <div><p>Vitrimers are a class of covalent adaptable networks (CANs) that undergo topology reconfiguration via associative exchange reactions, enabling reprocessing at elevated temperatures. Here, we show that cross-linker reactivity represents an additional design parameter to tune stress relaxation rates in vitrimers. Guided by calculated activation barriers, we prepared a series of cross-linkers with varying reactivity for the conjugate addition—elimination of thiols in a PDMS vitrimer. Surprisingly, despite a wide range of stress relaxation rates, we observe that the flow activation energy of the bulk material is independent of the cross-linker structure. Superposition of storage and loss moduli from frequency sweeps can be performed for different cross-linkers, indicating the same exchange mechanism. We show that we can mix different cross-linkers in a single material in order to further modulate the stress relaxation behavior.</p></div> | Bassil El-Zaatari; Jacob Ishibashi; Julia Kalow | Physical Organic Chemistry; Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748c7ee301c97ccc7993d/original/cross-linker-control-of-vitrimer-flow.pdf |
6157def146030aeddec58896 | 10.26434/chemrxiv-2021-w2c7b | Dimensional control over metal halide perovskite crystallization guided by active learning | Metal halide perovskite (MHP) derivatives, a promising class of optoelectronic materials, have been synthesized with a range of dimensionalities that govern their optoelectronic properties and determine their applications. We demonstrate a data-driven approach combining active learning and high-throughput experimentation to discover, control, and understand the formation of phases with different dimensionalities in the morpholinium (morph) lead iodide system. Using a robot-assisted workflow, we synthesized and characterized two novel MHP derivatives that have distinct optical properties: a one-dimensional (1D) morphPbI3 phase ([C4H10NO][PbI3]) and a 2D (morph)2PbI4 phase ([C4H10NO]2[PbI4]). To efficiently acquire the data needed to construct a machine learning (ML) model of the reaction conditions where the 1D and 2D phases are formed, data acquisition was guided by a diverse-mini-batch-sampling active learning algorithm, using prediction confidence as a stopping criterion. Querying the ML model uncovered the reaction parameters that have the most significant effects on dimensionality control. Based on these insights, we propose a reaction scheme that rationalizes the formation of different dimensional MHP derivatives in the morph-Pb-I system. The data-driven approach presented here, including the use of additives to manipulate dimensionality, will be valuable for controlling the crystallization of a range of materials over large reaction-composition spaces. | Zhi Li; Philip Nega; Mansoor Najeeb; Chaochao Dun; Matthias Zeller; Jeffrey Urban; Wissam Saidi; Joshua Schrier; Alexander Norquist; Emory Chan | Theoretical and Computational Chemistry; Materials Science; Hybrid Organic-Inorganic Materials; Machine Learning; Artificial Intelligence; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6157def146030aeddec58896/original/dimensional-control-over-metal-halide-perovskite-crystallization-guided-by-active-learning.pdf |
668c3bac5101a2ffa8c7b8ac | 10.26434/chemrxiv-2024-p2pxr-v2 | Leveraging Asymmetric Catalysis Data for Mechanistic Interrogation of Nickel-Photoredox THF Arylation | This manuscript details the development of an asymmetric variant for the Ni-photoredox α-arylation of tetrahydrofuran (THF), which was originally reported in a racemic fashion by Doyle and Molander. Leveraging the enantioselectivity data that we obtained, a complex mechanistic scenario different from those originally proposed is uncovered. Specifically, an unexpected dependence of the product enantiomeric ratio on both the halide identity (aryl chloride vs. bromide substrates) and the Ni source was observed. Stoichiometric experiments and time course analyses of the evolution of product enantioselectivity with time revealed a different initial behavior for reactions carried out with Ni(II) and Ni(0) pre-catalysts that later converge into a common mechanism. For studying the predominant pathway, this paper describes a rare example of the syntheses of chiral bisoxazoline Ni(II) aryl halide complexes, which proved essential for probing enantioselectivity via stochiometric experiments. These experiments identify the Ni(II) aryl halide complex as the primary species involved in the key THF radical trapping event. A multivariate linear regression model is presented that further validates the dominant mechanism and delineates structure-selectivity relationships between ligand properties and enantioselectivity. EPR analysis of Ni(0)/aryl halide mixtures highlights the fast access to a variety of Ni complexes in 0,+1, and +2 oxidation states that are proposed to be responsible for the initial divergence in mechanism observed when using Ni(0) pre-catalysts. More broadly, beyond advancing the mechanistic understanding of this THF arylation protocol, this work underscores the potential of leveraging enantioselectivity data to unravel intricate mechanistic manifolds within Ni-photoredox catalysis. | Brennan McManus; Lang Hung; Olivia Taylor; Paul Nguyen; Alfredo Cedeno; Kyle Arriola; Robert Bradley; Paul Saucedo; Robert Hannan; Yvette Luna; Phillip Farias; Ana Bahamonde | Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668c3bac5101a2ffa8c7b8ac/original/leveraging-asymmetric-catalysis-data-for-mechanistic-interrogation-of-nickel-photoredox-thf-arylation.pdf |
6204e47ebd05a06d5301f422 | 10.26434/chemrxiv-2022-t748w-v2 | A Prodrug Strategy for the In Vivo Imaging of Aldehyde Dehydrogenase Activity | Therapy resistance is one of the biggest challenges facing clinical oncology. Despite a revolution in new anti-cancer drugs targeting multiple components of the tumour microenvironment, acquired or innate resistance frequently blunts the efficacy of these treatments. Non-invasive identification of drug-resistant tumours will enable modification of the patient treatment pathway through the selection of appropriate second-line treatments. Here, we have designed a pro-drug radiotracer for the non-invasive imaging of aldehyde dehydrogenase 1A1 (ALDH1A1) activity. Elevated ALDH1A1 activity is a marker of drug-resistant cancer cells, modelled here with matched cisplatin-sensitive and -resistant human SKOV3 ovarian cancer cells. The aromatic aldehyde of our prodrug radiotracer was intracellularly liberated by esterase cleavage of the geminal diacetate and specifically trapped by ALDH through its conversion to the charged carboxylic acid. Through this mechanism of action, ALDH-specific retention of our pro-drug radiotracer in the drug-resistant tumour cells was twice as high as the drug-sensitive cells. Acylal masking of the aldehyde afforded a modest protection from oxidation in the blood, which was substantially improved in carrier-added experiments. In vivo positron emission tomography imaging of tumour-bearing mice produced high tumour-to-background images and radiotracer uptake in high ALDH-expressing organs but was unable to differentiate between drug-sensitive and drug-resistant tumours. Alternative strategies to protect the labile aldehyde are currently under investigation. | Raul Pereira; Renee Flaherty; Richard Edwards; Hannah Greenwood; Adam Shuhendler; Timothy Witney | Biological and Medicinal Chemistry; Biochemistry; Cell and Molecular Biology; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2022-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6204e47ebd05a06d5301f422/original/a-prodrug-strategy-for-the-in-vivo-imaging-of-aldehyde-dehydrogenase-activity.pdf |
6244941258f7afc187ad23a6 | 10.26434/chemrxiv-2022-zwctv-v2 | Automated Stereocontrolled Assembly-Line Synthesis of Organic Molecules | Automation has fuelled dramatic advances in fields such as proteomics and genomics (e.g., in preparation of proteins and nucleic acids),1,2 enabling non-experts to prepare, test and analyse complex biological molecules. However, the field of automated organic synthesis lags far behind, partly because of the complexity and variety of organic molecules. As a result, only a handful of relatively simple organic molecules, requiring a small number of synthetic steps, have been made in an automated fashion. Herein, we report an automated assembly-line synthesis that allows iterative, stereocontrolled formation of C(sp3)–C(sp3) bonds with high stereochemical fidelity and reproducibility, enabling access to complex organic molecules even by non-synthesis experts. This was achieved on a commercially available robotic platform capable of handling air sensitive reactants and performing low temperature reactions, which enabled six sequenced one-carbon homologations of organoboron substrates to be performed iteratively without human intervention. Together with other automated functional group manipulations, this methodology has been exploited to rapidly build the core fragment of the natural product (+)-kalkitoxin, thus leading the way towards automated organic synthesis. | Valerio Fasano; Rory Mykura; James Fordham; Jack Rogers; Borys Banecki; Adam Noble; Varinder Aggarwal | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6244941258f7afc187ad23a6/original/automated-stereocontrolled-assembly-line-synthesis-of-organic-molecules.pdf |
60c74d92ee301cf47ac7a2f7 | 10.26434/chemrxiv.12639032.v1 | Durability of Mo-Ni Intermetallic Compounds in the Hydrogen Evolution Reaction | Molybdenum-nickel materials are catalysts of industrial interest for the hydrogen evolution reaction (HER). This contribution investigates the potential influence of ordered crystal structures on the catalytic activity. Well-characterized surfaces of the single-phase intermetallic compounds Ni7Mo7, Ni3Mo and Ni4Mo were subjected to accelerated durability tests (ADTs) and thorough characterization to unravel, whether crystallographic ordering affects the activity. Due to their intrinsic instability, molybdenum is leached resulting in higher specific surface areas and nickel-rich surfaces. The gain in surface area scales with the applied potential and the molybdenum content of the pristine samples. The nickel-enriched surfaces are more prone to form Ni(OH)2 layers, which leads to deactivation of the Mo-Ni materials. The crystal structure of the intermetallic compounds has, due to the intrinsic instability of the materials in alkaline media, no effect on the activity. The earlier as durable identified Ni7Mo7 proves to be highly unstable in the applied ADTs. The results indicate that the enhanced activity of unsupported bulk Mo-Ni electrodes can solely be ascribed to increased specific surface areas. | Leonard Rößner; Holger Schwarz; Igor Veremchuk; Ridha Zerdoumi; Thomas Seyller; Marc Armbrüster | Alloys; Catalysts; Electrochemistry; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d92ee301cf47ac7a2f7/original/durability-of-mo-ni-intermetallic-compounds-in-the-hydrogen-evolution-reaction.pdf |
6569d40bcf8b3c3cd790cf49 | 10.26434/chemrxiv-2023-2jx24 | Targeted Photodynamic Therapy: Gluconamide-Modified Cellulose Nanocrystals as Efficient Photosensitizer Delivery Platforms Against Gram-Negative Bacteria | Antimicrobial Photodynamic Therapy (aPDT) is an emerging strategy to fight against resistant pathogenic bacteria, which is considered a serious health problem. In this work, we described the functionalization of cellulose nanocrystals (CNC) with two photosensitizers (PS): one cationic and the other anionic, Rose Bengal (RB) and Toluidine Blue O (TBO), respectively, together with a specific target, gluconamide, as potential nanosystem for a PDT against Gram-negative bacteria such as Escherichia Coli (E. coli). The nanosystems loaded with the photosensitizers (PS@CNC) are chemically and photophysically characterized and tested in E. coli bacteria comparing their cyto- and phototoxicity with the PSs in solution. The resultant PS@CNC have reduced the inherent cytotoxicity of PSs in dark conditions maintaining their phototoxicity activity under green and red irradiation for RB@CNC and TBO@CNC, respectively. The presence of gluconamide as the target has improved the phototoxic of the nanosystem.
| Ruth Prieto-Montero; Maite Tejón; Andrea Albaya; Teresa Arbeloa; Jose Luis Chiara; Mónica L. Fanárraga; VIRGINIA MARTINEZ-MARTINEZ | Physical Chemistry; Photochemistry (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6569d40bcf8b3c3cd790cf49/original/targeted-photodynamic-therapy-gluconamide-modified-cellulose-nanocrystals-as-efficient-photosensitizer-delivery-platforms-against-gram-negative-bacteria.pdf |
6441034471383d092101da69 | 10.26434/chemrxiv-2023-1ngg4 | Sensitizer-free photochemical regeneration of benzimidazoline organohydride | Organohydrides are an important class of organic compounds that can provide hydride anions for chemical and biochemical reactions, as demonstrated by reduced nicotinamide adenine dinucleotide serving as an important natural redox cofactor. The coupling of hydride transfer from the organohydride to the substrate and subsequent regeneration of the organohydride from its oxidized form can realize organohydride-catalyzed reduction reactions. Depending on the structure of the organohydride, its hydridicity and ease of regeneration vary. Benzimidazoline (BIH) is one of the strongest synthetic C–H hydride donors; however, its reductive regeneration requires highly reducing conditions. In this study, we synthesized various oxidized and reduced forms of BIH derivatives with aryl groups at the 2-position and investigated their photophysical and electrochemical properties. 4-(Dimethylamino)phenyl-substituted BIH exhibited salient red-shifted absorption compared to other synthesized BIH derivatives, and visible-light-driven regeneration without using an external photosensitizer was achieved. This knowledge has significant implications for the future development of solar-energy-based catalytic photoreduction technologies that utilize organohydride regeneration strategies. | Ryosuke Matsubara; Tatsuhiro Harada; Weibin Xie; Tatsushi Yabuta; Jiasheng Xu; Masahiko Hayashi | Organic Chemistry; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6441034471383d092101da69/original/sensitizer-free-photochemical-regeneration-of-benzimidazoline-organohydride.pdf |
64feb8aab6ab98a41c3cf57c | 10.26434/chemrxiv-2023-1sdkl-v2 | EnzyKR: A Chirality-Aware Deep Learning Model for Predicting the Outcomes of the Hydrolase-Catalyzed Kinetic Resolution | Hydrolase-catalyzed kinetic resolution is a well-established biocatalytic process. However, the computational tools that predict the favorable enzyme scaffolds for separating racemic substrate mixture are underdeveloped. To address this challenge, we trained a deep learning framework, EnzyKR, to automate the selection of hydrolases for stereoselective biocatalysis. EnzyKR adopts a classifier-regressor architecture that first identifies the reactive binding conformer of an enantiomer-hydrolase complex, and then predicts its activation free energy. A structure-based encoding strategy was used to depict the chiral interactions between hydrolases and enantiomers. Different from existing models trained on protein sequence and substrate SMILES strings, EnzyKR was trained using 204 enantiomer-hydrolase complexes, which were constructed by docking based on the enzyme and substrate structures curated from IntEnzyDB. EnzyKR was tested using a held-out dataset of 20 complexes on the task of active free energy prediction. EnzyKR achieved a Pearson correlation coefficient (R) of 0.72, a Spearman rank correlation coefficient (Spearman R) of 0.72, and a mean absolute error (MAE) of 1.54 kcal/mol in its active free energy prediction task. Furthermore, EnzyKR was tested on the task of predicting enantiomeric excess ratios for 28 hydrolytic kinetic resolution reactions catalyzed by fluoroacetate dehalogenase RPA1163, halohydrin HheC, A. mediolanus epoxide hydrolase, and P. fluorescens esterase. The performance of EnzyKR was compared against a recently developed kinetic predictor, DLKcat. EnzyKR correctly predicts the favored enantiomer and outperforms DLKcat in 18 out of 28 reactions, occupying 64% of the test cases. These results demonstrate EnzyKR as a new approach for prediction of enantiomeric outcomes in hydrolase-catalyzed kinetic resolution reactions. | Xinchun Ran; Yaoyukun Jiang; Qianzhen Shao; Zhongyue J. Yang | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64feb8aab6ab98a41c3cf57c/original/enzy-kr-a-chirality-aware-deep-learning-model-for-predicting-the-outcomes-of-the-hydrolase-catalyzed-kinetic-resolution.pdf |
676d0c116dde43c9085fb79e | 10.26434/chemrxiv-2024-mxwwl | Cytosolic Protein Delivery via Protein-Bound Microparticles Based on Anionic Boron Clusters and Cationic Polymers | Direct protein delivery to the cytosol facilitates immediate functional expression of proteins without the risks associated with gene introduction. However, the technology for delivering various proteins to the cytosol is still in its infancy. Herein, the formation of microparticles comprising anionic boron clusters and the cationic polymer hexadimethrine bromide (HDB) was demonstrated. In particular, the microparticles formed from dodecabromododecaborate clusters and HDB were confirmed to be bound with proteins. The protein-bound boron cluster/polymer-based microparticles (protein-bound BPMs) were internalized into cells via endocytosis. Upon internalization, the protein-bound BPMs released the proteins with different isoelectric points and sizes into the cytosol. Furthermore, an enzyme was delivered by protein-bound BPMs into the cytosol of various cell types while maintaining its functional activity. This method shows considerable promise for delivering diverse proteins to a variety of cell types, potentially advancing the field of protein-based therapeutics. Our findings open new avenues for utilizing boron clusters in cytosolic delivery systems. | Yuya Hirai; Yoshimasa Makita; Makoto Nakagawa; Rie Kakehashi; Shin-ichi Fujiwara | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676d0c116dde43c9085fb79e/original/cytosolic-protein-delivery-via-protein-bound-microparticles-based-on-anionic-boron-clusters-and-cationic-polymers.pdf |
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