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60c75769ee301cc71ec7b523 | 10.26434/chemrxiv.14399213.v1 | Room-Temperature Reduction of Sulfur Hexafluoride with Metal Phosphides | Upon treatment with sulfur hexafluoride, alkali metal diphenyl or dicyclohexyl phosphides are
oxidized within seconds to tetraphenyl or tetracyclohexyl diphosphines. In a hindered example,
di-tert-butylphosphide, fluorophosphine intermediates are detected. This is the first reported
reaction of sulfur hexafluoride with metal phosphides, and a rare example of reactivity of sulfur
hexafluoride at ambient temperature. | Blake S. N. Huchenski; Alex Speed | Frustrated Lewis Pairs; Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75769ee301cc71ec7b523/original/room-temperature-reduction-of-sulfur-hexafluoride-with-metal-phosphides.pdf |
65bc7f16e9ebbb4db97ef296 | 10.26434/chemrxiv-2024-jfdjj-v2 | The neglected tautomerism in “Study of the electronic effect and quantitative spectra predictions of o-methoxyanilineterminated monoazonaphthols: a combined experimental and DFT study” by Guoxun Zhu, Yan Lin, Wenxian Zhou, Huacan Song and Zhengquan Li, RSC Advances, 2023, 13, 33736 | In the paper of Zhu and co-workers, cited in the title, the authors derived a protocol for the absorption spectra prediction is sulphonated azo naphthols assuming that they exist as single azo tautomers. However, as shown by the available experimental data and the calculations, performed in this note, the studied dyes exist almost solely in hydrazone tautomeric form, which unavoidably affects the conclusions and linear relations made in the original paper. | Liudmil Antonov | Theoretical and Computational Chemistry; Organic Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bc7f16e9ebbb4db97ef296/original/the-neglected-tautomerism-in-study-of-the-electronic-effect-and-quantitative-spectra-predictions-of-o-methoxyanilineterminated-monoazonaphthols-a-combined-experimental-and-dft-study-by-guoxun-zhu-yan-lin-wenxian-zhou-huacan-song-and-zhengquan-li-rsc-advan.pdf |
64d6cf844a3f7d0c0d05ed13 | 10.26434/chemrxiv-2023-2rn2p | Secondary Ion Mass Spectrometry of Single Giant Unilamellar Vesicles Reveals Compositional Variability | Giant unilamellar vesicles (GUVs) are a widely used model system to interrogate lipid phase behavior, study biomembrane mechanics, reconstitute membrane proteins, and provide a chassis for synthetic cells. It is generally assumed that the composition of individual GUVs is the same as the nominal stock composition, however, there may be significant compositional variability between individual GUVs. Although this compositional heterogeneity likely impacts phase behavior, the function and incorporation of membrane proteins, and the encapsulation of biochemical reactions, it has yet to be directly quantified. To assess heterogeneity, we use secondary ion mass spectrometry (SIMS) to probe the composition of individual GUVs using non-perturbing isotopic labels. Both 13C- and 2H-labeled lipids are incorporated into a ternary mixture, which is then used to produce GUVs via gentle hydration or electroformation. Simultaneous detection of seven different ion species via SIMS allows for the concentration of 13C- and 2H-labeled lipids in single GUVs to be quantified using calibration curves, which correlate ion intensity to composition. Additionally, the relative concentration of 13C- and 2H-labeled lipids is assessed for each GUV via the ion ratio 2H-/13C-, which is highly sensitive to compositional differences between individual GUVs and circumvents the need for calibration using standards. Both quantification methods suggest that gentle hydration produces GUVs with greater compositional variability than those formed by electroformation. However, both gentle hydration and electroformation display compositional variability on the order of 5-15 mol percent. | Dashiel Grusky; Ahanjit Bhattacharya; Steven Boxer | Physical Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry; Biophysical Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d6cf844a3f7d0c0d05ed13/original/secondary-ion-mass-spectrometry-of-single-giant-unilamellar-vesicles-reveals-compositional-variability.pdf |
60c752df702a9b487e18c26e | 10.26434/chemrxiv.13200176.v3 | Molecular Recognition of SARS-CoV-2 Spike Glycoprotein: Quantum Chemical Hot Spot and Epitope Analyses | <div>Due to the COVID-19 pandemic, researchers have attempted to identify complex structures of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein (S-protein) with angiotensin-converting enzyme 2 (ACE2) or a blocking antibody. However, the molecular recognition mechanism - critical information for drug and antibody design - has not been fully clarified at the amino acid residue level. Elucidating such a microscopic mechanism in detail requires a more accurate molecular interpretation that includes quantum mechanics to quantitatively evaluate hydrogen bonds, XH/π interactions (X = N, O, and C), and salt bridges. In this study, we applied the fragment molecular orbital (FMO) method to characterize the SARS-CoV-2 S-protein binding interactions with not only ACE2 but also the B38 Fab antibody involved in ACE2-inhibitory binding. By analyzing FMO-based interaction energies along a wide range of binding inter-faces carefully, we identified amino acid residues critical for molecular recognition between S-protein and ACE2 or B38 Fab antibody. Importantly, hydrophobic residues that attribute to weak interactions such as CH-O and XH/π interactions, as well as polar residues that construct conspicuous hydrogen bonds, play important roles in molecular recognition and binding ability. Moreover, through these FMO-based analyses, we also clarified novel hot spots and epitopes that had been overlooked in previous studies by structural and molecular mechanical approaches. Altogether, these hot spots/epitopes identified between S-protein and ACE2/B38 Fab antibody may provide useful information for future anti-body design and small or medium drug design against the SARS-CoV-2. </div><div><br /></div> | Chiduru Watanabe; Yoshio Okiyama; Shigenori Tanaka; Kaori Fukuzawa; Teruki Honma | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752df702a9b487e18c26e/original/molecular-recognition-of-sars-co-v-2-spike-glycoprotein-quantum-chemical-hot-spot-and-epitope-analyses.pdf |
60c75622ee301c00aec7b2c3 | 10.26434/chemrxiv.14215871.v1 | Time-Dependent Influence of High Glucose Environment on the Metabolism of Neuronal Immortalized Cells | In this work the effect of glucose concentration on the metabolome of living hippocampal HN9.10e neurons was studied. This cell line represents a reliable, <i>in vitro </i>model of one of the most vulnerable regions of central nervous system. Targeted metabolites were analyzed in the cell culture medium by two direct methods, namely liquid chromatography – diode array detection and headspace – solid phase micro extraction – gas chromatography – mass spectrometry. Twenty-two metabolites were simultaneously identified and quantified in the growth medium of the cells, treated with 25, 50 or 75 mM glucose, sampled along 8 days to mimic a prolonged hyperglycemia. The results of statistical analysis showed the clear impairment of neuronal metabolism already after 48 hours, represented by a significant reduction of the metabolic activity. | Laura Colombaioni; Beatrice Campanella; Riccardo Nieri; Massimo Onor; Edoardo Benedetti; Emilia Bramanti | Biochemical Analysis; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75622ee301c00aec7b2c3/original/time-dependent-influence-of-high-glucose-environment-on-the-metabolism-of-neuronal-immortalized-cells.pdf |
60f5d2320b093e026be22366 | 10.26434/chemrxiv-2021-p9f5h | PNA Microprobe for Label-Free Detection of Nucleic Acid Repeat Mutations | We present a PNA-based microprobe sensing platform to detect nucleic acid repeat mutations by electrochemical impedance spectroscopy. The microprobe platform discriminated Huntington’s disease-associated CAG repeats in cell-derived total RNA. This sensitive, label-free, and PCR-free detection strategy has the potential to detect a plethora of length mutation disorders. | Mohtashim Shamsi; Narges Asefifeyzabadi; Grace Durocher; Kizito-Tshitoko Tshilenge; Lisa Ellerby | Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Electrochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f5d2320b093e026be22366/original/pna-microprobe-for-label-free-detection-of-nucleic-acid-repeat-mutations.pdf |
60d48befc622957acc1adbee | 10.26434/chemrxiv-2021-h28j4-v2 | Preparation of Recyclable and Versatile Porous Poly-Arylthioethers by Reversible Pd-Catalysed C–S/C–S Metathesis | Porous organic polymers have shown a number of promising properties; however, their application is usually hampered due to the lability of their linkages. Inspired by the outstanding chemical, mechanical and thermal resistance of the 1D polymer polyphenylene sulphide (PPS), we have designed a new family of 2D and 3D poly-arylthioethers, synthesised via a mild Pd-catalysed C–S/C–S metathesis-based method, that merges the attractive features common to porous polymers and PPS in a single material. In addition, the method is highly modular, allowing to easily introduce application-oriented functionalities in the materials for a series of environmentally relevant applications including metal capture, metal sensing and heterogeneous catalysis. Moreover, despite their extreme chemical resistance, the polymers can be easily recycled to recover the original monomers, offering an attractive perspective for their sustainable use. | Miguel A. Rivero-Crespo; Georgios Toupalas; Bill Morandi | Catalysis; Heterogeneous Catalysis; Homogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d48befc622957acc1adbee/original/preparation-of-recyclable-and-versatile-porous-poly-arylthioethers-by-reversible-pd-catalysed-c-s-c-s-metathesis.pdf |
629e160982f956d93ad25d51 | 10.26434/chemrxiv-2022-cj13g | From dopamine 4 to sigma 1: synthesis, SAR and biological characterization of a piperidine scaffold of s1 modulators | The sigma 1 receptor is a multifunctional receptor with wide distribution in the nervous system and its function has been implicated with a number of neurological disorders including dementia and Alzheimer’s disease (AD) and other neurodegenerative disorders. In addition, modulators of s1 have been advanced into clinical trials for the treatment of pain. Starting from our previously disclosed piperidine scaffold, we have identified a class of potent sigma 1 modulators. This work highlights the key SAR components that lead to the divergence in D4 and s1 activity. In addition, we further profile lead compounds in panel of off-target receptors, in vitro and in vivo pharmacokinetic studies. This has culminated in the discovery of multiple s1 receptor modulators with properties that will allow for study in animal models. | Corey Hopkins; Kirsten Tolentino; Viktoriya Mashinson | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629e160982f956d93ad25d51/original/from-dopamine-4-to-sigma-1-synthesis-sar-and-biological-characterization-of-a-piperidine-scaffold-of-s1-modulators.pdf |
60c74efc842e65a67fdb3758 | 10.26434/chemrxiv.12827966.v1 | HUMAN SARS CoV-2 SPIKE PROTEIN MUTATIONS | <p>The human SARS-CoV-2 spike
protein sequences from Asia, Africa, Europe, North America, South America and
Oceania were analyzed by comparing with the reference SARS-CoV-2 protein sequence
from Wuhan-Hu-1, China. Out of 10,333 spike protein sequences analyzed, 8,155 proteins
comprised one or more mutations. A total of 9,654 mutations were observed that correspond
to 400 distinct mutation sites. The receptor binding domain
(RBD) which is involved in the interactions with human ACE-2 receptor and causes
infection leading to the COVID-19 disease comprised 44 mutations that included residues
within 3.2 Å interacting distance from the ACE-2 receptor. The mutations observed
in the spike proteins are discussed in the context of their distribution
according to the geographical locations, mutation sites, mutation types, distribution
of the number of mutations at the mutation sites and mutations at the glycosylation
sites. The density of mutations in different regions of the spike protein sequence
and location of the mutations in protein three-dimensional structure corresponding
to the RBD are discussed. The mutations identified in the present work are important
considerations for antibody, vaccine and drug development.</p> | Lalitha Guruprasad | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74efc842e65a67fdb3758/original/human-sars-co-v-2-spike-protein-mutations.pdf |
6696bccb01103d79c52ff142 | 10.26434/chemrxiv-2024-tsrvm | Ring-to-Chain Transformation of Elemental Sulfur: Nonadiabatic Dynamics Simulations | The emergence of high-sulfur content polymeric materials and their diverse applications underscore the need for a comprehensive understanding of the ring-to-chain transformation of elemental sulfur. In this study, we delve into the ultra-fast transformation of the elemental sulfur S8 ring upon photoexcitation employing advanced non-adiabatic dynamics simulations. Our findings reveal that the bond breaking of the S8 ring occurs within tens of femtoseconds. At the time of bond breaking, most molecules are in the lowest singlet excited state S1. S1 survives for 40 to 450 fs before relaxing to the quasi-degenerate manifolds formed by the T1 and S0 states of the S8 chain. This suggests that upon photoexcitation the polymerization of the S8 chains might proceed before the chains relax to their lowest energy states. The derived temporal resolution provides a detailed perspective on the dynamics of S8 rings upon photoexcitation, shedding light on the intricate processes involved in its excited-state transformations. | Qi Sun; Jean-Luc Brédas; Veaceslav Coropceanu | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6696bccb01103d79c52ff142/original/ring-to-chain-transformation-of-elemental-sulfur-nonadiabatic-dynamics-simulations.pdf |
671b8e681fb27ce124925504 | 10.26434/chemrxiv-2024-97w8l-v2 | Analysis of battery-like and pseudocapacitive ion intercalation kinetics via distribution of relaxation times | Improving the kinetics of electrochemical ion intercalation processes is of interest for realizing high-power electrochemical energy storage. This includes classical battery-like intercalation and pseudocapacitive intercalation processes with a capacitor-like electrochemical signature. Electrochemical methods are needed to probe the kinetics of such complex multistep processes in detail. Here, we present the use of the Distribution of Relaxation Times (DRT) analysis of electrochemical impedance data to identify the kinetic limits of intercalation reactions. We study the lithium intercalation reaction in TiS2 from organic and aqueous electrolytes as a model system. The material can exhibit both battery-like and pseudocapacitive intercalation regimes depending on the potential range, variable diffusion lengths by adjusting its particle size, and a tunable degree of solvent cointercalation by choosing the electrolyte solvent. Using DRT, we can distinguish between the kinetic limitations imposed by solid-state ion diffusion, interfacial ion adsorption and transport, and ion desolvation processes. Thus, DRT analysis can complement existing methods, such as voltammetry or 3D-Bode analysis, to better understand the kinetics of intercalation reactions. | Yoga Trianzar Malik; Michael Braig; Patrice Simon; Roswitha Zeis; Simon Fleischmann | Physical Chemistry; Energy; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Transport phenomena (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671b8e681fb27ce124925504/original/analysis-of-battery-like-and-pseudocapacitive-ion-intercalation-kinetics-via-distribution-of-relaxation-times.pdf |
6415656faad2a62ca1f37751 | 10.26434/chemrxiv-2023-712fl | Concentrated zwitterion interfaces for the selective promotion of ionic electrocatalysis | The electrode/electrolyte interfacial structure is a seminal component that governs the activity of electrochemical reactions. Concentrated interfaces can typically retard the local electrocatalytic reactions to extend the voltage window for high-voltage batteries, whereas in this study we demonstrated that a dense interface constituting of zwitterionic betaine could selectively promote the electrocatalytic transformation of anionic species, especially electrocatalytic hydroxide oxidation in alkaline water splitting. Under concentrated betaines, the state-of-the-art oxygen evolution reaction (OER) electrocatalysts of nickel and nickel-iron oxyhydroxide exhibited overpotential gains of 138 mV and 97 mV, corresponding to two orders of magnitude higher current densities. The activity increment was stemmed from both the static dehydration effect that the hygroscopic betaine rips off the anionic hydration shell to promote its downstream reaction and the dynamic double layer effect that the ultra-dense betaine layer accelerates the accumulation of underhydrated anions in the inner Helmholtz plane. This enhancement is highly specific to ions for enabling the selective ionic transformation in complex media. The concentrated betaine interface effectively segregates the reactive zones to improve the durability of water electrolysis in aniline-containing electrolytes by at least an order of magnitude, opening up new possibilities for next-generation unconventional water splitting. | Jianxiang Wu; Yuxin Chen; Yaming Hao; Shaoyan Wang; Ran Wang; Wei Du; Shuangshuang Cha; Xuejing Yang; Qiang Yang; Cheng Lian; Honglai Liu; Ming Gong | Catalysis; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6415656faad2a62ca1f37751/original/concentrated-zwitterion-interfaces-for-the-selective-promotion-of-ionic-electrocatalysis.pdf |
658176f39138d231610852ac | 10.26434/chemrxiv-2023-6r8s7-v2 | Co-evolved ligands to ORF8. Could they reduce SARS-COV-2-excesive inflammation? | ORF8 is an asymmetric-homodimer SARS-COV-2 accessory protein implicated in excesive human inflammation causing numerous deaths. There is no approved drug targeting ORF8, nor it is known whether any anti-ORF8 drugs could reduce human excesive inflammation. Computationally combining ligand co-evolution of parent molecules with affinity-consensus docking, children candidates for docking to ORF8 cavities were generated. Targeting the homodimer interface with the highest affinity children scaffolds, hundreds of grandchildren predicting nanoMolar affinities, unique scaffolds, high specificities and low toxicity risks were generated. Although remaining hypothetical without experimental confirmation, this constitute a new methodological attempt to search for drug-like candidates to interfere with SARS-COV-2-dependent excessive inflammation. | Melissa Bello-Perez; Julio Coll | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2023-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658176f39138d231610852ac/original/co-evolved-ligands-to-orf8-could-they-reduce-sars-cov-2-excesive-inflammation.pdf |
63330291114b7e0a741f5899 | 10.26434/chemrxiv-2022-3cx6g-v2 | Xanthate-supported photo-iniferter (XPI)-RAFT polymerization: Facile and rapid access to complex macromolecules | Xanthate-supported photo-iniferter (XPI)-reversible addition-fragmentation chain-transfer (RAFT) polymerization is introduced as a fast and versatile photo-polymerization strategy. Small amounts of xanthate are added to conventional RAFT polymerizations to act as a photo-iniferter under light irradiation. Radical exchange is facilitated by the main CTA ensuring control over the molecular weight distribution, while the xanthate enables an efficient photo-(re)activation. The photo-active moiety is thus introduced into the polymer as an end group, which makes chain extension of produced polymers possible directly by irradiation. This is in sharp contrast to conventional photo-initiators, or photo electron transfer (PET)-RAFT polymerizations, where radical generation depends on added small molecules. In contrast to regular photo-iniferter-RAFT polymerization, photo-activation is decoupled from polymerization control, rendering XPI-RAFT an elegant tool for the fabrication of defined and complex macromolecules. The method is oxygen tolerant and robust and was used to perform screenings in a well-plate format, and it was even possible to produce multiblock copolymers in a coffee mug under open-to-air conditions. XPI-RAFT does not rely on highly specialized equipment and qualifies as a universal tool for the straightforward synthesis of complex macromolecules. | Anne-Catherine Lehnen; Johannes Gurke; Alain Bapolisi; Martin Reifarth; Marek Bekir; Matthias Hartlieb | Polymer Science; Organic Polymers; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63330291114b7e0a741f5899/original/xanthate-supported-photo-iniferter-xpi-raft-polymerization-facile-and-rapid-access-to-complex-macromolecules.pdf |
60c74f029abda24e84f8d783 | 10.26434/chemrxiv.12837635.v1 | Comparative Life Cycle Assessment of Electrochemical Upgrading of CO2 to Fuels and Feedstocks | <p>Development
of electrochemical pathways to convert CO<sub>2</sub> into fuels and feedstock is
rapidly progressing over the past decade. Here we present a comparative
cradle-to-gate life cycle assessment (LCA) of one and two-step electrochemical conversion
of CO<sub>2 </sub>to eight major value-added products; wherein we consider CO<sub>2</sub>
capture, conversion and product separation in our process model. We measure the
carbon intensity (i.e., global warming impact) of one and two-step electrochemical
routes with its counterparts – thermochemical CO<sub>2</sub> utilization and
fossil-fuel based conventional synthesis routes for those same products. Despite
inevitable carbonate formation in one-step CO<sub>2</sub> electrolysis, this analysis reveals one-step electrosynthesis
would be equally compelling (through the lens of climate benefits) as compared
to two-step route. This analysis further reveals that the carbon
intensity of electrosynthesis products is due to significant energy requirement
for the conversion (70-80% for gas products) and product separation (40-85% for
liquid products) phases. Electrochemical route is highly sensitive to the
electricity emission factor and is compelling only when coupled with
electricity with low emission intensity (<0.25 kg CO<sub>2</sub>e/kWh). As
the technology advances, we identify the near-term products that would provide
climate benefits over fossil-based routes, including syngas, ethylene and n-propanol.
We further identify technological goals required for electrochemical route to
be competitive, notably achieving liquid product concentration >20 wt%. It
is our hope that this analysis will guide the CO<sub>2</sub> electrosynthesis
community to target achieving these technological goals, such that when coupled
with low-carbon electricity, electrochemical route would bring climate benefits
in near future. </p> | Shariful Nabil; Sean McCoy; Md Kibria | Electrocatalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f029abda24e84f8d783/original/comparative-life-cycle-assessment-of-electrochemical-upgrading-of-co2-to-fuels-and-feedstocks.pdf |
67b33018fa469535b9b68f8e | 10.26434/chemrxiv-2024-8v8km-v2 | A method to identify small molecule/protein pairs susceptible to protein ubiquitination by the CRBN E3 ligase | Although using DNA-encoded libraries (DELs) to find small molecule binders of target proteins is well-established, identifying molecules with functions beyond binding remains challenging in pooled screens. Here, we develop an approach for multiplexing functional screens that simultaneously evaluates encoded small molecules and encoded collections of protein targets in functional selections. We focus on ubiquitin (Ub) transfer with the cereblon-bound CRL4 E3 ligase because of its proven versatility in drug discovery. The functional selections recover small molecule/G-hairpin loop pairs based on their ability to promote Ub-transfer onto the G-hairpin loop. As Ub-transfer is the first step in tagging proteins for proteasomal destruction, finding small molecules capable of selectively reprogramming it is a significant challenge in contemporary drug development. Our work lays the foundation for functional DEL selections that match small molecule Ub-transfer catalysts with their optimal protein substrates. | Pinwen Cai; Chiara Disraeli; Basilius Sauter; Saule Zhanybekova; Dennis Gillingham | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b33018fa469535b9b68f8e/original/a-method-to-identify-small-molecule-protein-pairs-susceptible-to-protein-ubiquitination-by-the-crbn-e3-ligase.pdf |
6719143183f22e4214eab7e7 | 10.26434/chemrxiv-2024-ll474-v2 | Electronic Structures of Late versus Early Transition Metal Imido Complexes from 15N NMR Signatures | Imido ligand is a ubiquitous motif in organometallic chemistry, serving roles spanning from ancillary ligands to reactive sites. The nature of M=N bond is highly depended on the metal centres and their d-electron configuration, with late transition metal (TM) imido complexes exhibiting contrasting features when compared to their early TM analogues. Envisioning to uncover general electronic descriptor for the nature of imido ligands, we computationally investigate the solid-state 15N NMR signatures of late TM imido complexes with various central metals, geometries and d-electron counts, and compare them against these of the corresponding early TM systems. The spectroscopic signatures are mostly driven by the presence of filled, π-symmetry orbitals in late TM imido complexes, suggesting the development of high-lying π(M=N) and low-lying σ/σ*(M=N) orbitals. This contrasts with what is observed for the reported early TM systems, for which high-lying σ-type orbitals determine the NMR signature. Noteworthily, Ni- and Pd-imido complexes with d10 configurations exhibit highly asymmetric nitrogen-15 NMR signature with extremely deshielded principal components, because of the presence of filled, high-lying antibonding π*(M=N) orbitals, consistent with their high reactivity. The sensitive response of 15N NMR signature to the nature of metal sites further highlights that chemical shift is a useful reactivity descriptor. | Yuya Kakiuchi; Christophe Copéret | Inorganic Chemistry; Bonding; Coordination Chemistry (Inorg.); Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6719143183f22e4214eab7e7/original/electronic-structures-of-late-versus-early-transition-metal-imido-complexes-from-15n-nmr-signatures.pdf |
62055a0fcbb4f462cabc7bc5 | 10.26434/chemrxiv-2022-26pjd | Seeded Growth of Mesoscale Quantum-Confined Semiconductor Nanoplatelets | Colloidally grown (II-VI) semiconductor nanoplatelets display significantly smaller lateral dimensions than their mechanically exfoliated 2D van der Waal (vdW) semiconductor counterparts. Here, we show that a seeded growth procedure allows us to significantly extend the lateral area of atomically precise nanoplatelets to the mesoscale (>1 μm^2). Using CdTe nanoplatelets as a model system, we optimize reaction parameters to expand a variety of nanoplatelets with different thickness and compositions. In situ spectroscopy results demonstrate that large NPLs grow through a mechanism of lateral ripening of seeds. Correlative optical spectroscopy and electron microscopy measurements show that the photoluminescence displays resolvable spatial inhomogeneities, similar to 2D semiconductors. Overall, these mesoscale nanoplatelets can be analogized to vdW semiconductors, with the added advantages of scalable colloidal synthesis, thickness tunability and solution processability. | Stephanie Tenney; Lauren Tan; Mikayla Sonnleitner; Anthony Sica; Ashley Shin; Timothy Atallah; Justin Caram | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62055a0fcbb4f462cabc7bc5/original/seeded-growth-of-mesoscale-quantum-confined-semiconductor-nanoplatelets.pdf |
628cd61287d01f5fe5f07639 | 10.26434/chemrxiv-2022-bl6rx | Aryl Dance Reaction of Arylheteroles | We have discovered a 1,2-migration (aryl dance reaction) of the aryl group on heteroles. AlCl3 can efficiently convert C3-arylheteroles to C2-arylheteroles. Depending on the electron density of the substrate, conversion from C2- to C3-arylheteroles was also possible with catalytic Zn(OTf)2. A one-pot aryl dance/acylation or bromination, and arylation/aryl dance was also demonstrated. | Hikaru Nakahara; Junichiro Yamaguchi | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2022-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628cd61287d01f5fe5f07639/original/aryl-dance-reaction-of-arylheteroles.pdf |
60c742e0567dfe5478ec3fa9 | 10.26434/chemrxiv.8796779.v1 | Discovering Ferro- and Piezoelectricity in Lead-Free Oxyhydrides Ln2H4O (Ln = Y, La) | One of the most significant aspects of crystal chemistry of multianionic oxyhydrides is the possibility of flexible regulation of the composition-structure-function relationships. In the context of competitive coordinations of different anions in the crystal lattice, this may afford formation of a number of stable stoichiometric phases without inversion symmetry. In the present work, we demonstrated that semiconducting yttrium and lantanium oxyhydrides with the composition Ln<sub>2</sub>H<sub>4</sub>O (Ln=Y, La) have an attractive potential for the design of novel lead-free ferro- and piezoelectric systems. By means of advanced DFT-based computational simulations we predicted that several polar monoclinic and orthorhombic phases of Ln<sub>2</sub>H<sub>4</sub>O may exhibit exceptional ferro- and piezoelectric properties as well as electromechanical coupling characteristics that are especially suitable for the piezoelectric devices working in a shear mode. Structure-dependent theoretical evaluations of the relevant physical responses demonstrated estimates of ferro- and piezoelectric characteristics that are comparable with the specifications of advanced ferroelectric solid solutions. Thus, our prediction of lead-free piezoelectric systems forms a solid and technologically reliable basis for the future development of effective and non-hazardous materials. | Aleksandr Pishtshev; Evgenii Strugovshchikov | Ceramics; Thin Films; Solid State Chemistry; Theory - Inorganic; Computational Chemistry and Modeling; Piezoelectricity and Thermoelectricity; Structure; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742e0567dfe5478ec3fa9/original/discovering-ferro-and-piezoelectricity-in-lead-free-oxyhydrides-ln2h4o-ln-y-la.pdf |
60c754a7bb8c1a3bbc3dc279 | 10.26434/chemrxiv.13705516.v1 | Cycloparaphenylene-Phenalenyl Radical and Its Dimeric Double Nanohoop | <p>We report the first example of a neutral spin-delocalized carbon-nanoring radical, achieved by integration of an open-shell graphene fragment phenalenyl into cycloparaphenylene (CPP). We show that spin distribution in this hydrocarbon partially extends from the phenalenyl onto the CPP segment as an interplay of steric and electronic effects. The resulting geometry is reminiscent of a diamond ring, with pseudo-perpendicular arrangement of the radial and the planar π-surface. Remarkably, this geometry gives rise to a steric effect that governs a highly selective dimerization pathway, yielding a giant double nanohoop. Its π-framework made of 158 sp2-carbon atoms was unambiguously elucidated by single crystal X-ray diffraction, which revealed a three-segment CPP–peropyrene–CPP structure. This nanocarbon shows a fluorescence profile characteristic of peropyrene, regardless of which segment gets excited. These results in conjunction with DFT suggest that adjustment of the size of the CPP segments in this double nanohoop could deliver true donor–acceptor systems.</p> | Yong Yang; Olivier Blacque; Sota Sato; Michal Juricek | Organic Synthesis and Reactions; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754a7bb8c1a3bbc3dc279/original/cycloparaphenylene-phenalenyl-radical-and-its-dimeric-double-nanohoop.pdf |
634e8e6933997208578f58c9 | 10.26434/chemrxiv-2022-54ccs | In Operando investigations of oscillatory water and carbonate effects in MEA-based CO2 electrolysis devices | Membrane electrode assembly (MEA) CO2 electrolysis (CO2E) is a promising route towards producing carbon-neutral chemicals, however, they often have stability issues related to flooding of the gas diffusion electrode (GDE). Thus, there is an urgent need to comprehend water management in these devices and to engineer electrodes that allow both stable and efficient electrocatalytic performance. Here, we investigated the possible causes of suppression in the CO2 reduction reaction (CO2RR) selectivity on Cu via in operando X-ray diffraction (XRD) analysis. The in operando XRD allowed us to monitor water and bicarbonate formation in the GDE, while in-line gas and mass chromatographs allowed us to correlate those changes to the cathode and anode product distribution during CO2E. We found direct evidence for salt precipitation in the cathode GDEs, which causes water build-up and an increase in hydrogen evolution reaction (HER). We also observed that the increase in HER is related to a drop in total cell potential, caused by a shift in ion transport through the membrane from carbonates to more conductive hydroxide ions. Our results reported here also do not show any substantial catalyst-induced effects on CO2RR. Thus this work suggests proper ion management is an important key to enhanced durability throughout the device. | Asger Moss; Sahil Garg; Marta Mirolo; Carlos Giron; Roosa Ilvonen; Ib Chorkendorff; Jakub Drnec; Brian Seger | Materials Science; Catalysis; Energy; Catalysts; Electrocatalysis; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634e8e6933997208578f58c9/original/in-operando-investigations-of-oscillatory-water-and-carbonate-effects-in-mea-based-co2-electrolysis-devices.pdf |
617812fdd7e1eee0a0357745 | 10.26434/chemrxiv-2021-81d73 | Enhancement of photoacoustic spectroscopy with
sorption enrichment for ppt-level benzene
detection | A real time trace gas detector for benzene is demonstrated. The measurement system
takes an advantage of modest enrichment through short adsorption periods to reach a
ppt-level detection limit with a sampling cycle of 90 s, which includes sample adsorption,
desorption and a spectroscopic measurement. Benzene is collected on Tenax TA sorbent
for 30 s and then detected from the enriched samples with photoacoustic spectroscopy. A
high sensitivity is achieved using cantilever-enhanced photoacoustic spectroscopy and a
continuous-wave quantum cascade laser emitting at the wavelength 14.8 μm, which corresponds
to the absorption wavelength of the strongest benzene infrared band. We reach a
detection limit of 150 ppt of benzene, over one sampling cycle. Interference from humidity
and other common petrochemicals is evaluated. | Juho Karhu; Tuomas Hieta | Physical Chemistry; Analytical Chemistry; Analytical Apparatus; Spectroscopy (Anal. Chem.); Optics | CC BY 4.0 | CHEMRXIV | 2021-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617812fdd7e1eee0a0357745/original/enhancement-of-photoacoustic-spectroscopy-with-sorption-enrichment-for-ppt-level-benzene-detection.pdf |
675b3e72f9980725cfdfae56 | 10.26434/chemrxiv-2024-rpf17-v2 | Why Ti3C2Tx MXenes Are Conductive but Not
Plasmonic in the Optical Domain | MXenes have shown great potential in electronic and optoelectronic applications. However, optical properties of these highly conductive two-dimentional materials are not fully understood. The near-infrared (IR) optical peak (∼1.5
eV) in Ti3C2Tx with mixed terminations (T: O, OH, F, Cl) has sparked debates, attributing the peak to a localized surface plasmon resonance (LSPR) or an inter-band transition (IBT). Here, density functional theory calculations conclusively assign the peak to an IBT that exists only in Ti3C2O2. Both experiments and calculations corroborate that this peak is absent in Ti3C2Cl2. Moreover, calculations predict SPR in the mid-IR (∼0.5 eV, outside optical domain) for Ti3C2O2, but not for Ti3C2Cl2. Our results reconcile conflicting interpretations of the debate, allowing for optimized use of Ti3C2Tx MXenes, by leveraging their IBT optical signature, which is size-independent and distinct from the size-dependent plasmonic effect. | Hui Fang; Zhenyao Fang; Anupma Thakur; Vahid Rad; Nithin Chandran B S; Paweł Michałowski; Masoud Soroush ; Babak Anasori; Andrew M. Rappe; Zahra Fakhraai | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Optical Materials; Computational Chemistry and Modeling; Physical and Chemical Properties | CC BY NC 4.0 | CHEMRXIV | 2024-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675b3e72f9980725cfdfae56/original/why-ti3c2tx-m-xenes-are-conductive-but-not-plasmonic-in-the-optical-domain.pdf |
617ad28081c4fc220fe41ddd | 10.26434/chemrxiv-2021-np7xj-v4 | Active site sequence representation of human kinases outperforms full sequence for affinity prediction and inhibitor generation: 3D effects in a 1D model | Recent advances in deep learning have enabled the development of large-scale multimodal models for virtual screening and de novo molecular design. The human kinome with its abundant sequence and inhibitor data presents an attractive opportunity to develop proteochemometric models that exploit the size and internal diversity of this family of targets. Here we challenge a standard practice in sequence-based affinity prediction models: instead of leveraging the full primary structure of proteins, each target is represented by a sequence of 29 residues defining the ATP binding site. In kinase-ligand binding affinity prediction, our results show that the reduced active site sequence representation is not only computationally more efficient but consistently yields significantly higher performance than the full primary structure. This trend persists across different models, datasets, performance metrics and holds true when predicting affinity for both unseen ligands and kinases. Our interpretability analysis further demonstrates that, even without supervision, the full sequence model can learn to focus on the active site residues to a higher extent. We then investigate a de novo molecular design task and find that the active site provides benefits in the computational efficiency, but otherwise, both kinase representations yield similar optimized affinities (for both SMILES and SELFIES-based molecular generators). Our work challenges the assumption that full primary structure is indispensable for modelling human kinases. We hope that these results will inspire additional investigation into hybrid mechanistic-DL modeling approaches to support the identification and optimization of kinase inhibitors’ candidates. | Jannis Born; Tien Huynh; Astrid Stroobants; Wendy Cornell; Matteo Manica | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Drug Discovery and Drug Delivery Systems; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617ad28081c4fc220fe41ddd/original/active-site-sequence-representation-of-human-kinases-outperforms-full-sequence-for-affinity-prediction-and-inhibitor-generation-3d-effects-in-a-1d-model.pdf |
6421742762fecd2a8382cbae | 10.26434/chemrxiv-2023-s8ft1 | Copper (II) bromide/NMO system for α-amination of esters in solvent-free condition | Copper (II) bromide/ N-methylmorpholine N-oxide promoted α-amination of esters in solvent-free condition is reported. The α-amino esters are precursors for α-amino acids. This method provides α-amino esters in 58-83% yields. The polar solvent dimethyl sulfoxide was avoided and the reactions were performed in solvent-free condition. NMO successfully oxidizes Cu(I)Br to regenerate the Cu(II)Br catalyst. The isolated CuBr2 catalyst was recycled twice. | Kankanala Naveen Kumar; Yaman Chauhan; V. Ravichandiran; Sharada Prasanna Swain | Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6421742762fecd2a8382cbae/original/copper-ii-bromide-nmo-system-for-amination-of-esters-in-solvent-free-condition.pdf |
67042dc251558a15ef65ca58 | 10.26434/chemrxiv-2024-p6tm4 | Comparative DFT Studies of Optoelectronic Properties of MTPA Derivatives | Accurate prediction of optical and electronic properties of methyl triphenyl amine (MTPA) and its derivatives was investigated as these properties are essential for designing efficient electron donor material for organic solar cell applications. Specifically, we have investigated ten different density functionals used in the Density Functional Theory (DFT) and Time Dependent DFT (TD-DFT) calculations to determine the best functional for predicting the HOMO, LUMO, Egap and UV-Vis absorption spectra of MTPA and its derivatives accurately. The ten density functionals namely, B3LYP, B3PW91, HSEH1PBE, MPW1PW91, CAMB3LYP, B97XD, BPV86, PBE, TPSS, and HCTH were investigated with the 6-31g+(d,p) basis set. MTPA and six MTPA derivatives in dichloromethane solvent were studied. Results show that among the ten functionals, HSEH1PBE is the best functional in predicting HOMO, LUMO and Egap of MTPA and MTPA derivatives with an overall MAE of 0.43 eV for all three properties mentioned. MAE for HOMO, LUMO and Egap of MTPA derivatives tend to decrease as the functional group attached becomes more electron-withdrawing. This trend was observed to be opposite for TD-DFT excitation calculations used for UV-Vis absorption spectra. Absorption wavelength MAE increases as the functional group attached to MTPA becomes more electron-withdrawing. The best functional in predicting absorption spectra of MTPA and MTPA derivatives is CAMB3LYP with MAE of 26nm. | Pemela Ubaldo; Lichang Wang | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67042dc251558a15ef65ca58/original/comparative-dft-studies-of-optoelectronic-properties-of-mtpa-derivatives.pdf |
667e81a3c9c6a5c07aaa740b | 10.26434/chemrxiv-2024-bfv3d | A Foundational Model for Reaction Networks on Metal Surfaces | Process optimization in heterogeneous catalysis relies on the control of competing reactions. The reaction mechanisms based on chemical knowledge can be evaluated via density functional theory unveiling experimental catalytic trends. However, this approach finds its limits when applied to complex reaction networks or large molecules, disregarding alternative paths and rare events. Here we present CARE, a foundational model for catalysis on metal surfaces with a rule-based reaction network generator for CxHyOz species built with GAME-Net-UQ, a graph neural network with uncertainty quantification targeting thermodynamic and kinetic parameters, coupled to microkinetic modeling. CARE reproduces experimental activity trends in methanol decomposition, selectivity to C3 products in electrochemical reduction processes, and models the Fischer-Tropsch synthesis to C6 products, including 370k reactions, breaking the current limits of network exploration. This comprehensive model opens the path towards the exploration of thermal and electrocatalytic surface processes previously not amenable to atomistic simulations. | Santiago Morandi; Oliver Loveday; Tim Renningholtz; Sergio Pablo-García; Rodrigo A. Vargas-Hernández; Ranga Rohit Seemakurthi; Pol Sanz Berman; Rodrigo García-Muelas; Alán Aspuru-Guzik; Núria López | Theoretical and Computational Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Artificial Intelligence; Chemoinformatics - Computational Chemistry; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667e81a3c9c6a5c07aaa740b/original/a-foundational-model-for-reaction-networks-on-metal-surfaces.pdf |
64a27b1d9ea64cc1675c02f0 | 10.26434/chemrxiv-2023-x7qmd | Dip Coating of Water-Resistant PEDOT:PSS Films Based on Physical Crosslinking | Water-resistant poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) films are valuable in biomedical applications; however, they typically require crosslinkers to stabilize the films, which can introduce undesired aggregation or phase separation reactions. Herein, we developed a dipping-based processes to prepare PEDOT:PSS films on non-planar surfaces without crosslinker. Sequential soaking of a dip-coated PEDOT:PSS film in ethanol and water imparted water resistance to the film. Microscopic and spectroscopic techniques were used to monitor the process and confirmed that the ethanol soaking eluted the excess PSS from the film bulk, which stabilized the film prior to the water-soaking process. The obtained films acted as conductors and semiconductors on curved surfaces, including three-dimensional (3D)-printed objects. A film deposited on a curved surface was successfully applied as the channel layer in a neuromorphic organic electrochemical transistor. This approach will enable integrated bioelectronic and neuromorphic applications that can be readily deployed for facile prototyping. | Shunsuke Yamamoto; Ryusei Miyako; Ryota Maeda; Yuya Ishizaki; Masaya Mitsuishi | Physical Chemistry; Materials Science; Thin Films; Interfaces; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a27b1d9ea64cc1675c02f0/original/dip-coating-of-water-resistant-pedot-pss-films-based-on-physical-crosslinking.pdf |
60c74c52337d6c32b1e27c09 | 10.26434/chemrxiv.12445226.v1 | Cyclic, Cell-Penetrating Peptides Tailor-Made for the Creation of Peptide Libraries with Intrinsic Cell Permeability | <p>The discovery of high-affinity peptides to many
intracellular targets has become feasible
through the development of diverse macrocyclic peptide libraries. But lack of
cell permeability is a key feature
hampering the use of these peptides as therapeutics. Here, we develop a set of
small, cyclic peptide carriers that efficiently carry cargoes into the cytosol.
These peptides are cyclized via side-chain alkylation, which makes them ideal for the creation of
diverse mRNA or phage-displayed libraries with intrinsic cell permeability.</p> | Nicolas A. Abrigo; Kara Dods; Koushambi Mitra; Kaylee Newcomb; Anthony Le; Matthew Hartman | Biochemistry; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c52337d6c32b1e27c09/original/cyclic-cell-penetrating-peptides-tailor-made-for-the-creation-of-peptide-libraries-with-intrinsic-cell-permeability.pdf |
67c456376dde43c90823c06c | 10.26434/chemrxiv-2025-nss12 | Regioselective 1,2-Di(hetero)arylation of Activated and Unactivated Alkenes with (Hetero)aryl Chlorides | Aryl chlorides are more commercially available and lower cost compared with aryl bromides and iodides. However, the use of (hetero)aryl chlorides as aryl radical precursors for the di(hetero)arylation of alkenes remains an underdeveloped area. Furthermore, existing examples of theses reactions are predominantly confined to activated alkenes. In this study, we introduce a benzophenone-catalyzed 1,2-di(hetero)arylation process that is applicable to both activated and unactivated alkenes, utilizing (hetero)aryl chlorides and cyanoarenes as aryl sources. Importantly, this method allows for the simultaneous introduction of two heterocycles to alkenes with high regioselectivity. | Yingjun Lan; Siqi Xie; Bin Liu | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c456376dde43c90823c06c/original/regioselective-1-2-di-hetero-arylation-of-activated-and-unactivated-alkenes-with-hetero-aryl-chlorides.pdf |
67c569596dde43c90845febe | 10.26434/chemrxiv-2025-pksq8 | Towards a Global Model for Diabetic Kidney Disease Screening using ATR-FTIR | Infrared (IR) spectroscopy of urine extracts coupled with Machine Learning (ML) methods has been proposed as a promising technique for Diabetic Kidney Disease (DKD) screening. However, for clinical translation, predictive models based on machine learning techniques necessitate substantial sets of samples for calibration and testing under various experimental parameters and populations, posing a critical barrier to the development of globally deployable tools. Here, we aim to assess the methodology's ability to establish DKD diagnostic models applicable across diverse populations, instruments and experimental conditions worldwide. Two datasets were compared. The Australian set included 155 DKD and 22 control samples from a 24-hour urine collection, with preconcentrated proteins measured on a Bruker spectrometer. The Spanish set, comprising 35 DKD and 26 control spot urine samples, was analyzed using a Perkin-Elmer spectrometer. Different ML methods were developed to identify DKD and microalbuminuria, aiming to compare their performance in terms of generalization and adaptation to different datasets. Models developed using Australian spectra successfully predicted Spanish samples, achieving AUROC values of 0.87 and 0.98 for DKD and microalbuminuria identification, respectively. Both values improved to 0.99 when a global model was calibrated and independently tested with a combined set integrating samples from both countries. Results evidence that the spectral markers found in the IR spectra, based on signals arising from albumin and other glycoproteins, have proven to be robust, minimizing the effects of population and instrument variability. Results exemplify the potential of developing global big-data spectroscopic datasets to facilitate the deployment of IR-based diagnostic methods in real-world settings. | Víctor Navarro-Esteve; Ángel Sánchez-Illana; José Pórtoles; María Marqués-Vidas; Josep Ventura-Gayete; Nuria Estañ Capell; Iris Viejo-Boyano; Francisco Valero-Mena; Antonio J. Sánchez-López; Bayden R. Wood; David Pérez-Guaita | Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Chemistry - General; Spectroscopy (Anal. Chem.) | CC BY 4.0 | CHEMRXIV | 2025-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c569596dde43c90845febe/original/towards-a-global-model-for-diabetic-kidney-disease-screening-using-atr-ftir.pdf |
624ab7bf804882827f0330f5 | 10.26434/chemrxiv-2022-78cvz | The onset of CVD graphene formation on γ-Al2O3 is promoted by unsaturated CH2 end | Chemical vapor deposition of methane onto a template of alumina (Al2O3) nanoparticles is a prominent synthetic strategy of graphene meso-sponge, a new class of nanoporous carbon materials consisting of single-layer graphene walls. However, the elementary steps controlling the early stages of graphene growth on Al2O3 surfaces are still not well understood. In this study, density functional calculations provide insights into the initial stages of graphene growth. We have modelled the mechanism of CH4 dissociation on (111), (110), (100), and (001) γ-Al2O3 surfaces. Subsequently, we have considered the reaction pathway leading to the formation of a C6 ring. We found the γ-Al2O3(110) and γ-Al2O3(100) are both active for CH4 dissociation, but the (100) surface has a higher catalytic activity towards the carbon growth reaction. The overall mechanism involves the formation of the reactive intermediate CH2* that then can couple to form CnH2n* (n = 2-6) species. The unsaturated CH2 end promotes the sustained carbon growth in a nearly barrierless process. Also, the short length between terminal carbon atoms leads to strong interactions, which might lead to the high activity among unsaturated CH2* of hydrocarbon chain. Analysis of the electron localization and geometries of the carbon chains reveal the formation of C-Al-σ bonds with the chain growing towards the gas rather than C-Al-π bonds covering the γ-Al2O3(100) surface. This growth behaviour prevents catalysis poison during the initial stage of graphene nucleation. | Qi Zhao; Masanori Yamamoto; Kaoru Yamazaki; Hirotomo Nishihara; Rachel Crespo-Otero; Devis Di Tommaso | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624ab7bf804882827f0330f5/original/the-onset-of-cvd-graphene-formation-on-al2o3-is-promoted-by-unsaturated-ch2-end.pdf |
67b01c0e6dde43c908ef6311 | 10.26434/chemrxiv-2025-dh55p | Harnessing CO₂ for the Development of Biodegradable Polymers: A Review of Innovations in Green Chemistry | The increasing environmental impact of plastic waste has prompted the exploration of sustainable alternatives, particularly CO₂-based biodegradable polymers. These polymers, synthesized from CO₂, offer an innovative approach to both reducing greenhouse gas emissions and mitigating plastic pollution. This review provides a comprehensive overview of recent advancements in CO₂-derived biodegradable polymers, with a focus on catalyst development, polymerization methods, and material properties. Various catalysts, including metal-based, organic, photocatalysts, and enzymes, are evaluated for their effectiveness in CO₂ activation and polymer synthesis. The structural, thermal, and mechanical properties of CO₂-based polymers are discussed, with comparisons to conventional petroleum-based plastics to highlight their potential advantages and limitations. Additionally, the biodegradability of these materials is assessed through soil burial, enzymatic degradation, and hydrolysis studies. Challenges in scalability, catalyst efficiency, and cost-effectiveness are also examined. Despite these challenges, CO₂-based biodegradable polymers hold significant promise for reducing plastic pollution, particularly in short-lifetime applications. This review concludes by discussing the future potential of CO₂-based polymers and the need for continued research to enhance their commercial viability and environmental impact. | Jerusha Evangeline Nallarajah | Organometallic Chemistry; Polymer Science; Biopolymers; Organic Polymers; Polymerization (Polymers); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b01c0e6dde43c908ef6311/original/harnessing-co2-for-the-development-of-biodegradable-polymers-a-review-of-innovations-in-green-chemistry.pdf |
60c73db7469df4c9a3f4276d | 10.26434/chemrxiv.6026795.v1 | Artificial Intelligence Recognizes β-Lapachone as an Allosteric 5- Lipoxygenase Inhibitor | <div>
<div>
<div>
<p>Chemical matter with often-discarded moieties entails opportunities for drug discovery. Relying
on orthogonal ligand-centric machine learning methods, targets were consensually identified as
potential counterparts for the fragment-like natural product β-lapachone. Resorting to a
comprehensive range of biophysical and biochemical assays, the natural product was validated
as a potent, ligand efficient, allosteric and reversible modulator of 5-lipoxygenase (5-LO).
Moreover, we provide a rationale for 5-LO-inhibiting chemotypes inspired in the β-lapachone
scaffold through a focused analogue library. This work demonstrates the power of artificial
intelligence technologies to deconvolute complex phenotypic readouts of clinically relevant
chemical matter, leverage natural product-based drug discovery, as an alternative and/or
complement to chemoproteomics and as a viable approach for systems pharmacology studies. </p>
</div>
</div>
</div> | Gonçalo Bernardes; Tiago Rodrigues; Markus Werner; Jakob Roth; Eduardo H. G. da Cruz; Marta C. Marques; Susana A. Lobo; Andreas Koeberle; Francisco Corzana; Eufrânio N. da Silva Júnior; Oliver Werz | Biophysics; Chemical Biology; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2018-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73db7469df4c9a3f4276d/original/artificial-intelligence-recognizes-lapachone-as-an-allosteric-5-lipoxygenase-inhibitor.pdf |
62ac9586f70c2111c631abe4 | 10.26434/chemrxiv-2022-fkj67-v2 | Identifying Limitations in Screening High-Throughput Photocatalytic Bimetallic Nanoparticles with Machine-Learned Hydrogen Adsorptions | The Sabatier principle is of fundamental importance to computational catalyst discovery, saving
researchers time and expense by predicting catalytic activity in silico at scale. However, as
polycrystalline and nanoscale catalysts increasingly dominate industry, computational screening tools
must be adapted to these uses. In this work, we demonstrate the effectiveness of computational
adsorption energy screening in nanocatalysis by comparing a multisite adsorption energy prediction
workflow against a large experimental dataset of hydrogen evolution activities over bimetallic
nanoparticles. Comparing 16 million hydrogen adsorption energy predictions with the hydrogen evolution
activity of 5,300 experiments across 84 monometallic and bimetallic systems, we discover that favorable
adsorption energies are a necessary condition for experimental activity, but other factors often determine
trends in practice. About half of the bimetallic search space can be excluded from experimental screens
using hydrogen adsorption predictions, but these tools may become significantly more powerful when
combined with other screening tools. | Kirby Broderick; Eric Lopato; Brook Wander; Stefan Bernhard; John Kitchin; Zachary Ulissi | Catalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2022-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ac9586f70c2111c631abe4/original/identifying-limitations-in-screening-high-throughput-photocatalytic-bimetallic-nanoparticles-with-machine-learned-hydrogen-adsorptions.pdf |
67c81c3281d2151a0226c06c | 10.26434/chemrxiv-2025-6gxq5 | Fine-tuning of physicochemical properties of 3,3-disubstituted oxetanes on the building blocks level | Fluorinated oxetane derivatives garner significant attention due to their unique physicochemical properties and diverse bioisosteric possibilities for potential applications in medicinal chemistry. We developed robust methodologies for the synthesis of 3-fluoroalkyl-substituted oxetanes, leveraging nucleophilic substitution, deoxy- and deoxofluorination, as well as fluoroiodination as key steps of introduction of fluorine atoms directly to the oxetane core or adjacent alkyl groups. Optimized reaction sequences enabled the gram-scale synthesis of various small building blocks, i.e. amines, carboxylic acids, terminal alkynes, alcohols, thiols, aldehydes, etc. Physicochemical studies revealed that fluorination significantly impacts acidity, with oxetane derivatives demonstrating the decrease of pKa values on up to three units in the case of replacement of gem-dimethyl, cyclopropyl- or cyclobutylidene moieties. These findings underscore the utility of fluorinated oxetanes as versatile building blocks for future applications in drug design and advanced materials. | Eduard Litskan; Serhii Lynnyk; Roman Shypov; Bohdan Vashchenko; Anastasiia Hoida; Oleksii Klymenko-Ulianov; Alina Gorlova; Dmitry Granat; Oleksandr Grygorenko; Dmytro Volochnyuk; Serhiy Ryabukhin | Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c81c3281d2151a0226c06c/original/fine-tuning-of-physicochemical-properties-of-3-3-disubstituted-oxetanes-on-the-building-blocks-level.pdf |
60c73e57bb8c1a41953d98d9 | 10.26434/chemrxiv.6871628.v1 | Learning Continuous and Data-Driven Molecular Descriptors by Translating Equivalent Chemical Representations | <p></p><p>There has been a recent surge of interest in using machine
learning across chemical space in order to predict properties of molecules or
design molecules and materials with desired properties. Most of this work
relies on defining clever feature representations, in which the chemical graph
structure is encoded in a uniform way such that predictions across chemical
space can be made. In this work, we propose to exploit the powerful ability of
deep neural networks to learn a feature representation from low-level encodings
of a huge corpus of chemical structures. Our model borrows ideas from neural
machine translation: it translates between two semantically equivalent but
syntactically different representations of molecular structures, compressing
the meaningful information both representations have in common in a
low-dimensional representation vector. Once the model is trained, this representation
can be extracted for any new molecule and utilized as descriptor. In fair
benchmarks with respect to various human-engineered molecular fingerprints and
graph-convolution models, our method shows competitive performance in modelling
quantitative structure-activity relationships in all analyzed datasets.
Additionally, we show that our descriptor significantly outperforms all
baseline molecular fingerprints in two ligand-based virtual screening tasks.
Overall, our descriptors show the most consistent performances over all
experiments. The continuity of the descriptor space and the existence of the
decoder that permits to deduce a chemical structure from an embedding vector
allows for exploration of the space and opens up new opportunities for compound
optimization and idea generation.</p><br /><p></p> | Robin Winter; Floriane Montanari; Frank Noé; Djork-Arné Clevert | Chemoinformatics; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2018-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e57bb8c1a41953d98d9/original/learning-continuous-and-data-driven-molecular-descriptors-by-translating-equivalent-chemical-representations.pdf |
60f7e5cc0b093e5fb2e284a4 | 10.26434/chemrxiv-2021-t2wqk | Data-driven discovery of small electroactive molecules for energy storage in aqueous redox flow batteries | Owing to advancements in computing power and improvements in automation of modelling, high-throughput virtual screening (HTVS) has increasingly been used for materials data generation. Here, we applied a HTVS-guided experimental study for the large-scale exploration of quinone-like anolytes for aqueous redox flow batteries (ARFBs). This includes the design of a focused virtual chemical library inspired by small colorant molecules, quantum chemical prediction of redox properties, machine learning prediction of aqueous solubility, automated search for commercial availability on vendor databases, and electrochemical characterization of the most promising compounds. Screening efforts in a chemical space of 3,257 redox pairs led to 205 predicted candidates with higher solubility and lower redox potential than that of the state-of-the-art anthraquinone-2,7- disulfonic acid (AQDS) anolyte used in ARFBs. Through the electrochemical studies on the commercially available compounds, we identified the molecules that show good performance in an ARFB setup. Among them, indigo trisulfonate [Indigo-3(SO3H)] showed higher solubility, capacity retention, and coulombic efficiency than AQDS and its predecessors. The data-driven material design methodology presented here is flexible and applicable for the future exploration of small compounds for electrochemical energy storage. | Qi Zhang; Abhishek Khetan; Elif Sorkun; Fang Niu; Andrea Loss; Ilaria Pucher; Süleyman Er | Theoretical and Computational Chemistry; Materials Science; Energy; Computational Chemistry and Modeling; Machine Learning; Energy Storage | CC BY NC 4.0 | CHEMRXIV | 2021-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f7e5cc0b093e5fb2e284a4/original/data-driven-discovery-of-small-electroactive-molecules-for-energy-storage-in-aqueous-redox-flow-batteries.pdf |
60c74e51337d6c1278e27f6a | 10.26434/chemrxiv.12736505.v1 | Non-toxic Cobalt(III) Schiff Base Complexes with Broad Spectrum Antifungal Activity | Resistance to currently available antifungal drugs has quietly been on the rise but overshadowed
by the alarming spread of antibacterial resistance. There is a striking lack of attention to the threat
of drug resistant fungal infections, with only a handful of new drugs currently in development.
Given that metal complexes have proven to be useful new chemotypes in the fight against
diseases such as cancer, malaria, and bacterial infections, it stands to reason to explore their
possible utility in treating fungal infections. Herein we report a series of cobalt(III) Schiff base
complexes with broad spectrum antifungal activity. Some of these complexes (1-3) show
minimum inhibitory concentrations (MIC) in the low micro- to nanomolar range against a series of
Candida and Cryptococcus yeasts. Additionally, we demonstrate that these compounds show no
cytotoxicity against both bacterial and human cells. Finally, we report first in vivo toxicity data on
these compounds in Galleria mellonella, showing that doses as high as 266 mg/kg are tolerated
without adverse effects, paving the way for further in vivo studies of these complexes.
<br /> | Angelo Frei; A. Paden King; Gabrielle J. Lowe; Amy K. Cain; Francesca L. Short; Hue Dinh; Alysha Elliott; Johannes Zuegg; Justin J. Wilson; Mark Blaskovich | Bioinorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e51337d6c1278e27f6a/original/non-toxic-cobalt-iii-schiff-base-complexes-with-broad-spectrum-antifungal-activity.pdf |
60c74293f96a0006e728662f | 10.26434/chemrxiv.8312324.v1 | Gold-Aptamer-Nanoconstructs Engineered to Detect Conserved Enteroviral Nucleic Acid Sequences | <p>Enteroviruses
are a ubiquitous mammalian pathogen that can produce mild to life-threatening
disease. Bearing this in mind, we have developed a rapid, accurate and
economical point-of-care biosensor that can detect a nucleic acid sequences
conserved amongst 96% of all known enteroviruses. The biosensor harnesses the
physicochemical properties of gold nanoparticles and aptamers to provide
colourimetric, spectroscopic and lateral flow-based identification of an
exclusive enteroviral RNA sequence (23 bases), which was identified through in
silico screening. Aptamers were designed to demonstrate specific
complementarity towards the target enteroviral RNA to produce aggregated
gold-aptamer nanoconstructs. Conserved target enteroviral nucleic acid sequence
(≥ 1x10<sup>-7</sup> M, ≥1.4×10<sup>-14</sup> g/mL), initiates gold-aptamer-nanoconstructs
disaggregation and a signal transduction mechanism, producing a colourimetric
and spectroscopic blueshift (544 nm (purple) > 524 nm (red)). Furthermore,
lateral-flow-assays that utilise gold-aptamer-nanoconstructs were unaffected by
contaminating human genomic DNA, demonstrated rapid detection of conserved target
enteroviral nucleic acid sequence (< 60 s) and could be interpreted with a
bespoke software and hardware electronic interface. We anticipate our
methodology will translate in-silico screening of nucleic acid databases to a
tangible enteroviral desktop detector, which could be readily translated to
related organisms. This will pave-the-way forward in the clinical evaluation of
disease and complement existing strategies at overcoming antimicrobial
resistance.</p> | Veeren Chauhan; Mohamed M Elsutohy; C Patrick McClure; Will Irving; Neil Roddis; Jonathan W Aylott | Nanostructured Materials - Materials; Analytical Chemistry - General; Biochemical Analysis; Nanofabrication | CC BY 4.0 | CHEMRXIV | 2019-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74293f96a0006e728662f/original/gold-aptamer-nanoconstructs-engineered-to-detect-conserved-enteroviral-nucleic-acid-sequences.pdf |
6276cb6b809e3278e78733a6 | 10.26434/chemrxiv-2022-tfqnn | Visualization of Electron Density Changes Along Chemical Reaction Pathways | We propose a simple procedure for visualizing the electron density changes (EDC) during a chemical reaction, which is based on a mapping of rectangular grid points for a stationary structure into (distorted) positions around atoms of another stationary structure. Specifically, during a small step along the minimum energy pathway (MEP), the displacement of each grid point is obtained as a linear combination of the motion of all atoms, with the contribution from each atom scaled by the corresponding Hirshfeld weight. For several reactions (identity SN2, Claisen rearrangement, Diels-Alder reaction, [3+2] cycloaddition, and phenylethyl mercaptan attack on pericosine A), our EDC plots showed an expected reduction of electron densities around severed bonds (or those with the bond-order lowered), with the opposite observed for newly-formed or enhanced chemical bonds. The EDC plots were also shown for copper triflate catalyzed N2O fragmentation, where the N–O bond weakening initially occurred on a singlet surface, but continued on a triplet surface after reaching the minimum-energy crossing point (MECP) between the two potential energy surfaces. | Chance Lander; Vardhan Satalkar ; Junjie Yang; Xiaoliang Pan; Zheng Pei ; Aayushi Chatterji ; Chungen Liu; Kenneth Nicholas ; Robert Cichewicz ; Zhibo Yang; Yihan Shao | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6276cb6b809e3278e78733a6/original/visualization-of-electron-density-changes-along-chemical-reaction-pathways.pdf |
662cd64321291e5d1ddbb192 | 10.26434/chemrxiv-2024-7vlzq | Dyotropic Rearrangement of an Iron–Aluminium Complex | Ligand exchange processes at metal complexes underpin their reactivity and catalytic applications. While mechanisms of ligand exchange at single site complexes are well established, occurring through textbook associative, dissociative and interchange mechanisms, those involving heterometallic complexes are less well developed. Here we report the reactions of a well-defined Fe–Al hydride complex with exogeneous ligands (CO and CNR, R = Me, tBu, Xyl = 2,6-Me2C6H3). Based on DFT calculations we suggest that these reactions occur through a dyotropic rearrangement, this involves initial coordination of the exogeneous ligand at Al followed by migration to Fe, with simultaneous migration of a hydride ligand from Fe to Al. Such processes are rare for heterometallic complexes. We study the bonding and mechanism of the dyotropic rearrangement through in-depth computational analysis (NBO, IBOs, CLMO analysis, QTAIM, NCIplot, IMGH), shedding new light on how the electronic structure of the heterometallic core responds to the migration of ligands between metal sites. The dyotropic rearrangement fundamentally changes the nature of the hydride ligands, exposing new nucleophilic reactivity as evidenced by insertion reactions with CO2, isocyanates, as well as isocyanides. | Benedek Stadler; Nikolaus Gorgas; Stuart Elliot; Mark Crimmin | Organometallic Chemistry; Kinetics and Mechanism - Organometallic Reactions; Main Group Chemistry (Organomet.); Transition Metal Complexes (Organomet.) | CC BY 4.0 | CHEMRXIV | 2024-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662cd64321291e5d1ddbb192/original/dyotropic-rearrangement-of-an-iron-aluminium-complex.pdf |
60c750e1702a9b50ac18be7a | 10.26434/chemrxiv.13094012.v1 | Hydrogen Abstraction/Addition Reactions in Soot Surface Growth | <p>The hydrogen abstraction (HB) and
addition reactions (HD) by H radicals are examined on a series of polycyclic
aromatic hydrocarbon (PAH) monomers and models of quasi-surfaces using quasi-classical
trajectory (QCT) method. The QCT results reproduce the rate constants of HB
reactions on PAH monomers from density function theory (DFT) in the range of 1500-2700
K. The PAH size has a minor impact on the rates of HB reactions especially at
temperatures beyond 2100 K. By contrast, HD reactions have a clear size
dependence and a larger PAH yields a higher rate. It is also found that the
preferred reaction pathway changing from HB to HD reactions at ~1900 K. The
rates of surface HB and HD reactions exceed those in the gas phase by nearly a
factor of magnitude. Further analysis on the detailed trajectory of QCT method
reveals that about 50% of the surface reactions can be attributed
to the events of surface diffusion, which
depends on the local energy transfer in the gas-surface
interactions. However, this phenomenon is not preferred in PAH monomers as
expected. Our finding here highlights the
misinterpretation of surface reactions as the product of
the first collision between gaseous species and particle surface, and surface diffusion induced reactions should be
accounted for in the rates of surface HB and HD reactions. Rate
constants of HB and HD reactions on each reactive site (surface zig-zag, surface
free-edge and pocket free-edge sites) are calculated by QCT method, which are
recommended for the further development of surface chemistry models in soot
formation.</p> | Qingzhao Chu; Baolu Shi; Hongyu Wang; Dongping Chen; Lijuan Liao | Fuels - Energy Science; Chemical Kinetics; Clusters; Physical and Chemical Processes; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750e1702a9b50ac18be7a/original/hydrogen-abstraction-addition-reactions-in-soot-surface-growth.pdf |
60c75073f96a007422287e23 | 10.26434/chemrxiv.13042115.v1 | Complementary Base Lowers the Barrier in SuFEx Click Chemistry for Primary Amine Nucleophiles | The Sulfur (VI) Fluoride Exchange (SuFEx) reaction is an emerging scheme for connecting molecular building blocks. Due to its broad functional group tolerance and rather stable resulting linkage it is seeing rapid adoption in various fields of chemistry. Still, to date the reaction mechanism is poorly understood which hampers further development. Here, we show that the mechanism of the SuFEx reaction for the prototypical example of methanesulfonyl fluoride reacting with methylamine can be understood as an SN2-type reaction. By analyzing the reaction path with the help of density functional theory in vacuo and under consideration of solvent and co-reactant influence we identify the often used complementary base as crucial ingredient to lower the reaction barrier significantly by increasing the nucleophilicity of the primary amine. With the help of energy decomposition analysis (EDA) at the transition state structures we quantify the underlying stereo-electronic effects and propose new avenues for experimental exploration of the potential of SuFEx chemistry. | Jan-Niclas Luy; Ralf Tonner | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75073f96a007422287e23/original/complementary-base-lowers-the-barrier-in-su-f-ex-click-chemistry-for-primary-amine-nucleophiles.pdf |
65f158049138d231615d5851 | 10.26434/chemrxiv-2024-mftbp | Generic Conditions for Electromembrane Extraction of Acids with Low to Moderate Hydrophilicity in Human Plasma | The current paper reports the first set of generic conditions for electromembrane extraction of acidic substances from human plasma. Two systems were developed, based on eutectic solvents; A1 (“A” for acid) comprised dodecyl methyl sulfoxide and thymol in 1:2 ratio (w/w) as liquid membrane, while A2 used [6-methylcoumarin:thymol (1:2)]:2-nitrophenyl octyl ether in 2:1 ratio (w/w). A1 and A2 were applied for extraction of 31 acidic model analytes spiked into 100 µL human plasma diluted 1:1 (v/v) with phosphate buffer pH 7.4. The acceptor solution was 50 mM NH4HCO3 buffer pH 10.0, and extraction was performed at an agitation rate of 750 RPM. Voltage and extraction time were 30 V for 30 min and 10 V for 20 min for A1 and A2, respectively. Under optimal conditions, A1 extracted analytes with 1.8 ≤ log P ≤ 6.0 with an average recovery (R) of 85.1%, while A2 extracted in a range of 0.5 ≤ log P ≤ 6.0 with an average recovery of 79.9%. Meanwhile, extraction current was low at 9 and 26 µA, respectively, which is indicative of good system robustness. Using UHPLC-MS/MS analysis of the acceptor solution, repeatability of the A1 and A2 methods was determined to be 2.8-7.7% and 3.3-9.4% for R > 40%, matrix effects were 82-117% and 84-112%, respectively, and linear calibration curves were obtained. With these methods, generic conditions are now available for electromembrane extraction of bases in the range -2.0 ≤ log P ≤ 6.4 and acids in the range 0.5 ≤ log P ≤ 6.0. | Chenchen Song; Samira Dowlatshah; Somayeh Gaznawi; Anne Oldeide Hay; Grete Hasvold; Frederik André Hansen | Analytical Chemistry; Analytical Chemistry - General | CC BY 4.0 | CHEMRXIV | 2024-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f158049138d231615d5851/original/generic-conditions-for-electromembrane-extraction-of-acids-with-low-to-moderate-hydrophilicity-in-human-plasma.pdf |
653f7ef3c573f893f16d3113 | 10.26434/chemrxiv-2023-c2jkx | Experimental electronic structure of copper complexes with biphenyldiimino dithioether – model of blue copper proteins | Abstract The experimental electron density distribution in two coordination compounds, one with a central atom Cu(I) and the other with Cu(II), coordinated by the same biphenyldiimino dithioether-type ligand (bite) has been obtained from high-resolution X-ray diffraction data to model the possible electron predisposition for the redox reaction in blue copper proteins. The bite ligand has been adapted to the conformation required by the central atom | Jozef Kozisek; Martin Breza; Lukas Bucinsky; Marek Fronc; Ingrid Jelemenska | Physical Chemistry; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653f7ef3c573f893f16d3113/original/experimental-electronic-structure-of-copper-complexes-with-biphenyldiimino-dithioether-model-of-blue-copper-proteins.pdf |
62f0e79d5bdc683aacede6e8 | 10.26434/chemrxiv-2022-hgprp | A Universal Concept for Bright, Organic Solid State Emitters - Doping of Small Molecule Ionic Isolation Lattices with FRET Acceptors | Brightly fluorescent solid-state materials are highly desirable tools in bioimaging, optoelectronic applications and energy harvesting. However, close contact between π-systems leads to strong electronic coupling and often subse-quent quenching of the emitters in dense solid-state materials. Recently, we developed a method to prohibit strong coupling based on small molecule ionic isolation lattices (SMILES) that efficiently isolate fluorophores while in paral-lel ensuring very high densities of the dyes. Nevertheless, efficient FRET energy migration in such dense systems is inevitable. While attractive for energy harvesting applications, FRET also significantly compromises quantum yields of fluorescent solids by funneling excitation energy to dark trap states like crystal defects. Here we investigate the underlying property of FRET and exploit it to our favor by intentionally introducing fluorescent dopants into SMILES materials, acting as FRET acceptors with favorable photophysical properties. This doping is shown to outcompete en-ergy migration to dark trap states, while also ruling out reabsorption effects in dense SMILES materials, resulting in universal fluorescent solid state materials (thin films, powders, crystals) with superior properties. These include emission quantum yields reaching as high as 50-65 %, programmable fluorescence lifetimes with mono-exponential decay, and independent selection of absorption and emission maxima. The volume normalized brightness of these FRET-based SMILES now reach values up to 32200 M-1 cm-1 nm-3 and can deliver freely tunable spectroscopic properties for the fabrication of super bright advanced optical materials. | Laura Kacenauskaite; Stine G. Stenspil; Andrew H. Olsson; Amar H. Flood; Bo W. Laursen | Physical Chemistry; Organic Chemistry; Materials Science; Supramolecular Chemistry (Org.); Dyes and Chromophores; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f0e79d5bdc683aacede6e8/original/a-universal-concept-for-bright-organic-solid-state-emitters-doping-of-small-molecule-ionic-isolation-lattices-with-fret-acceptors.pdf |
673195f7f9980725cfcc1d36 | 10.26434/chemrxiv-2024-3v3jg | Membrane Technology for Pathogenic Virus Removal: A Comprehensive Review of Centralized and Decentralized Water Treatment Processes | The recent COVID-19 pandemic has once again drawn attention to the risks of pathogenic viruses, as viruses can be transmitted through water environments, posing a threat to human health. Membrane technology, as a novel, green, and effective water treatment process, has been widely applied in the removal of pathogenic viruses from wastewater and drinking water. However, compared to refined centralized water treatment processes in urban areas, rural areas still lack effective water treatment strategies for decentralized water supply and drainage systems. Therefore, this review provides a comprehensive analysis of the hazards and transmission pathways of viruses, the mechanisms and influencing factors of virus removal by membrane processes. Based on the characteristics of centralized and decentralized water treatment systems, it further summarizes the application scenarios and effectiveness of the most widely used membrane processes. We emphasize the need for context-specific development of membrane-based water treatment processes tailored to urban or rural areas, addressing both water supply and wastewater treatment processes, to ensure comprehensive public health safety in water environments. In addition, this review also discusses several challenges that membrane technology faces in virus removal, providing new insights for further research in membrane processes. | Rui Wang | Polymer Science; Earth, Space, and Environmental Chemistry; Environmental Science; Wastes | CC BY NC 4.0 | CHEMRXIV | 2024-11-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673195f7f9980725cfcc1d36/original/membrane-technology-for-pathogenic-virus-removal-a-comprehensive-review-of-centralized-and-decentralized-water-treatment-processes.pdf |
673e971af9980725cf212334 | 10.26434/chemrxiv-2024-dwsm8 | Interface Effects on Crystal Growth and Li Ion Dynamics in Sulfide Glass-Ceramics | Glass-ceramics are promising materials for use as solid electrolytes in all-solid-state batteries because of their high Li+ conductivity. This study investigated an interfacial model for glass-ceramics consisting of 75Li2S-25P2S5 glass and beta-Li3PS4 with seven different beta-Li3PS4 planes using molecular dynamics simulations. The equilibrated structure at 300 K and crystal growth at 500 K were analyzed in terms of interfacial enthalpy and crystallization rates. A novel method for identifying PS43- units as either glassy or crystalline was established based on the rotational motion of PS43- units. The rotational motion of PS43- units in the interfacial model was quantitatively indexed using sulfur trajectories within a 100 ps time window. The crystallization rate calculated using crystal growth simulations was found to depend on the crystalline plane forming the interface. The predicted crystal shape, derived from the interfacial enthalpy and growth rate, was analyzed using Wulff's theorem. The Li+ diffusivity in the crystalline, glassy, and interfacial regions of the interfacial model was evaluated through the time integration of velocity--velocity autocorrelation functions. Notably, the Li+ diffusivity in the crystalline regions varied depending on the interfacial model and differed from that of bulk beta-Li3PS4. This variation was attributed to differences in the degree of PS43- rotational motion in the crystalline regions of the interfacial model. The analytical methodologies developed in this study and the insights into the effects of interfaces on PS43- rotational motion, make valuable contributions to the understanding and design of glass-ceramics with interfaces. | Kazuki Fukuda; Futoshi Utsuno; Aoto Matsuo; Takahiro Ohkubo | Physical Chemistry; Inorganic Chemistry; Interfaces; Physical and Chemical Processes; Thermodynamics (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673e971af9980725cf212334/original/interface-effects-on-crystal-growth-and-li-ion-dynamics-in-sulfide-glass-ceramics.pdf |
60c75700bdbb89f460a3ab33 | 10.26434/chemrxiv.14355812.v1 | Formal Syntheses of Dictyodendrins B, C, and E by a Multi-substituted Indole Synthesis | The dictyodendrins are a family of marine alkaloids, which possess a highly substituted pyrrolo[2,3-<i>c</i>]carbazole core. This core structure can be regarded as a multi-substituted indole and aniline moiety. To achieve a concise synthesis of dictyodendrins, we planned to capitalize on our previously developed multi-substituted indole synthesis. By using this method along with two C–H functionalizations, formal syntheses of dictyodendrin B, C, and E were achieved. | AKira Kabuki; Junichiro Yamaguchi | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75700bdbb89f460a3ab33/original/formal-syntheses-of-dictyodendrins-b-c-and-e-by-a-multi-substituted-indole-synthesis.pdf |
6500437fb338ec988a589fd1 | 10.26434/chemrxiv-2023-k704b | Enhancing Stability and Efficacy of Trichoderma Bio-Control Agents through Layer-by-Layer Encapsulation for Sustainable Plant Protection | Agricultural fungicide pollution poses a significant environmental challenge and carries adverse consequences for human health. Therefore, strategies to limit fungicide usage have gained paramount importance. Trichoderma fungi, owing to their antagonistic activity against various pathogenic fungi, have emerged as prospective candidates for enhancing both the effectiveness and sustainability of plant protection. Nevertheless, the utilization of bio-control agents like Trichoderma has unveiled new challenges, notably their vulnerability to physical stimuli and diminished efficacy during prolonged storage.
To overcome these drawbacks, we present a mild and scalable encapsulation method for Trichoderma spores, employing a layer-by-layer (LbL) encapsulation approach using biobased lignin derivates. Our investigations demonstrate that the LbL-encapsulation technique imparts remarkable improvements in spore stability, even under adverse conditions such as variable temperature and prolonged exposure to UV irradiation compared to unencapsulated spores. Notably, encapsulated Trichoderma spores exhibit increased efficiency in the cultivation of tomato plants when compared to their unencapsulated counterparts. Additionally, our findings reveal that the in planta efficacy of encapsulated spores is contingent upon the specific Trichoderma strain employed.
The results outlined herein suggest that Trichoderma spores, encapsulated within lignin through the LbL approach, exhibit potential as promising and sustainable alternative to chemical fungicides and potential commercialization.
| Kaja Borup Løvschall; Sara T. R. Velasquez; Beata Kowalska; Magdalena Ptaszek; Anna Jarecka; Magdalena Szczech; Frederik R. Wurm | Polymer Science; Biopolymers; Polyelectrolytes - Polymers; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6500437fb338ec988a589fd1/original/enhancing-stability-and-efficacy-of-trichoderma-bio-control-agents-through-layer-by-layer-encapsulation-for-sustainable-plant-protection.pdf |
60c744fe4c8919de0fad28f9 | 10.26434/chemrxiv.9946925.v1 | N-Heterocyclic Carbene-Catalyzed Synthesis of Ynones via C–H Alkynylation of Aldehydes with Alkynyliodonium Salts | Alkynylation of aldehydes with alkynyl(aryl)iodonium salts catalyzed by an N-heterocyclic carbene (NHC) has been developed. The application of the organocatalyst and the hypervalent iodine group-transfer reagent allowed for metal-free C–H functionalization and C–C bond formation. The reaction proceeds under exceptionally mild conditions, at –40 ⁰C and in the presence of an amine base, providing access to an array of heteroaryl-propargyl ketones containing various substituents in good to excellent yields. The mechanism of the reaction was investigated by means of both experiments and density functional theory calculations. 13C-labelling and computations determined that the key alkynyl transfer step occurs via an unusual direct SN2 substitution of iodine-based leaving group by Breslow intermediate nucleophile at an acetylenic carbon. Moreover, kinetic studies revealed that the turnover-limiting step of the catalytic cycle is the generation of the Breslow intermediate, whereas the subsequent C–C bond-formation is a fast process. These results were fully reproduced and rationalized by the computed full free energy profile of the reaction, showing that the largest energy span is located between protonated NHC and the transition state for the carbene attack on the aldehyde substrate.<br /> | Adam A. Rajkiewicz; Natalia Wojciechowska; Marcin Kalek | Organic Synthesis and Reactions; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744fe4c8919de0fad28f9/original/n-heterocyclic-carbene-catalyzed-synthesis-of-ynones-via-c-h-alkynylation-of-aldehydes-with-alkynyliodonium-salts.pdf |
6685a420c9c6a5c07a30fbb3 | 10.26434/chemrxiv-2024-lnc5x | The Sooting Behavior of Lactones as Sustainable Fuels | Lactones are an interesting category of sustainable fuels since they have the same carbon backbones as sugars but are liquids at room temperature. Engine studies have shown that lactones can reduce soot emissions as well as net carbon dioxide emissions. In this study quantitative sooting tendencies were measured for 10 lactones with a wide range of molecular structures. They included compounds with ring sizes varying from three to six carbons, unsubstituted compounds, substituted compounds with side chain lengths ranging from one to seven carbons, and one compound with a double bond in the ring. Two alkenoic acids were also tested since they are possible isomerization products of lactones. The sooting tendencies were characterized by yield sooting index (YSI), which is based on the soot yield when a methane/air nonpremixed flame is doped with 1000 μmol/mol of the test fuel. The results show that the lactones have lower sooting tendencies than conventional gasoline, diesel fuel, and Jet A aviation fuel, even when accounting for their lower heats of combustion. However, the sooting tendencies depend strongly on molecular structure, so the right lactones must be chosen to maximize the emissions benefits. The measured sooting tendencies are generally larger than those predicted with a group contribution method, which indicates that the lactones have high sooting tendencies given the set of atoms they contain. To explain this observation, reactive molecular dynamics simulations and quantum chemistry calculations were performed. The results show that the lactones tend to decompose directly to CO2, so the oxygen atoms are being used inefficiently to sequester only one carbon atom. | Zhanhong Xiang; Mehmet Acikel; Collin Hansen; Ga-Un Jeong; Seonah Kim; Charles McEnally; Raúl Pérez-Soto; Lisa Pfefferle; David Wang; Vivian Whoriskey; Yuan Xuan | Chemical Engineering and Industrial Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6685a420c9c6a5c07a30fbb3/original/the-sooting-behavior-of-lactones-as-sustainable-fuels.pdf |
617134f2ac379f130db63c64 | 10.26434/chemrxiv-2021-rxqz8 | Molecular Simulations of Surfactant Adsorption on Iron Oxide from Hydrocarbon Solvents | The performance of lubricant additives, such as organic friction modifiers (OFMs), depends critically on their ability to adsorb onto the surfaces of moving components and form protective self-assembled layers (SAMs). Therefore, understanding the relationship between the concentration of the additive in the base oil and the resulting surface coverage is extremely important for lubricant formulations, as well as many other surfactant applications. Here, we use molecular dynamics (MD) simulations to study the adsorption isotherms of three different OFMs, stearic acid (SA), glycerol monoostearate (GMS), and glycerol monooleate (GMO), onto a hematite surface from hydrocarbon solvents, n-hexadecane and poly-α-olefin (PAO). First, we calculate the potential of mean force (PMF) of the adsorption process using MD simulations with the adaptive biasing force (ABF) algorithm. Our MD simulations show that SA has the weakest adsorption energy on hematite, followed by GMS, and finally GMO, due to the increasing number of functional groups available to bind to the surface. We also estimate the area occupied by each OFM molecule on the surface in the high-coverage limit using MD simulations of the annealing of OFM films with different initial surface coverages. We obtain a similar hard-disk area for GMS and GMO, but a lower value for SA, which is due to its smaller headgroup size. Based on the adsorption energy and surface area, we determine the corresponding adsorption isotherms using the molecular thermodynamic theory (MTT), which agree well with one available experimental data-set for SA. Two other experimental data-sets for SA require lateral interactions between surfactant molecules to be accounted for. SA forms monolayers with lower surface coverage than GMO and GMS at low concentrations (due to a smaller adsorption energy), but also has the highest plateau coverage (due to a smaller hard-disk area). We validate the adsorption energies from the MD simulations using high frequency reciprocating rig (HFRR) friction experiments with different concentrations of the OFMs in PAO. We use the Jahanmir and Beltzer model to estimate the surface coverage at each concentration and the adsorption energy of each OFM from the HFRR friction data. For OFMs with saturated tailgroups (SA and GMS), we obtain good agreement between the predictions made by the simulations and the experiments. The MD simulation and experimental results deviate for OFMs containing Z-unsaturated tailgroups (GMO), with the former suggesting stronger adsorption for GMO than GMS, while the latter predicts the opposite trend. We suggest that this is can be attributed to the higher steric barrier of adsorption of the OFMs with kinked Z-unsaturated tailgroup through a partially formed monolayer, an aspect which was not captured in the current simulations. This study demonstrates that MD simulations with the ABF algorithm, alongside MTT, are an accurate and efficient tool to predict adsorption isotherms at solid-liquid interfaces. | Pablo Navarro Acero; Stephan Mohr; Marco Bernabei; Carlos Fernandez; Beatriz Dominguez; James Ewen | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Surface | CC BY 4.0 | CHEMRXIV | 2021-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617134f2ac379f130db63c64/original/molecular-simulations-of-surfactant-adsorption-on-iron-oxide-from-hydrocarbon-solvents.pdf |
65eb433666c1381729915eac | 10.26434/chemrxiv-2024-sh0nq | Activation of Primary C-H Bonds in Oxidative Cyclizations of Tambjamines Catalyzed by Rieske Oxygenases TamC and PtTamC | Tambjamines are complex bipyrrole-containing natural prod-ucts that possess promising bioactive properties. Although Pseudoalteromonas citrea is known to produce both cyclic tambjamine MYP1 and the linear precursor (YP1), the biosynthetic machinery used to catalyze the site-selective oxidative carbocyclization at the unactivated 1° carbon of YP1 has re-mained unclear. Here, we demonstrate that a three-component Rieske system consisting of an oxygenase (TamC) and two redox partner proteins is responsible for this unprecedented activity on YP1 and a non-native substrate (BE-18591). We also show that a homologous oxidase from Pseudoalteromonas tunicata (PtTamC) can function together with the partner proteins from P. citrea to process both YP1 and BE-18591. These reactions represent the first Rieske oxygenase-catalyzed activations of C-H bonds at 1° carbons. The use of TamC and PtTamC to generate the new-to-Nature cyclic analogue of BE-18591 illustrates the enormous biocatalytic potential of these Rieske systems to facilitate late-stage oxidative cyclizations at terminal C(sp3)-H bonds. | Manasa Ramachandra; Jian Yu; Graeme Howe; Francoise Sauriol; Richard Oleschuk; Avena Ross | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Natural Products; Biochemistry; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65eb433666c1381729915eac/original/activation-of-primary-c-h-bonds-in-oxidative-cyclizations-of-tambjamines-catalyzed-by-rieske-oxygenases-tam-c-and-pt-tam-c.pdf |
6516a83b00659409121c0bc2 | 10.26434/chemrxiv-2023-dpx9n-v3 | Development of First-in-Class Dual Sirt2/HDAC6 Inhibitors as Molecular Tools for Dual Inhibition of Tubulin Deacetylation | Dysregulation of both tubulin deacetylases sirtuin 2 (Sirt2) and the histone deacetylase 6 (HDAC6) has been associated with the pathogenesis of cancer and neurodegeneration, thus making these two enzymes promising targets for pharmaceutical intervention. Herein, we report the design, synthesis, and biological characterization of the first-in-class dual Sirt2/HDAC6 inhibitors as molecular tools for dual inhibition of tubulin deacetylation. Using biochemical in vitro assays and cell-based methods for target engagement, we identified Mz325 (33) as a potent and selective inhibitor of both target enzymes. Inhibition of both targets was further confirmed by x-ray crystal structures of Sirt2 and HDAC6 in complex with building blocks of 33. In ovarian cancer cells, 33 evoked enhanced effects on cell viability compared to single or combination treatment with the unconjugated Sirt2 and HDAC6 inhibitors. Thus, our dual Sirt2/HDAC6 inhibitors are important new tools to study the consequences and the therapeutic potential of dual inhibition of tubulin deacetylation. | Laura Sinatra; Anja Vogelmann; Florian Friedrich; Margarita Tararina; Emilia Neuwirt; Arianna Colcerasa; Philipp König; Lara Toy; Talha Yesiloglu; Sebastian Hilscher; Lena Gaitzsch; Niklas Papenkordt; Shiyang Zhai; Lin Zhang; Christophe Romier; Oliver Einsle; Wolfgang Sippl; Mike Schutkowski; Olaf Groß; Gerd Bendas; David Christianson; Finn Hansen; Manfred Jung; Matthias Schiedel | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6516a83b00659409121c0bc2/original/development-of-first-in-class-dual-sirt2-hdac6-inhibitors-as-molecular-tools-for-dual-inhibition-of-tubulin-deacetylation.pdf |
6360496c1db0bdf3da414cbc | 10.26434/chemrxiv-2022-9r8hl | A Purification-Free Method for the Synthesis of Thiazolium Salts Using P2S5-Py2 Complex or P4S10 | An expedient method to prepare thiazolium salts using the P2S5-Py2 complex or P4S10 has been studied. A variety of thiazolium salts can be rapidly accessed by the clean reaction between readily available α-formamido ketones and these reagents. The pure thiazolium salts are obtained via simple filtration followed by salt metathesis with sodium tetrafluoroborate or sodium tetraphenylborate. The method is suitable for a variety of substituents on the heterocycle. The use of these reagents confers a practical advantage over the use of Lawesson’s reagent, making the purification of the thiazolium salt straightforward. | Tianqi Ji; Venkata Krishna Rao Garapati; Michel Gravel | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6360496c1db0bdf3da414cbc/original/a-purification-free-method-for-the-synthesis-of-thiazolium-salts-using-p2s5-py2-complex-or-p4s10.pdf |
6753669bf9980725cf474d31 | 10.26434/chemrxiv-2024-3w2np | Crystalline 1D Coordination Polymer Inhibitor Layer Leads to Vertical Sidewalls in
Selectively Deposited ZnO on Nanoscale Patterns | Area-selective atomic layer deposition (AS-ALD) is a promising technique for the fabrication of
next generation nanoelectronics. There are two main challenges in AS-ALD: (1) achieving high
selectivity of deposition on the growth regions and (2) preventing mushrooming of the growth
material onto the nongrowth regions and achieving well-defined interfaces. In this work, we use
benzenethiol (BT) as an inhibitor in the selective deposition of ZnO on SiO2 in the presence of
copper with and without a native oxide (Cu/CuOx). We observe that BT forms a monolayer on the
Cu surface and a Cu-thiolate multilayer structure on CuOx. Using grazing incidence x-ray
diffraction combined with simulations, we find that the multilayer structure is crystalline and
composed of 1D coordination polymers of Cu-thiolate. Using ellipsometry and x-ray photoelectron
spectroscopy, we show that the BT consumes the entirety of the CuOx present in forming the
multilayer, and thus the thickness of the multilayer can be tuned by the thickness of the original
oxide. Both the monolayer BT and the multilayer BT prove to be effective inhibitors of ZnO ALD,
blocking nearly 500 ALD cycles, which is more than twice that achieved with other thiol inhibitors.
Finally, we demonstrate that the multilayer structure can prevent mushrooming of the ALD
material onto the nongrowth surface of nanoscale patterns, creating vertical sidewalls with welldefined material interfaces and providing excellent pattern transfer even for a relatively thick
deposited film. As such, these results demonstrate not only that BT is an effective inhibitor, but
also that its ability to form tunable multilayers lends itself towards highly precise nanopatterning
applications.
| Alexander Shearer; Yukio Cho; Miso Kim; Andreas Werbrouck; Tzu-Ling Liu; Chris Takacs; Bonggeun Shong; Stacey F Bent | Materials Science; Chemical Engineering and Industrial Chemistry; Hybrid Organic-Inorganic Materials; Materials Processing; Thin Films; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6753669bf9980725cf474d31/original/crystalline-1d-coordination-polymer-inhibitor-layer-leads-to-vertical-sidewalls-in-selectively-deposited-zn-o-on-nanoscale-patterns.pdf |
65f04b0a66c1381729d720e5 | 10.26434/chemrxiv-2022-m6qhd-v13 | Transition Energy, Orientation Force and Work Done in Transitional Behavior Atoms: Formulating New Principles in Thermodynamics | Studying the basic parameters of heat and thermodynamics can lead to new insights. Gaseous and solid atoms under transitional conditions are candidates for exploring remarkable advances in chemical and physical sciences. There is an anomaly in the first law of thermodynamics when studying the transitional behaviors of atoms. By gaining transition energy, gaseous atoms undergo a transition state. Thus, they perform the work self. Symbolically, a plus sign is needed. However, a transition in solid atoms occurs because of the absorbing transition energy, where electrons decrease the potential energy. Therefore, the work rating is a minus sign. The force exerted at the electron level in a gaseous atom is different than that in a solid atom. The potential energy of the electron changes from the transitional energy, thus controlling the orientation. An anomaly resolves by changing the equations of internal energy. Gaseous and solid atoms introduce cooling and heat effects under elastically driven electronic states when reaching the mid-states. A transition state between re-crystallization and liquid states can be considered a mid-state. In generating cooling or heating energy, an electron executes dynamics by remaining within the occupied energy knot. Thus, constantly driven electronic states of atoms cause disorder and irreversible cycling. This study provides a basic understanding of the first law of thermodynamics, cold and heat energy, entropy, and condensed matter science at the atomic and electronic levels. | Mubarak Ali | Inorganic Chemistry; Kinetics and Mechanism - Inorganic Reactions; Solid State Chemistry; Theory - Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f04b0a66c1381729d720e5/original/transition-energy-orientation-force-and-work-done-in-transitional-behavior-atoms-formulating-new-principles-in-thermodynamics.pdf |
60c74479842e6579a6db2472 | 10.26434/chemrxiv.9821846.v1 | Efficient Z-Selective Semi-Hydrogenation of Internal Alkynes Catalyzed by Cationic Iron(II) Hydride Complexes | We
describe here the application of
the well-defined bench-stable cationic aminoborane complex as highly efficient pre-catalysts for the
semi-hydrogenation of internal alkynes, 1,3-diynes and 1,3-enynes with molecular hydrogen under mild conditions. | Nikolaus Gorgas; Julian Brünig; Berthold Stöger; Stefan Vanicek; Mats Tilset; Luis F. Veiros; Karl Kirchner | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74479842e6579a6db2472/original/efficient-z-selective-semi-hydrogenation-of-internal-alkynes-catalyzed-by-cationic-iron-ii-hydride-complexes.pdf |
60c746ec469df41a8ff43736 | 10.26434/chemrxiv.11439558.v1 | Computational Strategies and Challenges for Using Native Ion Mobility Mass Spectrometry in Biophysics and Structural Biology | <p>Native mass spectrometry (MS) allows the interrogation of structural aspects of macromolecules in the gas phase, under the premise of having initially maintained their solution-phase non-covalent interactions intact. In the more than 25 years since the first reports, the utility of native MS has become well established in the structural biology community. The experimental and technological advances during this time have been rapid, resulting in dramatic increases in sensitivity, mass range, resolution, and complexity of possible experiments. As experimental methods are improved, there have been accompanying developments in computational approaches for analysing and exploiting the profusion of MS data in a structural and biophysical context. Here, based on discussions within the <i>EU COST Action </i><i>BM1403 </i><i>on Native MS and Related Methods for Structural Biology</i> with broad participation from Europe and North America, we consider the computational strategies currently being employed by the community, aspects of best practice, and the challenges that remain to be addressed. </p> | Timothy Allison; Perdita Barran; Sarah Cianferani; Matteo Degiacomi; Valerie Gabelica; Rita Grandori; Erik Marklund; Thomas Menneteau; Lukasz Migas; Argyris Politis; Michal Sharon; Frank Sobott; Konstantinos Thalassinos; Justin Benesch | Biochemical Analysis; Mass Spectrometry; Bioinformatics and Computational Biology; Biophysics; Computational Chemistry and Modeling; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746ec469df41a8ff43736/original/computational-strategies-and-challenges-for-using-native-ion-mobility-mass-spectrometry-in-biophysics-and-structural-biology.pdf |
60c74a97f96a0098c528747f | 10.26434/chemrxiv.12228831.v1 | Drug Repurposing Studies Targeting SARS-nCoV2: An Ensemble Docking Approach on Drug Target 3C-like Protease (3CLpro) | <p>The
COVID-19 pandemic has been responsible for several deaths worldwide. The
causative agent behind this disease is the Severe Acute Respiratory Syndrome –
novel Coronavirus 2 (SARS-nCoV2). SARS-nCoV2 belongs to the category of RNA
viruses. The main protease, responsible for the cleavage of the viral
polyprotein is considered as one of the hot targets for treating COVID-19.
Earlier reports suggest the use of HIV anti-viral drugs for targeting the main
protease of SARS-CoV, which caused SARS in the year 2002-03. Hence, drug
repurposing approach may prove to be useful in targeting the main protease of
SARS-nCoV2. The high-resolution crystal structure of 3CL<sup>pro</sup> (main protease) of
SARS-nCoV2 (PDB ID: 6LU7) was used as the target. The Food and Drug
Administration (FDA) approved and SWEETLEAD database of drug molecules were
screened. The apo form of the main protease was simulated for a cumulative of
150 ns and 10 μs open source simulation data was used, to obtain conformations
for ensemble docking. The representative structures for docking were selected using
RMSD-based clustering and Markov State Modeling analysis. This ensemble docking
approach for main protease helped in exploring the conformational variation in
the drug binding site of the main protease leading to efficient binding of more
relevant drug molecules. The drugs obtained as best hits from the ensemble
docking possessed anti-bacterial and anti-viral properties. Small molecules
with these properties may prove to be useful to treat symptoms exhibited in
COVID-19. This <i>in-silico</i> ensemble docking approach would support identification
of potential candidates for repurposing against COVID-19.</p> | Shruti Koulgi; Vinod Jani; Mallikarjunachari Uppuladinne; Uddhavesh Sonavane; Asheet Kumar Nath; Hemant Darbari; Rajendra Joshi | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a97f96a0098c528747f/original/drug-repurposing-studies-targeting-sars-n-co-v2-an-ensemble-docking-approach-on-drug-target-3c-like-protease-3c-lpro.pdf |
614c9feca7b24910bc364aa7 | 10.26434/chemrxiv-2021-m9c8j | Small Peptides for Inhibiting Serum Amyloid A Aggregation | Deposition of human Serum Amyloid A (SAA) amyloids in blood vessels, causing inflammation, thrombosis and eventually organ damage, are a commonly seen as a consequence of certain cancers and inflammatory diseases. Several attempts have been made to develop peptide-based drugs that inhibit or at least slow down SAA amyloidosis. We use extensive all-atom molecular dynamic simulations to compare three of these drug candidates for their ability to destabilize SAA fibrils, and to propose for the best candidate, the N-terminal sequence SAA1-5, a mechanism for inhibition. As the life-time of peptide drugs can be increased by replacing L-amino acids with their mirror D- amino acids, we have also studied corresponding D-peptides. We find that DRI-SAA1-5, formed of D-amino acids with the sequence of the peptide reversed, has similar inhibitory properties than the original L-peptide, and therefore may be a promising candidate for drugs targeting SAA amyloidosis. | Asis Jana; Augustus Greenwood; Ulrich H.E. Hansmann | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614c9feca7b24910bc364aa7/original/small-peptides-for-inhibiting-serum-amyloid-a-aggregation.pdf |
6656639b21291e5d1d80682f | 10.26434/chemrxiv-2024-2tvc6 | Cryogenic Ion Vibrational Spectroscopy of Protonated Valine: Messenger Tag Effects | We report the infrared photodissociation spectrum of tagged protonated valine in the range 1000 – 1900 cm-1, prepared in a cryogenic ion trap. Comparison of experimental results with calculated infrared spectra based on density functional theory shows that the hydroxyl group of the carboxylic acid functionality and the protonated amine group adopt a trans configuration. Nitrogen and methane molecules were used as messenger tags, with optimal tagging temperatures of 30 K for N2 and 60 K for CH4. While the calculated infrared spectra of the tagged ion suggest only a weak influence of the messenger tag on the frequency positions of ValH+, the measured intensities for N2-tagged ValH+ are strongly suppressed for all but the highest frequency features at 1773 cm-1. We trace this behavior to the binding energy of the N2 tag, which is significantly higher than that of CH4, based on CCSD(T) calculations and rate estimates for photoinduced unimolecular dissociation from statistical theory. | Lane M. Terry; Maddie K. Klumb; Deacon J. Nemchick; Robert Hodyss; Frank Maiwald; J. Mathias WEBER | Physical Chemistry; Earth, Space, and Environmental Chemistry; Space Chemistry; Clusters; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6656639b21291e5d1d80682f/original/cryogenic-ion-vibrational-spectroscopy-of-protonated-valine-messenger-tag-effects.pdf |
6734f2e95a82cea2fa06c6d5 | 10.26434/chemrxiv-2024-d6hl7 | From Micro-Environments to Macroscopic Effects: How the Alkaline Hydrogen Evolution Reaction Drives Cu Cathodic Corrosion | Cathodic corrosion of copper (Cu) has posed a significant challenge for over a century, impeding various technological progresses such as electrochemical conversion of CO2 (eCO2RR) into fuels and other value-added carbon products. In this study, employing a combined Density Functional Theory (DFT) and kinetic Monte Carlo (kMC) simulation approach, we delve into the atomistic level mechanism driving this phenomenon in Cu. Our hypothesis posits the pivotal role of alkaline hydrogen evolution reaction (HER) in facilitating cathodic corrosion in Cu. We rigorously develop a pH-dependent hydroxide (OH) adsorption mechanism and calculate the equilibrium OH coverage (𝜃OH) at varying pH levels, the thermodynamic stability of subsurface oxygen (Osub), as well as the Cu-vacancy mediated diffusion of subsurface oxygens (Osub). Through comprehensive analysis, we establish correlation among various microenvironments, including oxygen diffusion in subsurface layers, pH-dependent OH adsorption, and Cu dissolution into the electrolyte as (Cu- OH) complexes. Furthermore, our investigation explores the correlation between surface coordination environment of active sites and cathodic corrosion of Cu. Finally, by integrating DFT- derived thermodynamic data into a kMC model, we successfully predict the formation of experimentally observed corrosion pits on Cu-surfaces. This combined approach not only advances our fundamental understanding of Cu cathodic corrosion but also offers insights crucial for developing effective corrosion mitigation strategies. | Hori Pada Sarker; Anshuman Goswami; Michael Tang; Frank Abild-Pedersen | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6734f2e95a82cea2fa06c6d5/original/from-micro-environments-to-macroscopic-effects-how-the-alkaline-hydrogen-evolution-reaction-drives-cu-cathodic-corrosion.pdf |
66b5e14801103d79c556db92 | 10.26434/chemrxiv-2024-ns1l4 | High Specific Activity during Electrochemical CO2 Reduction through Homogeneous Deposition of Gold Nanoparticles on Gas Diffusion Electrodes | The electrochemical CO2 reduction reaction (CO2RR) has attracted attention as a promising strategy for converting CO2 into value-added products. Gas diffusion electrodes (GDEs) loaded with metallic nanoparticles as electrocatalysts are expected to efficiently reduce CO2 due to the high specific surface area of such particles and the superior mass transport characteristics of GDEs. In the present study, GDEs loaded with homogeneous layers of sub-nanometer gold (Au) nanoparticles were fabricated using a radio frequency sputtering technique that had a low deposition rate. This allowed precise control of the catalyst loading. The Au-loaded GDEs exhibited significantly higher CO production efficiency compared with the electrodes fabricated by conventional deposition methods using dispersed Au nanoparticles. Additionally, a Au-loaded GDE having a catalytic layer thickness of 10 nm demonstrated a mass-based CO production activity of 1882 A g-¹ at -0.85 V. This is the highest value yet reported. This work confirmed that the uniform deposition of sub-nanometer metallic particles gives enhanced catalyst utilization. The results of this research provide important insights into the design of efficient CO2RR electrodes and highlight the potential of radio frequency sputtering to fabricate high-performance CO2RR electrodes as an approach to realizing carbon-neutral technologies. | Takuya Yamada; Kazuyuki Iwase; Naoto Todoroki; Itaru Honma | Catalysis; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b5e14801103d79c556db92/original/high-specific-activity-during-electrochemical-co2-reduction-through-homogeneous-deposition-of-gold-nanoparticles-on-gas-diffusion-electrodes.pdf |
60c7525bee301c0820c7aba9 | 10.26434/chemrxiv.13289222.v1 | COVID-19 Knowledge Extractor (COKE): A Tool and a Web Portal to Extract Drug - Target Protein Associations from the CORD-19 Corpus of Scientific Publications on COVID-19 | <p><b>Objective:</b> The COVID-19
pandemic has catalyzed a widespread effort to identify drug candidates and
biological targets of relevance to SARS-COV-2 infection, which resulted in
large numbers of publications on this subject. We have built the <b><u>CO</u></b>VID-19
<b><u>K</u></b>nowledge <b><u>E</u></b>xtractor (COKE), a web application to
extract, curate, and annotate essential drug-target relationships from the
research literature on COVID-19 to assist drug repurposing efforts.</p>
<p><b>Materials and Methods:</b> SciBiteAI
ontological tagging of the COVID Open Research Dataset (CORD-19), a repository
of COVID-19 scientific publications, was employed to identify drug-target
relationships. Entity identifiers were resolved through lookup routines using
UniProt and DrugBank. A custom algorithm was used to identify co-occurrences of
protein and drug terms, and confidence scores were calculated for each entity
pair.</p>
<p><b>Results:</b> COKE processing of
the current CORD-19 database identified about 3,000 drug-protein pairs, including
29 unique proteins and 500 investigational, experimental, and approved drugs. Some of these drugs are presently undergoing clinical
trials for COVID-19.</p>
<p><b>Discussion:</b> The rapidly
evolving situation concerning the COVID-19 pandemic has resulted in a dramatic growth
of publications on this subject in a short period. These circumstances call for
methods that can condense the literature into the key concepts and
relationships necessary for insights into SARS-CoV-2 drug repurposing. </p>
<p><b>Conclusion:</b> The COKE
repository and web application deliver key drug - target protein relationships
to researchers studying SARS-CoV-2. COKE
portal may provide comprehensive and critical information on studies concerning
drug repurposing against COVID-19. COKE is freely available at <a href="https://coke.mml.unc.edu/">https://coke.mml.unc.edu/</a> and the code is
available at <a href="https://github.com/DnlRKorn/CoKE">https://github.com/DnlRKorn/CoKE</a>.
</p> | Daniel Korn; Vera Pervitsky; Tesia Bobrowski; Vinicius Alves; Charles Schmitt; Cristopher Bizon; Nancy Baker; Rada Chirkova; Artem Cherkasov; Eugene Muratov; Alexander Tropsha | Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7525bee301c0820c7aba9/original/covid-19-knowledge-extractor-coke-a-tool-and-a-web-portal-to-extract-drug-target-protein-associations-from-the-cord-19-corpus-of-scientific-publications-on-covid-19.pdf |
63da6cd7d1857ca6d6a5d3e6 | 10.26434/chemrxiv-2023-hpxg0 | Triplet Phenylarsinidene and Its Oxidation to Dioxophenylarsine | Diradicals are key intermediates involved in numerous chemical processes and have attracted considerable attention in synthetic chemistry, biochemistry, and materials science. Even though parent arsinidene (H-As) has been characterized well, the high reactivity of subsituted arsinidenes has prohibited their isolation and characterization to date. Here, we report the preparation of triplet phenylarsinidene through the photolysis of phenylarsenic diazide, isolated in an argon matrix, and its subsequent characterization by infrared and UV/Vis spectroscopy. Doping the matrices containing phenylarsinidene with molecular oxygen leads to the formation of hitherto unknown anti-dioxyphenylarsine. The latter undergoes isomerization to novel dioxophenylarsine upon 465 nm irradiation. The assignments were validated by isotope-labeling experiments combined with B3LYP/def2-TZVP computations. | Weiyu Qian; Peter R. Schreiner; Artur Mardyukov | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63da6cd7d1857ca6d6a5d3e6/original/triplet-phenylarsinidene-and-its-oxidation-to-dioxophenylarsine.pdf |
662b65f6418a5379b0c517e5 | 10.26434/chemrxiv-2024-8b9sz-v2 | Extracellular vesicles in the pathogenesis of Campylobacter jejuni | Bacteria in genus Campylobacter are the leading cause of foodborne infections worldwide. Here we describe the roles of extracellular vesicles in the pathogenesis of these bacteria and current knowledge of vesicle biogenesis. We also discuss the advantages of this alternative secretion pathway for bacterial virulence. | Jeanne Malet-Villemagne; Jasmina Vidic | Biological and Medicinal Chemistry; Biochemistry; Cell and Molecular Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662b65f6418a5379b0c517e5/original/extracellular-vesicles-in-the-pathogenesis-of-campylobacter-jejuni.pdf |
65670c7acf8b3c3cd762f49e | 10.26434/chemrxiv-2023-8z10s | Temperature-dependent NIR-CPL spectra of chiral Yb(III) complexes | Chiral, enantiopure Yb(III) complexes are able to emit circularly polarized luminescence (CPL) in the near infrared (NIR) wavelength region, quantified by the dissymmetry factor (glum). Due to crystal field splitting (CFS), the excited state 2F5/2 consists of three mj' sublevels, which are populated in accordance with the Boltzmann distribution. Consequently, room temperature CPL spectra are the sum of various - either positive or negative – contributions, that are practically impossible to quantify. Thanks to the use of an advanced setup enabling CPL measurements over a range of temperatures (300 to 4 K), the interrelation of CFS, glum and temperature was demonstrated on the example of a pair of enantiopure Yb(III) com-plexes. It was thereby confirmed that each mJ’ sublevel gives an independent contribution to the overall CPL spectrum. Hence, the CPL spectra of chiral lanthanide complexes were found to be indeed strongly temperature-dependent, as is the glum dissymmetry factor, as a consequence of the variation in thermal sublevel population. These results were additional-ly interpreted in the framework of multireference wave-function calculations. | Annika Sickinger; Maxime Grasser; Bruno Baguenard; Amina Bensalah-Ledoux; Laure Guy; Anh Thy Bui; Yannick Guyot; Vincent Dorcet; Fabrice Pointillart; Olivier Cador; Stéphan Guy; Olivier Maury; Boris Le Guennic; François Riobé | Physical Chemistry; Organic Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65670c7acf8b3c3cd762f49e/original/temperature-dependent-nir-cpl-spectra-of-chiral-yb-iii-complexes.pdf |
6417a90e2bfb3dc251090187 | 10.26434/chemrxiv-2023-xmjbn | Comprehensive Fluorescence Profiles of Contamination-prone Foods Applied to the Design of Microcontact-printed in situ Functional Oligonucleotide Sensors | With both foodborne illness and food spoilage detrimentally impacting human health and the economy, there is growing interest in the development of in situ sensors that offer real-time monitoring of food quality within enclosed food packages. While oligonucleotide-based fluorescent sensors have illustrated significant promise, the development of such on-food sensors requires consideration towards sensing-relevant fluorescence properties of target food products – information that has not yet been reported. To address this need, comprehensive fluorescence profiles for various contamination-prone food products are established in this study across several wavelengths and timepoints. The intensity of these food backgrounds is further contextualized to biomolecule-mediated sensing using overlaid fluorescent oligonucleotide arrays, which offer perspective towards the viability of distinct wavelengths and fluorophores for in situ food monitoring. Results show that biosensing in the Cy3 range is optimal for all tested foods, with the Cy5 range offering comparable performance with meat products specifically. Moreover, recognizing that mass fabrication of on-food sensors requires rapid and simple deposition of sensing agents onto packaging substrates, RNA-cleaving fluorescent nucleic acid probes are successfully deposited via microcontact printing for the first time. Direct incorporation onto food packaging yields cost-effective sensors with performance comparable to ones produced using conventional deposition strategies. | Shadman Khan; Amid Shakeri; Jonathan Monteiro; Simrun Tariq; Akansha Prasad; Jimmy Gu; Carlos Filipe; Yingfu Li; Tohid Didar | Materials Science; Nanoscience; Agriculture and Food Chemistry; Biocompatible Materials; Coating Materials; Food | CC BY 4.0 | CHEMRXIV | 2023-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6417a90e2bfb3dc251090187/original/comprehensive-fluorescence-profiles-of-contamination-prone-foods-applied-to-the-design-of-microcontact-printed-in-situ-functional-oligonucleotide-sensors.pdf |
60ddb56c6b8d894c856ab35c | 10.26434/chemrxiv-2021-2cls6 | Kinetic Resolution of Sulfur-Stereogenic Sulfoximines by Pd(II)-MPAA Catalyzed C-H Arylation and Olefination | A direct Pd(II)-catalyzed kinetic resolution of heteroaryl-enabled sulfoximines through an ortho-C-H alkenylation/arylation of arenes has been developed for the first time. The coordination of sulfoximine pyridyl-motif and the chiral amino acid MPAA ligand to the Pd(II)-catalyst controls the enantio-discriminating C(aryl)-H activation. This method provides access to a wide range of enantiomerically enriched unreacted aryl-pyridyl-sulfoximine precursors and C(aryl)-H alkenylation/arylation products in good yields with high enantioselectivity (up to >99% ee), and selectivity factor up to >200; which are inaccessible by conventional methods. The coordination preference of the directing group, ligand effect, geometry constraints, and the transient six-membered concerted-metalation-deprotonation species dictate the stereoselectivity; DFT studies validate this hypothesis. | Kallol Mukherjee; Nicolas Grimblat; Somratan Sau; Koushik Ghosh; Majji Shankar; Vincent Gandon; Akhila Sahoo | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60ddb56c6b8d894c856ab35c/original/kinetic-resolution-of-sulfur-stereogenic-sulfoximines-by-pd-ii-mpaa-catalyzed-c-h-arylation-and-olefination.pdf |
66a8cd5801103d79c5391446 | 10.26434/chemrxiv-2024-wgvzq | Establishing a 1:1 charge stoichiometry and rheological investigations for novel pH- induced polyelectrolyte complex coacervate xerogels | In order to explore new options for colon targeting, this study designs new polyelectrolyte complex (PEC) coacervate xerogels of chitosan (Ch) with Albizia procera (AP). It was determined by potentiometric titration tests that a 1:5 Ch/AP weight ratio was necessary for 1:1 charge stoichiometry. Rheological characterizations experiments were carried out for the pH independent coacervates and 1:5 coacervate was found to be having the highest G/ value in the strain sweep experiment. In the frequency sweep experiments the coacervate (1:5) with the highest storage modulus (G/) values was produced at pH 4.5. | Dr. Partha Sarathi Roy | Analytical Chemistry; Chemical Engineering and Industrial Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a8cd5801103d79c5391446/original/establishing-a-1-1-charge-stoichiometry-and-rheological-investigations-for-novel-p-h-induced-polyelectrolyte-complex-coacervate-xerogels.pdf |
62acb13504a3a965064a4a2a | 10.26434/chemrxiv-2022-07br7 | Development of a MARTINI Coarse-Grained Model of the Rosette Nanotubes | A significant challenge in healthcare is providing effective treatments with minimal side effects. This is particularly true in chemotherapies, where side effects can range from nausea to chemo-induced seizures. As a result, the area of nanotechnology can provide targeted drug delivery systems to boost the efficacy of the drugs and potentially minimize the side effects for more personalized treatment. To develop these systems, building models can complement experiments and provide guidance on which systems could be more effective to reduce research and development costs and potentially speed up the process. In this paper, the first-of-its-kind coarse-grained MARTINI v2.2 model of a biocompatible rosette nanotube was developed, tested, and compared to previ- ous simulation and experimental work. The coarse-grained model structure was in good agreement with the all-atom structure based on the nanotube characterizations performed (eg. axial rise was approximately 0.39 nm, which is close to experimen- tal values). However, more optimization is needed, especially for when the RNT is functionalized. | Vyshnavi Karra; Francisco Hung; Hicham Fenniri | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Thermodynamics (Chem. Eng.) | CC BY 4.0 | CHEMRXIV | 2022-06-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62acb13504a3a965064a4a2a/original/development-of-a-martini-coarse-grained-model-of-the-rosette-nanotubes.pdf |
6698e118c9c6a5c07a97d651 | 10.26434/chemrxiv-2024-sfp3b-v2 | Raman Broad Scans of Glasses with Rare Earth Element (REE) Oxides and their Decomposition with q-BWF Line Shapes | RRUFF database is proposing the Raman broad scans of glasses CaO-Al2O3-SiO2 with rare earth element (REE) oxides, that is of CaO-RE2O3-Al2O3-SiO2 glasses. Raman data are courtesy of E. Cairns, University of Edinburgh. Here we show how we can use the q-BWF functions to decompose these spectra. The q-BWF functions are generalizing the Breit-Wigner-Fano line shape in the framework of the q-exponential function proposed by Constantino Tsallis and his statistics. Besides asymmetry, the decompositions with q-BWF line shapes are stressing Gaussian and non-Gaussian behaviors of components. The data analysis of CaO-RE2O3-Al2O3-SiO2 glasses is highlighting the presence of photoluminescence regular patterns in the Raman broad scans. | Amelia Carolina Sparavigna | Materials Science | CC BY 4.0 | CHEMRXIV | 2024-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6698e118c9c6a5c07a97d651/original/raman-broad-scans-of-glasses-with-rare-earth-element-ree-oxides-and-their-decomposition-with-q-bwf-line-shapes.pdf |
65492430c573f893f1ef468d | 10.26434/chemrxiv-2023-k994h | ROBERT: Bridging the Gap between Machine Learning and Chemistry | Beyond addressing technological demands, the integration of machine learning (ML) into human societies has also promoted sustainability through the adoption of digitalized protocols. Despite these advantages and the abundance of available toolkits, a substantial implementation gap is preventing the widespread incorporation of ML protocols into the computational and experimental chemistry communities. In this work, we introduce ROBERT, a software carefully crafted to make ML more accessible to chemists of all programming skill levels, while achieving results comparable to those of field experts. We conducted benchmarking using six recent ML studies in chemistry containing 18–4,149 entries. Furthermore, we demonstrated the program’s ability to initiate workflows directly from SMILES strings, which simplifies the generation of ML predictors for common chemistry problems. To assess ROBERT’s practicality in real-life scenarios, we employed it to discover new luminescent Pd complexes with a modest dataset of 23 points, a frequently encountered scenario in experimental studies. | David Dalmau; Juan Vicente Alegre Requena | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65492430c573f893f1ef468d/original/robert-bridging-the-gap-between-machine-learning-and-chemistry.pdf |
67ae0af06dde43c908b96d99 | 10.26434/chemrxiv-2025-gxtfp-v2 | Synthesis of tetra-porphyrin tubes for catalysis and host-guest chemistry | We report a reaction between tetra-3-pyridyl porphyrin and tetra-3-bromomethylphenyl porphyrin leading to the formation of a tetra-porphyrin tube with alkylpyridinium linkers. The 24-hour synthesis resulted in a 26% isolated yield. The free-base tube (FB4-tube) was characterized using 1D NMR, 2D NMR, HR-MS, UV-Vis, and single-crystal X-ray diffraction. This architecture was subsequently metalated with zinc(II) and cobalt(II) resulting in tetra-nuclear cores. Cobalt porphyrins are often used as catalysts for the Oxygen Reduction Reaction (ORR). Therefore, we evaluated the tube as a homogenous ORR catalyst. The Co4-tube showed a Ecat1/2 value of –1.0 V versus FcH+/FcH. Additionally, porphyrin cages with large cavities have been used to sequester pollutants and other organic molecules like fullerenes. With our tube, encapsulation of C60 and C70 occurred with high binding affinity, which was verified via NMR and HR-MS. Due to the large cavity of the tube, the fullerenes sit off-centered, breaking the symmetry to C2v from D2h. This was confirmed by proton NMR shifts associated with through-space interactions. | John Pinti; Owen Szeglowski; Rachel Snider; Matthew Crawley; Timothy Cook | Inorganic Chemistry; Coordination Chemistry (Inorg.); Electrochemistry; Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ae0af06dde43c908b96d99/original/synthesis-of-tetra-porphyrin-tubes-for-catalysis-and-host-guest-chemistry.pdf |
66ade8065101a2ffa8fdeb82 | 10.26434/chemrxiv-2024-gwpw5 | Electrified Nutrient Recovery at Municipal Wastewater Facilities: Sampling, Screening and Multivariate Analyses | Municipal wastewater facilities can contain recycle streams with high nutrient content, that both increase the overall energy consumption in the facility and cause environmental pollution when not properly handled. Reducing the nutrient load of these streams through recovery is a promising solution that enhances the Food-Energy-Water nexus by producing sustainable fertilizer. In this study, the potential for nutrient recovery at municipal wastewater facilities was investigated through a 1-year sampling of nutrient, ionic, organic and heavy metal composition of three wastewater streams influent to or effluent from two types of digesters. Subsequently, electrochemical nutrient recovery was evaluated for these streams through multivariate screening of three groups of variables – operational, stream and design – and the effect of these variables on optimal nutrient recovery in the form of phosphorus. Results showed that Orthophosphate (Ortho-P) and ammonia concentrations do not show significant correlation in any tested streams. On the other hand, major ions exhibited interdependence with Ortho-P concentration, while the stream pH was found to correlate with Ortho-P and Cl- in the anaerobic digester effluent. Screening analyses identified 5 – anode type, cathodic potential, initial P concentration, initial NH4+ concentration and temperature – of the 11 variables evaluated were the variables that most significantly affected P recovery efficiency and specific energy consumed during this recovery. Finally, the optimum conditions for high phosphorus recovery and low energy consumption from the anaerobic digester effluent during a 2-hour experiment were a cathodic potential of -0.805 V vs Ag/AgClsat, an electrode area to electrolyte volume ratio of 0.145 1/cm, and a temperature of 41.3°C, with a solid product that was predominantly struvite. Overall, the demonstrated 95% P recovery efficiency and 0.03 kWh/kg P are characteristic of an emerging process that could be competitive at scale with state-of-the-art synthetic nutrient routes, if applied to the right stream. | Sana Heydarian; Lawrence Ajayi; Asad Abbas; Kody Wolfe; Rida Benhaddou; Jason Trembly; Damilola Daramola | Physical Chemistry; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Hydrology and Water Chemistry; Electrochemistry - Mechanisms, Theory & Study; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ade8065101a2ffa8fdeb82/original/electrified-nutrient-recovery-at-municipal-wastewater-facilities-sampling-screening-and-multivariate-analyses.pdf |
62209a5697f21085c5fb89ab | 10.26434/chemrxiv-2022-5kr7s-v2 | Defining the Temperature of an Isolated Molecule | The microcanonical temperature of an isolated molecule is derived in terms of Boltzmann and Gibbs volume entropies within the quantum harmonic vibrational approximation. The effects of the entropy functional choice and various approximations are examined. The difference between Boltzmann and Gibbs volume temperatures is negligible for molecules as small as ten atoms. However, it is significant for smaller systems, opening a way to probe them experimentally. A simple, analytical expression of the temperature as a function of the vibrational energy is provided, allowing predictions with a 3% margin of error. The microcanonical temperature is discussed and exemplified with polycyclic aromatic hydrocarbon molecules and other molecules of astrophysical interest. | Mario BARBATTI | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62209a5697f21085c5fb89ab/original/defining-the-temperature-of-an-isolated-molecule.pdf |
66c71ba620ac769e5f7290e9 | 10.26434/chemrxiv-2024-2h48p-v3 | Structural transformations of metal-organic cages through tetrazine-alkene reactivity | The assembly of metal-organic cages is governed by metal ion coordination preferences and the geometries of the typically rigid and planar precursor ligands. PdnL2n cages are amongst the most structurally diverse, with subtle differences in the metal-ligand coordination vectors resulting in drastically different assemblies, however almost all rely on rigid aromatic linkers to avoid the formation of intractable mixtures. Here we exploit the inverse electron-demand Diels-Alder (IEDDA) reaction between tetrazine linker groups and alkene reagents to trigger structural changes induced by post-assembly modification. The structure of the 1,4-dihydropyridazine produced by IEDDA (often an afterthought in click chemistry) is crucial; its two sp3 centers increase flexibility and non-planarity, drastically changing the range of accessible coordination vectors. This triggers an initial Pd4L8 tetrahedral cage to transform into different Pd2L4 lantern cages, with both the transformation extent (thermodynamics) and rate (kinetics) dependent on the alkene dienophile selected. With cyclopentene, the unsymmetrical 1,4-dihydropyridazine ligands undergo integrative sorting in the solid state, with both head-to-tail orientation and enantiomer selection, leading to a single isomer from the 39 possible. This preference is rationalized through entropy, symmetry, and hydrogen bonding. Subsequent oxidation of the 1,4-dihydropyridazine to the aromatic pyridazine rigidifies the ligands, restoring planarity. The oxidized ligands no longer fit in the lantern structure, inducing further structural transformations into Pd4L8 tetrahedra and Pd3L6 double-walled triangles. The concept of controllable addition of limited additional flexibility and then its removal through well-defined reactivity we envisage being of great interest for structural transformations of any class of supramolecular architecture. | Martin Black; Soumalya Bhattacharyya; Stephen Argent; Ben Pilgrim | Organic Chemistry; Inorganic Chemistry; Supramolecular Chemistry (Org.); Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c71ba620ac769e5f7290e9/original/structural-transformations-of-metal-organic-cages-through-tetrazine-alkene-reactivity.pdf |
60c7567a702a9be92318c8fe | 10.26434/chemrxiv.14254289.v1 | Revisiting the Electronic Structure of Cobalt-Porphyrin Nitrene and Carbene Radicals with NEVPT2-CASSCF Calculations: Doublet versus Quartet Ground States | Cobalt-porphyrin complexes are established catalysts for carbene and nitrene radical group transfer reactions. The key carbene, mono- and bis-nitrene radical complexes coordinated to [Co(TPP)] (TPP = tetraphenylporphyrin) have previously been investigat-ed with a variety of experimental techniques and supporting (single-reference) DFT calculations that indicated doublet (S = ½) ground states for all three species. In this contribution we revisit their electronic structures with multireference NEVPT2-CASSCF calculations to investigate possible multireference contributions to the ground state wavefunctions. The carbene ([Co<sup>III</sup>(TPP)(•CHCO<sub>2</sub>Et)]) and mono-nitrene ([Co<sup>III</sup>(TPP)(•NNs)]) radical complexes were confirmed to have uncomplicated doublet ground states, although a higher carbene or nitrene radical character and a lower Co‒C/N bond order was found in the NEVPT2-CASSCF calculations. Supported by EPR analysis and spin counting, paramagnetic molar susceptibility determination and NEVPT2-CASSCF calculations, we report that the cobalt-porphyrin bis-nitrene complex ([Co<sup>III</sup>(TPP•)(•NNs)<sub>2</sub>]) has a quartet (S = 3/2) spin ground state, with a thermally assessable multireference & multideterminant ‘broken-symmetry’ doublet spin excited state. A spin flip on the porphyrin-centered unpaired electron allows for interconversion between the quartet and broken-symmetry doublet spin states, with an approximate 10- and 200-fold higher Boltzmann population of the quartet at room tempera-ture or 10 K, respectively.<br /> | Nicolaas P. van Leest; Bas de Bruin | Spectroscopy (Inorg.); Theory - Inorganic; Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7567a702a9be92318c8fe/original/revisiting-the-electronic-structure-of-cobalt-porphyrin-nitrene-and-carbene-radicals-with-nevpt2-casscf-calculations-doublet-versus-quartet-ground-states.pdf |
67615a7e6dde43c9086c2d10 | 10.26434/chemrxiv-2024-4qfd4 | Arriving at Short Wavelength Infrared: Beyond 1000 nm Reversible Photoswitching of peri-Anthracenethioindigo Using Aggregation Induced Bathochromism | The development of modern molecular photoswitches has made tremendous progress with the advent of low-energy responsive variants able to use visible and red light for reversible photoresponses. Dedicated approaches have been developed to achieve such highly desired properties including push-pull substitution, new chromophore designs, and physical means such as two-photon absorptions, sensitization, or upconversion. However, reaching further into the near infrared (NIR) has proven to be extremely challenging so far, raising the question whether viable photoswitching can actually go beyond 1000 nm. Here we use the concept of aggregation induced bathochromism (AIB) to enable direct excitation beyond 1000 nm for reversible photoswitching. Derivatives of the recently reported peri-anthracenethioindigo (PAT) can be aggregated into ca. 500 nm large particles, which shifts their absorption far beyond 1000 nm and into the short wavelength infrared (SWIR) region. Upon irradiation with 1020 nm light, the metastable Z isomer is obtained while at the same time the aggregates are dissolved. Photoisomerization of the Z isomer with orange or red light allows to return to the aggregated state establishing reversible beyond 1000 nm photoswitching. Further, a secondary and independent level of control is enabled via pH-dependent aggregation and deaggregation and corresponding absorption shifting. The resulting multi-stimuli responsiveness was applied in advanced molecular logic operations in the red and NIR absorption regime. AIB thus offers a highly promising way to realize extremely low-energy responsive photoswitching while at the same time allowing to control aggregation and dissolution behavior at the SWIR end of the electromagnetic spectrum. | Verena Josef; Fabian Harenz; Maria Eugenia Perez-Ojeda Rodriguez; Henry Dube | Physical Chemistry; Organic Chemistry; Nanoscience; Photochemistry (Org.); Physical Organic Chemistry; Self-Assembly | CC BY 4.0 | CHEMRXIV | 2024-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67615a7e6dde43c9086c2d10/original/arriving-at-short-wavelength-infrared-beyond-1000-nm-reversible-photoswitching-of-peri-anthracenethioindigo-using-aggregation-induced-bathochromism.pdf |
66a37ffe01103d79c5bfc858 | 10.26434/chemrxiv-2024-0ws9m | Electrochemical Imaging of Thermochemical Catalysis | Thermochemical redox catalysis is critical to a wide array of key chemical transformations and is known to be sensitive to catalyst surface structure. Yet there exist limited operando tools for quantitatively imaging heterogeneities in catalytic rate across a surface. Since many thermochemical redox reactions can proceed via the coupling of electrochemical half-reactions, electrochemical microscopies can, in principle, be used to image heterogeneities in thermochemical redox catalysis. Herein, we develop a methodology for imaging variations in the rate of thermochemical redox catalysis using electrochemical microscopy. Using Pt-catalyzed aerobic oxidation of formic acid oxidation as a test reaction, scanning electrochemical cell microscopy (SECCM) imaging reveals grain-dependent variations in catalytic rate for the underlying oxygen reduction and formic acid oxidation half-reactions, implying inter-grain cooperativity during ensemble thermochemical catalysis via lateral current flows that galvanically couple disparate active sites. Tafel analysis of current-potential profiles in the presence of both reactants reveals the nature of cross-talk between the two half-reactions and provides quantitative spatially-resolved images of catalytic rates for the net thermochemical reaction. These studies establish a methodology for using electrochemical microscopy to image thermochemical catalysis and expose how electrochemical half-reactions couple and interact across surface structures to enable redox transformations. | Xiangdong Xu; William Howland; Daniel Martín-Yerga; Cole Cadaram; Deiaa Harraz; Geoff West; Patrick Unwin; Yogesh Surendranath | Catalysis; Analytical Chemistry; Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a37ffe01103d79c5bfc858/original/electrochemical-imaging-of-thermochemical-catalysis.pdf |
60c747429abda26962f8c89c | 10.26434/chemrxiv.11560137.v1 | 4-Step Total Synthesis of (−)-Pavidolide B | (−)-Pavidolide B is a complex
tetracyclic diterpenoid with seven contiguous stereocenters, and classical
total syntheses have recently been reported. In this work, an annulation strategy
of carbanion cascade reaction is formulated for accomplishing an asymmetric
total synthesis of (−)-pavidolide B in just 4 linear steps. The key reaction
is a tandem intramolecular Michael addition, which constructs two 5-membered
rings and five stereocenters in a highly selective fashion in one step. This
work represents one of the most efficient cases of total synthesis and
demonstrates that synthetic access to complex therapeutic natural product can
be greatly simplified. | Yaoqiu Zhu; Elkin L. Romero; Kolluru Srinivas; Elizabeth Noriega | Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747429abda26962f8c89c/original/4-step-total-synthesis-of-pavidolide-b.pdf |
64197fbd2bfb3dc2511d5a38 | 10.26434/chemrxiv-2022-mkx92-v7 | Basic principle from electrospray ionization to soft ionization mass spectrometry and development of ion source | Since the electrospray phenomenon was discovered, there is still an unsolved mystery about the prinple of generating charged analyte in the soft ionization phenomenon which represented by ESI. Scientists have described this process from different perspectives, but current theories still can not explain many experimental phenomena. At the same time, the slow development of the theory restricts the design and development of ion source, making it encounter many bottlenecks from the laboratory to commercialization. In this paper, the principle of electrospray ionization and soft ionization mass spectrometry is briefly introduced, and the application of ion migrate and transport mechanism is discussed, all are expected to be used in the development of ion sources. | jiehong luo | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64197fbd2bfb3dc2511d5a38/original/basic-principle-from-electrospray-ionization-to-soft-ionization-mass-spectrometry-and-development-of-ion-source.pdf |
6645505f418a5379b064c02e | 10.26434/chemrxiv-2024-m7t4c | Theory of Resonance Suppression in Vibrational Polariton Chemistry | Recent experiments have demonstrated that it is possible to modify ground-state chemical reactivities by placing an ensemble of molecules in an optical microcavity through resonant coupling between the cavity and vibrational degrees of freedom (DOF) of the molecules. This new strategy of vibrational strong coupling (VSC), if feasible, will offer a paradigm shift in synthetic chemistry through cavity-enabled bond-selective chemical transformations. This so-called VSC regime operates in the absence of any light source, occurs under the resonance condition when cavity frequency matches the molecular vibrational frequency, and only occurs at the normal incidence when considering in-plane momentum inside a Fabry-Perot cavity. In this work, we provide a potential mechanism that explains all observed phenomena. Using numerically exact quantum dynamics simulations and an analytic rate theory, we have demonstrated the resonant suppression of the rate constant when coupling the cavity mode to a vibrational spectator mode in a model reaction. Both the analytic theory and the simulations can explain previously observed phenomena, including the non-linear change of the rate constant when increasing Rabi splitting, modification of both reactive enthalpy and entropy, and for a reason why with a very low barrier, there is a lack of the cavity modification. The analytic theory can also explain the normal incidence condition, and collective coupling effects when solvents are collectively coupled to both cavity mode and reaction coordinate. | Sebastian Montillo Vega; Wenxiang Ying; Pengfei Huo | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Chemical Kinetics | CC BY 4.0 | CHEMRXIV | 2024-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6645505f418a5379b064c02e/original/theory-of-resonance-suppression-in-vibrational-polariton-chemistry.pdf |
656f2dbacf8b3c3cd7d62097 | 10.26434/chemrxiv-2023-124lf | Visible Organic Thermoluminescence above Room Temperature in Small Molecule Crystals | Thermoluminescence (TL) is commonly observed in inorganic luminescent materials at elevated temperatures, with applications in radiation dosimetry, archaeology, geological dating, and defect studies. However, the understanding of TL in organic small molecules above room temperature is still limited. Here, we experimentally discovered and theoretically analyzed the unusual TL exhibited by organic scintillation crystals in air. It exhibits an onset temperature of ~300 K, reaching its maximum intensity at 348 K (heating rate of 2 K s-1). Upon 365 nm ultraviolet light excitation at room temperature, the material gradually released stored energy through phosphorescence, achieving a record-breaking organic afterglow lasting over 10 hours. The exceptional luminescence originates from excited states generated by thermally driven back electron-transfer (BET). Crucially, this work reveals that certain instances of previously reported ultralong organic afterglow are, in reality, specific cases of organic TL occurring at room temperature. These findings prompt a reevaluation of the similarities and differences between organic and inorganic phosphors. Specifically, in the absence of a comprehensive understanding of above-room-temperature thermoluminescence in organics, the information gained from this work holds significant practical implications for organic emitters and fields involving back electron transfer. | Yunsheng Wang ; Jie Yang; Liwei Wang; Aisen Li; Yalei Cao; Xiaoze Wang; Manman Fang; Qiushui Chen; Huang-Hao Yang; Zhen Li | Organic Chemistry; Organic Compounds and Functional Groups; Photochemistry (Org.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656f2dbacf8b3c3cd7d62097/original/visible-organic-thermoluminescence-above-room-temperature-in-small-molecule-crystals.pdf |
60c75824567dfe2b6dec67d0 | 10.26434/chemrxiv.14502744.v1 | Development of an Efficient Route to 2-Ethynylglycerol for the Synthesis of Islatravir | The unnatural, alkyne-containing nucleoside analog islatravir
(MK-8591) is synthetically accessed through a biocatalytic cascade starting from
2-ethynylglycerol as a building block. Herein, we describe the development of an
efficient synthesis of this building block including the initial route, route
scouting and final process development. Key challenges that have been overcome are
the development of an efficient and safe acetylenic nucleophile addition to an appropriate
ketone, and the identification of a 2-ethynylpropane-1,2,3-triol derivative
with favorable physical properties. An acid-catalyzed cracking of commercially
available 1,3-dihydroxyacetone dimer and subsequent 1,2-addition of an
acetylenic nucleophile has been discovered and optimized into the manufacturing
process | Stephan M. Rummelt; Ji Qi; Yonggang Chen; James F. Dropinski; Gregory Hughes; Jeffrey T. Kuethe; Donghong Li; Kevin M. Maloney; Eric Margelefsky; Rose Mathew; Daniel J. Muzzio; Christopher C. Nawrat; Justin A. Newman; Honggui Ouyang; Niki R. Patel; Zhen Qiao; Gao Shang; Eric Sirota; Zhiguo Jake Song; Lushi Tan; Richard J. Varsolona; Baoqiang Wan; Brian M. Wyvratt; Feng Xu; Yingju Xu; Jingjun Yin; Shaoguang Zhang; Ralph Zhao | Process Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75824567dfe2b6dec67d0/original/development-of-an-efficient-route-to-2-ethynylglycerol-for-the-synthesis-of-islatravir.pdf |
60c7422b4c89194739ad23f4 | 10.26434/chemrxiv.7334564.v3 | Computational evidence for kinetically controlled radical coupling during lignification | Lignin is an alkyl-aromatic biopolymer that, despite its abundance, is underutilized as a renewable feedstock because of its highly complex structure. An approach to overcome this challenge that has gained prominence in recent years leverages the plasticity and malleability of lignin biosynthesis to tune lignin structure in planta through genetic approaches. An improved understanding of lignin biosynthesis can thus provide fundamental insights critical for the development of effective tailoring and valorization strategies. Although it is widely accepted that lignin monomers and growing chains are oxidized enzymatically into radicals that then undergo kinetically-controlled coupling in planta, direct experimental evidence has been scarce because of the difficulty of exactly replicating in planta lignification conditions. Here, we computationally investigate a set of radical reactions representative of lignin biosynthesis. We show that, contrary to the widely held notion that radical coupling reactions should be barrierless and dynamically controlled, the computed activation energies can be qualitatively consistent with key structural observations made empirically for native lignin in a variety of biomass types. We also rationalize the origins of regioselectivity in coupling reactions through structural and activation strain analyses. Our findings lay the groundwork for more detailed multiscale simulations of the lignification process.<br /> | Terry Gani; Michael Orella; Eric Anderson; Michael Stone; Fikile Brushett; Gregg Beckham; Yuriy Román-Leshkov | Biopolymers; Plant Biology; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7422b4c89194739ad23f4/original/computational-evidence-for-kinetically-controlled-radical-coupling-during-lignification.pdf |
62559e61d048edb1e240881a | 10.26434/chemrxiv-2022-rz8m6 | Not all aggregates are made the same: Distinct structures of solution aggregates drastically modulate assembly pathways, morphology and electronic properties of
conjugated polymers | Tuning structures of solution-state aggregation and aggregation-mediated assembly pathways of conjugated polymers is crucial for optimizing their solid-state morphology and charge transport property. However, it remains challenging to unravel and control the exact structures of solution aggregates, let alone to modulate assembly pathways in a controlled fashion. Herein, we largely modulate aggregate structures by tuning selectivity of the solvent towards the side chain vs. the backbone, which leads to three distinct assembly pathways: direct crystallization from side-chain associated amorphous aggregates, chiral liquid crystal (LC)-mediated assembly from semicrystalline aggregates with side-chain and backbone stacking, random agglomeration from backbone-stacked semicrystalline aggregates. Importantly, we demonstrate for the first time that the amorphous solution aggregates, compared with semicrystalline ones, lead to significantly improved alignment and reduced paracrystalline disorder in solid-state due to direct crystallization during the meniscus-guided coating process. Alignment quantified by dichroic ratio obtained from grazing incidence X-ray diffraction (GIXD) is enhanced by up to fourteen-fold, and the charge carrier mobility increases by a maximum of twenty-fold in films printed from amorphous aggregates compared to those from semicrystalline aggregates. This work shows that by tuning the precise structure of solution aggregates, one can drastically tune assembly pathways, and the resulting thin film morphology and device properties. | Zhuang Xu; Kyung Sun Park; Justin J. Kwok; Oliver Lin; Bijal B. Patel; Prapti Kafle; Daniel W. Davies; Qian Chen; Ying Diao | Materials Science; Chemical Engineering and Industrial Chemistry; Aggregates and Assemblies; Liquid Crystals; Thin Films; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62559e61d048edb1e240881a/original/not-all-aggregates-are-made-the-same-distinct-structures-of-solution-aggregates-drastically-modulate-assembly-pathways-morphology-and-electronic-properties-of-conjugated-polymers.pdf |
66ec447c12ff75c3a1d503ab | 10.26434/chemrxiv-2024-5b3pf | Key Aspects in Designing High-Throughput Workflows in Electrocatalysis Research: A Case Study on IrCo Mixed-Metal Oxides | With the growing interest of the electrochemical community in high-throughput (HT) experimentation as a powerful tool in accelerating materials discovery, the implementation of HT methodologies and the design of HT workflows has gained traction. We identify 6 aspects essential to HT workflow design in electrochemistry and beyond to ease the incorporation of HT methods in the community’s research and to assist in their improvement. We study IrCo mixed-metal oxides (MMOs) for the oxygen evolution reaction (OER) in acidic media using the mentioned aspects to provide a practical example of possible workflow design pitfalls and strategies to counteract them. | Joanna Magdalena Przybysz; Ken Jenewein; Mária Minichová; Tomáš Hrbek; Thomas Böhm; Tatiana Priamushko; Serhiy Cherevko | Materials Science; Catalysis; Energy; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ec447c12ff75c3a1d503ab/original/key-aspects-in-designing-high-throughput-workflows-in-electrocatalysis-research-a-case-study-on-ir-co-mixed-metal-oxides.pdf |
60c7505c0f50db78cb397571 | 10.26434/chemrxiv.13027955.v1 | The Molecular Mechanisms of Photoactivation of Orange Carotenoid Protein Revealed by Molecular Dynamics | Light-harvesting in photosynthesis is accompanied by photoprotective processes. In cyanobacteria, the photoprotective role is played by a specialized complex, the Orange Carotenoid Protein which is activated by strong blue-green light. This photoactivation involves a unique series of structural changes which terminate with an opening of the complex into two separated domains, one of which acts as a quencher for the light-harvesting complexes. Many experimental studies have tried to reveal the molecular mechanisms through which the energy absorbed by the carotenoid finally leads to the large conformational change of the complex. Here for the first time, these mechanisms are revealed by simulating at atomistic level the whole dynamics of the complex through an effective combination of enhanced sampling techniques. On the basis of our findings, we can conclude that the carotenoid does not act as a spring that, releasing its internal strain, induces the dissociation, as it was previously proposed but as a "latch" locking together the two domains. The photochemically triggered displacement of the carotenoid breaks this balance, allowing the complex to dissociate. <br /> | Mattia Bondanza; Lorenzo Cupellini; Pietro Faccioli; Benedetta Mennucci | Computational Chemistry and Modeling; Biophysical Chemistry; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7505c0f50db78cb397571/original/the-molecular-mechanisms-of-photoactivation-of-orange-carotenoid-protein-revealed-by-molecular-dynamics.pdf |
637f46744b1a5faf1a8b9217 | 10.26434/chemrxiv-2022-mk21t | A catalyst acceleration platform towards realizing the energy transition | The climate emergency has made it necessary to rethink our economy which relies heavily on fossil fuels. Currently, sustainable processes are too costly, but catalysis as a key enabling technology has the potential to reduce process costs to a level that makes them economically viable. In spite of that, the existing catalyst discovery paradigm depends heavily on serendipity and trial and error methods. What is urgently needed to transform the energy transition is a catalyst acceleration platform (CAP) that expedites the development of next-generation sustainable processes. To advance the field, we need to use state-of-the-art robotic and algorithmic tools to look beyond the well-established systems that dominate the current research landscape. Herein, we discuss the requirements for a successful catalyst acceleration concept and the societal impact of breakthrough catalytic materials. | Marcus Tze-Kiat Ng; Ahmed S. M. Ismail; Alexander J. S. Hammer | Physical Chemistry; Catalysis; Electrocatalysis; Physical and Chemical Properties; Robotics; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637f46744b1a5faf1a8b9217/original/a-catalyst-acceleration-platform-towards-realizing-the-energy-transition.pdf |
60c757bcbdbb8996c7a3ac6d | 10.26434/chemrxiv.14454681.v1 | Free-base Porphyrin Polymer for Bifunctional Electrochemical Water Splitting | Projected future global energy demands require sustainable energy sources as alternatives to the current world dependence on hydrocarbon fuels. The production of hydrogen and oxygen gas from water is a promising approach. Currently, water-splitting electrolyzers require precious metals as electrocalysts because they are active and stable. Yet, replacement of these precious metals by cost-effective alternatives is necessary for the economic feasibility of this approach. Here, we describe a molecular based polymeric approach that effectively removes the need to use any metal to electrochemically split water. The incorporation of free-base porphyrin units into a 2D network structure yields a stable and efficient bifunctional electrocatalyst for water oxidation and water reduction that can operate for days at competitive overpotentials comparable to metal based ones. <br /><br /><br /> | Yulu Ge; Zhenhua Lyu; Mariana Marcos Hernandez; Dino Villagran | Catalysts; Fuels - Materials; Organic Polymers; Electrochemistry; Electrocatalysis; Heterogeneous Catalysis; Redox Catalysis; Fuels - Energy Science; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757bcbdbb8996c7a3ac6d/original/free-base-porphyrin-polymer-for-bifunctional-electrochemical-water-splitting.pdf |
67d31046fa469535b919a616 | 10.26434/chemrxiv-2025-2nnnk | Reaction Mechanism and Metal Selectivity of Human SAMHD1 Elucidated by QM/MM Calculations | 2'-deoxynucleoside-5'-triphosphate triphosphohydrolases (dNTPases) constitute a crucial enzyme family that plays a pivotal role in antiviral innate immunity. Among these enzymes, human SAMHD1 has emerged as a novel dNTPase, demonstrating special catalytic structure and property. This metalloenzyme regulates cellular dNTP concentration through its ability to hydrolyze all four canonical dNTPs into their corresponding 2'-deoxynucleosides and inorganic triphosphates, a reaction requiring coordinated iron and magnesium ions for enzymatic activity. In the present work, molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations are employed to investigate the mechanistic details of dATP hydrolysis mediated by two metal ions. Starting from the resolved crystal structure, Model1, containing a Fe2+ in the active site, was constructed. Our calculations demonstrate that SAMHD1 employs a bridging hydroxide anion OH− to attack Pα site of dNTP, triggering the cleavage of Pα–O5' bond via a trigonal-bipyramidal transition state. Simultaneously, His215 donates a proton to O5' of the leaving group, leading to the formation of 2'-deoxyadenosine and triphosphate. It is further demonstrated that the native Fe2+-Mg2+ bi-metallic centre help catalyse this hydrolysis reaction with a barrier of 13.4 kcal/mol, while the substitution from Fe2+ to Fe3+ abolishes the catalytic activity of SAMHD1. The comparisons between different QM/MM models highlight the high affinity of SAMHD1 for Fe2+ relative to Mn2+ and Mg2+ at one of bi-metallic sites. In addition, the metal ion swapping between Fe2+ and Mg2+ from their crystallographic positions is shown to elevate the energy of the reactant state, underscoring the critical influence of metal coordination geometry on catalytic activity. These computational insights not only expand the understanding of how SAMHD1 wisely modulates catalytic reactivity and metal selectivity by binding suitable metal ions, but also provide valuable foundation for guiding the design of novel drugs for antiviral therapies. | Edina Rosta; Rong-Zhen Liao; Wen-Hao Deng; Harry Lewin | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d31046fa469535b919a616/original/reaction-mechanism-and-metal-selectivity-of-human-samhd1-elucidated-by-qm-mm-calculations.pdf |
60c74a1aee301c7a9bc79bc6 | 10.26434/chemrxiv.12152835.v1 | Functionalization of Bis-Diazaphospholene P-P Bonds with Diverse Electrophiles | <p>Readily prepared bis-diazaphospholenes are shown to react with several classes of electrophiles, resulting in cleavage of the phosphorus-phosphorus bond and formation of functionalized diazaphospholenes. Phosphorus – sp<sup>3</sup> or sp<sup>2</sup> carbon and phosphorus – sulfur bonds were formed using this protocol. Experimental evidence with aryl and alkyl halides suggests the intermediacy of radicals in some cases, however other evidence suggests either radical or polar mechanisms may be operative for certain substrates, with a dependence on reaction conditions. In some cases, the substituted diazaphospholenes can transfer the substituent to electrophiles via previously unknown reactions. These results show diazaphospholene dimers are potent participants in radical chemistry at room temperature without requiring chemical initiators.</p> | Blake S. N. Huchenski; Katherine N. Robertson; Alex Speed | Photochemistry (Org.); Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a1aee301c7a9bc79bc6/original/functionalization-of-bis-diazaphospholene-p-p-bonds-with-diverse-electrophiles.pdf |
60f8ebe6393cc945f04e290e | 10.26434/chemrxiv-2021-tld2h | Pre- and post-industrial levels of polycyclic aromatic hydrocarbons in sediments from the Estuary and Gulf of St. Lawrence (eastern Canada) | The concentrations of 23 polycyclic aromatic hydrocarbons (PAHs; 16 parent PAHs and 7 alkyl-PAHs) were determined in 45 surface sediment and 7 basal sediment box core samples retrieved from the Estuary and Gulf of St. Lawrence in eastern Canada. The concentration sums of 16 priority PAHs (Σ16PAHs) in the surface sediments ranged from 71 to 5672 ng g−1. Σ16PAHs in the basal sediments ranged from 93 to 172 ng g−1 among the pre-industrial samples and from 1216 to 1621 ng g−1 among the early post-industrial samples. The highest Σ16PAH values occurred in samples retrieved from the Baie-Comeau-Matane area, an area affected by intense industrial anthropogenic activities. Source-diagnostic PAH ratios suggest a predominance of pyrogenic sources via atmospheric deposition, with a minor contribution of petrogenic seabed pockmark sources. The PAH concentrations in the sediments from the study areas reveal low ecological risks to benthic or other organisms living near the water-sediment interface. | Anne Corminboeuf ; Jean-Carlos Montero-Serrano; Richard St-Louis ; Allyson Dalpé ; Yves Gélinas | Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f8ebe6393cc945f04e290e/original/pre-and-post-industrial-levels-of-polycyclic-aromatic-hydrocarbons-in-sediments-from-the-estuary-and-gulf-of-st-lawrence-eastern-canada.pdf |
661e545d418a5379b0f4fbac | 10.26434/chemrxiv-2024-pfh2g | A Native Mass Spectrometry Approach to Qualitatively Elucidate Interfacial Epitopes of Transient Protein-Protein Interactions | Native mass spectrometric analysis of TPR2A and GrpE with unpurified peptides derived from limited proteolysis of their respective PPI partners (HSP90 C-terminus and DnaK) facilitated efficient, qualitative identification of interfacial epitopes involved in transient PPI formation. Application of this approach can assist in elucidating interfaces of currently uncharacterised transient PPIs. | Clinton Veale; Abir Chakraborty; Richwell Mhlanga; Fernando Albericio; Beatriz de la Torre; Adrienne Edkins; David Clarke | Biological and Medicinal Chemistry; Biophysics; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661e545d418a5379b0f4fbac/original/a-native-mass-spectrometry-approach-to-qualitatively-elucidate-interfacial-epitopes-of-transient-protein-protein-interactions.pdf |
60c74e26bdbb892d8da39b37 | 10.26434/chemrxiv.12706235.v1 | Ultra-Fine Ni2P Nanoparticles Decorated R-GO: Novel Phosphidation Approach and Dibenzothiophene Hydrodesulfurization | Nanostructured transition metal phosphides gathered
last years an elevated scientific interest, due to their unique
physical-chemical properties. Nickel phosphide nanoparticles, with the
controllable crystal structure, from the metal rich tetragonal Ni<sub>12</sub>P<sub>5</sub>
to the phosphorous rich hexagonal Ni<sub>2</sub>P, and <i>hcp</i> Ni<sub>2</sub>P decorated r-GO (reduced graphene oxide), nano-hybrid
materials have been synthesized via a novel one step organometallic approach in
primary-tertiary aliphatic amines mixture. The nanoparticles are monodispersed,
with spherical shape and controllable size in the sub-10 nm regime and decorate
uniformly the surface of the r-GO, leading to the formation of Ni<sub>2</sub>P/r-GO
hybrid materials. The materials were characterized by powder XRD, TEM and Raman
spectroscopy and catalytically evaluated for the dibenzothiophene
hydrodesulphurization (HDS) reaction.
The results show that the role of the tertiary amine is crucial for the
phosphidation process and the r-GO is an ideal alternative, to the traditional inorganic
ones, support for the immobilization of the catalytically active component,
preventing significantly sintering effects. | Vasileios Tzitzios; Vishnu Pillai; Christina Gioti; Marios Katsiotis; Thomas Karagiannis; Dimitrios Gournis; Michael A Karakassides; Saeed Alhassan | Carbon-based Materials; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e26bdbb892d8da39b37/original/ultra-fine-ni2p-nanoparticles-decorated-r-go-novel-phosphidation-approach-and-dibenzothiophene-hydrodesulfurization.pdf |
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