id
stringlengths 24
24
| doi
stringlengths 28
32
| title
stringlengths 8
495
| abstract
stringlengths 17
5.7k
| authors
stringlengths 5
2.65k
| categories
stringlengths 4
700
| license
stringclasses 3
values | origin
stringclasses 1
value | date
stringdate 1970-01-01 00:00:00
2025-03-24 00:00:00
| url
stringlengths 119
367
⌀ |
|---|---|---|---|---|---|---|---|---|---|
610ad1db4cb47932ea287e28 | 10.26434/chemrxiv-2021-x46f8 | The presence and role of the intermediary CO reservoir in heterogeneous electroreduction of CO2 | Despite the importance of the microenvironment in heterogeneous electrocatalysis, its role remains unclear due to a lack of suitable characterization techniques. Multi-step reactions like the electroconversion of CO2 to multicarbons (C2+) are especially relevant considering the potential creation of a unique microenvironment as part of the reaction pathway. To elucidate the significance of the microenvironment during CO2 reduction, we develop on-stream substitution of reactant isotope (OSRI), a new method which relies on the subsequent introduction of CO2 isotopes. Combining electrolytic experiments with a numerical model, this method reveals the presence of a reservoir of CO molecules concentrated near the catalyst surface that influences C2+ formation. Application of OSRI on a Cu nanoparticle (NP) ensemble and an electropolished Cu foil demonstrates that a CO monolayer covering the surface does not provide the amount of CO intermediates necessary to facilitate C-C coupling. Specifically, the C2+ turnover increases only after reaching a density of ~100 CO molecules per surface Cu atom. The Cu NP ensemble satisfies this criterion at an overpotential 100 mV lower than the foil, making it a better candidate for efficient C2+ formation. Furthermore, given the same reservoir size, the ensemble’s intrinsically higher C-C coupling ability is highlighted by the 4-fold higher C2+ turnover it achieves at a more positive potential. The OSRI method provides an improved understanding of how the presence of CO intermediates in the microenvironment impacts C2+ formation during the electroreduction of CO2 on Cu surfaces. | Sheena Louisia; Dohyung Kim; Yifan Li; Mengyu Gao; Sunmoon Yu; Peidong Yang | Catalysis; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610ad1db4cb47932ea287e28/original/the-presence-and-role-of-the-intermediary-co-reservoir-in-heterogeneous-electroreduction-of-co2.pdf |
63c6afbdf604d16125591e45 | 10.26434/chemrxiv-2023-5chkk | Total Disruption of Au Cores and the Formation of Hollow Voids in Au-Pt Bimetallic Nanoparticles | When homogenized as core-shell structures, the structural instability of Au cores in bimetallic nanoparticles (NPs) has been well documented in the theoretical calculations, yet there are limited examples in the experiments. It is presented in this study that in the presence of Ag(I), Au cores with the average size of 33.0 nm are annihilated with crystalline Au being hardly found when Au NPs are coated with Pt shells, while the crystallinity and size of Au cores remain intact when they are coated with Pd. Strains follow when heterogeneous metals are embedded around Au cores with relatively large size and relatively large interfacial area, and there are ways for releasing the interface energy for Pd: i) twin boundaries and stacking faults on the surface of Pd shells, and ii) small voids around Au cores. When Au NPs are coated with Pt, however, porous structures rather than crystalline structures are observed with twin defects being hardly found, and for alleviating the high surfaces energies of Pt, Au atoms diffuse actively outward. In the absence of Ag(I), significant alloying progresses with no hollow cores observed. Ag(I) is believed to facilitate the segregation of Au to the surfaces, and during this rapid movement, Pt does not diffuse as quickly as Au and consequently hollow cores are generated in the presence of Ag(I). | Hyon-Min Song; Dalaver H. Anjum; Jeffrey I. Zink | Materials Science; Core-Shell Materials | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c6afbdf604d16125591e45/original/total-disruption-of-au-cores-and-the-formation-of-hollow-voids-in-au-pt-bimetallic-nanoparticles.pdf |
66472a7391aefa6ce13d5d6c | 10.26434/chemrxiv-2024-4z0xg-v2 | STRUCTURE CONFIRMATION, REACTIVITY, BACTERIAL MUTAGENICITY AND QUANTIFICATION OF 2,2,4-TRIBROMO-5-HYDROXYCYCLOPENT-4-ENE-1,3-DIONE IN DRINKING WATER | Non-target chemical analysis of drinking water revealed the presence of two new disinfectant by-product (DBP) groups in the UK, halogenated-hydroxycyclopentenediones and halogenated-methanesulfonic acids. We unequivocally identified 2,2,4-tribromo-5-hydroxycyclopent-4-ene-1,3-dione (TBHCD), and quantified it together with dibromomethanesulfonic acid at 122±34 and 326±157 ng L-1 in London drinking water, respectively (N=21). We found TBHCD to be photolabile and unstable in tap water and at alkaline pH. Furthermore, spectral and computational data for TBHCD and three other halogenated-hydroxycyclopentenediones indicated they could act as a source of radicals and form other DBPs as a result. Importantly, TBHCD was calculated to have a 14.5 kcal mol-1 lower C-Br bond dissociation enthalpy than the N-Br bond of N-bromosuccinimide, a common radical substitution reagent used in organic synthesis. TBHCD was mutagenic in Salmonella/microsome assays using strains TA98, TA100 and TA102. This work reveals the unique features, activity and toxicity of trihalogenated hydroxycyclopent-4-ene-1,3-diones, prompting a need to more comprehensively assess their risks. | Davide Ciccarelli; Ben Lancaster; D. Christopher Braddock; Matteo Calvaresi; Miroslav Mišík; Siegfried Knasmuller; Edoardo Jun Mattioli; Francesco Zerbetto; Andrew J.P. White; Tim Marczylo; Timothy W. Gant; Leon Barron | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Chemoinformatics; Environmental Analysis; Mass Spectrometry | CC BY NC 4.0 | CHEMRXIV | 2024-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66472a7391aefa6ce13d5d6c/original/structure-confirmation-reactivity-bacterial-mutagenicity-and-quantification-of-2-2-4-tribromo-5-hydroxycyclopent-4-ene-1-3-dione-in-drinking-water.pdf |
66cc3af8f3f4b052902355c4 | 10.26434/chemrxiv-2024-w40xh | Silicon Oxide Microchips Functionalized with Fluorescent Probes for Quantitative Real-Time Glutathione Sensing in Living Cells | Glutathione (GSH) plays a vital role in the regulation of intracellular functions which alterations in physiological glutathione levels are associated to various diseases. Molecular imaging using fluorescent probes is a sensitive method for glutathione detection. Despite significant progress, challenges persist in the development of fluorescent probes, notably concerning potential aggregation in polar environments, quantitative GSH detection, and long-term tracking of intracellular GSH concentration. Engineered nanomaterials have shown great promise for increasing the disease diagnosis accuracy. Microchips generated by advanced microfabrication techniques can be applied in designing biomedical devices due to control over size, shape, and bioactive coatings utilization. In the current work, the synthesis and characterization of two GSH probes, Bdpy1 and Bdpy2, is reported, each offering irreversible and reversible GSH reactions, respectively. These GSH probes are immobilized on silicon oxide microchips (SOµC), micro-fabricated using photolithographic techniques, to give SOµC-Bdpy1 and SOµC-Bdpy2. Both functionalized microchips exhibited sensitivity to GSH, and, notably, the reversible SOµC-Bdpy2 showed less time dependency, making it more suitable for long-term intracellular GSH sensing. In vitro experiments in HeLa cells reveal both SOµC-Bdpy1 and SOµC-Bdpy2 were internalized in living cells, showing SOµC-Bdpy2 more reliable results (due to its less time dependency) for quantifying intracellular GSH. Remarkably, the intracellular GSH measurement was monitored by SOµC-Bdpy2 for 48h, indicating the functionalized microchips capability to detect GSH amount in different time intervals. This study introduces a promising approach for long term real-time quantification of intracellular GSH, overcoming current limitations in fluorescent probes and offering valuable insights into microchip-based sensing methodologies. | Saman Bagherpour; Patricia Vázquez; Marta Duch; Juan Pablo Agusil; José Antonio Plaza; Mariano Redondo-Horcajo; Teresa Suárez; Lluïsa Pérez-García | Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-08-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cc3af8f3f4b052902355c4/original/silicon-oxide-microchips-functionalized-with-fluorescent-probes-for-quantitative-real-time-glutathione-sensing-in-living-cells.pdf |
65cedfa49138d231613a7fe4 | 10.26434/chemrxiv-2024-qlfk9 | Narrowband Green Thermally-activated Delayed Fluorescence Emitters Based on Bis-fused Indolo[3,2,1-jk]carbazole with Peripheral Donor Decoration | Fused indolo[3,2,1-jk]carbazole (fICZ) framework has emerged as a new paradigm for developing narrowband emitters, but red-shifting the emission and triggering reverse intersystem crossing (RISC) for thermally-activated delayed fluorescence (TADF) have remained challenges. Here, narrowband green TADF emitters based on a fICZ framework are reported with a peripheral donor decoration strategy. By attaching electron-donating diphenylamino-type groups onto the highest occupied molecular orbital (HOMO)-dominating positions of bis-fused indolo[3,2,1-jk]carbazole, the HOMO is largely destabilized and the emission is markedly red-shifted (by > 70 nm) with retained narrow bandwidth. In toluene solution, the emitters show green emission with emission maximums at 500−523 nm and small full-widths at half maximums at 26−28 nm. Importantly, the donor decoration narrows the singlet-triplet energy gap and introduces a higher-lying long-range charge-transfer triplet state having considerable spin-orbital coupling with the emissive singlet state, which behaves as an intermediate triplet state to facilitate RISC. In doped films, the emitters show efficient narrowband green TADF emission. Solution-processed organic light-emitting diodes (OLEDs) using the emitters afford green emission close to the NTSC standard and high external quantum efficiencies up to 24.7%, which are among the most efficient solution-processed narrowband green OLEDs. | Ke Zhang; Pingping Wang; Yuan Cao; Yongjun Song; Yue Xiu; Yibo Li; Hao Ren; Lei He; Dongdong Zhang; Lian Duan | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cedfa49138d231613a7fe4/original/narrowband-green-thermally-activated-delayed-fluorescence-emitters-based-on-bis-fused-indolo-3-2-1-jk-carbazole-with-peripheral-donor-decoration.pdf |
65e75705e9ebbb4db9f75bf1 | 10.26434/chemrxiv-2024-m8dtd | Accelerated screening of gas diffusion electrodes for carbon dioxide reduction | The electrochemical conversion of carbon dioxide to chemicals and fuels is expected to be a key sustainability technology. Electrochemical carbon dioxide reduction technologies are challenged by several factors, including the limited solubility of carbon dioxide in aqueous electrolyte as well as the difficulty in utilizing polymer electrolytes. These considerations have driven systems designs to incorporate gas diffusion electrodes (GDEs) to bring the electrocatalyst in contact with both a gaseous reactant/product stream as well as a liquid electrolyte. GDE optimization typically results from manual tuning by select experts. Automated preparation and operation of GDE cells could be a watershed for the systematic study of, and ultimately the development of a materials acceleration platform (MAP) for, catalyst discovery and system optimization. Toward this end, we present the automated GDE (AutoGDE) testing system. Given a catalyst-coated GDE, AutoGDE automates the insertion of the GDE into an electrochemical cell, the liquid and gas handling, the quantification of gaseous reaction products via online mass spectroscopy, and the archiving of the liquid electrolyte for subsequent analysis. | Ryan Jones; Yungchieh Lai; Dan Guevarra; Kevin Kan; Joel Haber; John Gregoire | Catalysis; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2024-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e75705e9ebbb4db9f75bf1/original/accelerated-screening-of-gas-diffusion-electrodes-for-carbon-dioxide-reduction.pdf |
60c7422a9abda26972f8bf77 | 10.26434/chemrxiv.8226068.v1 | Named Entity Recognition and Normalization Applied to Large-Scale Information Extraction from the Materials Science Literature | <div><div><div>Over the past decades, the number of published materials science articles has increased manyfold. Now, a major bottleneck in the materials discovery pipeline arises in connecting new results with the previously established literature. A potential solution to this problem is to map the unstructured raw-text of published articles onto a structured database entry that allows for programmatic querying. To this end, we apply text-mining with named entity recognition (NER), along with entity normalization, for large-scale information extraction from the published materials science literature. The NER is based on supervised machine learning with a recurrent neural network architecture, and the model is trained to extract summary-level information from materials science documents, including: inorganic material mentions, sample descriptors, phase labels, material properties and applications, as well as any synthesis and characterization methods used. Our classifer, with an overall accuracy (f1) of 87% on a test set, is applied to information extraction from 3.27 million materials science abstracts - the most information-dense section of published articles.</div><div>Overall, we extract more than 80 million materials-science-related named entities, and the content of each abstract is represented as a database entry in a structured format. Our database shows far greater recall in document retrieval when compared to traditional text-based searches due to an entity normalization procedure that recognizes synonyms. We demonstrate that simple database queries can be used to answer complex \meta-questions" of the published literature that would have previously required laborious, manual literature searches to answer. All of our data has been made freely available for bulk download; we have also made a public facing application programming interface (https://github.com/materialsintelligence/matscholar) and website http://matscholar.herokuapp.com/search for easy interfacing with the data, trained models and functionality described in this paper. These results will allow researchers to access targeted information on a scale and with a speed that has not been previously available, and can be expected to accelerate the pace of future materials science discovery.</div></div></div> | Leigh Weston; Vahe Tshitoyan; John Dagdelen; Olga Kononova; Kristin Persson; Gerbrand Ceder; Anubhav Jain | Chemoinformatics | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7422a9abda26972f8bf77/original/named-entity-recognition-and-normalization-applied-to-large-scale-information-extraction-from-the-materials-science-literature.pdf |
64560a9e1ca6101a45de0782 | 10.26434/chemrxiv-2023-mw9cf | Anisotropy-Driven Crystallization of Dimensionally Resolved Quasi-1D van der Waals Nanostructures | Unusual behavior in solids emerge from the complex interplay between crystalline order, composition, and dimensionality. In crystals comprising of weakly-bound one-dimensional (1D) or quasi-1D (q-1D) chains, properties such as charge density waves, topologically protected states, and indirect-to-direct band gap crossovers have been predicted to arise. However, the experimental demonstration of many of these nascent physics in 1D or q-1D van der Waals (vdW) crystals is obscured by the highly anisotropic bonding between the chains, stochasticity of top-down exfoliation, and lack of synthetic strategies to control bottom-up growth. Herein, we report the directed crystallization of a model q-1D vdW phase, Sb2S3, into dimensionally resolved nanostructures. We demonstrate the uncatalyzed growth of highly crystalline Sb2S3 nanowires, nanoribbons, and quasi-2D nanosheets with thicknesses in the range of 10 to 100 nm from the bottom-up crystallization of [Sb4S6]n chains. We found that dimensionally resolved nanostructures emerge from two distinct chemical vapor growth pathways defined by diverse covalent intra-chain and anisotropic vdW inter-chain interactions and precise precursor ratios. At sub-100 nm nanostructure thicknesses, we observe the hardening of phonon modes, blue-shifting of optical band gaps, and emergence of a new high-energy photoluminescence peak, suggesting a confinement-induced indirect-to-direct optical band gap crossover. The directional growth of weakly bound 1D ribbons or chains into well-resolved nanocrystalline morphologies provides opportunities to develop ordered nanostructures and hierarchical assemblies that are suitable for a wide range of optoelectronic and quantum devices. | Dmitri Cordova; Kenneth Chua; Rebecca Huynh; Toshihiro Aoki; Maxx Arguilla | Materials Science; Nanoscience; Nanostructured Materials - Materials; Optical Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64560a9e1ca6101a45de0782/original/anisotropy-driven-crystallization-of-dimensionally-resolved-quasi-1d-van-der-waals-nanostructures.pdf |
60c744e8ee301c5feec791eb | 10.26434/chemrxiv.9924806.v1 | SAMPL6 Octanol-Water Partition Coefficients from Alchemical Free Energy Calculations with MBIS Atomic Charges | In molecular modeling the description of the interactions between molecules forms the basis for a correct prediction of macroscopic observables. Here, we derive atomic charges from the implicitly polarized electron density of eleven molecules in the SAMPL6 challenge using the Hirshfeld-I and Minimal Basis Set Iterative Stockholder(MBIS) partitioning method. These atomic charges combined with other parameters in the GAFF force field and different water/octanol models were then used in alchemical free energy calculations to obtain hydration and solvation free energies, which after correction for the polarization cost, result in the blind prediction of the partition coefficient. From the tested partitioning methods and water models the S-MBIS atomic charges with the TIP3P water model presented the smallest deviation from the experiment. Conformational dependence of the free energies and the energetic cost associated with the polarization of the electron density are discussed. | Maximiliano Riquelme; Esteban Vöhringer-Martinez | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744e8ee301c5feec791eb/original/sampl6-octanol-water-partition-coefficients-from-alchemical-free-energy-calculations-with-mbis-atomic-charges.pdf |
673ccc975a82cea2fab626c6 | 10.26434/chemrxiv-2024-kwx47 | Collective Coordinates and Facilitated Conformational Opening during Translocation of Human Mitochondrial RNA Polymerase (POLRMT) from Atomic Simulations | Collective coordinate (CV) identification is challenging in complex dynamical systems. To study translocation of a single-subunit RNA polymerase (RNAP) during human mitochondrial transcription, we employed all-atom molecular dynamics (MD) as a vehicle to illustrate CV refinement in conformational samplings and dimension reduction analyses. The RNAP translocation is an essential mechanical step of the transcription elongation that dictates gene expression. The translocation generally follows from polymerization product release and proceeds to initial binding or pre-insertion of incoming nucleotides. The human mitochondrial DNA-dependent RNAP (or POLRMT) plays a critical role in cellular metabolism and can be a key molecular off-target in the design of nucleotide analogue antiviral and antitumor drugs due to its structural similarities with many viral RNAPs or RNA dependent RNA polymerases (RdRps). While POLRMT shares particularly high structural similarity with bacteriophage T7 RNAP, previous experimental studies and our current simulations suggest that POLRMT’s mechano-chemical coupling mechanisms may be distinct. In our current work, we modeled POLRMT elongation complexes and performed equilibrium MD simulations on the pre- and post-translocation models, with extensive samplings around different potential translocation paths (with or without coupling to the fingers subdomain conformational change). We then compared time-lagged independent component analysis (tICA) and the neural network implementation of the variational approach for Markov processes (VAMPnets) as dimensional reduction methods on selected atomic CV sets to best represent the sampled data from the MD simulations. Our results indicate that POLRMT translocation is likely coupled with and facilitated by NTP binding to enable fingers subdomain opening at post-translocation which would otherwise be non-stabilized, or the translocations may proceed in futile without leading to the fingers opening for incoming NTP initial binding or incorporation. The timescale of the NTP binding-coupled or facilitated translocation reaches over hundreds of microseconds as predicted by the VAMPnets analyses. Such a timescale seems to match a last post-catalytic kinetic step suggested for the POLRMT elongation cycle by previous experimental detections. By inclusion of NTP binding/catalytic motifs into the analyses, the predicted time scale slightly increases as if additional protein dynamics related to NTP binding activities are considered. Thus, our MD simulation studies combining CV refinements and dimension reduction analyses on top of extensive conformational samplings suggest a distinct mechano-chemical coupling mechanism of POLRMT translocation as if the Brownian motions are slightly assisted by NTP binding. | Shannon McElhenney; Jin Yu | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673ccc975a82cea2fab626c6/original/collective-coordinates-and-facilitated-conformational-opening-during-translocation-of-human-mitochondrial-rna-polymerase-polrmt-from-atomic-simulations.pdf |
629678fe80f81c9c5197411a | 10.26434/chemrxiv-2022-8rq77-v2 | Solvent-Controlled Switchable Synthesis of gem-Difluoro Compounds from Anhydrides under Photoredox Catalysis | The outstanding impact of fluorine atom in drug discovery cannot be overestimated. Substantially, the incorporation of the gem-difluoro (CF2) group into organic frameworks is highly sought due to the influence of this unit on physicochemical and pharmacological properties of molecules. Yet, introduction of CF2 moiety into organic structures is a step-intensive preparation, and known approaches are often limited to certain classes of molecules. Development of strategies for a rapid incorporation of gem-difluoro synthon that utilizes inexpensive commercial reagents is highly desirable. In the context of divergency and applicability of such reagents, switchable synthesis can be beneficial to access a wide range of fluorinated compounds. Herein we report a mild and operationally simple protocols to access various gem-difluoro compounds that employs chlorodifloroacetic anhydride (CDFAA) as a low cost and versatile fluoroalkylating reagent. Detailed mechanistic investigations revealed that electron-transfer photocatalysis triggers mesolytic cleavage of a C−Cl bond generating a gem-difluoro carboxy radical. In the presence of alkene molecule, this radical species acts as an efficient and unique bifunctional reagent that, under solvent-controlled reaction conditions, delivers a wide range of gem-difluorinated γ-lactams, γ-lactones, as well as promotes oxy-perfluoroalkylation. These protocols are flow and batch scalable, possess excellent chemo- and regioselectivity, and can be used for the late-stage diversification of biorelevant molecules. | Rahul Giri; Ivan Mosiagin; Ivan Franzoni; Nicolas Yannick Nötel; Subrata Patra; Dmitry Katayev | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629678fe80f81c9c5197411a/original/solvent-controlled-switchable-synthesis-of-gem-difluoro-compounds-from-anhydrides-under-photoredox-catalysis.pdf |
60c73d0d4c89198ff8ad1b39 | 10.26434/chemrxiv.5327677.v1 | How toxicity of nanomaterials towards different species could be simultaneously evaluated: Novel multi-nano-read-across approach | Application of predictive modeling approaches is able solve the problem of the missing data. There are a lot of studies that investigate the effects of missing values on qualitative or quantitative modeling, but only few publications have been<br />discussing it in case of applications to nanotechnology related data. Current project aimed at the development of multi-nano-read-across modeling technique that helps in predicting the toxicity of different species: bacteria, algae, protozoa, and mammalian cell lines. In this study, the experimental toxicity for 184 metal- and silica oxides (30 unique chemical types) nanoparticles from 15 experimental datasets was analyzed. A hybrid quantitative multi-nano-read-across approach that combines interspecies correlation analysis and self-organizing map analysis was developed. At the first step, hidden patterns of toxicity among the nanoparticles were identified using a combination of methods. Then the developed model that based on categorization of metal oxide nanoparticles’ toxicity outcomes was evaluated by means of combination of supervised and unsupervised machine learning techniques to find underlying factors responsible for toxicity. | Natalia Sizochenko; Alicja Mikolajczyk; Karolina Jagiello; Tomasz Puzyn; Jerzy Leszczynski; Bakhtiyor Rasulev | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2017-08-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0d4c89198ff8ad1b39/original/how-toxicity-of-nanomaterials-towards-different-species-could-be-simultaneously-evaluated-novel-multi-nano-read-across-approach.pdf |
64a37ef26e1c4c986bc43a78 | 10.26434/chemrxiv-2023-fsh24 | Using ML to repurpose FDA drugs for the treatment of Diabetic Cardiomyopathy | PARP-1 (Poly ADP Ribose polymerase) functions to repair damage to DNA and is implicated in a variety of diseases including Diabetic Cardiomyopathy (DCM). Unfortunately, there are few treatments for this disease, and the expenses associated with these drugs present barriers to many. With this project, we developed a neural network that was able to distinguish between inhibitors and non-inhibitors of PARP-1 in order to uncover more accessible treatments of DCM. We collected confirmed inhibitors of PARP-1 from PubChem, clustered these compounds, and performed attribute selection. This data was used to develop the neural network which was able to predict inhibitors of PARP-1 with an accuracy of 97% and an AUROC of 0.98. The model was then run on all FDA drugs, and the top 37 predictions were taken. In protein ligand docking simulations, the predicted inhibitors had a significantly better binding affinity for PARP-1 than the control group. | Vishnu Aravind; Alex Kumar | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2023-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a37ef26e1c4c986bc43a78/original/using-ml-to-repurpose-fda-drugs-for-the-treatment-of-diabetic-cardiomyopathy.pdf |
61af457e7ada9542fb6c2d42 | 10.26434/chemrxiv-2021-nz14l-v2 | Iodine determination in mineral water using ICP-MS: method development and analysis of brands available in Israeli stores | Reliable iodine determination in drinking water samples has gained importance in the last few decades, mostly due to intensive use of both desalinized water that lacks several important nutritional elements, and bottled mineral water. ICP-MS is a sensitive, high-throughput method for iodine determination that must be performed under alkaline conditions because of the volatile nature of some iodine species. However, in water samples with high pH (>10), slow precipitation of calcium (Ca) and/or magnesium (Mg) carbonates leads to clogging of the ICP-MS nebulizer. We propose preventing this precipitation by adding the chelating agent ethylenediaminetetraacetic acid (EDTA) at 0.1% to a 2% ammonium hydroxide matrix. This concentration of EDTA sufficed for most drinking water samples studied, as long as a 1:1 molar ratio of EDTA to Ca+Mg concentration in the water was maintained. The limit of quantitation of the developed method for iodine was <0.1 µg L-1. The average iodine concentration in various brands of bottled mineral water sold in Israel was relatively low (7.67 ± 6.38 µg I L-1). Regular consumption of either desalinated water or bottled mineral water may induce iodine deficiency in Israeli consumers. Therefore, continuous follow-up of the iodine status in both tap and bottled water is strongly recommended. | Vasiliy Rosen; Orit Gal Garber; Yona Chen | Analytical Chemistry; Environmental Analysis; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61af457e7ada9542fb6c2d42/original/iodine-determination-in-mineral-water-using-icp-ms-method-development-and-analysis-of-brands-available-in-israeli-stores.PDF |
60c73f1e9abda23cf1f8b9e6 | 10.26434/chemrxiv.7125497.v1 | Discovery of Calcium-Metal Alloy Anodes for Reversible Ca-Ion Batteries | Ca-ion batteries (CIBs) show promise to achieve the high energy density required by emerging applications like electric vehicles because of their potentially improved capacities and high operating voltages. The development of CIBs has been hindered by the failure of traditional graphite and calcium metal anodes due to the intercalation difficulty and lacking efficient electrolyte. Recently a high voltage (4.45 V) CIB cell using Sn as the anode was reported achieving a remarkable cyclability (> 300 cycles). The calciation of Sn was observed to end at Ca7Sn6, which is surprising, since higher Ca-content compounds are known (e.g. Ca2Sn). Here, we investigate computationally the Sn electrochemical calciation reaction process and explore the reaction driving force as a function of Ca content using density functional theory (DFT) calculations. This exploration allows us to identify threshold voltages which govern the limits of the calciation process. We then use this information to design a four-step screening strategy and use high-throughput DFT to search for anode materials with higher properties. We predict that many metalloids (Si, Sb, Ge), (post-)transition metals (Al, Pb, Cu, Cd, CdCu2) are promising inexpensive anode candidates and warrant further experimental investigations. | Zhenpeng Yao; Vinay I. Hegde; Alan Aspuru-Guzik; Christopher Wolverton | Theory - Computational; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1e9abda23cf1f8b9e6/original/discovery-of-calcium-metal-alloy-anodes-for-reversible-ca-ion-batteries.pdf |
60c745ecf96a006432286c6a | 10.26434/chemrxiv.10288553.v1 | Molecular Engineering Strategies for Symmetric Aqueous Organic Redox Flow Batteries | <p>Symmetric aqueous organic redox flow batteries (RFBs) are potentially a cheap, durable and safe energy storage technology. Unlike normal asymmetric flow batteries, they are based on electrolytes that exist in at least three oxidation states and can undergo a minimum of two distinct redox processes. We compute the redox potentials of selected electrolytes intending to understand how the interaction between the redox units affects the potentials. We find that electronic interaction between redox units and intramolecular hydrogen bonding can both be exploited to tune the difference between the redox potentials, i.e. the theoretical voltage of the battery. The redox potentials can be further fine-tuned in either direction by adding substituents. Starting from these observations we formulate a set of rules which will help finding ideal candidates for symmetric RFBs.</p> | Rocco Peter Fornari; Murat Mesta; Johan Hjelm; Tejs Vegge; Piotr de Silva | Carbon-based Materials; Computational Chemistry and Modeling; Theory - Computational; Energy Storage; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745ecf96a006432286c6a/original/molecular-engineering-strategies-for-symmetric-aqueous-organic-redox-flow-batteries.pdf |
629a202197e76a75d0c4c570 | 10.26434/chemrxiv-2022-hx4c7 | MetalWalls: Simulating electrochemical interfaces between polarizable electrolytes and metallic electrodes | Electrochemistry is central to many applications, ranging from biology to energy science. Studies now involve a wide range of techniques, both experimental and theoretical. Modelling and simulations methods, such as density functional theory or molecular dynamics, provide key information on the structural and dynamic properties of the systems. Of particular importance are polarization effects the electrode/electrolyte interface, which are difficult to simulate accurately. Here we show how these electrostatic interactions are taken into account in the framework of the Ewald summation method. We discuss, in particular, the formal set up for calculations that enforce periodic boundary conditions in two directions, a geometry that more closely reflects the characteristics of typical electrolyte/electrode systems and presents some differences with respect to the more common case of periodic boundary conditions in three dimensions. These formal developments are implemented and tested in MetalWalls, a molecular dynamics software which captures the polarization of the electrolyte and allows the simulation of electrodes maintained at a constant potential. We also discuss the technical aspects involved in the calculation of two sets of coupled degrees of freedom, namely the induced dipoles and the electrode charges. We validate the implementation, first on simple systems, then on the well-known interface between graphite electrodes and a room-temperature ionic liquid. We finally illustrate the capabilities of MetalWalls by studying the adsorption of a complex functionalized electrolyte on a graphite electrode. | Alessandro Coretti; Camille Bacon; Roxanne Berthin; Alessandra Serva; Laura Scalfi; Iurii Chubak; Kateryna Goloviznina; Matthieu Haefele; Abel Marin-Laflèche; Benjamin Rotenberg; Sara Bonella; Mathieu Salanne | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629a202197e76a75d0c4c570/original/metal-walls-simulating-electrochemical-interfaces-between-polarizable-electrolytes-and-metallic-electrodes.pdf |
60c743f6702a9ba0c818a70f | 10.26434/chemrxiv.9161789.v2 | Ligand Mediated Nanocluster Formation with Classical and Autocatalytic Growth | We describe a kinetic model of ligand-mediated nanocluster (diameter < 2 nm) formation. We investigate two growth pathways: classical single-monomer addition, and autocatalytic growth. We compare our results to some relevant experiments and we discuss and generally describe the optimal conditions for "bottom up" nanocluster synthesis.<br /> | Mohsen Farshad; Dylan Suvlu; Jayendran C. Rasaiah | Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743f6702a9ba0c818a70f/original/ligand-mediated-nanocluster-formation-with-classical-and-autocatalytic-growth.pdf |
67116f11cec5d6c142728bad | 10.26434/chemrxiv-2024-mk3dq | A Deoxyfluoroalkylation-Aromatization Strategy to Access Fluoroalkyl Arenes | Fluoroalkyl arenes (Ar–RF) are valuable substructures present in several FDA-approved drugs, patents, agrochemicals, and materials, and complementary strategies that enable access to a broad spectrum of Ar–RF compounds benefit these applied fields. Herein, we report a deoxyfluoroalkylation-aromatization strategy to convert cyclohexanones into a broad-spectrum Ar–RF containing compounds. Generally, the fluoroalkyl sources were activated to participate in a 1,2-addition reaction followed by aromatization in a sequence that contrasts more common preparations of these Ar–RF compounds, such as i) transition-metal catalyzed cross-coupling reactions of aryl electrophiles and nucleophiles, and ii) radical fluoroalkylation reactions of C–H bonds of arenes. Considering the range of cyclohexanone-derived substrates that could be prepared and used, this strategy can be creatively employed to deliver a broad spectrum of highly substituted fluoroalkyl arenes. | Pankaj Bhattarai; Suvajit Koley; Krttika Goel; Ryan Altman | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67116f11cec5d6c142728bad/original/a-deoxyfluoroalkylation-aromatization-strategy-to-access-fluoroalkyl-arenes.pdf |
674487def9980725cfd313af | 10.26434/chemrxiv-2024-50bfz-v2 | Efficient Crystallization of Apo Sirt2 for Small Molecule Soaking and Structural Analysis of Ligand Interactions | The selectivity pocket is a key binding site for inhibitors of the NAD+-dependent lysine deacylase Sirtuin 2 (Sirt2), a promising drug target due to its involvement in diseases like cancer and neurodegeneration. While small molecule soaking could advance inhibitor development, the selectivity pocket is absent in current Sirt2 apo structures, and existing soaking systems like Sirt2-ADPribose (ADPR) suffer from disadvantageous crystal contacts that hinder ligand binding. We developed a method to rapidly generate high-quality Sirt2 apo crystals with an open selectivity pocket, suitable for high-throughput soaking experiments. The pocket formation is induced by seeding with a Sirtuin Rearranging ligand (SirReal) and is retained in the final apo structure without the presence of the ligand. Screening the Maybridge Ro3 library using fluorescence polarization and thermal shift assays yielded three novel Sirt2-fragment structures. These crystals can accommodate ligands at the acyl-lysine channel entrance and the cofactor binding site, as further confirmed with KT9 and NAD+, facilitating SAR studies and the optimization of inhibitors. | Florian Friedrich; Matthias Schiedel; Sören Swyter; Lin Zhang; Wolfgang Sippl; Mike Schutkowski; Oliver Einsle; Manfred Jung | Biological and Medicinal Chemistry; Biochemistry | CC BY NC 4.0 | CHEMRXIV | 2024-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674487def9980725cfd313af/original/efficient-crystallization-of-apo-sirt2-for-small-molecule-soaking-and-structural-analysis-of-ligand-interactions.pdf |
636d058333f73324ade213f1 | 10.26434/chemrxiv-2022-b8pdw | Oxidation-controlled, Strain-Promoted Tellurophene-Alkyne Cycloaddition (OSTAC): A Bioorthogonal Reaction for Fast and Selective Protein Conjugation | Noncanonical amino acids (ncAAs) bearing functional groups for bioorthogonal labelling are useful tools for the downstream analysis of nascent polypeptides. However, the methionine analogues commonly used are not optimally recognized by the endogenous protein synthesis machinery. TePhe, a tellurophene bearing phenylalanine analogue, is a promising alternative to the methionine analogues as it is readily accepted, and incorporated, during protein synthesis. However, a bioorthogonal reaction to label TePhe was required to enable protein tagging to facilitate analysis. Here we establish that the tellurophene side chain of TePhe is a potent partner in an oxidation-controlled, strain-promoted tellurophene-alkyne cycloaddition (OSTAC) reaction. Mild oxidation of the tellurophene ring with N-chlorosuccinimide produces a Te(IV) species which undergoes rapid (k > 100 M-1s-1) cycloaddition with bicyclo[6.1.0]nonyne (BCN) resulting in a benzo-fused cyclooctane. Selective reaction of TePhe containing proteins can be achieved in complex protein mixtures. OSTAC reactions can be combined with strain-promoted azide alkyne cycloaddition (SPAAC) and copper catalyzed azide alkyne click (CuAAC) reactions. The favorable properties of the OSTAC reaction will likely find wide application beyond its use with TePhe in chemical biology. | Yong Jia Bu; Mark Nitz | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636d058333f73324ade213f1/original/oxidation-controlled-strain-promoted-tellurophene-alkyne-cycloaddition-ostac-a-bioorthogonal-reaction-for-fast-and-selective-protein-conjugation.pdf |
6744fc737be152b1d0d1337d | 10.26434/chemrxiv-2024-4sqd3-v2 | Improvements in glycoproteomics through architecture changes to the Orbitrap Tribrid MS platform | Hardware changes introduced on the Orbitrap Ascend MultiOmics Tribrid MS include dual ion routing multipoles (IRMs) that can enable parallelized accumulation, dissociation, and Orbitrap mass analysis of three separate ion populations. The balance between these instrument functions is especially important in glycoproteomics, where complexities of glycopeptide fragmentation necessitate large precursor ion populations and, consequently, long ion accumulation times for quality MS/MS spectra. To compound matters further, dissociation methods like electron transfer dissociation (ETD) that benefit glycopeptide characterization come with overhead times that also slow down scan acquisition. Here we explored how the dual IRM architecture of the Orbitrap Ascend can improve glycopeptide analysis, with a focus on O-glycopeptide characterization using ETD with supplemental collisional activation (EThcD). We found that parallelization of ion accumulation and EThcD fragmentation – uniquely enabled by the Orbitrap Ascend – increased scan acquisition speed without sacrificing spectral quality, subsequently increasing the number of O-glycopeptides identified relative to analyses on the Orbitrap Eclipse (i.e., the previous generation Tribrid MS). Additionally, we systematically evaluated ion-ion reaction times and supplemental activation energies used for EThcD to understand how best to utilize acquisition time in the dual IRM architecture. We observed that shorter-than-expected ion-ion reaction times minimized scan overhead time without sacrificing c/z•-fragment ion generation, and that higher supplemental collision energies can generate combinations of glycan-retaining and glycan-neutral-loss peptide backbone fragments that benefit O-glycopeptide identification. We also saw improvements in N-glycopeptide analysis using collision-based dissociation, especially with methods using faster scan acquisition speeds. Overall, these data show how architectural changes to the Tribrid MS platform benefit glycoproteomic experiments by parallelizing scan functions to minimize overhead time and improve sensitivity. | Tim S. Veth; Emmajay Sutherland; Kayla A. Markuson; Ruby Zhang; Anna G. Duboff; Jingjing Huang; David Bergen; Amanda E. Lee; Rafael D. Melani; Jesse D. Canterbury; Vlad Zabrouskov; Graeme C. McAlister; Christopher Mullen; Nicholas M. Riley | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6744fc737be152b1d0d1337d/original/improvements-in-glycoproteomics-through-architecture-changes-to-the-orbitrap-tribrid-ms-platform.pdf |
646e4588e64f843f41b49bbc | 10.26434/chemrxiv-2023-m5rzw | Chemoenzymatic Photoreforming: A Sustainable Approach for Solar-fuel Generation from Plastic Feedstocks | Plastic upcycling through catalytic transformations is an attractive concept to valorise waste. However, the clean and energy-efficient production of high-value products from plastics remains challenging. We introduce chemoenzymatic photoreforming, a new process coupling enzymatic pre-treatment and solar-driven reforming of polyester plastics under mild temperature and pH to produce clean H2 and value-added chemicals. Chemoenzymatic photoreforming demonstrates versatility in upcycling polyester films and nanoplastics to produce H2 at high yields reaching ~103‒104 µmol gsub–1 and activities at >500 µmol gcat–1 h–1. Enzyme-treated plastics were also used for the first time for photocatalytic CO2-to-syngas conversion with a phosphonated cobalt bis(terpyridine) catalyst immobilised on TiO2 nanoparticles (TiO2|CotpyP). Finally, techno-economic analyses reveal that the chemoenzymatic photoreforming approach has the potential to drastically reduce green H2 production costs to levels comparable to market prices of H2 produced from fossil fuels while maintaining low CO2-equivalent emissions. | Subhajit Bhattacharjee; Chengzhi Guo; Erwin Lam; Josephin Holstein; Mariana Pereira; Christian Pichler; Chanon Pornrungroj; Motiar Rahaman; Taylor Uekert; Florian Hollfelder; Erwin Reisner | Catalysis; Energy; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2023-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646e4588e64f843f41b49bbc/original/chemoenzymatic-photoreforming-a-sustainable-approach-for-solar-fuel-generation-from-plastic-feedstocks.pdf |
6659978c418a5379b0bd75f1 | 10.26434/chemrxiv-2024-c61xt | Digital Skills in Chemical Education | The role of computing in the chemical sciences is changing. Previously the domain of the theoretical or computational chemist, advanced digital skills, including data analysis and simulation, are becoming extremely relevant to all. Here, we discuss the importance of integrating computing and digital skills into an undergraduate chemistry program and highlight some work currently being carried out to achieve this. | Andrew McCluskey; Miguel Rivera; Antonia Mey | Theoretical and Computational Chemistry; Chemical Education; Chemical Education - General; Theory - Computational; Machine Learning | CC BY 4.0 | CHEMRXIV | 2024-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6659978c418a5379b0bd75f1/original/digital-skills-in-chemical-education.pdf |
615df20df718dffc59d5cfd5 | 10.26434/chemrxiv-2021-v0bv6-v2 | Biocatalytic oxidative cross-coupling reactions for biaryl bond formation | Despite their varied purposes, many indispensable molecules in medicine, materials, and asymmetric catalysis share a biaryl core. The necessity of joining arene building blocks to access these valuable compounds has inspired multiple approaches for biaryl bond formation and challenged chemists to develop increasingly concise and robust methods for this task. Oxidative coupling of two C–H bonds offers an efficient strategy for the formation of a biaryl C–C bond, however, fundamental challenges remain in controlling the reactivity and selectivity for uniting a given pair of substrates. Biocatalytic oxidative cross-coupling reactions have the potential to overcome limitations inherent to small molecule- mediated methods by providing a paradigm with catalyst-controlled selectivity. In this article, we disclose a strategy for biocatalytic cross-coupling through oxidative C–C bond formation using cytochrome P450 enzymes. We demonstrate the ability to catalyze cross-coupling reactions on a panel of phenolic substrates using natural P450 catalysts. Moreover, we engineer a P450 to possess the desired reactivity, site- selectivity, and atroposelectivity by transforming a low-yielding, unselective reaction into a highly efficient and selective process. This streamlined method for constructing sterically hindered biaryl bonds provides a programmable platform for assembling molecules with catalyst-controlled reactivity and selectivity. | Lara Zetzsche; Jessica Yazarians; Suman Chakrabarty; Meagan Hinze; April Lukowski; Leo Joyce; Alison Narayan; Lauren Murray | Catalysis; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615df20df718dffc59d5cfd5/original/biocatalytic-oxidative-cross-coupling-reactions-for-biaryl-bond-formation.pdf |
60c74c83bb8c1a57d83db41f | 10.26434/chemrxiv.12488804.v1 | In Silico Docking Studies of Antimalarial Drug Hydroxychloroquine to SARS-CoV Proteins :An Emerging Pandemic Worldwide | <p>This computational
study comprises screening and prediction of interaction of selected
antimalarial drug hydroxychloroquine with targeted two proteins of coronavirus.
One is SARS enveloped E pantameric ion channel protein and another is SARS-CoV-2
main apoprotein protease. Both are vital for viral attachment and entry to the
host cell for infection. After molecular protein docking with different
confirmations, stable interacting complex of ligand and macromolecules were
obtained. Interacting Lysine, Threonine and Tyrosine of E protein were found
for participation of stable interaction with selected drug having docking
affinity energy of -6.3kcal/mol. For apoprotein protease stable confirmation
was screened out having bonding Threonine residue with same drug of energy -6.0
kcal/mol. Irreversible covalent bond formation and van der Waals interaction
favours the selectivity and stability of both targeted proteins towards selected
drug. Conventional as well as hydrophobic interactions are found in Ligplot and
Discovery studio analysis also indicates stabilized confirmations between
ligand and drug. Thus, this study delivers the putative mechanism of the drug
interactions to target proteins hence comprising landmark for future
investigation for antimalarial hydroxychloroquine as anti COVID 19 drug in this
experimental time.</p> | Priyanka H. Jokhakar; Rishee Kalaria; Hiren K. Patel | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c83bb8c1a57d83db41f/original/in-silico-docking-studies-of-antimalarial-drug-hydroxychloroquine-to-sars-co-v-proteins-an-emerging-pandemic-worldwide.pdf |
613a8326ac3219738976976f | 10.26434/chemrxiv-2021-kj8n3 | The Importance of Decarbonylation Mechanisms in the Atomic Layer Deposition of High-Quality Ru Films by Zero-Oxidation State Ru(DMBD)(CO)3 | Achieving facile nucleation of noble metal films through atomic layer deposition (ALD) is extremely challenging. To this end, η4-2,3-dimethylbutadiene ruthenium tricarbonyl (Ru(DMBD)(CO)3), a zero-valent complex, has recently been reported to achieve good nucleation by ALD at relatively low temperatures and mild reaction conditions. We study the growth mechanism of this precursor by in situ quartz-crystal microbalance and quadrupole mass spectrometry during Ru ALD, complemented by ex situ film characterization and kinetic modeling. These studies reveal that Ru(DMBD)(CO)3 produces high-quality Ru films with excellent nucleation properties. This results in smooth, coalesced films even at low film thicknesses, all important traits for device applications. However, Ru deposition follows a kinetically limited decarbonylation reaction scheme, akin to typical CVD processes, with a strong dependence on both temperature and reaction timescale. The non-self-limiting nature of the kinetically driven mechanism presents both challenges for ALD implementation and opportunities for process tuning. By surveying reports of similar precursors, we suggest that the findings can be generalized to the broader class of zero-oxidation state carbonyl-based precursors used in thermal ALD, with insight into the design of effective saturation studies. | Joel Schneider; Camila de Paula; Jacqueline Lewis; Jacob Woodruff; James Raiford; Stacey Bent | Materials Science; Inorganic Chemistry; Nanoscience; Thin Films; Reaction (Inorg.); Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613a8326ac3219738976976f/original/the-importance-of-decarbonylation-mechanisms-in-the-atomic-layer-deposition-of-high-quality-ru-films-by-zero-oxidation-state-ru-dmbd-co-3.pdf |
616252a235b406642b0ebbf2 | 10.26434/chemrxiv-2021-4b291 | Enhancing Cysteine Chemoproteomic Coverage Through Systematic Assessment of Click Chemistry Product Fragmentation | Mass spectrometry-based chemoproteomics has enabled functional analysis and small molecule screening at thousands of cysteine residues in parallel. Widely adopted chemoproteomic sample preparation workflows rely on the use of pan-cysteine reactive probes such as iodoacetamide alkyne combined with biotinylation via copper-catalyzed azide–alkyne cycloaddition (CuAAC) or ‘click chemistry’ for cysteine capture. Despite considerable advances in both sample preparation and analytical platforms, current techniques only sample a small fraction of all cysteines encoded in the human proteome. Extending the recently introduced labile mode of the MSFragger search engine, here we report an in-depth analysis of cysteine biotinylation via click chemistry (CBCC) reagent gas-phase fragmentation during MS/MS analysis. We find that CBCC conjugates produce both known and novel diagnostic fragments and peptide remainder ions. Among these species, we identified a candidate signature ion for CBCC peptides, the oxonium-biotin fragment ion that is generated upon fragmentation of the N(triazole)–C(alkyl) bond together with cyclization. Guided by our empirical comparison of the fragmentation patterns of five CBCC reagent combinations, we achieved enhanced coverage of cysteine labeled peptides. For larger, fragmentation-prone biotinylation reagents, implementation of labile search afforded unique PSMs and provides a roadmap for the utility of such searches in enhancing chemoproteomic peptide coverage. | Tianyang Yan; Andrew Palmer; Daniel Geiszler; Dan Polansky; Ernest Armenta; Alexey Nesvizhskii; Keriann Backus | Biological and Medicinal Chemistry; Analytical Chemistry; Mass Spectrometry; Bioinformatics and Computational Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616252a235b406642b0ebbf2/original/enhancing-cysteine-chemoproteomic-coverage-through-systematic-assessment-of-click-chemistry-product-fragmentation.pdf |
677f61726dde43c908d148c9 | 10.26434/chemrxiv-2025-2q127 | Novel Approach to Pre-Exposure Prophylaxis (PrEP) of COVID-19: Development of S-892216 Long-acting Injectable Suspension | S-892216 is a small-molecule compound developed by Shionogi & Co., Ltd. as a second-generation 3CLpro inhibitor against severe acute respiratory syndrome coronavirus 2. In this study, we evaluated the feasibility of developing a long-acting injectable suspension formulation of S-892216 towards future development of coronavirus disease 2019 pre-exposure prophylaxis medicine for immunocompromised patients. We found that the S-892216 drug substance had a low solubility suitable for long-acting injectable suspension development. The developed S-892216 injectable suspension showed prolonged plasma exposure in both rats and beagle dogs when formulated as a nanosuspension. Selecting polysorbate 20 as a stabilizer enabled manufacturing the nanosuspension with less wet-milling time than that of poloxamer P338. The developed injectable suspension was stable for 12 months at 5°C and 25°C/60% relative humidity after terminal sterilization by gamma irradiation. Thus, the developed injectable suspension shows potential for further development for human use. | Ryo Ohashi; Ryosuke Watari; Daisuke Kondo; Shuichi Otake; Tatsuhiko Murata; Go Kimura | Chemical Engineering and Industrial Chemistry; Pharmaceutical Industry | CC BY 4.0 | CHEMRXIV | 2025-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677f61726dde43c908d148c9/original/novel-approach-to-pre-exposure-prophylaxis-pr-ep-of-covid-19-development-of-s-892216-long-acting-injectable-suspension.pdf |
60c74b379abda243a4f8d005 | 10.26434/chemrxiv.12100968.v4 | Interaction of drugs candidates with various SARS-CoV-2 receptors: an in silico study to combat COVID-19 | The world is currently facing the COVID-19 pandemic caused by the SARS-CoV-2 virus. The pandemic is causing the death of people around the world and public and social health measures to slow or prevent the spread of COVID-19 are being implemented with the involvement of all members of society. Research institutions are accelerating the discovery of vaccines and therapies for the COVID-19. In this work, molecular docking was used to study (in silico) the interaction of twenty-four ligands, divided into four groups, with four important SARS-CoV-2 receptors. The results showed that Metaquine (group 01), antimalarial substance and the anti-HIV antiretroviral Saquinavir (group 03), presented interaction with all the studied receptors, indicating that they are potentials candidates for muti-target drugs for COVID-19. | Romulo O. Barros; Fabio L. C. C. Junior; Wildrimak S. Pereira; Neiva M. N. Oliveira; Ricardo Ramos | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b379abda243a4f8d005/original/interaction-of-drugs-candidates-with-various-sars-co-v-2-receptors-an-in-silico-study-to-combat-covid-19.pdf |
658d471ce9ebbb4db9e7b18a | 10.26434/chemrxiv-2023-v5g58-v2 | Constructing Dynamical Symmetries | Optical excitation in the dipole approximation and other probes couple two quantum states of an unaddressed finite quantum mechanical discrete system. Thereby the interaction of the system with the probe is bilinear in the coherence between the two states and in the time-dependent strength of the probe. The total Hamiltonian is a sum of such bilinear terms and of terms linear in the populations. The terms in the Hamiltonian form a basis for a Lie algebra that can be represented as a direct product of individual two state systems each using the population and the coherence between two states. Dynamical symmetries can be used to advantage to describe the progress of such systems in time. They also offer a compact and efficient representation for a density matrix of maximal entropy that evolves in time. Using the factorization approach of Wei and Norman, (J. Wei and E. Norman, Lie Algebraic Solution of Linear Differential Equations, J. Math. Phys. 4, 575 (1963)), we construct a unitary quantum mechanical evolution operator that is a factored contribution of individual two state systems. Thereby one can propagate, to all orders in perturbation theory, both the wave function and the density matrix with special reference to dynamical symmetries. | James R. Hamilton; Francoise Remacle; Raphael D. Levine | Theoretical and Computational Chemistry; Theory - Computational; Quantum Computing | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658d471ce9ebbb4db9e7b18a/original/constructing-dynamical-symmetries.pdf |
6299fd9123bf1f5226b38719 | 10.26434/chemrxiv-2022-tbmz3 | Highly dispersed mesoporous Au/SiO2 catalysts obtained by a direct aerosol-assisted sol-gel process | Supported gold nanoparticles play a fundamental role in modern heterogeneous catalysis. However, controlling their fine dispersion remains a challenge, in particular when using silica supports. Here, we report a simple one-pot aerosol route to Au-SiO2 catalysts featuring small gold nanoparticles and calibrated mesoporous texture. To achieve such result, we rely on the strong interactions between gold and the thiol function of a mercapto-silane. We show that the addition of this gold-stabilizer during synthesis enhances the stability of the gold precursor and is the key to control the formation of small gold nanoparticles in the one-pot synthesis. After calcination, the catalyst displays advantageous textural properties (SSA = 440 m².g-1; Vp = 0.5 cm³.g-1; Dp = 5 nm) with small gold nanoparticles (3.7 nm, compared to 13.7 nm without the stabilizer). The dispersion of gold in the material reaches 21 % (compared to 3 % without the stabilizer). The selective oxidation of glycerol to dihydroxyacetone was employed as a test reaction, of importance in the context of sustainable chemistry. We show that the highly dispersed catalyst obtained via gold stabilization outcompetes benchmark catalysts, reaching a glycerol conversion of 59 % after 8 hours (vs. 5 % without stabilization). | Margot Van der Verren; Vit Vykoukal; Ales Styskalik; Carmela Aprile; Damien Debecker | Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Heterogeneous Catalysis; Redox Catalysis; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6299fd9123bf1f5226b38719/original/highly-dispersed-mesoporous-au-si-o2-catalysts-obtained-by-a-direct-aerosol-assisted-sol-gel-process.pdf |
649e0aa39ea64cc16730cfa7 | 10.26434/chemrxiv-2023-kdg9p | Merged molecular switches excel as optoacoustic dyes: azobenzene-cyanines are loud and photostable NIR imaging agents | Optoacoustic imaging, also known as photoacoustic imaging, promises micron-resolution noninvasive imaging in biology at much deeper penetration (>cm) depths than e.g. fluorescence. However, the loud, photostable, NIR-absorbing molecular contrast agents which would be needed for optoacoustic imaging of enzyme activity remain unknown: most organic molecular contrast agents are simply repurposed fluorophores, with severe shortcomings of photoinstability or phototoxicity under optoacoustic imaging conditions, which are consequences of their slow S1→S0 electronic relaxation rates. We now disclose that known fluorophores can be rationally modified to reach ultrafast S1→S0 rates, without much extra molecular complexity, simply by merging them with molecular switches. Here, we merge azobenzene switches to cyanine dyes to give ultrafast relaxation (<10 ps, >100-fold faster). Even without adapting instrument settings, these azohemicyanine optoacoustic imaging agents deliver outstanding improvements in signal longevity (>1000-fold increase of photostability) and signal loudness (here: >3-fold even at time zero). We show why this still-unexplored design strategy can offer even stronger performance in the future, as a simple method that will also increase the spatial resolution and the quantitative linearity of photoacoustic response even over extended longitudinal imaging. By bringing the world of molecular switches and rotors to bear on unsolved problems that have faced optoacoustic agents, this practical strategy may be a crucial step towards unleashing the full potential, in fundamental studies and in translational uses, of optoacoustic imaging. | Markus Müller; Nian Liu; Vipul Gujrati; Abha Valavalkar; Sean Hartmann; Andras Telek; Benjamin Dietzek-Ivanšić; Achim Hartschuh; Vasilis Ntziachristos; Oliver Thorn-Seshold | Physical Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Photochemistry (Org.); Chemical Biology; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2023-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649e0aa39ea64cc16730cfa7/original/merged-molecular-switches-excel-as-optoacoustic-dyes-azobenzene-cyanines-are-loud-and-photostable-nir-imaging-agents.pdf |
60c74a4e4c89195569ad31e4 | 10.26434/chemrxiv.12179202.v1 | Identification of Potent Inhibitors of COVID-19 Main Protease Enzyme by Molecular Docking Study | <p>Within
the span of a few months, the severe acute respiratory syndrome coronavirus,
COVID-19 (SARS-CoV-2), has proven to be a pandemic, affecting the world at an
exponential rate. It is extremely pathogenic and causes communicable infection
in humans. Viral infection causes difficulties in breathing, sore throat,
cough, high fever, muscle pain, diarrhea, dyspnea, and may lead to death.
Finding a proper drug and vaccines against this virus is the need of the hour. The
RNA genome of COVID19 codes for the main protease M<sup>pro</sup>, which is
required for viral multiplication. To identify possible antiviral drug(s), we
performed molecular docking studies. Our screen identified ten biomolecules
naturally present in <i>Aspergillus flavus</i> and <i>Aspergillus oryzae</i>
fungi. These molecules include Aspirochlorine, Aflatoxin B1,
Alpha-Cyclopiazonic acid, Sporogen, Asperfuran, Aspergillomarasmine A,
Maltoryzine, Kojic acid, Aflatrem and Ethyl 3-nitropropionic acid, arranged in
the descending order of their docking score. Aspirochlorine exhibited the
docking score of – 7.18 Kcal/mole, higher than presently used drug Chloroquine (-6.2930522 Kcal/mol) and out of ten ligands
studied four has docking score higher than chloroquine. These natural bioactive
compounds could be tested for their ability to inhibit viral growth <i>in- vitro</i> and <i>in-vivo</i>.<b> </b></p> | Pooja Singh; Angkita Sharma; Shoma Paul Nandi | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a4e4c89195569ad31e4/original/identification-of-potent-inhibitors-of-covid-19-main-protease-enzyme-by-molecular-docking-study.pdf |
614a482a4853d205b9add1d0 | 10.26434/chemrxiv-2021-2b4bj | Binding methylarginines and methyllysines as free amino acids: a comparative study of multiple supramolecular host classes | Methylated free amino acids are an important class of targets for host-guest chemistry that have recognition properties distinct from those of methylated peptides and proteins. We present comparative binding studies for three different host classes that are each studied with multiple methylated arginines and lysines to determine fundamental structure-function relationships. The hosts studied are all anionic and include three calixarenes, two acyclic cucurbiturils, and two cleft-like hosts. We determined the binding association constants for a panel of methylated amino acids using indicator displacement assays. The calixarene hosts show weak binding that favours the higher methylation states, with the strongest binding observed for trimethyllysine. The acyclic cucurbiturils display stronger binding to the methylated amino acids, and some unique patterns of selectivity. The cleft-like hosts follow two different trends, one shallow host following similar trends to the calixarenes, and the other more closed host binding certain less-methylated amino acids stronger than their per-methylated counterparts. Molecular modeling sheds some light on the different preferences of different hosts. The results identify hosts with selectivities that will be useful for certain biomedical applications. The overall selectivity patterns are explained by a common framework that considers the topology, depth of binding pockets, and functional group participation across all host classes. | Zoey Warmerdam; Bianca Kamba; My-Hue Le; Thomas Schrader; Lyle Isaacs; Peter Bayer; Fraser Hof | Biological and Medicinal Chemistry; Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614a482a4853d205b9add1d0/original/binding-methylarginines-and-methyllysines-as-free-amino-acids-a-comparative-study-of-multiple-supramolecular-host-classes.pdf |
643ee80783fa35f8f6dcdfdb | 10.26434/chemrxiv-2023-ltb8q-v2 | Formation of Highly Stable 1,2-Dicarbonyl Organic Radicals from Cyclic (Alkyl)(amino)carbenes | The synthesis of air-persistent organic radicals (APORs) is challenging because of the presence of highly reactive species in air. It was found that N-heterocyclic carbenes (NHCs) are effective in stabilizing radical centers because of their bulky substituents and low-lying empty orbitals, thereby leading to the development of several APORs. Herein, we report the synthesis of two air-stable organic radicals derived from oxalyl chloride and cyclic (alkyl)(amino)carbene (cAAC), which included the unexpected formation of a known (amino)(carboxy) radical cation ([2]BF4) and a 1,2-dicarbonyl radical cation ([3]BF4). Most importantly, the reduced 3-oxetanone compound (4) was discovered as a new product originating from [3]BF4, which differs from the generation of NHC-based 1,2-dicarbonyl radicals. The highly strained 3-oxetanone 4 was obtained by a single-electron reduction of [3]BF4 with a mild reducing agent, chloride salt, and vice versa with a AgBF4 oxidant. Both [2]BF4 and [3]BF4 retained their intrinsic blue color and exhibited high air stability. Furthermore, [3]BF4 produced a temperature-dependent electron paramagnetic resonance spectrum. | Solhye Choe; Hayoung Song; Hyeonjeong Choi; Seunghyuk Yoo; Jaelim Kim; Young Ho Ko; Eunsung Lee | Organic Chemistry; Inorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643ee80783fa35f8f6dcdfdb/original/formation-of-highly-stable-1-2-dicarbonyl-organic-radicals-from-cyclic-alkyl-amino-carbenes.pdf |
60c7536e842e65470cdb3f5d | 10.26434/chemrxiv.13489857.v1 | A Robust, Open-Flask, Moisture-Tolerant, and Scalable Route to Unprotected α/β-Amino Acid N-Carboxyanhydrides | Synthetic polypeptides, commonly prepared by the ring-opening polymerization
(ROP) of amino acid N-carboxyanhydrides (NCA), are a family of biomimetic materials with vast
biomedical applications. A great hurdle in the pro-duction of synthetic polypeptides is the synthesis
of NCA, which requires ultra-dry solvents, Schlenk line/gloveboxes, and the protection of sidechain functional groups. Herein, we report a robust and scalable new method for the production of
unpro-tected NCA monomers in air and under moisture. The method employs propylene oxide or
epichlorohydrin as an inexpensive and ultra-fast scavenger of hydrogen chloride to prevent NCA
from acid-catalyzed decomposition under moist conditions. The broad scope and outstanding
functional group tolerance of the method are demonstrated by the successful synthesis of more than
30 different NCAs, including many otherwise inaccessible compounds with reactive functional
groups (e.g. hy-droxyl, thiol, and carboxylic acid), at high yield and up to ten-gram scale. The scope
of the method can be further extended to various α-hydroxyl acid O-carboxyanhydrides (OCA) and
β-amino acid NCAs (βNCA). Given these merits, our strategy holds great potential for
revolutionizing the synthesis of NCA and polypeptides, and dramatically expanding the industrial
application of synthetic polypeptides | Zi-You Tian; HUA LU | Organic Synthesis and Reactions; Polymerization (Polymers); Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7536e842e65470cdb3f5d/original/a-robust-open-flask-moisture-tolerant-and-scalable-route-to-unprotected-amino-acid-n-carboxyanhydrides.pdf |
666cd74c01103d79c53f1c4d | 10.26434/chemrxiv-2024-k295n | Multifunctional Chiral Silanol Ligands for Enantioselective Catalysis | We report transition metal catalysis using novel chiral metal-chelating ligands featuring a silanol coordinating group and peptide-like aminoamide scaffold. The catalytic properties of the silanol ligands are demonstrated through an enantioselective Cu-catalyzed N−H insertion affording unnatural amino acid derivatives in high selectivity. Our investigations into the silanol coordination mode include DFT calculations, ligand analogs, NMR and X-ray structure analyses, which support the formation of an H-bond stabilized silanol-chelating copper carbenoid complex. A π-π stacking interaction revealed by DFT calculations is proposed to enable selectivity for aryl diazoacetate substrates, overcoming the traditional limitations of using these substrates. | Yun-Pu Chang; Kevin Blanco-Herrero; Turki Alturaifi; James Fettinger; Peng Liu; Annaliese Franz | Organic Chemistry; Catalysis; Organometallic Chemistry; Ligand Design; Ligands (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666cd74c01103d79c53f1c4d/original/multifunctional-chiral-silanol-ligands-for-enantioselective-catalysis.pdf |
60c73d0d9abda20edef8b663 | 10.26434/chemrxiv.5372992.v1 | Electrochemical Cell Equipment for Salinity Gradient Power Generation | Extraction of electricity from the salinity gradient of sea water-river water interface has drawn the key interest of sustainable energy researchers. Different technologies are in the spot light − such as pressure retarded osmosis, reverse electrodialysis, ionic diode membrane, mixing entropy battery, microbial fuel cell, etc. In the present work, electrochemical cell equipment is used for this purpose. Two different techniques are described − galvanic cell equipment (GCEQ) and concentration cell equipment (CCEQ). It is observed that, the extracted energy density is very high (up to 95 W m<sup>−2</sup> ) compared with the other methods of the same kind reported so far. Implementation of these methods is trivial. Thus, we may conclude that present method will fulfill our requirement of sustainable energy resource.<br /><br /> | Arijit Bag | Fuels - Materials; Power | CC BY 4.0 | CHEMRXIV | 2017-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0d9abda20edef8b663/original/electrochemical-cell-equipment-for-salinity-gradient-power-generation.pdf |
6178956c0c0480094846a1b3 | 10.26434/chemrxiv-2021-tfdmc | Active Meta-Learning for Predicting and Selecting Perovskite Crystallization Experiments | Autonomous experimentation systems use algorithms and data from prior experiments to select and perform new experiments in order to meet a specified objective. In most experimental chemistry situations there is a limited set of prior historical data available, and acquiring new data may be expensive and time consuming, which places constraints on machine learning methods. Active learning methods prioritize new experiment selection by using machine learning model uncertainty and predicted outcomes. Meta-learning methods attempt to construct models that can learn quickly with a limited set of data for a new task. In this paper, we applied the model-agnostic meta-learning (MAML) model and Probabilistic LATent model for Incorporating Priors and Uncertainty in few-Shot learning (PLATIPUS) approach, which extends MAML to active learning, to the problem of halide perovskite growth by inverse temperature crystallization. Using a dataset of 1870 reactions conducted using 19 different organoammoniumn lead iodide systems, we determined the optimal strategies for incorporating historical data into active and meta-learning models. We then evaluated the best three algorithms (PLATIPUS, and active-learning k-Nearest Neighbor and Decision Tree algorithms) with four new chemical systems in experimental laboratory tests. With a fixed budget of 20 experiments, PLATIPUS makes superior predictions of reaction outcome compared to other active-learning algorithms and a random baseline. | Venkateswaran Shekar; Gareth Nicholas; Mansoor Ani Najeeb; Margaret Zeile; Vincent Yu; Xiaorong Wang; Dylan Slack; Zhi Li; Philip Nega; Emory Chan; Alexander Norquist; Joshua Schrier; Sorelle Friedler | Materials Science; Hybrid Organic-Inorganic Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6178956c0c0480094846a1b3/original/active-meta-learning-for-predicting-and-selecting-perovskite-crystallization-experiments.pdf |
677cc38081d2151a022a77bf | 10.26434/chemrxiv-2025-z7w2k | Conductance measurements of polar molecules in a non-conducting solvent | Solution-based single-molecule conductance measurements of 𝛼,ω-bis(carboxylic acids) are conveniently performed using high-boiling point, non-conducting ethereal solvents. Tunnel coupling calculations support experimental observations that linear oligoalkanes exhibit the expected exponential decay of conductance with length, whereas junctions comprising cyclic bridge hydrocarbons of different length and/or structure exhibit a similar conductance. | Clark Otey; Mukund Sharma; Jazmine Prana; Thomas Czyszczon-Burton; Alejandro Hernandez; Michael Inkpen | Physical Chemistry; Nanoscience; Nanodevices; Interfaces; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677cc38081d2151a022a77bf/original/conductance-measurements-of-polar-molecules-in-a-non-conducting-solvent.pdf |
62c530729195490387e0ae70 | 10.26434/chemrxiv-2022-59zzw-v2 | Stereoselective Synthesis of 2-Oxyenamides | An improved route for the highly stereoselective synthesis of (Z)-2-oxyenamides is reported. The desired products can be accessed in only three steps from aminoacetaldehyde dimethyl acetal as common, readily available building block in a highly modular fashion. The improved procedure has been applied to the synthesis of various acylated and sufonylated oxyenamides. Mechanistic and theoretical studies provide a conclusive rationale for the observed stereoselectivities. | Sara-Cathrin Krieg; Jennifer Grimmer; Annika Maria Pick; Harald Kelm; Martin Breugst; Georg Manolikakes | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c530729195490387e0ae70/original/stereoselective-synthesis-of-2-oxyenamides.pdf |
677e9e6581d2151a0251cf27 | 10.26434/chemrxiv-2025-7glks | Poly(lactic acid) nanoplastics through laser ablation:
Establishing a reference model for mimicking biobased
nanoplastics in aquatic environments | Due to the well-documented negative environmental impacts of conventional plastics,
the use of bioplastics has been increasing. Poly(lactic acid) (PLA) is currently among the
most common and industrially available bioplastics. Although PLA is compostable under
industrial conditions and generally degrades more quickly than conventional plastics, its
breakdown in typical environmental settings remains problematic. PLA’s potential to
contribute to plastic pollution through the release of microplastics and nanoplastics makes
it crucial to understand how these particles behave, especially in marine environments.
However, as for all nanoplastics, identifying, isolating, and quantifying PLA nanoplastics
in water presents significant challenges. This study proposes a versatile approach to
fabricate PLA nanoplastics through laser ablation in a water environment to mimic realworld
samples. Commencing with bulk PLA films, this top-down method yields the
formation of nanoplastics with an average diameter of 54.7 ± 26.7 nm. Surface and
chemical analyses confirm the presence of carboxylic groups on their surface, potentially
resembling the environmental degradation pathway of PLA under exposure to sunlight
and humid environments. This indicates that the proposed process results in a PLA
nanoplastics system that serves as an invaluable reference model, enabling realistic
environmental scenario explorations and simulations for risk assessment evaluations on
bio-based nanoplastics. | Malavika Manju Sudheer; Arezou Fazli; Stefania Sganga; Nicolla Tirelli; Riccardo Carzino; Marina Veronesi; Kirill Khabarov; Athanassia Athanassiou; Despina Fragouli | Physical Chemistry; Polymer Science; Earth, Space, and Environmental Chemistry; Biopolymers; Environmental Science | CC BY NC 4.0 | CHEMRXIV | 2025-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677e9e6581d2151a0251cf27/original/poly-lactic-acid-nanoplastics-through-laser-ablation-establishing-a-reference-model-for-mimicking-biobased-nanoplastics-in-aquatic-environments.pdf |
643ef74b83fa35f8f6dd4ec5 | 10.26434/chemrxiv-2023-3wmtp | DFT studies of proton transfer of 2, 4-dihydroxybenzoic acid derivatives | In this work, the proton transfer and photophysical properties of 2,4-dihydroxybenzoic acid and its chlorinated and brominated derivatives were studied using Density Functional Theory (DFT) to understand the proton transfer mechanism of these molecules as matrices in matrix-assisted laser desorption-ionization (MALDI). Structures, IR, UV-Vis, and fluorescence spectra were obtained together with the energies of frontier orbitals from DFT and time-dependent DFT calculations. In addition, the proton affinity (PA) and gas phase acidity (GPA) of the molecules were determined to understand the heavy atom substitution effect. Upon substitution of Cl and Br, the UV-Vis absorption at ~330 nm increases with heavy atom substitutions. While no apparent change in the OH bond strength at the ground state, it is substantially weakened upon electronic excitation at both the first singlet and triplet excited states under heavy atom substitution. These results demonstrate that both the UV-Vis absorption and intersystem crossing play important roles in facilitating proton transfer in heavy atom substitution of 2,4-dihydroxybenzoic acid. | Chelsea Bridgmohan; Lichang Wang | Physical Chemistry; Analytical Chemistry; Mass Spectrometry; Physical and Chemical Properties; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643ef74b83fa35f8f6dd4ec5/original/dft-studies-of-proton-transfer-of-2-4-dihydroxybenzoic-acid-derivatives.pdf |
60c745a1ee301cd3eac79375 | 10.26434/chemrxiv.10078943.v1 | Unusual Structures, Phase Behavior, and Fluorescent Properties of 3-phenyl-1-(pyridin-2-yl)-1H-pyrazol-5-amine and Its’ ZnCl2 Complex | The synthesis and single crystal structures of
3-phenyl-1-(pyridin-2-yl)-1<i>H</i>-pyrazol-5-amine (<b>L1</b>) and its complex with ZnCl<sub>2 </sub>are reported. <b>L1</b> exhibits supercooling, with a
difference in melting and solidification points of over 100 <sup>o</sup>C. The complex [<b>L1</b>ZnCl<sub>2</sub>] has a room-to-low temperature single
crystal-to-crystal phase transition in the solid state, while a birefringent
fluid phase mixed with crystalline domains is observed at high temperatures. Significant
fluorescence enhancement is observed upon formation of the ZnCl<sub>2</sub>
complex. | Lana K. Hiscock; Delara Joekar; Zachary W. Schroeder; Victoria Jarvis; Kenneth E. Maly; Louise Dawe | Coordination Chemistry (Inorg.); Ligands (Inorg.); Sensors; Supramolecular Chemistry (Inorg.); Transition Metal Complexes (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745a1ee301cd3eac79375/original/unusual-structures-phase-behavior-and-fluorescent-properties-of-3-phenyl-1-pyridin-2-yl-1h-pyrazol-5-amine-and-its-zn-cl2-complex.pdf |
60c754cd702a9b38d618c5b7 | 10.26434/chemrxiv.13727857.v1 | One-Pot Synthesis and Characterization of Biomimetic Copper(I) Complexes | A modular one-pot synthesis yielding tetracoordinated-N,N,N,N-copper(I)
complexes bearing imine and diimine ligands was developed. Copper aids the condensation of a
pyridine or imidazole carbaldehyde with a biphenyl amine and even stabilizes labile ligands.
Tetradentate and bidentate ligands were formed, the latter forming homoleptic CuL2 complexes.
The identity and purity of the compounds were assessed by NMR, elemental analysis and mass
spectrometry. The interconversion of different species in solution was studied by variable
temperature NMR. The complexes aim to mimic the histidine copper brace of lytic polysaccharide
monooxygenases (LPMOs) and bond lengths obtained from XAS and single crystal XRD for the
complexes were compared to reported photoreduced LPMOs. | Isabelle Gerz; Chiara Negri; David Wragg; Sigurd Øien-Ødegaard; Mats Tilset; Unni Olsbye; Mohamed Amedjkouh | Organic Synthesis and Reactions; Physical Organic Chemistry; Heterogeneous Catalysis; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754cd702a9b38d618c5b7/original/one-pot-synthesis-and-characterization-of-biomimetic-copper-i-complexes.pdf |
60c751fabb8c1a16423dbddc | 10.26434/chemrxiv.13237307.v1 | Photoelectron Spectra of Gd2O2− and Non-Monotonic Photon-Energy Dependent Variations in Populations of Close-Lying Neutral States | <p>Photoelectron spectra of Gd<sub>2</sub>O<sub>2</sub><sup>−</sup> obtained with photon energies from 2.033 eV to 3.495 eV exhibit numerous close-lying neutral states with photon-energy-dependent relative intensities. Transitions to states falling within the electron binding energy window of 0.9 and 1.6 eV are attributed to one- or two-electron transitions to the ground and low-lying excited neutral states. An additional, manifold of electronic states observed in the 2.1 to 2.8 eV window cannot be assigned to any simple one-electron transitions. Because of the relatively simple electronic structure from the half-filled 4<i>f<sup>7</sup> </i>subshell occupancy in Gd<sub>2</sub>O<sub>2</sub><sup>–</sup>, the numerous transitions observed in the spectra are fairly well-resolved, allowing a detailed view of the changes in relative intensities of individual transitions with photon energy. With supporting calculations on the numerous close-lying electronic states, we suggest a description of strong photoelectron-valence electron interactions that result in the photon-energy dependent shake-up transitions and switching between ferro- and antiferromagnetic coupling. </p> | Jarrett
L. Mason; Hassan Harb; Ali Abou Taka; Abbey McMahon; Caleb D. Huizenga; Hector H. Corzo; Hrant Hratchian; Caroline Chick Jarrold | Computational Chemistry and Modeling; Clusters; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751fabb8c1a16423dbddc/original/photoelectron-spectra-of-gd2o2-and-non-monotonic-photon-energy-dependent-variations-in-populations-of-close-lying-neutral-states.pdf |
667597945101a2ffa826a43c | 10.26434/chemrxiv-2024-z9g39-v3 | Assessing the accuracy and efficiency of free energy differences obtained from reweighted flow-based probabilistic generative models | Computing free energy differences between metastable states characterized by non-overlapping Boltzmann distributions is often a computationally intensive endeavour, usually requiring chains of intermediate states to connect them. Targeted free energy perturbation (TFEP) can significantly lower the computational cost of FEP calculations by choosing a set of invertible maps used to directly connect the distributions of interest, achieving the necessary statistically significant overlaps without sampling any intermediate states. Probabilistic generative models (PGMs) based on normalising- flow architectures can make it much easier via machine learning to train invertible maps needed for TFEP. However, the accuracy and applicability of approaches based on empirically learned maps depend crucially on the choice of reweighting method adopted to estimate the free energy differences. In this work, we assess the accuracy, rate of convergence, and data efficiency of different free energy estimators, including exponential averaging, BAR, and MBAR, in reweighting PGMs trained by maximum likelihood on limited amounts of molecular dynamics data sampled only from end-states of interest. We carry out the comparisons on a set of simple but representative case studies, including conformational ensembles of alanine dipeptide and ibuprofen. Our results indicate that BAR and MBAR are both data efficient and robust, even in the presence of significant model overfitting in the generation of invertible maps. This analysis can serve as a stepping stone for the deployment of efficient and quantitatively accurate ML-based free energy calculation methods in complex systems. | Edgar Olehnovics; Yifei Michelle Liu; Nada Mehio; Ahmad Y Sheikh; Michael Shirts; Matteo Salvalaglio | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2024-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667597945101a2ffa826a43c/original/assessing-the-accuracy-and-efficiency-of-free-energy-differences-obtained-from-reweighted-flow-based-probabilistic-generative-models.pdf |
65cccfc1e9ebbb4db9596442 | 10.26434/chemrxiv-2024-5pwx9 | Unveiling the nature of lignin’s interaction with molecules: a mechanistic understanding of adsorption of complex organic molecules | The valorization of lignin into advanced materials for water and soil remediation is experiencing a surge in demand. However, it is imperative that material research and manufacturing are sustainable to prevent exacerbating environmental issues. Meeting these requirements necessitates a deeper understanding of the role of lignin’s functional groups in attracting targeted species. This research delves into the interaction mechanisms between lignin and organic molecules, using the adsorption of the cationic dye Methylene Blue (MB+) as a case study. Herein, we aim to quantitatively estimate the contribution of different interaction types in the overall adsorption process. While carbonyl groups were found to have no significant role in attraction, carboxylic groups (–COOH) exhibited significantly lower adsorption compared to hydroxyl groups (–OH). Through alternately blocking aliphatic and phenolic –OH groups, we determined that 61% of the adsorption occurred through H-bonding and 38% via electrostatic interactions. Performance studies of modified lignin, along with spectroscopic methods (XPS, FTIR) confirmed the negligible role of π-π interactions in adsorption. This study offers fundamental insights into the mechanistic aspects of MB adsorption on lignin, laying the groundwork for potential modifications to enhance the performance of lignin-based adsorbents. The findings underscore the importance of hydroxyl groups and provide a roadmap for future studies examining the influence of steric factors and interactions with other organic molecules. | Oleg Tkachenko; Daryna Diment; Davide Rigo; Maria Strømme; Tetyana Budnyak | Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cccfc1e9ebbb4db9596442/original/unveiling-the-nature-of-lignin-s-interaction-with-molecules-a-mechanistic-understanding-of-adsorption-of-complex-organic-molecules.pdf |
66445b59418a5379b055d5cf | 10.26434/chemrxiv-2024-2qw5x | Solving the vibrational Schrödinger equation with artificial neural networks | Artificial neural networks (NN) are universal function approximators and have shown great ability in computing the ground state energy of the electronic Schrödinger equation, yet NN has not established itself as a practical and accurate approach to solve the vibrational Schrödinger equation for realistic polyatomic molecules to obtain vibrational energies and wave functions for the excited states. Here we purpose an efficient approach to use NN to solve the vibrational Schrödinger equation and demonstrate the new method on CH4, a five atom molecule with 9 degree of freedom. By using a NN with < 3,000 parameters, we are able to achieve vibration energies for the ground and excited states with an accuracy of less than 1 cm-1 as compared to the reference values obtained by using more than 109 basis functions. It is anticipated the new method is capable of providing highly accurate vibrational energies and wave functions for molecules with more than 10 atoms, beyond the limit for all the existing computational approaches. | Shuaishuai Zhao; Dong H. Zhang | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Quantum Computing | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66445b59418a5379b055d5cf/original/solving-the-vibrational-schrodinger-equation-with-artificial-neural-networks.pdf |
6378224153ab804ba92af800 | 10.26434/chemrxiv-2022-49xgz | Role of Vibronic Couplings and Energy Gap in the Internal Conversion Process of a Molecule | In this study, an analytical expression for the rate constant of the internal conversion (IC) in a molecule was derived based on the crude adiabatic representation.
All vibrational modes were considered to be on equal footing in the rate constant expression.
Based on this expression, we investigated the role of vibronic couplings and electronic energy gap in IC processes, using 9-fluorenone as an illustrative example.
Vibrational modes with strong off-diagonal vibronic coupling constants (VCCs) give rise to non-radiative transitions.
Contrastingly, vibrational modes with strong diagonal VCCs constitute the final vibronic states that accept the excess energy between the initial and final electronic states.
Therefore, vibrational modes are classified into promoting and accepting modes based on their roles.
We identified important promoting modes responsible for the one-phonon emission/absorption and accepting modes that contribute greatly to the final state.
A Franck-Condon (FC) envelope describes the final density of vibronic states and explains the dependence of the rate constant on the energy gap.
VCC can be visualized as a spatial distribution of its density form, i.e., vibronic coupling density (VCD), obtained from the electronic wave functions and vibrational modes.
Using the concept of VCD, the IC process can be understood and controlled in terms of the electronic states and vibrational modes.
This approach provides new chemical insights into IC processes.
It has the advantage that the VCD concept facilitates the design of functional molecules with IC processes controlled. | Wataru Ota; Motoyuki Uejima; Tohru Sato | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6378224153ab804ba92af800/original/role-of-vibronic-couplings-and-energy-gap-in-the-internal-conversion-process-of-a-molecule.pdf |
67bf2101fa469535b908b62b | 10.26434/chemrxiv-2025-pqdvc | Tetracarboxylic aromatic acid-based self-healing metallosupramolecular flexible nano-scaffold: Exploring rheological features, stimuli-responsiveness and anti-bacterial efficiency | Tetracarboxylic acid-directed formation strategy of Zn(II)-metallogel has been achieved through supramolecular interactions among gel-forming Zn(II) acetate dihydrate, pyromellitic acid and N,N′-dimethyl formamide (DMF). Role of pyromellitic acid as low molecular weight gelator in forming stable Zn(II)-metallogel has been established through the work. Mechanical stability of Zn(II)-metallogel has been characterized through several rheological analyses including frequency sweep, strain sweep, time sweep (i.e., thixotropic analysis), and Creep recovery tests. The morphological feature of the xerogel sample of Zn(II)-metallogel gets scrutinized through field emission scanning electron microscopy (FESEM) investigation. The elemental analyses associated to FESEM system has also been performed for getting the role of different metallogel-forming chemical ingredients. The stimuli-responsiveness of the prepared metallogel has been deciphered by applying several influences like mechanical shaking, sonication, heating effect, chemical factors like acid, base, UV-light exposure. The metallogel construction pathway has been explored through the employment of FT-IR and ESI-Mass spectral analyses. The biological effectiveness of the metallogel is also explored. Different kinds of bacteria including Gram +/- ve species such as Bacillus cereus (ATCC 13061), Listeria monocytogenes (MTCC 657), and Staphylococcus aureus (MTCC 96), Salmonella typhimurium (MTCC 98) and Escherichia coli (MTCC 1667) are subjected for exploring the bioactivity of synthesized Zn(II)-metallogel. | Biswajit Dey; Subhajoy Sadhu; DEBLINA SAHA; Sai Jyoti Behera; Anupam Kundu; Ritu Ranjan Kumar; Suresh Kumar Yatirajula; Jnanendra Rath | Materials Science; Biocompatible Materials; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials | CC BY 4.0 | CHEMRXIV | 2025-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bf2101fa469535b908b62b/original/tetracarboxylic-aromatic-acid-based-self-healing-metallosupramolecular-flexible-nano-scaffold-exploring-rheological-features-stimuli-responsiveness-and-anti-bacterial-efficiency.pdf |
615c4cbeaa918d2b28209aa4 | 10.26434/chemrxiv-2021-mhj20-v2 | Targeted Fluorogenic Cyanine Carbamates Enable In Vivo Analysis of Antibody-Drug Conjugate Linker Chemistry | Antibody-drug conjugates (ADCs) are a rapidly emerging therapeutic platform. The chemical linker between the antibody and the drug payload plays an essential role in the efficacy and tolerability of these agents. New methods that quantitively assess cleavage efficiency in complex tissue settings could provide valuable insights into the ADC design process. Here we report the development of a near-infrared (NIR) optical imaging approach that measures the site and extent of linker cleavage in mouse models. This approach is enabled by a superior variant of our recently devised cyanine carbamate (CyBam) platform. We identify a novel tertiary amine-containing norcyanine, the product of CyBam cleavage, that exhibits dramatically in-creased cellular signal due to improved cellular permeability and lysosomal accumulation. The resulting cyanine lysosome-targeting carbamates (CyLBams) are ~50X brighter in cells, and we find this strategy is essential for high-contrast in vivo targeted imaging. Finally, we compare a panel of several common ADC linkers across two antibodies and tumor models. These studies indicate that cathepsin-cleavable linkers provide dramatically higher tumor activation relative to hindered or non-hindered disulfides – an observation that is only apparent with in vivo imaging. This strategy enables quantitative comparisons of cleavable linker chemistries in complex tissue settings with implications across the drug delivery landscape. | Syed Usama; Sierra Marker; Donald Caldwell; Nimit Patel; Yang Feng; Joseph Kalen; Brad St Croix; Martin Schnermann | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2021-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615c4cbeaa918d2b28209aa4/original/targeted-fluorogenic-cyanine-carbamates-enable-in-vivo-analysis-of-antibody-drug-conjugate-linker-chemistry.pdf |
60c74d4b4c89198557ad37c1 | 10.26434/chemrxiv.12611438.v1 | Cherrypicking Resolvents: A General Strategy for Convergent Coupled-Cluster Damped Response Calculations of Core-Level Spectra | Damped response theory calculations within the higher-level coupled cluster methods such as EOM-CCSD are typically divergent in the X-ray regime due to the coupling of response states with the valence ionization continuum. We provide a novel strategy for convergent response calculations in the X-ray regime within the damped response EOM-CCSD framework that include contributions from both the core and valence states to the response. | Kaushik Nanda; Anna Krylov | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d4b4c89198557ad37c1/original/cherrypicking-resolvents-a-general-strategy-for-convergent-coupled-cluster-damped-response-calculations-of-core-level-spectra.pdf |
63a080fba53ea609ab5092be | 10.26434/chemrxiv-2022-txfgj | High-entropy oxides in the mullite-type structure | High-entropy materials (HEM) represent a new class of solid solutions containing at least five different elements. Their compositional diversity makes them promising as platforms for development of functional materials. We synthesized HEMs in a complex mullite-type structure challenging previous assumptions that HEMs only form in simple structures. We present five new HEMs i.e., Bi2(Al0.25Ga0.25Fe0.25Mn0.25)4O9, and A2Mn4O10 with variations of A = Nd, Sm, Y, Er, Eu, Ce, Bi demonstrating the vast accessible composition space. By combining scattering, microscopic, and spectroscopic techniques, we show that our materials are mixed solid solutions. Remarkably, when following their crystallization in situ using X-ray diffraction and X-ray absorption spectroscopy we find that the HEMs form through a metastable amorphous phase without the formation of any crystalline intermediates. We believe that our synthetic route is excellently suited to synthesize diverse HEMs and therefore will have a significant impact on their future exploration. | Andrea Kirsch; Espen D. Bøjesen; Niels Lefeld; Rasmus Larsen; Jette K. Mathiesen; Susanne L. Skjærvø; Rebecca K. Pittkowski; Denis Sheptyakov; Kirsten M. Ø. Jensen | Inorganic Chemistry; Lanthanides and Actinides; Solid State Chemistry; Spectroscopy (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a080fba53ea609ab5092be/original/high-entropy-oxides-in-the-mullite-type-structure.pdf |
60c753d9bdbb8964f5a3a525 | 10.26434/chemrxiv.13564748.v1 | Unveiling Potent Photooxidation Behavior of Catalytic Photoreductants | We describe a photocatalytic system that reveals latent photooxidant behavior from one of the most reducing conventional photoredox catalysts, <i>N</i>-phenylphenothiazine<i> </i>(<b>PTH</b>). This aerobic photochemical reaction engages difficult to oxidize feedstocks, such as benzene, in C(sp<sup>2</sup>)–N coupling reactions through direct oxidation. Mechanistic studies are consistent with activation of <b>PTH</b> via photooxidation and that Lewis acid co-catalysts scavenge inhibitors formed upon catalyst activation. | Karina Targos; Oliver P. Williams; Zachary Wickens | Organic Synthesis and Reactions; Homogeneous Catalysis; Organocatalysis; Photocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753d9bdbb8964f5a3a525/original/unveiling-potent-photooxidation-behavior-of-catalytic-photoreductants.pdf |
65dfca5d66c1381729cd9f31 | 10.26434/chemrxiv-2024-1342w | Unlocking the Secrets of Porous Silicon Formation: Insights into Magnesiothermic Reduction Mechanism using In-situ Powder X-ray Diffraction Studies | The magnesiothermic reduction of SiO2 is an important reaction as it is a bulk method that produces porous Si for a wide range of applications directly from SiO2. While its main advantage is potential tunability, the reaction behavior and final product properties are heavily dependent on many parameters including feedstock type. However, a complete understanding of the reaction pathway has not yet been achieved. Here, using in-situ X-ray diffraction analysis, we map for the first time, various pathways through which the magnesiothermic reduction reaction proceeds. Further, we identified the key parameters and conditions that determine which pathways are favored. We discovered that the reaction onset temperatures can be as low as 348 ± 7°C, which is significantly lower than previously reported values. The onset temperature is dependent on the size of Mg particles. Further, Mg2Si was identified as a key intermediate rather than a reaction byproduct during the reduction process. Its rate of consumption is determined by the reaction temperature which needs to be >535°C. These findings can enable process and product optimization of the magnesiothermic reduction process to manufacture and tune porous Si for a range of applications. | Sarah Martell; Maximilian Yan; Robert Coridan; Kevin Stone; Siddharth Patwardhan; Mita Dasog | Materials Science; Inorganic Chemistry; Materials Processing; Nanostructured Materials - Materials; Solid State Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65dfca5d66c1381729cd9f31/original/unlocking-the-secrets-of-porous-silicon-formation-insights-into-magnesiothermic-reduction-mechanism-using-in-situ-powder-x-ray-diffraction-studies.pdf |
63f8098a897b18336f06fbdf | 10.26434/chemrxiv-2023-nq2p3 | The Superformula and model quantum systems as tools for learning | Our understanding of quantum phenomena often begins with simple particle-in-a-box style problems, the solutions of which introduce the student to foundational quantum concepts such as degeneracy and quantization. Simple model geometries of confinement afford analytic solutions, which are readily derivable, easily manipulable, and provide a unique sandbox of exploration accessible at the undergraduate level. In the current work, these model problems are explored in a variety of ways. Firstly, through a historical lens - orienting them to the birth and development of quantum physics. Then, via an organizing syntax. This framework allows the interested student to orient the diverse multidisciplinary literature that has evolved around these problems. Finally, through consideration of the shape element of the syntax, the superformula a simple extension of the equation describing a circle is introduced and discussed. | David Thompson; Johan Gielis | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Education; Chemical Education - General; Computational Chemistry and Modeling; Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2023-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f8098a897b18336f06fbdf/original/the-superformula-and-model-quantum-systems-as-tools-for-learning.pdf |
63bbe1b32840d87b79aa1623 | 10.26434/chemrxiv-2023-3dfw6 | Reaching the Fundamental Limitation in CO2 Reduction to CO with Single Atom Catalysts | The electrochemical CO2 reduction reaction (CO2RR) to value-added chemicals with renewable electricity is a promising method to decarbonise parts of the chemical industry. Recently, single metal atoms in nitrogen-doped carbon (MNC) have emerged as potential electrocatalysts for CO2RR to CO with high activity and faradaic efficiency, although the reaction limitation for CO2RR to CO is unclear. To understand the comparison of intrinsic activity of different MNCs, we synthesized two catalysts through a decoupled two-step synthesis approach of high temperature pyrolysis and low temperature metalation (Fe or Ni). The highly meso-porous structure resulted in the highest reported electrochemical active site utilisation based on in situ nitrite stripping; up to 59±6% for NiNC. Ex-situ X-ray absorption spectroscopy confirmed the penta-coordinated nature of the active sites. The catalysts are amongst the most active in the literature for CO2 reduction to CO. Our density functional theory calculations (DFT) show that their binding to the reaction intermediates approximates to that of Au surfaces. However, we find that the TOFs of the most active catalysts for CO evolution converge, suggesting a fundamental ceiling to the catalytic rates. | Saurav Chandra Sarma; Jesus Barrio; Alexander Bagger; Angus Pedersen; Mengjun Gong; Hui Luo; Mengnan Wang; Silvia Favero; Chang-Xin Zhao; Qiang Zhang; Anthony Kucernak; Maria-Magdalena Titirici; Ifan Stephens | Catalysis; Energy; Electrocatalysis; Nanocatalysis - Reactions & Mechanisms; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bbe1b32840d87b79aa1623/original/reaching-the-fundamental-limitation-in-co2-reduction-to-co-with-single-atom-catalysts.pdf |
60fe89b97bf0c9ccad60d1e4 | 10.26434/chemrxiv-2021-qvr57-v3 | Fast and Automated Identification of Reactions with Low Barriers: The Decomposition of 3-Hydroperoxypropanal | We show how fast semiempirical QM methods can be used to significantly decrease the CPU requirements for automated reaction mechanism discovery, using two different method for generating reaction products: graph-based systematic enumeration of all possible products and the meta-dynamics approach by Grimme (J. Chem. Theory. Comput. 2019, 15, 2847). We test the two approaches on the low-barrier reactions of 3-hydroperoxypropanal, which have been studied by a large variety of reaction discovery approaches and therefore provides a good benchmark. By using PM3 and GFN2-xTB for reaction energy and barrier screening the systematic approach identifies 64 reactions (out of 27,577 possible reactions) for DFT refinement, which in turn identifies the three reactions with lowest barriers plus a previously undiscovered reaction. With optimised hyperparameters meta-dynamics followed by PM3/GFN2-xTB-based screening identifies 15 reactions for DFT refinement, which in turn identifies the three reactions with lowest barrier. The number of DFT refinements can be further reduced to as little as six for both approaches by first verifying the transition states with GFN1-xTB. The main conclusion is that the semiempirical methods are accurate and fast enough to automatically identify promising candidates for DFT refinement for the low barrier reactions of 3-hydroperoxypropanal in about 15-30 minutes using relatively modest computational resources. | Maria Harris Rasmussen; Mads Madsen; Jan H. Jensen | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2021-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60fe89b97bf0c9ccad60d1e4/original/fast-and-automated-identification-of-reactions-with-low-barriers-the-decomposition-of-3-hydroperoxypropanal.pdf |
667ba36a01103d79c524bb0a | 10.26434/chemrxiv-2024-k5bf2 | Exploring Novel Quantum Embedding Methods with a Non-orthogonal Decomposition of Slater Determinants | The Schmidt decomposition of quantum many-body states, which is the basis of many powerful quantum many-body techniques, relies on a partition of the whole system in terms of orthogonal local basis functions. By carefully investigating the spectrum of the truncated density matrices in a non-orthogonal basis, we propose in this work a non-orthogonal decomposition of Slater determinants, which reduces to the conventional Schmidt decomposition in the orthogonal limit. The new decomposition provides a natural tool for building local correlation spaces when the orbitals are overlapping, and we are able to extend some existing embedding methods based on the Schmidt decomposition like density matrix embedding theory (DMET) to overlapping subsystem partitions to achieve greater flexibility and efficiency. We also propose a new quantum embedding strategy as another utility of the non-orthogonal decomposition that bridges the \textit{ab initio} model potential (AIMP) theory and DMET, which does not require a mean-field calculation of the whole system like AIMP, and is able to capture quantum entanglement like DMET. | Yuhang Ai; Hong Jiang | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667ba36a01103d79c524bb0a/original/exploring-novel-quantum-embedding-methods-with-a-non-orthogonal-decomposition-of-slater-determinants.pdf |
64cf698469bfb8925a770708 | 10.26434/chemrxiv-2023-nxmmn | Defining the molecular architecture, metal dependence, and distribution of metal-dependent class II sulfofructose-1-phosphate aldolases | Sulfoquinovose (SQ or 6-deoxy-6-sulfoglucose) is a sulfosugar that is the anionic head group of plant and cyanobacterial sulfolipids: sulfoquinovosyl diacylglycerols. SQ is produced within photosynthetic tissues, forms a major terrestrial reservoir of biosulfur, and is an important species within the biogeochemical sulfur cycle. A major pathway for the breakdown of SQ is the sulfoglycolytic Embden-Meyerhof-Parnas (sulfo-EMP) pathway, which involves cleavage of the 6-carbon chain of the intermediate sulfofructose-1-phosphate (SFP) into dihydroxyacetone and sulfolactaldehyde, catalyzed by class I or II SFP aldolases. While the molecular basis of catalysis is well studied for class I SFP aldolases, comparatively little is known about class II SFP aldolases. Here, we report the molecular architecture and biochemical basis of catalysis of two metal-dependent class II SFP aldolases from Hafnia paralvei and Yersinia aldovae. 3D X-ray structures in complex with the substrate SFP and product DHAP reveal a dimer-of-dimers (tetrameric) assembly, and identify the sulfonate binding pocket that defines the substrate specificity of these enzymes, two metal binding sites, and flexible loops that are implicated in catalysis. Both enzymes were metal dependent and exhibited high KM values for SFP, consistent with their role in a unidirectional nutrient acquisition pathway. Bioinformatic analysis identified a range of sulfo-EMP gene clusters containing class I/II SFP aldolases. The class I and II SFP aldolases occur exclusively within Actinobacteria and Firmicutes phyla, respectively, while both classes of enzyme occur within Proteobacteria. This work emphasizes the importance of SQ as a nutrient for diverse bacterial phyla and the different chemical strategies they use to harvest carbon from this sulfosugar. | Mahima Sharma; Arashdeep Kaur; Niccolay Madiedo Soler; James Lingford; Ruwan Epa; Ethan Goddard-Borger; Gideon Davies; Spencer Williams | Biological and Medicinal Chemistry; Catalysis; Earth, Space, and Environmental Chemistry; Biochemistry; Chemical Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64cf698469bfb8925a770708/original/defining-the-molecular-architecture-metal-dependence-and-distribution-of-metal-dependent-class-ii-sulfofructose-1-phosphate-aldolases.pdf |
60c742ba842e652311db2113 | 10.26434/chemrxiv.8636414.v1 | Parallel Synthesis and Screening of Supramolecular Chemosensors that Achieve Fluorescent Turn-On Detection of Drugs in Saliva | <div><div><div><p>We report here a parallel synthesis-driven approach to create a family of self-assembling dimeric sensors that we call DimerDyes, and its use for the rapid identification of salt-tolerant sensors for illicit drugs. We developed an efficient method that involves parallel synthesis and screening in crude form without the need to purify each potential sensor. Structurally diverse “hit” DimerDyes were re-synthesized, purified and were each shown to assemble into homodimers in water in the programmed way. DimerDyes provided a “turn-on” fluorescence detection of multiple illicit drugs at low micromolar concentrations in water and in saliva. The combination of multiple agents into a sensor array was successfully able to detect and discriminate between closely related drugs and metabolites in multiple important drug families. This report includes extensive NMR data on synthetic characterization, and on binding and assembly processes. It also includes UV-Vis and fluorescence spectroscopy data, and their use for quantitation and identification of drug-related analytes using multivariate statistical analysis. </p></div></div></div> | Meagan Beatty; Allison Selinger; YuQi Li; Fraser Hof | Bioorganic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Supramolecular Chemistry (Org.); Analytical Chemistry - General; Biochemical Analysis; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742ba842e652311db2113/original/parallel-synthesis-and-screening-of-supramolecular-chemosensors-that-achieve-fluorescent-turn-on-detection-of-drugs-in-saliva.pdf |
60c74751bdbb89bf3aa38db4 | 10.26434/chemrxiv.11627451.v1 | A Lattice Dynamical Approach for Finding the Lithium Superionic Conductor Li3ErI6 | <p>Driven by the increasing attention that the superionic conductors Li<sub>3</sub>MX<sub>6</sub> (M = Y, Er, In, La; X = Cl, Br, I) have gained recently for the use of solid-state batteries, and the idea that a softer, more polarizable anion sublattice is beneficial for ionic transport, here we report Li<sub>3</sub>ErI<sub>6</sub>, the first experimentally-obtained iodine-based compound within this material system of ionic conductors. Using a combination of synchrotron and neutron diffraction, we elucidate the structure, the lithium positions and possible diffusion pathways of Li<sub>3</sub>ErI<sub>6</sub>. Temperature-dependent impedance spectroscopy shows low activation energies of 0.37 and 0.38 eV alongside promising ionic conductivities of 0.65 mS·cm<sup>-1</sup> and 0.39 mS·cm<sup>-1</sup>directly after ball milling and the subsequently annealed Li<sub>3</sub>ErI<sub>6</sub>, respectively. Speed of sound measurements are used to determine the Debye frequency of the lattice as a descriptor of the lattice dynamics and overall lattice softness, and Li<sub>3</sub>ErI<sub>6</sub> is compared to the known material Li<sub>3</sub>ErCl<sub>6</sub>. The softer, more polarizable framework from the iodide anion leads to improved ionic transport, showing that the idea of softer lattices holds up in this class of materials. This work provides Li<sub>3</sub>ErI<sub>6</sub> as an interesting novel framework for optimization in the class of halide-based ionic conductors.</p> | Roman Schlem; Tim Bernges; Cheng Li; Marvin Kraft; Nicolo Minafra; Wolfgang Zeier | Fuels - Materials; Solid State Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74751bdbb89bf3aa38db4/original/a-lattice-dynamical-approach-for-finding-the-lithium-superionic-conductor-li3er-i6.pdf |
66db946ecec5d6c1425cd490 | 10.26434/chemrxiv-2024-p24xf | Fast event-based electron counting for small molecule structure determination by MicroED | Electron counting helped realize the resolution revolution in single particle cryoEM and is now accelerating the determination of MicroED/3DED structures. Its advantages are best demonstrated by new direct electron detectors capable of fast (kilohertz) event-based electron counting (EBEC). This strategy minimizes the inaccuracies introduced by coincidence loss (CL) and promises fast, accurate structures. We use the Direct Electron Apollo camera to leverage EBEC technology for MicroED data collection. Given its ability to count single electrons, the Apollo collects high quality MicroED data from organic small molecule crystals illuminated with incident electron beam flux values as low as 0.01–0.045 e-/Å2/s. Under even the lowest flux (0.01 e-/Å2/s) condition, fast EBEC data produced ab initio structures of a salen ligand (268 Da) and biotin (244 Da). Each structure was determined from 100–degree wedge of data collected from a single crystal in as few as 50 seconds, with a delivered fluence of only ~0.5 e-/Å2. Fast EBEC data collected with a fluence of 2.25 or 3.33 e-/Å2 also facilitated a 1.5Å structure of thiostrepton (1,665 Da). While refinement of those structures appeared unaffected by CL, a CL-adjustment applied to gain-normalized EBEC data further improved the distribution of intensities measured from salen ligand and biotin crystals. However, CL-adjustment only marginally improved the refinement of their corresponding structures, signaling the already high counting accuracy of detectors with counting rates in the kilohertz range. Overall, by delivering low-dose structure-worthy data, fast EBEC collection strategies open new possibilities for high-throughput MicroED. | Niko Vlahakis; Songrong Qu; Logan Richards; Lygia Silva deMoraes; Duilio Cascio; Hosea Nelson; Jose Rodriguez | Analytical Chemistry; Imaging; Microscopy | CC BY 4.0 | CHEMRXIV | 2024-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66db946ecec5d6c1425cd490/original/fast-event-based-electron-counting-for-small-molecule-structure-determination-by-micro-ed.pdf |
62bdff6808a0f9bda7578734 | 10.26434/chemrxiv-2022-knt5m | The covalent reactivity of functionalized 5-hydroxy-butyrolactams is the basis for targeting of fatty acid binding protein 5 (FABP5) by the neurotrophic agent MT-21 | Covalently acting compounds experience a strong interest within chemical biology both as molecular probes in studies of fundamental biological mechanisms and/or as novel drug candidates. In this context, the identification of new classes of reactive groups are particularly important as these can expose novel reactivity modes and, consequently, expand the ligandable proteome. Here, we investigated the electrophilic reactivity of the 3-acyl-5-hydroxy-1,5-dihydro-2H-pyrrole-2-one (AHPO) scaffold, a heterocyclic motif that is e.g. present in various bioactive natural products. Our investigations were focused on the compound MT-21 - a simplified structural analogue of the natural product epolactaene - which is known to have both neurotrophic activity and ability to trigger apoptotic cell death. We found that the central N-acyl hemiaminal group of MT-21 can function as an electrophilic centre enabling divergent reactivity with both amine- and thiol-based nucleophiles, which furthermore translated to reactivity with proteins in both cell lysates and live cells. We found that in live cells MT-21 strongly engaged the lipid transport protein fatty acid-binding protein 5 (FABP5) by direct binding to a cysteine residue in the bottom of the ligand binding pocket. Through preparation of a series of MT-21 derivatives, we probed the specificity of this interaction which was found to be strongly dependent on subtle structural changes. Our study suggests that MT-21 may be employed as a tool compound in future studies of the biology of FABP5, which remains incompletely understood. Furthermore, our study has also made clear that other natural products containing the AHPO-motif may likewise possess covalent reactivity and that this property may underlie their biological activity. | Esben Svenningsen; Rasmus Ottosen; Katrine Jørgensen; Marija Nisavic; Camilla Larsen; Bente Hansen; Yong Wang; Kresten Lindorff-Larsen; Thomas Tørring; Stephan Hacker; Johan Palmfeldt; Thomas Poulsen | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bdff6808a0f9bda7578734/original/the-covalent-reactivity-of-functionalized-5-hydroxy-butyrolactams-is-the-basis-for-targeting-of-fatty-acid-binding-protein-5-fabp5-by-the-neurotrophic-agent-mt-21.pdf |
60c73fc4f96a0028a128615b | 10.26434/chemrxiv.7482098.v1 | Quasi-fractal Gold Nanoparticles for Sers: Effect of Nanoparticle Morphology and Concentration | <p>Quasi-fractal gold nanoparticles can be synthesized via a modified
and temperature controlled procedure initially used for the synthesis of star-like
gold nanoparticles. The surface features of nanoparticles leads to improved
enhancement of Raman scattering intensity of analyte molecules due to the
increased number of sharp surface features possessing numerous localized
surface plasmon resonances (LSPR). The LSPR is affected by the size and shape
of surface features as well as inter-nanoparticle interactions, as these affect
the oscillation modes of electrons on the nanoparticle surfaces. The effect of
the particle morphologies on the LSPR and further on the surface-enhancing
capabilities of these nanoparticles is explored by comparing different
nanoparticle morphologies and concentrations. We show that in a fixed nanoparticle
concentration regime, Quasi-fractal gold nanoparticles provide the highest
level of surface enhancement, whereas spherical nanoparticles provide the
largest enhancement in a fixed gold concentration regime. The presence of
highly branched features enables these nanoparticles to couple with a laser
wavelength despite having no strong absorption band and hence no single surface
plasmon resonance. This cumulative LSPR may allow these nanoparticle to be used
in a variety of applications where laser wavelength flexibility is beneficial,
such as in medical imaging applications where fluorescence at short laser
wavelengths may be coupled with non-fluorescing long laser wavelengths for
molecular sensing. </p> | Richard Darienzo; Olivia Chen; Maurinne Sullivan; Tatsiana Mironava; Rina Tannenbaum | Nanostructured Materials - Materials; Plasmonic and Photonic Structures and Devices | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fc4f96a0028a128615b/original/quasi-fractal-gold-nanoparticles-for-sers-effect-of-nanoparticle-morphology-and-concentration.pdf |
60c73dd74c8919625cad1ca8 | 10.26434/chemrxiv.6210110.v1 | Exploring the “Goldilocks Zone” of Semiconducting Polymer Photocatalysts via Donor-Acceptor Interactions | Water splitting using polymer photocatalysts is a
key technology to a truly sustainable hydrogen-based energy economy. Synthetic
chemists have intuitively tried to enhance photocatalytic activity by tuning
the length of π-conjugated domains of their semiconducting polymers, but the
increasing flexibility and hydrophobicity of ever-larger organic building
blocks leads to adverse effects such as structural collapse and inaccessible
catalytic sites. To reach the ideal optical bandgap of ~2.3 eV, we
synthesised a library of eight sulphur and nitrogen containing porous polymers
(SNPs) with similar geometries but with optical bandgaps ranging from 2.07 to
2.60 eV using Stille coupling. These polymers combine π-conjugated
electron-withdrawing triazine- (C<sub>3</sub>N<sub>3</sub>) and electron
donating, sulphur-containing moieties as covalently-bonded donor-acceptor frameworks
with permanent porosity. The remarkable optical properties of SNPs enable
fluorescence on-off sensing of volatile organic compounds and illustrate
intrinsic charge-transfer effects. Moreover, obtained polymers effectively
evolve H<sub>2</sub> gas from water under visible light irradiation with
hydrogen evolution rates up to 3158 µmol h<sup>-1</sup> g<sup>-1</sup> and high apparent
quantum efficiency which is the highest value obtained for microporous
organic polymers to-date. The design principles demonstrated here are
transferable to a new field of high-performance polymer photocatalysts based on
efficient donor-acceptor dyads. | Yaroslav S. Kochergin; Dana Schwarz; Amitava Acharjya; Arun Ichangi; Ranjit Kulkarni; Pavla Eliášová; Jaroslav Vacek; Johannes Schmidt; Arne Thomas; Michael J. Bojdys | Carbon-based Materials; Catalysts; Optical Materials; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd74c8919625cad1ca8/original/exploring-the-goldilocks-zone-of-semiconducting-polymer-photocatalysts-via-donor-acceptor-interactions.pdf |
6275237644bdd5fa9758e9c3 | 10.26434/chemrxiv-2022-lxdk2 | OOPS, the Ontology for Odor Perceptual Space: from molecular composition to sensory attributes of odor objects | When creating a flavor to elicit a specific odor object characterized by odor sensory attributes (OSA), expert perfumers or flavorists use mental combinations of odor qualities (OQ) such as Fruity, Green, Smoky. However, OSA and OQ are not directly related to the molecular composition in terms of odorants that constitute the chemical stimuli supporting odor object perception because of the complex non-linear integration of odor mixtures within the olfactory system. Indeed, single odorants are described with odor descriptors (OD), which can be found in various databases. Although classifications and aroma wheels studied the relationships between OD and OQ, the results are highly dependent of the studied products. Nevertheless, ontologies have proved to be very useful in sharing concepts across applications in a generic way but also to allow experts’ knowledge integration implying non-linear cognitive processes. In this paper we constructed the Ontology for Odor Perceptual Space (OOPS) to merge OD into a set of OQ best characterizing the odor further translated in a set of OSA thanks to expert knowledge integration. Results showed that OOPS can help to bridge molecular composition to odor perception and description as demonstrated in the case of wines. | Alice Roche; Nathalie Mejean Perrot; Thierry Thomas-Danguin | Agriculture and Food Chemistry; Food | CC BY NC 4.0 | CHEMRXIV | 2022-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6275237644bdd5fa9758e9c3/original/oops-the-ontology-for-odor-perceptual-space-from-molecular-composition-to-sensory-attributes-of-odor-objects.pdf |
60c73e17702a9b997e189cd9 | 10.26434/chemrxiv.6619223.v1 | Practical Intermolecular Hydroarylation of Terminal Alkenes via Reductive Heck Coupling | The hydroarylation of alkenes is an attractive approach to construct carbon–carbon (C–C) bonds from abundant and structurally diverse starting materials. Herein we report a palladium-catalyzed reductive Heck hydroarylation of unactivated and heteroatom-substituted terminal alkenes with an array of (hetero)aryl iodides. The reaction is anti-Markovnikov selective and tolerates a wide variety of functional groups on both the alkene and (hetero)aryl coupling partners. Additionally, applications of this method to complex molecule diversifications were demonstrated. Deuterium-labeling experiments are consistent with a mechanism in which the key alkylpalladium(II) intermediate is intercepted with formate and undergoes a decarboxylation/C–H reductive elimination cascade to afford the saturated product and turn over the cycle. <br /> | John A. Gurak; Keary M. Engle | Organic Synthesis and Reactions; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-06-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e17702a9b997e189cd9/original/practical-intermolecular-hydroarylation-of-terminal-alkenes-via-reductive-heck-coupling.pdf |
649b1e3fba3e99daef21aa2b | 10.26434/chemrxiv-2023-3mzgh | Photocatalytic dechlorination of unactivated chlorocarbons including PVC using organolanthanide complexes | Simple lanthanide cyclopentadienyl (Cp) complexes can photochemically cleave the sp3 carbon-chlorine bond of unactivated chlorinated hydrocarbons including polyvinyl chloride (PVC). The excited state lifetimes of these simple complexes are long (175 ns for (CpMe4)2CeCl) and the light absorption by the Cp ligand is efficient, so photocatalytic reactivity is enhanced for cerium and now also made possible for neighboring, normally photoinactive, lanthanide congeners. | Amy Kynman; Stella Christodoulou; Erik Ouellette; Appie Peterson; Sheridon Kelly; Laurent Maron; Polly Arnold | Catalysis; Organometallic Chemistry; Photocatalysis; Bond Activation; Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649b1e3fba3e99daef21aa2b/original/photocatalytic-dechlorination-of-unactivated-chlorocarbons-including-pvc-using-organolanthanide-complexes.pdf |
67a1def1fa469535b90311cb | 10.26434/chemrxiv-2025-vrxkw | Decoding Hairpin Structure Stability in Lin28-mediated Repression | Lin28 protein is well-known for its role in inhibiting biogenesis of micro-RNAs (miRNAs) that belong to the let-7 family. The Lin28 and let-7 axis is associated with several types of cancer. It is imperative to understand the underlying mechanism to treat these cancer in a more efficient way. In this study, we employed all-atom molecular dynamics simulation as research tool to investigate the interaction formed between Lin28 and precursor element of let-7d, one of the 12 members of the let-7 family. By constructing systems of intact sequence length of preE-let-7d, our simulations suggest that both the loop region of hairpin structure and GGAG sequence can form stable interactions with the CSD and ZKD region of the protein, respectively. The system with deleting the nucleotides GGAG at the 3' terminal indicates that the loop region is more responsible for its ability in bypassing the binding and repression of Lin28. Additionally, using let-7c-2, which can bypass Lin28 regulation, as a template, we constructed systems with mutated loop region sequences in miRNAs and tested their stabilities. Our simulations results coincide well with experimental observations. Based on both simulation results and statistical analysis from two databases, we hypothesized that two factors, namely, interaction between terminal nucleotides and ring tension originating from the middle nucleotides, can significantly influence their stabilities. Systems combining strong and weak terminal interactions with large and small ring tensions were recruited to validate our hypothesis. Our findings offer a new perspective and shed lights on strategies for design sequences to regulate the interactions formed between proteins and hairpin structures. | Qiang Zhu; Limu Hu; Chang Cui; Min Zang; Hao Dong; Jing Ma | Theoretical and Computational Chemistry; Physical Chemistry; Biophysical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a1def1fa469535b90311cb/original/decoding-hairpin-structure-stability-in-lin28-mediated-repression.pdf |
60c756f8bb8c1a4fa63dc6e2 | 10.26434/chemrxiv.14348117.v1 | State of the Art Iterative Docking with Logistic Regression and Morgan Fingerprints | <p>There
is renewed interest in docking campaigns for ligand-discovery since the advent
of ultra-large scale virtual libraries. Using brute-force search, the scale of
the libraries suggests highly parallelized compute should be used to avoid
years-long computations. This paper reports a re-analysis of docking data from
an ultra-large docking campaign at the D4 receptor and AmpC beta lactamase, and
demonstrates large reductions in computation time to identify the top-ranked
ligands. A search of ‘baseline’ featurizations shows that logistic regression
on Morgan fingerprints with pharmacophoric atom invariants can match the reported
performance on the same task using message-passing networks. With this approach,
an ultra-large docking campaign could be performed in a matter of weeks using
consumer-grade CPUs with <i>RDKit </i>and <i>scikit-learn</i>. All code and figures are available at <a href="https://github.com/ljmartin/dockop">https://github.com/ljmartin/dockop</a> </p><br /> | Lewis Martin | Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756f8bb8c1a4fa63dc6e2/original/state-of-the-art-iterative-docking-with-logistic-regression-and-morgan-fingerprints.pdf |
60f9738b880443f736e2e223 | 10.26434/chemrxiv-2021-w9g4h-v2 | Influence of Glass Composition on the Luminescence Mechanisms of CdSe Quantum Dot-Doped Glasses | In this work, we characterized the electronic structure of CdSe quantum dots embedded
in a series of x Na2O, (1–x) SiO2 glass matrices (x = 0, 0.25, 0.33 and 0.5). We analyzed
the impact of the glass matrix composition on both the atomic structure of the quantum
dot (QD) and the QD/glass interface, as well as the luminescence mechanisms, using
density functional theory (DFT) calculations. The increase of Na2O content in the glass
matrices was found to promote the formation of Cd–O and Se–Na interfacial bonds,
and disrupting the Cd–Se bonds network. In particular, we show that the glass
composition directly affects the nature of the highest occupied molecular orbitals
(HOMO). According to the atomic structure, the band gap distribution and the density
of states calculation, we find that there is significant reconstruction of the QD, and that
the picture sometimes proposed of a “pristine QD” surrounded by glass is not realistic.
The introduction of CdSe QD significantly decreased the bandgap of the glass
compared to pristine glasses, and the interfacial bonds greatly contributed to the frontier
orbitals without forming midgap states. We propose a new energy diagram, quite
different from the traditional model, to explain the luminescence of CdSe quantum dot-
doped glasses, originating from the intrinsic emission of this hybrid system {QD +
glass}. These results improve our understanding of the luminescence of CdSe quantum
dot-doped glasses, explaining the reason for the poor quantum efficiency and broad
emission linewidth compared with their colloidal counterparts. | Wenke Li; Xiujian Zhao; Chao Liu; François-Xavier Coudert | Theoretical and Computational Chemistry; Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f9738b880443f736e2e223/original/influence-of-glass-composition-on-the-luminescence-mechanisms-of-cd-se-quantum-dot-doped-glasses.pdf |
64ed9777dd1a73847fbe2335 | 10.26434/chemrxiv-2023-0bn4t-v2 | Metallaantiaromaticity of 10-Platinacorrole Complexes | The aromaticity of cyclic π-conjugated organometallic compounds is known as metallaaromaticity. π-Conjugated metallacycles, such as metallabenzenes and metallapentalenes, have been investigated in order to understand the involvement of the d electrons from the metal center in the π-conjugated systems of the organic ligands. Here, we report the synthesis of Pd(II) 10-platinacorrole complexes with cyclooctadiene (COD) and norbornadiene (NBD) ligands. While the Pd(II) 10-platinacorrole COD complex adopts a distorted structure without showing appreciable antiaromaticity, the corresponding NBD complex exhibits distinct antiaromatic character due to its highly planar conformation. Detailed density-functional-theory (DFT) calculations revealed that two d orbitals are involved in the macrocyclic π-conjugation. We furthermore demonstrated that Craig–Möbius antiaromaticity is not present in the studied system. The synthesis of 10-platinacorroles enables the systematic comparison of the antiaromaticity and aromaticity of closely related porphyrin analogues, providing a better understanding of π-conjugation that involves d orbitals. | Kazuki Miwa; Tomoya Yokota; Qian Wang; Takahiro Sakurai; Heike Fliegl; Dage Sundholm; Hiroshi Shinokubo | Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Organometallic Compounds; Theory - Organometallic; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ed9777dd1a73847fbe2335/original/metallaantiaromaticity-of-10-platinacorrole-complexes.pdf |
60c73e7c702a9b8663189d74 | 10.26434/chemrxiv.6987461.v1 | Decoration of Cellulose Nanowhiskers with Iron Oxide Nanoparticles | <p>Orientation of cellulose nanowhiskers (CNWs) within various
matrices is an effective approach that affords the exploitation of the high
stiffness of CNWs as a reinforcement phase in nanocomposites. One potential
engineering method to achieve orientation is to incorporate magnetic properties
into the CNWs by tethering magnetic nanoparticles onto the surface of these
nanoparticles, followed by their alignment in an externally-applied magnetic
field. In this work we report the successful in-situ tethering of iron oxide
nanoparticles (IONPs) onto CNWs by the thermal decomposition of Fe(CO)<sub>5 </sub>in
a H<sub>2</sub>O/DMF suspension. Following this procedure, IONPs consisting of
mixtures of Fe<sub>3</sub>O<sub>4</sub> and Fe<sub>2</sub>O<sub>3</sub> with an
average diameter of 20 nm were attached to the CNWs. The type of iron oxide
species that was generated was determined by selected area electron diffraction
(SAED) and energy dispersive spectroscopy (EDS) and the particle size was
evaluated by transmission electron microscopy (TEM). Raman spectroscopy was
used to characterize the presence and the nature of the molecular interaction between
the IONPs and the CNWs.</p> | Lyufei Chen; Shruti Sharma; Richard Darienzo; Rina Tannenbaum | Composites; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2018-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e7c702a9b8663189d74/original/decoration-of-cellulose-nanowhiskers-with-iron-oxide-nanoparticles.pdf |
62722edbed4d8838f722f250 | 10.26434/chemrxiv-2022-6dlsg | Flexible CO2 sensor architecture with selective nitrogen functionalities by one-step laser-induced conversion of versatile organic ink | Nitrogen-doped carbons (NC) are a class of sustainable materials for selective CO2 adsorption. We introduce a versatile concept to fabricate flexible NC-based sensor architectures for room-temperature sensing of CO2 in a one-step laser conversion of primary coatings cast from abundant precursors. By the unidirectional energy impact in conjunction with depth-dependent attenuation of the laser beam, a layered sensor heterostructure with porous transducer and active sensor layer is formed. Comprehensive microscopic and spectroscopic cross-sectional analyses confirm the preservation of a high content of imidazolic nitrogen in the sensor. The performance was optimized in terms of material morphology, chemical composition, and surface chemistry to achieve a linear relative resistive response of up to ∆R/R0 = -14.3% (10% of CO2). Thermodynamic analysis yields ΔadsH values of -35.6 kJ·mol-1 and 34.1 kJ·mol 1 for H2O and CO2, respectively. The sensor is operable even in humid environments (e.g., ∆R/R0,RH=80% = 0.53%) and shows good performance upon strong mechanical deformation. | Huize Wang; Charles Otieno Ogolla; Gyanendra Panchal; Marco Hepp; Simon Delacroix; Daniel Cruz; Danny Kojda; Jim Ciston; Colin Ophus; Axel Knop-Gericke; Klaus Habicht; Benjamin Butz; Volker Strauss | Materials Science; Nanoscience; Carbon-based Materials; Materials Processing; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62722edbed4d8838f722f250/original/flexible-co2-sensor-architecture-with-selective-nitrogen-functionalities-by-one-step-laser-induced-conversion-of-versatile-organic-ink.pdf |
61842be53c169de28b8e8e2d | 10.26434/chemrxiv-2021-3x8p2-v2 | A manipulative activity for exploring effective nuclear charge (Zeff) | High-school and undergraduate college students may often rely on memorization when learning periodic trends, leading to an ineffective understanding of introductory chemistry concepts like atomic radius, ionization energy, and electron affinity. Comprehension of effective nuclear charge (Zeff) is foundational to a complete understanding of periodic trends. Zeff remains an abstract concept for many students, indicating that a manipulative activity for teaching the phenomenon could be a useful way to explain the concept for greater student comprehension. Here we report a hands-on learning activity to target this knowledge gap using magnetic attraction as an analogy for electrostatic attraction within the atom. This approach enables students to explore the phenomenon of effective nuclear charge at a macroscopic level and apply their learning to periodic trends and related concepts. We anticipate that this activity will fill a long-standing hole in the active learning of chemical principles. Importantly, this activity is low-cost and can be assembled using readily accessible materials to allow implementation in most classrooms and virtual learning environments. | Jillian Kasman; Taylor Slouka; Alan Kiste; Javin Oza | Physical Chemistry; Chemical Education | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61842be53c169de28b8e8e2d/original/a-manipulative-activity-for-exploring-effective-nuclear-charge-zeff.pdf |
66694a7e12188379d8e81a78 | 10.26434/chemrxiv-2024-mn2rk | Tailoring the dynamics of DUT-5 nanocrystals: from rigid nanoparticles to flexible nanowires | Here we describe the synthesis of a series of 1D anisotropic DUT-5(Al) nanostructures differing by their crystal dimensions and aspect ratio. Very long and monodisperse DUT-5(Al) nanowires (NWs) with length exceeding 6 µm were designed by using graphene oxide (GO) nanoscrolls as structure directing agents while shorter DUT-5(Al) nanorods 50 nm in length or polydisperse DUT-5(Al) samples with a broad size distribution were prepared without any GO. Remarkably, these materials were also differing by their dynamic properties upon guest molecules adsorption. While DUT-5(Al) nanorods exhibited a rigid large pore (lp) phase, it was revealed that DUT-5(Al) NWs could present a gating behaviour upon guest adsorption involving a structural transition from a highly disordered narrow pore (np) phase to the lp phase. The structure of DUT-5(Al) NWs as well as their guest-responsive structural flexibility were fully characterized by coupling high resolution TEM, 3D electron diffraction, high resolution synchrotron PXRD and PDF, adsorption isotherms and in situ PXRD. To the best of our knowledge, this study delivers an unprecedented design of flexible DUT-5(Al) NWs whereas this MOF was previously regarded as a rigid porous hybrid material. Moreover, it demonstrates that tuning the aspect ratio of MOF particles can influence their structural flexibility. | Ali Saad; Frédéric Gobeaux; Volodymyr Bon; Sergi Plana-Ruiz; Clémence Sicard; Mathieu Frégnaux; Sanchari Dasgupta; Subharanjan Biswas; Khaled Dassouki; Benoît Baptiste; Stefano Canossa; Stefan Kaskel; Nicolas Menguy; Nathalie Guillou; Nathalie STEUNOU | Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66694a7e12188379d8e81a78/original/tailoring-the-dynamics-of-dut-5-nanocrystals-from-rigid-nanoparticles-to-flexible-nanowires.pdf |
61d5a0d9db4d9f3c6b8c687f | 10.26434/chemrxiv-2021-m67lk-v3 | Prediction of Thermal Properties of Zeolites through Machine Learning | The use of machine learning for the prediction of physical and chemical properties of crystals based on their structure alone is currently an area of intense research in computational materials science. In this work, we studied the possibility of using machine learning-trained algorithms in order to calculate the thermal properties of siliceous zeolite frameworks. We used as training data the thermal properties of 120 zeolites, calculated at the DFT level, in the quasi-harmonic approximation. We compared the statistical accuracy of trained models (based on the gradient boosting regression technique) using different types of descriptors, including ad hoc geometrical features, topology, pore space, and general geometric descriptors. While geometric descriptors were found to perform best, we also identified limitations on the accuracy of the predictions, especially for a small group of materials with very highly negative thermal expansion coefficients. We then studied the generalizability of the technique, demonstrating that the predictions were not sensitive to the refinement of framework structures at a high level of theory. Therefore, the models are suitable for the exploration and screening of large-scale databases of hypothetical frameworks, which we illustrate on the PCOD2 database of zeolites containing around 600,000 hypothetical structures. | Maxime Ducamp; François-Xavier Coudert | Theoretical and Computational Chemistry; Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d5a0d9db4d9f3c6b8c687f/original/prediction-of-thermal-properties-of-zeolites-through-machine-learning.pdf |
66fdb783cec5d6c142f765cd | 10.26434/chemrxiv-2024-nvl26 | Repartitioning the Hamiltonian in Many-Body Second-Order Brillouin-Wigner Perturbation Theory: Uncovering New Size-Consistent Models. | Second-order Møller-Plesset perturbation theory is well-known as a computationally inexpensive approach to the elec- tron correlation problem that is size-consistent, but fails to be regular. On the other hand, the less well-known many- body version of Brillouin-Wigner (BW) perturbation theory has the reverse properties: it is regular but fails to be size-consistent when used with the standard MP partitioning. For this reason it is not widely used. In this work, we analyze the ways in which it is possible to use alternative non-MP partitions of the Hamiltonian to yield variants of BW2 that are size-consistent as well as regular. We show that there is a vast space of such BW2 theories, and also show that it is possible to define a repartitioned BW2 theory from the ground state density alone, which regenerates the exact correlation energy. We also provide a general recipe for deriving regular, size-consistent and size-extensive partitions from physically meaningful components and we apply the result to small model systems. The scope of these results appears to further set the stage for a revival of BW2 in quantum chemistry. | Linus Bjarne Dittmer; Martin Head-Gordon | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2024-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fdb783cec5d6c142f765cd/original/repartitioning-the-hamiltonian-in-many-body-second-order-brillouin-wigner-perturbation-theory-uncovering-new-size-consistent-models.pdf |
60c73f5d567dfeca98ec39e3 | 10.26434/chemrxiv.7352459.v1 | Synthesis of (+)-Darwinolide, a Biofilm-Penetrating Anti-MRSA Agent | Darwinolide, a recently identified marine natural product from the Antarctic sponge Dendrilla membranosa, was shown to exhibit promising activity against the biofilm phase of methicillin-resistant Staphylococcus aureus. Its challenging tetracyclic rearranged spongian diterpenoid structure links a trimethylcyclohexyl subunit to a seven-membered core with two fused tetrahydrofurans. Here we describe the first synthesis of (+)-darwinolide featuring a convergent aldol fragment coupling, an Ireland-Claisen rearrangement and an organocatalytic desymmetrization as the key steps. Our results provide a foundation for the development of novel antibiofilm-specific antibiotics.<br /> | Thomas Siemon; Simon Steinhauer; Mathias Christmann | Natural Products; Organic Synthesis and Reactions; Stereochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f5d567dfeca98ec39e3/original/synthesis-of-darwinolide-a-biofilm-penetrating-anti-mrsa-agent.pdf |
60c74c339abda27211f8d236 | 10.26434/chemrxiv.12439967.v1 | In-Silico Molecular Docking Show Mitocurcumin can Potentially Block Innate Immune Evasion Mechanism of SARS-CoV-2 and Enhance Viral Load Clearance | In the present work, we have employed a molecular docking approach to
study the ability of mitocurcumin (MC), a triphenyl phosphonium conjugated curcumin
derivative, to inhibit SARS-CoV-2 infection. Computational analysis revealed
that MC can bind strongly to SARS-CoV-2 ADP Ribose Phosphatase (NSP3) with high
binding energy of -10.3 kcal/mol and to SARS-CoV-2 methyltransferase
(NSP10-NSP16 complex) with a high binding energy of -10.4 kcal/mol. We found
that MC interacts with critical residues of viral NSP3 macro-domain, known to suppress
host immune response, through hydrophobic interactions and occupies its active
site. Furthermore, MC interacts with the critical residues of NSP10-NSP16
complex, known to prevent innate immune detection of viral mRNA, through
hydrophobic and hydrogen bond interaction and occupies the methyl group donor
site. MC is also found to bind to main protease of SARS-CoV-2 and may potentially
act as an inhibitor of the viral protease. In conclusion, MC can potentially inhibit
the activity of multiple SARS-CoV-2 proteins and may accentuate the innate
immune system mediated clearance of viral load resulting in improved clinic
outcome in COVID-19 patients. | Debojyoti Pal; Rahul Checker; Vijay Kutala; Santosh Sandur | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c339abda27211f8d236/original/in-silico-molecular-docking-show-mitocurcumin-can-potentially-block-innate-immune-evasion-mechanism-of-sars-co-v-2-and-enhance-viral-load-clearance.pdf |
66d9eaafcec5d6c1423df2dc | 10.26434/chemrxiv-2024-4tcbv | Sustainable Natural Fiber Based Composites Materials: A Review | Natural fiber-based composite materials have emerged as sustainable alternatives to conventional composites, driven by the need for environmentally friendly solutions in various industries. This review provides a comprehensive overview of the natural fibers commonly used in composite manufacturing, including jute, flax, hemp, sisal, coir, and many more. The fiber characteristics such as tensile strength, elasticity, moisture absorption, and their mechanical and physical properties are presented and discussed, highlighting their influence on the overall performance of the composites. The interaction between these natural fibers and polymer matrices, including both thermoplastic and thermosetting polymers, is also focused on this review. Various manufacturing techniques employed to produce natural fiber composites are explored, including hand layup, compression molding, resin transfer molding, injection molding, extrusion molding, and automated fiber placement techniques. Lastly, the review explores the diverse applications of natural fiber-based composites across sectors such as automotive, construction, packaging, and sports equipment. | Imam Hossain Imon | Materials Science; Chemical Engineering and Industrial Chemistry; Composites; Fibers | CC BY NC 4.0 | CHEMRXIV | 2024-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d9eaafcec5d6c1423df2dc/original/sustainable-natural-fiber-based-composites-materials-a-review.pdf |
6152338087a02d9ab04af36a | 10.26434/chemrxiv-2021-ws71h | Accurate Simulations of Lipid Monolayers Require a Water Model With Correct Surface Tension |
Lipid monolayers provide our lungs and eyes their functionality, and serve as proxy systems in biomembrane research. Therefore, lipid monolayers have been studied intensively also using molecular dynamics simulations, which are able to probe their lateral structure and interactions with, e.g., pharmaceuticals or nanoparticles. However, such simulations have struggled in describing the forces at the air–water interface. Particularly the surface tension of water and long-range van der Waals interactions have been considered critical, but their importance in monolayer simulations has been evaluated only separately. Here we combine the recent C36/LJ-PME lipid force field that in- cludes long-range van der Waals forces with water models that reproduce experimental surface tensions to elucidate the importance of these contributions in monolayer simulations. Our results suggest that a water model with correct surface tension is necessary to reproduce experimental surface pressure–area isotherms and monolayer phase behavior, while standard cutoff-based CHARMM36 lipid model with the 4-point OPC water model still provides the best agreement with experiments. Our results emphasize the importance of using high quality water models in applications and parameter development in molecular dynamics simulations of biomolecules. | Carmelo Tempra; O.H. Samuli Ollila; Matti Javanainen | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Biophysical Chemistry; Interfaces; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-09-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6152338087a02d9ab04af36a/original/accurate-simulations-of-lipid-monolayers-require-a-water-model-with-correct-surface-tension.pdf |
65e90000e9ebbb4db918fff4 | 10.26434/chemrxiv-2024-78kc5 | Unprecedented Bonding Dynamics during THF and DMSO Molecular Hydration | Hydration of organic molecules determines the fascinating properties of aqueous solutions with challenges for understanding the bonding and electronic dynamics. We found three types of unusual interactions in terms of the O/C−H:O coupling hydrogen bonds, the charge-inverted H:O-C and H:O=S, and the HH repulsion bridged CHHO interactions at the THF and DMSO hydration interfaces. Perturbative differential phonon spectroscopy and the first-principles computations further unveiled that the polarization effects of solute dipoles and the inter- and intramolecular coupling interactions cooperatively and disparately relax these bonds. These findings shall enrich the connotation of hydration interfacial bonding profoundly by incorporating the inter- and intramolecular coupling, charge inversion, and the coupling-enabled cooperativity and polarizability upon perturbation, which should offer impacts on dealing with systems involving molecular interactions, such as cryoprotectants, electrolytes, etc. | Changqing Sun; Yong Zhou | Physical Chemistry; Chemical Kinetics | CC BY 4.0 | CHEMRXIV | 2024-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e90000e9ebbb4db918fff4/original/unprecedented-bonding-dynamics-during-thf-and-dmso-molecular-hydration.pdf |
617b6f2d8ac7a277d85fd007 | 10.26434/chemrxiv-2021-140tk | Universal promotion of heterogeneous olefin metathesis catalysts by controlling dynamic active site renewal | Olefin metathesis is a versatile strategy for large-scale olefin interconversion, yet mechanistic details over industrial heterogeneous catalysts have remained ambiguous for decades. Here, from rigorous kinetic measurements, spectroscopic studies, and computational modeling of propylene metathesis over model and industrial WOx/SiO2 catalysts, we identify a hitherto unknown site renewal and decay cycle, mediated by proton transfers involving proximal Brønsted acidic OH groups, which operates concurrently with the classical Chauvin cycle. We show how this cycle can be manipulated using small quantities of promoter olefins to drastically increase steady-state propylene metathesis rates by up to 30-fold at 250oC with negligible promoter consumption. The increase in activity and considerable reduction of operating temperature requirements were also observed on MoOx/SiO2 catalysts, showing that this strategy is general and can address major roadblocks associated with industrial metathesis processes. | Terry Z. H. Gani; Zachariah J. Berkson; Ran Zhu; Jong Hun Kang; John R. Di Iorio; Ka Wing Chan; Daniel F. Consoli; Sohel K. Shaikh; Christophe Copéret; Yuriy Román-Leshkov | Catalysis; Energy; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617b6f2d8ac7a277d85fd007/original/universal-promotion-of-heterogeneous-olefin-metathesis-catalysts-by-controlling-dynamic-active-site-renewal.pdf |
671f077583f22e421466a3e9 | 10.26434/chemrxiv-2024-19rj6-v2 | A Theoretical Framework for Absolute Quantification in Digital Immunoassays and the Advancements in Droplet-Based Digital Immunoassay Methodologies | Conventional single-molecule immunoassay models, which model on a single discrete Poisson distribution, are inadequate for achieving theoretical absolute quantification of target proteins. We introduce a novel approach that models the capture of target proteins by magnetic beads in digital immunoassays as a Poisson process, treating the beads as discrete units. The subsequent secondary sampling process is modeled using hypergeometric distributions. By implementing a droplet-based absolute quantification method, we establish two technical approaches, the bead-counting method and the external calibration method, that eliminate the necessity for traditional calibration curves. Comparative analyses with existing techniques, such as Single Molecule Immunoassays and Electrochemiluminescence Immunoassays, demonstrate enhanced feasibility and wide digital linear range of our methods. Furthermore, we explore the feasibility of an internal calibration method. Our theoretical framework effectively addresses the critical challenge of absolute quantification in protein immunoassays. It provides essential support for the development of precise protein quantification techniques and extends the capabilities of digital immunoassays in biomedical research and clinical diagnostics. | Liang Guo; Tianjiao Mao; Liang Lu; Yipi Xiao; Fanrong Ai; Jiani Wang; Jing Yao; Xiluan Yan; Huan Li | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Chemistry - General; Biochemical Analysis; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671f077583f22e421466a3e9/original/a-theoretical-framework-for-absolute-quantification-in-digital-immunoassays-and-the-advancements-in-droplet-based-digital-immunoassay-methodologies.pdf |
6711347c51558a15ef5b05e6 | 10.26434/chemrxiv-2024-sxzbn | Proton-transfer kinetics at liquid-liquid interfaces | Proton transfer at electrochemical interfaces is fundamentally important for many areas of science and technology, yet kinetic measurements of this elementary step are often convoluted by inhomogeneous electrode surface structures. We show that facilitated proton transfer at the interface between two immiscible electrolyte solutions (ITIES) can serve as a model system to study proton transfer kinetics in the absence of defects found at solid|electrolyte interfaces. Diffusion-controlled micropipette voltammetry revealed that 2,6-diphenylpyridine (DPP) facilitated interfacial proton-transfer across the HCl(aq)|Trifluorotoluene interface and voltammetry at nanopipette-supported interfaces yielded activation-controlled ion transfer currents. Fitting quasireversible voltammograms to a mixed diffusive-kinetic model allow for the extraction of kinetic parameters k0 and α, which were equal to 3.0 +/- 1.8 cm/s and 0.3 +/- 0.2, respectively for DPP facilitated proton transfer. Finite element simulations highlighted regimes of direct proton transfer and sequential proton transfer, where the current divided between these two possible pathways was shown to favor direct PT when the neutral partitioning step DPP(org) to DPP(aq) was rate determining. Understanding the kinetics of ion transfer at the ITIES will be important in the development of general theories of ion transfer in electrochemical science and technology.
| Nick D'Antona; Nadia Barnard; Shane Ardo; Yixian Wang; Yogesh Surendranath; Paul Kempler; Shannon Boettcher | Analytical Chemistry; Nanoscience; Energy; Electrochemical Analysis; Energy Storage; Fuels - Energy Science | CC BY 4.0 | CHEMRXIV | 2024-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6711347c51558a15ef5b05e6/original/proton-transfer-kinetics-at-liquid-liquid-interfaces.pdf |
65c0ed71e9ebbb4db9b83308 | 10.26434/chemrxiv-2023-43db8-v2 | Deuterium Labeling of Isoaspartic and Isoglutamic Acids for Mass Spectrometry Analysis | Isoaspartic acid (isoAsp) is a common protein modification that spontaneously arises from asparagine or aspartic acid, and it has been linked to various diseases and health conditions. However, current methods for identifying isoAsp sites in proteins often suffer from ambiguity and have not gained widespread adoption. We have developed a novel method that exclusively labels isoAsp with deuterium. This method capitalizes on the unique structural characteristics of isoAsp residues, which possess a free α-carboxyl group and can form an oxazolone ring. Once the oxazolone ring forms, it facilitates racemization at the Cα-position, incorporating a deuteron from a D2O solvent. The sites of deuterium-incorporated isoAsp in proteins can be unequivocally determined by comparing the precursor and product ion masses of the peptides from proteins reacted in H2O and D2O. The effectiveness of this method has been demonstrated through its application to model proteins, lysozyme and rituximab. Furthermore, we have confirmed that the isoAsp deuterium labeling reaction efficiently labels both L- and D-isoAsp without distinction, as well as isoglutamic acid (isoGlu), for which no effective detection methods currently exist. | MASARU MIYAGI; Evan Kiesel; Kelao Neumbo; Takashi Nakazawa | Analytical Chemistry; Biochemical Analysis; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c0ed71e9ebbb4db9b83308/original/deuterium-labeling-of-isoaspartic-and-isoglutamic-acids-for-mass-spectrometry-analysis.pdf |
635bc2d1ac45c73b369c0358 | 10.26434/chemrxiv-2022-brg1w | The hydroamination of TIPS-C≡C-SF5 –
A bench-top route to pentafluorosulfanylated enamines
| Synthetic access to a variety of aliphatic and vinylic pentafluorosulfanylated building blocks remains a major challenge in contemporary organofluorine chemistry hampering its broad investigation in the context of medicinal chemistry, agrochemistry and functional materials. Herein, we report a bench-top protocol to access the virtually unknown class of a-SF5-enamines under rather benign reaction conditions. This reaction combines the in-situ protodesilylation of the commercially available precursor TASP with the unprecedented hydroamination of HC≡C-SF5. The on-site use of highly toxic gases is completely avoided, granting access to a-SF5-enamines to conventional labs. Furthermore, employing a combined experimental and computational approach, we revealed a two-step cascade reaction. The excellent E-diastereoselectivity of the reaction is suggested to be the result of the convergence of the fast Z-/E- isomerization of a vinyl anion as well as isomerization of the iminium ion in the equilibrium. The remarkably thermal stability of these SF5-enamines encourages further studies of its synthetic utility. | Jonas Oliver Wenzel; Fabian Jester; David Rombach | Organic Chemistry; Inorganic Chemistry; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635bc2d1ac45c73b369c0358/original/the-hydroamination-of-tips-c-c-sf5-a-bench-top-route-to-pentafluorosulfanylated-enamines.pdf |
6506d11fb6ab98a41c99b024 | 10.26434/chemrxiv-2023-sbrrv | Reaction Mechanism of Hydrogen Generation and Nitrogen Fixation at Carbon Nitride/Double Perovskite Heterojunctions | Photocatalytically active heterojunctions based on metal halide perovskites (MHPs) are drawing significant interest for their chameleon ability to foster several redox reactions. The lack of mechanistic insights into their performance, however, limits the ability of engineering novel and optimized materials. Herein, we report on a composite system including a double perovskite, Cs2AgBiCl6/g-C3N4, used in parallel for solar-driven hydrogen generation and nitrogen reduction. The composite efficiently promotes the two reactions, but its activity strongly depends on the perovskite/carbon nitride relative amounts. Through advanced spectroscopic investigation and density function theory modelling we studied the H2 and NH3 production reaction mechanisms, finding perovskite halide vacancies as the primary reactive sites for hydrogen generation, withstanding a positive contribution of low loaded g-C3N4, in reducing carrier recombination. For nitrogen reduction, instead, the active sites are g-C3N4 nitrogen vacancies, and the heterojunction best performs at low perovskites loadings, as the composites maximizes light absorption and reduced carrier losses. We believe these insights are important add-ons towards universal exploitation of MHPs in contemporary photocatalysis. | Lorenzo Malavasi; Costanza Tedesco; Antonella Profumo; Andrea Speltini; Francesca Merlo; Edoardo Mosconi; Filippo De Angelis; Waldemar Kaiser; Asma Alothman; Andrea Listorti; Silvia Colella; Luca Gregori; Michele Saba; Angelica Simbula; Federico Pitzalis | Materials Science; Catalysis; Composites; Heterogeneous Catalysis; Photocatalysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6506d11fb6ab98a41c99b024/original/reaction-mechanism-of-hydrogen-generation-and-nitrogen-fixation-at-carbon-nitride-double-perovskite-heterojunctions.pdf |
60c75421ee301cdfb6c7aeff | 10.26434/chemrxiv.13618808.v1 | Logic and Symbolism of Switchable Porous Framework Materials | <p>Metal-Organic Frameworks (MOFs) are highly porous materials
composed of organic linkers connected by inorganic nodes. A unique subset of
MOFs shows switchability, the ability to switch between at least two distinct
structures differing significantly in porosity. These unique guest dependent
pore opening and closing processes offer new opportunities in gas separation,
selective recognition, sensing and energy storage. However, the factors
affecting switchability are poorly understood. Network topology, micromechanics
of building blocks and their hinges, but also particle size, defects,
agglomeration, desolvation conditions etc. are convoluted into the
responsiveness of the system. </p>
<p>In essence all factors are a consequence of the
materials history including synthesis procedure and desolvation but also all
subsequent handling steps such as mechanical and adsorption stress leading to a
complex interplay of factors which are difficult to express clearly by ordinary
writing systems, chemical or mathematical symbols without loss of intuitive
understanding. Here we propose a symbolic language for the rationalization of
switchability emphasizing the history dependent responsivity of many dynamic
frameworks and their stimuli induced 1<sup>st</sup> order phase transitions.
Color representations of the guest and host offer an intuitive understanding of
switchability phenomena even for non-experts. The system follows a bivalent
logic inspired by Freges <i>Begriffsschrift</i>
providing a fundamental logic structure for the rationalization of statements
and representation of logic gates. <b></b></p> | Leila Abylgazina; Irena Senkovska; Stefan Kaskel | Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75421ee301cdfb6c7aeff/original/logic-and-symbolism-of-switchable-porous-framework-materials.pdf |
67a552c46dde43c908db63ed | 10.26434/chemrxiv-2025-2nj2g | Photosynthetic Reaction Center: A Nonergodic, Dynamically Anisotropic, and Nonlinear Charge-Transport Engine | We ask the question of what is special about photosynthetic reaction-center proteins as media for transporting electrons across the lipid membrane. Ergodicity is broken for the statistics of electrostatic fluctuations in the heliobacterial reaction center studied here by atomistic simulations. It is not restored on the simulation time scale of ~ 1 us, and it allows low activation barriers for electron hops. The medium dynamics are highly anisotropic (depending on the oxidation state) at cofactors sites allowing unidirectional flow of charge. This nonlinear response of the protein to altering oxidation state combines with coupling of cofactor polarizabilities to strong intra-protein electric fields. Nonparabolic and nonergodic free energy surfaces of electron transfer allow low-barrier charge conductivity in proteins. | Mohammad Mehdi Pirnia; Dmitry Matyushov | Biological and Medicinal Chemistry; Biophysics | CC BY NC 4.0 | CHEMRXIV | 2025-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a552c46dde43c908db63ed/original/photosynthetic-reaction-center-a-nonergodic-dynamically-anisotropic-and-nonlinear-charge-transport-engine.pdf |
60c7491a567dfe4d0fec4b2b | 10.26434/chemrxiv.11865879.v2 | Nanocluster Growth and Coalescence Modulated by Ligands | We describe a model of nanocluster formation that incorporates competition between ligand adsorption and nanocluster growth. Growth occurs through the addition of a metal-ligand complex and coalescence of nanoclusters. The competition between ligands for binding sites on the nanoclusters and growth of the nanoclusters through coalescence creates interesting growth pathways. The patterns are reminiscent of those observed in the synthesis of gold thiolate nanoclusters. For a particular set of rate coefficients, described herein, we observe the formation of a kinetically stable nanocluster that participates in coalescent growth. This determines the size interval of the resulting nanoclusters in the size distribution. The kinetically stable cluster can be tuned by modifying the functional form of the number of surface sites on the nanoclusters, thereby changing the growth pathway and the final sizes of the clusters. | Dylan Suvlu; Mohsen Farshad; Jayendran C. Rasaiah | Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7491a567dfe4d0fec4b2b/original/nanocluster-growth-and-coalescence-modulated-by-ligands.pdf |
657cb14de9ebbb4db9fa0e13 | 10.26434/chemrxiv-2023-cpkfk | Domain adaptable language modeling of chemical compounds identifies potent pathoblockers for Pseudomonas aeruginosa. | Computational techniques for predicting molecular properties are emerging as pivotal components for streamlining drug development, optimizing time, and financial investments. Here, we introduce ChemLM, a transformer language model-based approach for this task. ChemLM further leverages self-supervised domain adaptation on chemical molecules to enhance its predictive performance across new domains of interest. Within the framework of ChemLM, chemical compounds are conceptualized as sentences composed of distinct chemical ‘words’, which are employed for training a specialized chemical language model. On the standard benchmark datasets, ChemLM has either matched or surpassed the performance of current state-of-the-art methods. Furthermore, we evaluated the effectiveness of ChemLM in identifying highly potent pathoblockers targeting Pseudomonas aeruginosa (PA), a pathogen that has shown an increased prevalence of multidrug-resistant strains and has been identified as a critical priority for the development of new medications. ChemLM demonstrated significantly higher accuracy in identifying highly potent pathoblockers against PA when compared to state-of-the-art approaches. An intrinsic evaluation demonstrated the consistency of the chemical language model’s representation concerning chemical properties. Our results from benchmarking, experimental data, and intrinsic analysis of the ChemLM space confirm the wide applicability of ChemLM for enhancing molecular property prediction within the chemical domain. | Georgios Kallergis; Ehsannedin Asgari; Behrooz Azarkhalili; Martin Empting; Anna Hirsch; Alice McHardy | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657cb14de9ebbb4db9fa0e13/original/domain-adaptable-language-modeling-of-chemical-compounds-identifies-potent-pathoblockers-for-pseudomonas-aeruginosa.pdf |
66cda3a520ac769e5ffc874a | 10.26434/chemrxiv-2024-fmbgk | UNIQUE: A Framework for Uncertainty Quantification Benchmarking | Machine learning (ML) models have become key in decision-making for many disciplines, including drug discovery and medicinal chemistry. ML models are generally evaluated prior to their usage for high-stake decisions, such as compound synthesis or experimental testing. However, no ML model is robust and predictive in all real-world scenarios. Therefore, uncertainty quantification (UQ) in ML predictions has gained importance in recent years. Many investigations have focused on developing methodologies that provide accurate uncertainty estimates for ML-based predictions. Unfortunately, there is no UQ strategy that consistently provides robust estimates about model’s applicability on new samples. Depending on the dataset, prediction task, and algorithm, accurate uncertainty estimations might be unfeasible to obtain. Moreover, the optimum UQ metric also varies across applications, and previous investigations have shown a lack of consistency across benchmarks. Herein, the UNIQUE (UNcertaInty QUantification bEnchmarking) framework is introduced to facilitate the comparison of UQ strategies in ML-based predictions. This Python library unifies the benchmarking of multiple UQ metrics, including the calculation of non-standard UQ metrics (combining information from the dataset and model), and providing a comprehensive evaluation. In such framework, UQ metrics are evaluated for different application scenarios, e.g. eliminate the predictions with the lowest confidence or obtain a reliable uncertainty estimate for an acquisition function. Taken together, this library will help to standardize UQ investigations and evaluate new methodologies. | Jessica Lanini; Minh Tam Davide Huynh; Gaetano Scebba; Nadine Schneider; Raquel Rodríguez-Pérez | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cda3a520ac769e5ffc874a/original/unique-a-framework-for-uncertainty-quantification-benchmarking.pdf |
60c74df9bdbb89bbfaa39acb | 10.26434/chemrxiv.12631496.v1 | The Discovery of Ketone-Based Covalent Inhibitors of Coronavirus 3CL Proteases for the Potential Therapeutic Treatment of COVID-19 | The novel coronavirus disease COVID-19 that emerged in 2019 is caused by the virus SARS CoV-2 and named for its close genetic similarity to SARS CoV-1 that caused severe acute respiratory syndrome (SARS) in 2002. Both SARS coronavirus genomes encode two overlapping large polyproteins which are cleaved at specific sites by a cysteine 3C-like protease (3CLpro) in a post-translational processing step that is critical for coronavirus replication. The 3CLpro sequences for CoV-1 and CoV-2 viruses are 100% identical in the catalytic domain that carries out protein cleavage. A research effort that focused on the discovery of reversible and irreversible ketone-based inhibitors of SARS CoV-1 3CLpro employing ligand-protease structures solved by X-ray crystallography led to the identification of 3 and 4. Preclinical experiments reveal 4 (PF-00835231) as a potent inhibitor of CoV-2 3CLpro with suitable pharmaceutical properties to warrant further development as an intravenous treatment for COVID-19. | Robert Hoffman; Robert S. Kania; Mary A. Brothers; Jay F. Davies; Rose A. Ferre; Ketan S. Gajiwala; Mingying He; Robert Jeff Hogan; Kirk Kozminski; Lilian Y. Li; Jonathan W. Lockner; Jihong Lou; Michelle T. Marra; Lennert J. Mitchell J. Mitchell Jr; Brion W. Murray; James A. Nieman; Stephen Noell; Simon P. Planken; Thomas Rowe; Kevin Ryan; George J. Smith III; James E. Solowiej; Claire M. Steppan; Barbara Taggart | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74df9bdbb89bbfaa39acb/original/the-discovery-of-ketone-based-covalent-inhibitors-of-coronavirus-3cl-proteases-for-the-potential-therapeutic-treatment-of-covid-19.pdf |
6637fa91418a5379b0885834 | 10.26434/chemrxiv-2024-j1xxr | Inner-bond-cleavage approach to figure-eight macrocycles from planar aromatic hydrocarbons | Contemporary synthetic strategies in organic chemistry rely heavily on the stepwise formation of bonds between fragments of the target compound (‘bottom-up’ approach). Figure-eight aromatic macrocycles represent a considerable challenge for the bottom-up approach, and the lack of versatile synthetic routes to such macrocycles prevents the use of their distinctive chiral D2-symmetric structures in advanced materials. Herein, we demonstrate the oxidative cleavage of internal double bonds of planar polycyclic aromatic hydrocarbons enables the scalable, catalytic, and enantioselective synthesis of figure-eight macrocycles. These macrocycles, with incorporated carbonyl groups, serve as a chiral electron-acceptor unit to furnish a thermally activated delayed fluorescence material with efficient circularly polarized luminescence. The inner-bond-cleavage approach is thus an effective alternative to the bottom-up approach, proving access to hitherto inaccessible materials. | Reiji Yoshina; Junichiro Hirano; Emiko Nishimoto; Yuki Sakamoto; Keita Tajima; Shunsuke Minabe; Muhammet Uyanik; Kazuaki Ishihara; Tomoyuki Ikai; Eiji Yashima; Takuya Omine; Fumitaka Ishiwari; Akinori Saeki; Jinseok Kim; Juwon Oh; Dongho Kim; Guanting Liu; Takuma Yasuda; Hiroshi Shinokubo; Norihito Fukui | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2024-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6637fa91418a5379b0885834/original/inner-bond-cleavage-approach-to-figure-eight-macrocycles-from-planar-aromatic-hydrocarbons.pdf |
6437a6a41d262d40ea5c75a7 | 10.26434/chemrxiv-2023-jskfd | Peptide-EBXs: Enabling Peptide Functionalization and Macrocyclization | Herein, we report a novel strategy for the modification of peptides based on the introduction of highly reactive hypervalent iodine reagents - ethynylbenziodoxolones (EBXs)- onto peptides. These peptide-EBXs can be easily accessed, both via solution and solid phase peptide synthesis (SPPS). They can be used to couple the peptide to other peptides or a protein via reaction with cysteine, leading to thioalkynes in organic solvents and hypervalent iodine adducts in water buffer. In addition, a photocatalytic decarboxylative coupling to the C-terminus of peptides was developed using an organic dye. This later reaction was also successful in an intramolecular way, leading to macrocyclic peptides of an unprecedented shape. The rigid linear aryl alkyne linker was essential to achieve high affinity to Keap1 at the Nrf2 binding site with potential protein-protein interaction inhibition. | Xingyu Liu; Xinjian Ji; Christian Heinis; Jerome Waser | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Biochemistry; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2023-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6437a6a41d262d40ea5c75a7/original/peptide-eb-xs-enabling-peptide-functionalization-and-macrocyclization.pdf |
Subsets and Splits
No saved queries yet
Save your SQL queries to embed, download, and access them later. Queries will appear here once saved.