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
⌀ |
|---|---|---|---|---|---|---|---|---|---|
66f2c333cec5d6c1420f1e8e
|
10.26434/chemrxiv-2024-mvvbc
|
A Critical Factor in Reactive Oxygen Species (ROS) Studies: The Need to Understand the Chemistry of the Solvent Used
|
Reactive oxygen species (ROS) play critical roles in normal physiological processes including cellular signaling and immune responses. Various pathological conditions including infections of various types, inflammation, cancer, and respiratory conditions are associated with elevated levels of ROS. Therefore, there is widespread interest in understanding ROS concentrations under various pathophysiological conditions for diagnostic and therapeutic applications including ROS-triggered drug delivery. However, in determining ROS concentration, there are major concerns of inappropriate use of various methods that lead to erroneous results; this has prompted the publication of a consensus paper in Nature Metabolism by a group of ROS experts stating “Unfortunately, the application and interpretation of these measurements are fraught with challenges and limitations. This can lead to misleading claims.” Along this line, we have identified an overlooked factor, which can significantly skew the results and results interpretation: the organic co-solvent. DMSO is one of the most widely used organic co-solvent to dissolve a reagent for bioassays. Herein, we describe the rapid oxidation of DMSO by hypochlorite and how this oxidation impacts results of ROS determination in buffer, cell culture media, cell culture, and cell lysates. We hope to use this one example to draw attention to the convoluted roles that DMSO and possibly other organic co-solvents can play and skew experimental results. We also hope to stimulate additional studies to bring more rigor to studying ROS concentration and biology.
|
Shubham Bansal; Binghe Wang
|
Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Analytical Chemistry - General; Chemical Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-09-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f2c333cec5d6c1420f1e8e/original/a-critical-factor-in-reactive-oxygen-species-ros-studies-the-need-to-understand-the-chemistry-of-the-solvent-used.pdf
|
66ec4c8351558a15ef7b45a2
|
10.26434/chemrxiv-2024-smx3g
|
Site-Selective C–H Bond Functionalization of Native Sugars
|
Non-typical C-functionalized sugars represent a prominent yet hardly accessible class of biologically-active compounds. The available synthetic methodologies towards such sugar derivatives suffer either from an extensive use of protecting groups, requiring long and laborious synthetic manipulations, or from limited predictability and non-controllable site-selectivity of the employed C-functionalization reactions. In this work, we disclose an alternative synthetic methodology towards non-typical sugars that allows facile, site-selective, and stereocontrolled C-functionalization of native sugars through a traceless tethering approach. The described silyl-based redox-active tethering group appends directly to the unprotected sugar substrate and mediates the C-functionalization reaction through a photochemically-promoted 1,6-hydrogen atom transfer (HAT) mechanism, while transforming into a readily-removable silyl protecting group. The protocol is compatible with a variety of unprotected carbohydrate substrates featuring sensitive aglycons and a diverse set of coupling partners, providing a straightforward and scalable route to pharmaceutically relevant C-functionalized carbohydrate conjugates.
|
Elena V. Stepanova; Andrey Shatskiy; Ivan Doroshenko; Peter Dinér; Markus D. Kärkäs
|
Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.)
|
CC BY 4.0
|
CHEMRXIV
|
2024-09-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ec4c8351558a15ef7b45a2/original/site-selective-c-h-bond-functionalization-of-native-sugars.pdf
|
6400d41863e8d44e594098bd
|
10.26434/chemrxiv-2023-c44ls
|
The Design, Synthesis, and Inhibition of Clostridioides difficile Spore Germination by Acyclic and Bicyclic Tertiary Amide Analogs of Cholate
|
Clostridioides difficile infection (CDI) is a major identifiable cause of antibiotic-associated diarrhea. In our previous study (J. Med Chem, 2018, 61, 6759-6778), we have identified N-phenyl-cholan-24-amide as a potent inhibitor of spore germination. The most potent compounds in our previous work are N-arylamides. We were interested in the role that the conformation of the amide plays in activity. Previous research has shown that secondary N-arylamides exist exclusively in the coplanar trans conformation while tertiary N-methyl-N-arylamides exist in a non-planar, cis conformation. The N-methy-N-phenyl-cholan-24-amide was 17-fold less active compared to the parent compounds suggesting the importance of the orientation of the phenyl ring. To lock the phenyl ring into a trans conformation, cyclic tertiary amides were prepared. Indoline and quinoline cholan-24-amides were both inhibitors of spore germination; however, the indoline analogs were most potent. Isoindoline and isoquinoline amides were inactive. We found that the simple indoline derivative gave an IC50 value of 1 M, while the 5-fluoro-substituted compound (5d) possessed an IC50 of 400 nM. To our knowledge, 5d is the most potent known spore germination inhibitor described to date. Taken together, our results indicate that the trans, coplanar conformation of the phenyl ring is required for potent inhibition.
|
Shiv Sharma; Angel Schilke; Jacqueline Phan; Christopher Yip; Prateek Sharma; Ernesto Abel-Santos; Steven Firestine
|
Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Microbiology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6400d41863e8d44e594098bd/original/the-design-synthesis-and-inhibition-of-clostridioides-difficile-spore-germination-by-acyclic-and-bicyclic-tertiary-amide-analogs-of-cholate.pdf
|
62334ce22c5010c4447e6554
|
10.26434/chemrxiv-2022-4knjf
|
Inter and Intramolecular Radical Additions of Aryl Halides Catalyzed by Diazaphospholenes
|
Diazaphospholenes have been widely used as hydride transfer catalysts, however their use in radical reactions and as photocatalysts is a recently emerging area. In this work, we show how stoichiometric radical cyclizations of aryl iodides mediated by diazaphospholene hydrides can be made catalytic by the combination of phenylsilane and alkali metal salts to regenerate the diazaphospholene hydride under the reaction conditions. The scope was expanded to include aryl bromides. These transformations required visible light irradiation, with twenty substrates undergoing cyclization, including a dearomative cyclization. Extension to six intermolecular radical hydroarylations with arenes, thiophenes, and a pyridine was also accomplished.
|
Robert Riley; Blake Huchenski; Karlee Bamford; Alex Speed
|
Catalysis; Organocatalysis; Photocatalysis; Redox Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62334ce22c5010c4447e6554/original/inter-and-intramolecular-radical-additions-of-aryl-halides-catalyzed-by-diazaphospholenes.pdf
|
66fd335412ff75c3a128dbdb
|
10.26434/chemrxiv-2024-lbnfw
|
“On-Water” enhanced base-catalytic oxidation of α-hydroxy ketone to diketone
|
The selective oxidation of alcohols to corresponding carbonyl compounds is essential in academia and industry. Benzil and BHMF have emerged as important classes of carbonyl compounds that have shown promising applications in materials and drug intermediates, especially in sustainable bio-based plastics. The traditional selective oxidation process generally uses equivalent amounts of oxidants or toxic reagents and generates a large amount of waste. Hence, it is very urgent to develop a greener, sustainable, practical, and industrially applicable selective oxidation process due to the environmental and sustainable requirements. Here, for the first time, we developed a water assistant base catalyzed selective oxidation of α-hydroxy ketone to the corresponding carbonyl compounds using air under mild reaction conditions. To the best of our knowledge, the only base K2CO3 catalytic selective oxidation of DHMF to BHMF under water using air as an oxidant has not been reported so far. Compared with the traditional selective oxidation, in this work, catalytic amounts of base, sustainable and green solvent water, and oxidant air were used for the first time.
|
Jian Han; Jie Wang; Jinsik Choi; Yong Xu; Jianguo Liu; Sang-Hyun Pyo
|
Catalysis
|
CC BY 4.0
|
CHEMRXIV
|
2024-10-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fd335412ff75c3a128dbdb/original/on-water-enhanced-base-catalytic-oxidation-of-hydroxy-ketone-to-diketone.pdf
|
64e818bc3fdae147fac33668
|
10.26434/chemrxiv-2023-w0z3r
|
Pulsed light induced trifluoromethylation of 1,3-dimethoxybenzene: A frequency controls chemoselectivity and chemical yield
|
Herein, we propose a new control method for photochemical reaction with the frequency of the light source as a parameter. Based on this proposal, we have developed a pulsed light induced trifluoromethylation reaction under the simple reaction condition which combined 1,3-dimethoxybenzene/anthraquinone/CF<sub>3</sub>SO<sub>2</sub>Na without any other additives, oxidant, and reductant. The yield and regioselectivity were improved and the excess reactions were also suppressed by pulsed light irradiation compared to use of conventional light source. Furthermore, it was found that the reaction yield and chemoselectivity changed with each frequency (length of light ON/OFF time) when only frequency of the pulsed light was varied from 1.4 x 10<sup>-5</sup> Hz (a period of 2 h on time and 18 h off time) to 10<sup>5</sup> Hz (a period of 1µs on time and 9 µs off time) while total irradiation time were fixed at 7200s for all reactions. The result shows that the pulsed light has the potential to control photochemical reactions and that the light irradiation method can be an important factor for the photochemical reaction in addition to conventional factor such as reagents, solution concentration, and temperature.
|
Mayaka Maeno; Katsuyuki Morii
|
Organic Chemistry; Photochemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e818bc3fdae147fac33668/original/pulsed-light-induced-trifluoromethylation-of-1-3-dimethoxybenzene-a-frequency-controls-chemoselectivity-and-chemical-yield.pdf
|
62392ca8d6d3ed023e9a498c
|
10.26434/chemrxiv-2022-k5xvx
|
An International Study Evaluating Elemental Analysis
|
A statistical study on C, H, N elemental analysis for 5 small organic compounds at 18 independent service providers across multiple countries demonstrates variation in the returned results that is outside journal guidelines (0.4%) in greater than 10% of measurements for C and N while H analyses return a high proportion of results within guidelines. The results clearly indicate that a deviation of 0.4% is not a realistic journal requirement for synthetic samples with the variability attributed to random error in the data collection process.
|
Jason Dutton; Rupert Kuveke; Lachlan Barwise; Yara van Ingen; Nicholas Roberts; Kanika Vashisth; Saurabh Chitnis; Caleb Martin; Rebecca Melen
|
Organic Chemistry; Analytical Chemistry; Organic Compounds and Functional Groups; Analytical Chemistry - General
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-03-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62392ca8d6d3ed023e9a498c/original/an-international-study-evaluating-elemental-analysis.pdf
|
60c743fd9abda2496af8c2d3
|
10.26434/chemrxiv.9733607.v1
|
Capturing Static and Dynamic Correlation with ΔNO-MP2 and ΔNO-CCSD
|
<p>The NO method for static correlation is combined with second-order Mller-Plesset perturbation theory (MP2) and coupled-cluster singles and doubles (CCSD) to account for dynamic correlation. The MP2 and CCSD expressions are adapted from nite-temperature CCSD, which includes orbital occupancies and vacancies, and expanded orbital summations. Correlation is partitioned with the aid of damping factors incorporated into the MP2 and CCSD residual equations. Potential energy curves for a selection of diatomics are in good agreement with extrapolated full conguration interaction results (exFCI), and on par with conventional multireference approaches.<br /></p>
|
joshua wallace hollett; Pierre-Francois Loos
|
Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-08-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743fd9abda2496af8c2d3/original/capturing-static-and-dynamic-correlation-with-no-mp2-and-no-ccsd.pdf
|
61f3c841191637319df6e304
|
10.26434/chemrxiv-2022-201jz
|
Biocatalytically active and stable cross-linked enzyme crystals of halohydrin dehalogenase HheG by protein engineering
|
A major drawback for practical application of halohydrin dehalogenase HheG in biocatalysis is its rather low thermal stability and low organic solvent tolerance. We therefore pursued a stabilization of HheG via immobilization as cross-linked enzyme crystals. Since glutaraldehyde inactivates HheG, we introduced a cysteine residue in the crystal interface, which enabled thiol-specific cross-linking at predefined cross-linking sites. Variant HheG D114C displayed improved crystallizability and yielded stable and catalytically active CLECs using bis-maleimidoethane as cross-linker. Effective cross-linking at the predefined site could be confirmed via the CLEC crystal structure. Compared to soluble enzyme, the CLECs displayed significantly improved stability and activity at higher temperatures, lower pH values and in the presence of water-miscible organic solvents, which enabled their reuse over 21 days in the azidolysis of cyclohexene oxide.
|
Marcel Staar; Steffi Henke; Wulf Blankenfeldt; Anett Schallmey
|
Catalysis; Biocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2022-01-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f3c841191637319df6e304/original/biocatalytically-active-and-stable-cross-linked-enzyme-crystals-of-halohydrin-dehalogenase-hhe-g-by-protein-engineering.pdf
|
611e25bfdff0ba60c5fb6fb1
|
10.26434/chemrxiv-2021-bnmmn
|
Self-limiting Nitrogen/Hydrogen Plasma Radical Chemistry in Plasma-Enhanced Atomic Layer Deposition of Cobalt
|
Cobalt (Co) is a potential candidate in replacing copper for interconnects and has been applied in the trenches in semiconductor industry over twenty years. A non-oxidizing reactant is required in plasma-enhanced atomic layer deposition (PE-ALD) of thin films of metals to avoid O-contamination. PE-ALD of Co has been demonstrated experimentally with plasma sources of NH3 or a mixture of N2 and H2, but the growth mechanism and key reactions are not clear. In this paper, we have investigated the reactions of plasma generated radicals H, N, NH and NH2 at metal precursor (CoCp2) terminated Co (001) and (100) surfaces using static DFT calculations at 0 K and molecular dynamics simulations at 600 K. N radicals play an important role in eliminating surface-bound Cp ligand (if any) via pyridine (C5H5N) formation and desorption, whereas H radicals have endothermic reactions for eliminating Cp ligand via CpH formation and desorption. The surface NHx species are eliminated by H radicals via NH3 formation and desorption. The simulations of these key reactions show that on Co(001) surface, the remaining Cp ligand and surface NHx species after the metal precursor pulse will be completely removed with N and H radicals, resulting in Co atoms deposited on Co(001) surface at a coverage of 3.03Co/nm2. Whereas, on Co(100) surface, the surface NH2 species cannot be completely removed via NH3 formation and desorption due to overall endothermic reactions. Instead, H radicals react with trench N species, contributed to H transfer at metal precursor pulse, to form NH. These trench N species cannot be eliminated completely on Co(100) surface, which will be the source of N impurities for the deposited Co thin films. At the post-plasma stage, the metal surface will be covered with NHx-terminations with plasma generated NH radicals, which is then ready for the next deposition cycle. Our results explain why ammonia or H2/N2 plasma, which produce NHx species are required to deposit Co thin films using Co metallocene precursors.
|
Ji Liu; Hongliang Lu; David Wei Zhang; Michael Nolan
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Processes; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2021-08-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611e25bfdff0ba60c5fb6fb1/original/self-limiting-nitrogen-hydrogen-plasma-radical-chemistry-in-plasma-enhanced-atomic-layer-deposition-of-cobalt.pdf
|
633731d1f764e6e535093041
|
10.26434/chemrxiv-2022-v5p6m-v3
|
Explaining molecular properties with natural language
|
We present a model-agnostic method that gives natural language explanations of molecular structure property predictions. Machine learning models are now common for molecular property prediction and chemical design. They typically are black boxes -- having no explanation for predictions. We show how to use surrogate models to attribute predictions to chemical descriptors and molecular substructures, independent of the black box model inputs. The method generates explanations consistent with chemical reasoning, like connecting existence of a functional group or molecular polarity. We see in a genuine test like blood brain barrier permeation, our descriptor explanations match biologically observed SARs with mechanistic support. We show these quantitative explanations can be further translated to natural language.
|
Heta A. Gandhi; Andrew D. White
|
Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633731d1f764e6e535093041/original/explaining-molecular-properties-with-natural-language.pdf
|
6615ae5291aefa6ce1359376
|
10.26434/chemrxiv-2024-dkvf8
|
3D-Pharma, A Ligand-based Virtual Screening tool
using 3D Pharmacophore Fingerprints
|
In this work, we introduced 3D-Pharma, a new Ligand-Based Virtual Screening method that uses fingerprints of pharmacophore triplets at atomic resolutions to build very simple and predictive models. Within 3D-Pharma the molecules are described by multiple representations that comprehend several prototropic species and conformations (multiple species, multiple mode approach). All the multiple representations of a compound are concatenated into a unique fingerprint that accounts for most of its chemical and conformational diversity. The biological activity of an ensemble of active molecules are represented by a single modal fingerprint or model, validated through a new exhaustive 10-fold cross-validation scheme, which improves robustness and internal consistency of the models, as well as its predictive power. We benchmark our method with 10 datasets of active compounds and decoys gathered from DUD database and compare its performance against seven state-of-the-art LBVS methods. To generate the models, we used three external and independent datasets of bioactive compounds (Drugs, PDB Ligands and WOMBAT). We concluded that 3D-Pharma overperforms all other state-of-the-art LBVS tools analyzed, in terms of global accuracy as well as scaffold hopping and early recovery capacities. Furthermore, the models produced by 3D-Pharma are simple, robust, consistent and predictive.
|
Bernardo F Domingues; Andrelly Martins-José; Julio CD LOPES
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Theory - Computational; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-04-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6615ae5291aefa6ce1359376/original/3d-pharma-a-ligand-based-virtual-screening-tool-using-3d-pharmacophore-fingerprints.pdf
|
60c74e5ff96a0020bb287ae1
|
10.26434/chemrxiv.12745097.v1
|
Extensive Screening of Green Solvents for Safe and Sustainable UiO-66 Synthesis
|
<p>Zirconium based Metal-Organic Framework
UiO-66 is to date considered one of the benchmark compound among stable MOFs
and it has attracted a huge attention for its employment in many strategic
applications. Large scale production of UiO-66 for industrial purposes requires
the use of safe and green solvents, fulfilling the green chemistry principles
and able to replace the use of <i>N,N</i>-Dimethyl-Formamide (DMF), which,
despite its toxicity, is still considered the most efficient solvent for
obtaining UiO-66 of high quality. Herein we report on a survey of about 40
different solvents with different polarity, boiling point and acidity, used for
the laboratory scale synthesis of high quality UiO-66 crystals. The solvents
were chosen according the European REACH
Regulation 1907/2006 among those having low cost, low
toxicity and fully biodegradable. Concerning MOF synthesis, the relevant
parameters chosen for establishing the quality of the results obtained are the
degree are the crystallinity, microporosity and specific surface area,
yield and solvent recyclability. Taking into account also the chemical physical
properties of all the solvents, a color code was assigned in order to give a
final green assessment for the UiO-66 synthesis. Defectivity of the obtained products, the use
of acidic modulators and the use of alternative Zr-salts have been also taken
into consideration. Preliminary
results lead to conclude that GVL (γ-valerolactone) is among the most promising
solvents for replacing DMF in UiO-66 MOF synthesis. </p>
|
Diletta Morelli Venturi; Filippo Campana; Fabio Marmottini; Ferdinando Costantino; Luigi Vaccaro
|
Coordination Chemistry (Inorg.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e5ff96a0020bb287ae1/original/extensive-screening-of-green-solvents-for-safe-and-sustainable-ui-o-66-synthesis.pdf
|
6386301194ff60aab943fc5a
|
10.26434/chemrxiv-2022-gd84k
|
Direct Imaging of Micrometer Thick Interfaces in Salt-Salt Aqueous Biphasic Systems
|
Unlike the interface between two immiscible electrolyte solutions (ITIES) formed between water and polar solvents, molecular understanding of the liquid-liquid interface formed for aqueous biphasic systems (ABSs) is relatively limited and mostly relies on surface tension measurements and thermodynamic models. Here, high-resolution Raman imaging is used to provide spatial and chemical resolution of the interface of LiCl-LiTFSI-water and HCl-LiTFSI-water, prototypical salt-salt ABSs found in a range of electrochemical applications. The concentration profiles of both TFSI anions and water are found to be sigmoidal, in agreement with an increasing surface tension as a function of concentration, both being typical of a negative adsorption mechanism. More striking, however, is the length at which the concentration profiles extend, ranging from 11 to 2 m with increasing concentrations, compared to a few nanometers for ITIES. We thus reveal that unlike ITIES, salt-salt ABSs do not have a molecularly sharp interface but rather form an interphase with a gradual change of environment from one phase to the other. This knowledge represents a major stepping-stone in the understanding of aqueous interfaces, key for mastering ion or electron transfer dynamics in a wide range of biological and technological settings including novel battery technologies such as membraneless redox flow and dual ion batteries.
|
Damien Degoulange; Raj Pandya; Michael Deschamps; Dhyllan Skiba; Betar Gallant; Sylvain Gigan; Hilton de Aguiar; Alexis Grimaud
|
Physical Chemistry; Inorganic Chemistry; Analytical Chemistry; Interfaces
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-11-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6386301194ff60aab943fc5a/original/direct-imaging-of-micrometer-thick-interfaces-in-salt-salt-aqueous-biphasic-systems.pdf
|
65fac53d66c138172962dc12
|
10.26434/chemrxiv-2024-dnmq7
|
Measuring density and viscosity of vanadium electrolytes: An exhaustive database with multivariate polynomial fits
|
The variation of the physical properties of vanadium electrolytes during vanadium redox flow batteries (VRFB) operation is known to have a significant impact on the flow of the electrolytes both in the cells and in the tanks. This study presents extensive accurate measurements of the density and viscosity of vanadium electrolytes for VRFBs spanning a four-dimensional parameter space, including State of Charge (SoC), total vanadium concentration, total sulfate concentration, and temperature. The experimental results reveal different trends in the density variations of the posolyte and negolyte. Specifically, while the density of the posolyte slightly increases with SoC, that of the negolyte decreases more significantly. Furthermore, temperature exerts a linear influence on the density of both electrolytes. The analysis also reveals complex and non-linear dependencies between viscosity and the parameters under study, with more pronounced variations being observed at higher vanadium concentrations. In particular, the viscosities of both electrolytes are seen to decrease with SoC, the viscosity of the negolyte being consistently higher than that of the posolyte. We also present multivariate regression fits accurately capturing the variations of electrolyte properties, aiming to provide valuable insights into the dynamic behavior of vanadium electrolytes and enable more accurate physics-based mathematical models.
|
Pablo Ángel Prieto-Díaz; Ange A. Maurice; Marcos Vera
|
Energy; Energy Storage
|
CC BY 4.0
|
CHEMRXIV
|
2024-03-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fac53d66c138172962dc12/original/measuring-density-and-viscosity-of-vanadium-electrolytes-an-exhaustive-database-with-multivariate-polynomial-fits.pdf
|
61724874ac379f032eb83268
|
10.26434/chemrxiv-2021-2x2tt
|
The Effect of Zero-Point Energy in Simulating Organic Reactions with Post-Transition State Bifurcation
|
Ambimodal reactions involve a single transition state leading to multiple products. To assess the ratio of the bifurcation products, quasiclassical trajectories (QCTs) are initiated from transition state geometries that are randomly sampled using the zero-point energy (ZPE) plus thermal energy of a molecule’s vibrational modes. However, in the QCTs, the influence of ZPE percentage in the resulting bifurcation ratio and time gap between formation of bonds is not well understood. To benchmark the effect of varying the percentage of the molecules’ inherent ZPE used in the simulation, three organic reactions with distinct mechanisms that all display post-transition state bifurcation were selected. The three reactions studied include an intramolecular [6+4]/[4+2] cycloaddition, an asynchronous nitrene insertion, and an SN2/addition to a carbonyl on an α-bromoketone. These reactions encompass various modes of bond formation and cleavage, offering a broad view of the influence of ZPE scaling in evaluating the product ratio resulted from post-transition state bifurcation. This work will establish a basis for future QCT studies of organic reactions.
|
Matthew Tremblay; Zhongyue John Yang
|
Theoretical and Computational Chemistry; Physical Chemistry; Physical and Chemical Processes
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-10-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61724874ac379f032eb83268/original/the-effect-of-zero-point-energy-in-simulating-organic-reactions-with-post-transition-state-bifurcation.pdf
|
60c7584d567dfe0ed4ec6828
|
10.26434/chemrxiv.14535315.v1
|
The Effect of Added Ligands on the Reactions of [Ni(COD)(dppf)] with Alkyl Halides: Halide Abstraction can be Reversible
|
The reactions of dppf-nickel(0) with alkyl halides proceed via three-coordinate nickel(0) intermediates of the form [Ni(dppf)(L)]. The effect of the identity of the added ligand (L) on catalyst speciation and the rates of reactions of [Ni(COD)(dppf)] with alkyl halides has been investigated using kinetic experiments and DFT calculations. A series of monodentate ligands have been investigated in attempts to identify trends in reactivity. Sterically bulky and electron donating ligands are found to decrease the reaction rate. It was found that (i) the halide abstraction step is not always irreversible, and the subsequent recombination of a nickel(I) complex with an alkyl halide can have a significant effect on the overall rate of the reaction; and (ii) some ligands lead to very stable<br />[Ni(dppf)(L) 2 ] species. The yields of prototypical (dppf)nickel-catalysed Kumada cross-coupling reactions of alkyl halides are significantly improved by the addition of free ligand, which provides another important variable to consider when optimizing nickel-catalysed reactions of alkyl halides.
|
Megan Greaves; Thomas O. Ronson; Feliu Maseras; David Nelson
|
Physical Organic Chemistry; Computational Chemistry and Modeling; Homogeneous Catalysis; Bond Activation; Catalysis; Kinetics and Mechanism - Organometallic Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7584d567dfe0ed4ec6828/original/the-effect-of-added-ligands-on-the-reactions-of-ni-cod-dppf-with-alkyl-halides-halide-abstraction-can-be-reversible.pdf
|
641d8ace62fecd2a835d1b9c
|
10.26434/chemrxiv-2023-g1b0d
|
Modular Synthesis of Bicyclic Twisted Amides and Anilines
|
Bridged amides and anilines display interesting properties owing to perturbation of conjugation of the nitrogen lone-pair with the adjacent π-system. A convergent approach to diazabicyclic scaffolds which contain either twisted amides or anilines is described, based on the photocatalysed hydroamination of cyclic enecarbamates and subsequent cyclisation. The modular nature of the synthesis allows for variation of the degree of ‘twist’ and hence the properties of the amides and anilines.
|
Alexandra Hindle; Krzysztof Baj; Jonathan Iggo; Daniel Cox; Christopher Pask; Adam Nelson; Stephen Marsden
|
Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.)
|
CC BY 4.0
|
CHEMRXIV
|
2023-03-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641d8ace62fecd2a835d1b9c/original/modular-synthesis-of-bicyclic-twisted-amides-and-anilines.pdf
|
67cda39081d2151a02bc5ea0
|
10.26434/chemrxiv-2025-fgr52
|
Scalable DOS-like Strategy to the δ-Amino Acids via Petasis/Cross Metathesis Reactions Sequence
|
A convenient and scalable approach to N-protected δ,δ-spirosubstituted δ-amino acids and their α,β-unsaturated analogues from bulk ketones was elaborated. The proposed routes include Petasis reaction of starting ketone with allylboronic acid pinacol ester and methanolic ammonia and cross metathesis with methyl acrylate or acrylic acid as key steps. The developed protocols are novel, robust and economically efficient, they avoid tedious separation and purification and were scaled up to 40 g of final compounds from a single synthetic run.
|
Мaksym Herasymchuk; Anastasiia Fedinchyk; Kostiantyn Melnykov; Eugeniy Ostapchuk; Tetiana Druzhenko; Dmytro Volochnyuk; Serhiy Ryabukhin
|
Organic Chemistry; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cda39081d2151a02bc5ea0/original/scalable-dos-like-strategy-to-the-amino-acids-via-petasis-cross-metathesis-reactions-sequence.pdf
|
6696d46801103d79c5315ccd
|
10.26434/chemrxiv-2024-9vl3w
|
High pH and Temperature Tolerant Molecular Mimics of Carbonic Anhydrase Towards Long-Term Carbonate Production in Enzymatic Construction Material
|
We recently applied carbonic anhydrase (CA) for the rapid catalytic conversion of carbon dioxide to enable the self-healing properties of concrete and in the development of a carbon-negative concrete replacement named Enzymatic Construction Material (ECM). Here, we explore the stability and carbonate generation ability of model molecular mimics of carbonic anhydrase under high pH and elevated temperatures relevant to long-term durability in cementitious and concrete-like materials. Molecular mimics include Zn2+-based organometallic complexes with an aromatic ligand tris(2-pyridylmethyl)amine, TPA, and with an aliphatic ligand cyclen, 1,4,7,10-tetraazacyclododecane. The Zn(TPA) and Zn(cyclen) complexes are stable in aqueous environments at standard pressures ranging from neutral to pH 13 and temperatures up to 120 °C, where CA is inactive. Under the temperature and pH conditions studied, organometallic degradation pathways do not involve the decomposition of either organic ligand, but rather dissociation of the complex that is reversible upon neutralization in the case of Zn(TPA). Zn(cyclen) is stable at high temperatures at pH 12 and above, resembling cementitious conditions for over 365 days with no signs of degradation. Separately, alkaline calcium-containing solutions with either 25 nM CA or 5 mM Zn(cyclen) catalyst demonstrated accelerated pH decreases compared to catalyst-free controls upon sparging with carbon dioxide because of the conversion of CO2 and H2O to HCO3– and H+. Notably, the inclusion of sub-molar concentrations of detergents, such as sodium dodecyl sulfate, in carbonate production reactions demonstrated no change in the reactivity of control solutions or those with the Zn(cyclen) catalyst, but severely attenuated the conversion in CA-containing solutions concomitant with CA denaturation and loss of enzymatic activity.
|
Rebecca J. Gilchrist; Peter G. Oni; Nima Rahbar; Suzanne F. Scarlata; Ronald L. Grimm
|
Physical Chemistry; Catalysis; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6696d46801103d79c5315ccd/original/high-p-h-and-temperature-tolerant-molecular-mimics-of-carbonic-anhydrase-towards-long-term-carbonate-production-in-enzymatic-construction-material.pdf
|
6791211c81d2151a026368d9
|
10.26434/chemrxiv-2025-kl68b
|
On the Role and Reality of Digital Reference Materials
|
The emergence of Laboratory 4.0 and digital twin technologies necessitates reconsideration of how reference materials (RMs) can support modern analytical workflows. Digital reference materials (dRMs), existing as validated digital twins of physical standards, represent the convergence of traditional metrology and modern information technology, enabling new quality assurance and quality control workflows. To translate the inherent promise of dRMs into analytical reality, this work aims to set a framework for their implementation and validation. In doing so, this paper attempts to clear the air regarding the understanding and harmonization of terms and concepts for practitioners across academia, industry, and regulatory bodies and provides practical examples of dRMs in analytical workflows. This work examines important considerations from a quality assurance perspective, mapping the requirements of ISO 17034 for the production of reference materials. Furthermore, it also proposes performance characteristics for evaluating dRMs, i.e., establishing confidence that digital “signatures” and their associated uncertainties are fit for contemporary analytical challenges. The discussion encompasses both technical and quality assurance aspects, addressing the needs of analytical chemists facing the challenges of digital transformation in their daily work. The integration of physical standards with their digital twins opens a pandora’s box of applications including high-throughput screening, non-targeted methods, digital proficiency testing and real-time process control in modern analytical laboratories. This transformation addresses contemporary challenges in analytical chemistry while preserving the fundamental role of RMs in ensuring measurement reliability and traceability.
|
Kapil Nichani; Frederik Fleissner; Bertrand Colson; Coralie Leonard; Steffen Uhlig
|
Analytical Chemistry; Chemoinformatics; Spectroscopy (Anal. Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6791211c81d2151a026368d9/original/on-the-role-and-reality-of-digital-reference-materials.pdf
|
60c743dd4c89191994ad26f7
|
10.26434/chemrxiv.9679028.v1
|
Protein Flexibility Catalyzes a Cell Signaling Reaction of the Ras-GAP Complex
|
Many enzyme molecules exhibit characteristic global and slow dynamics which furnish them with allostery realizing remarkable molecular functionalities more than simple chemical catalysis. However, molecular mechanism of a catalytic reaction associated with the molecular flexibility of enzymes is not well-understood. Here we report a hybrid molecular simulation study on GTPase activity of a Ras-GAP protein complex for cell signaling termination. We unveiled that extensive conformational changes of the protein complex and exclusion of internal water molecules are induced upon the transition state (TS) formation in the catalytic reaction and significantly lower the reaction activation free energy. We also revealed that tumor-related mutations perturb those conformational changes upon the TS formation, leading to reduction of the catalytic activity. The findings of the remarkably dynamic protein conformation directly linking to the catalytic reaction have broad implications for understanding of enzyme mechanism and for developments of allosteric drugs and novel catalysts.
|
Keiei Kumon; Masahiro Higashi; Shinji Saito; Shigehiko Hayashi
|
Biochemistry; Bioinformatics and Computational Biology; Biophysics; Computational Chemistry and Modeling; Biocatalysis; Biophysical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-08-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743dd4c89191994ad26f7/original/protein-flexibility-catalyzes-a-cell-signaling-reaction-of-the-ras-gap-complex.pdf
|
631b72c949042af13dd19f67
|
10.26434/chemrxiv-2022-h60w1
|
An improved protocol for the selection of structures from molecular dynamics of organic systems in solution: the value of investigating different wavelet families
|
Wavelets are mathematical tools used to decompose and represent another function described in the time domain, allowing the study of each component of the original function with a scale-compatible resolution. Thus, these transforms have been used to select conformations from Molecular Dynamics (MD) trajectories in systems of fundamental and technological interest. Recently our research group has used wavelets to develop and validate a method, meant to select structures from MD trajectories, which we named OWSCA (Optimal Wavelet Signal Compression algorithm). Here we moved forward on this project by demonstrating the efficacy of this method on the study of 3 different systems (non-flexible organic, flexible organic and protein). For each system, 93 wavelets were investigated in order to verify which is the best one for a given organic system. The results show that the best wavelets were different for each system and, also, very close to the experimental values, with the wavelets db1, rbio 3.1 and bior1.1 being selected for the non-flexible, flexible organic, and protein systems, respectively. This reinforces our OWSCA as a very efficient and promising method for the selection of structures from MD trajectories of different classes of compounds. Our findings also point out that additional studies considering wavelets families is needed for defining the best wavelet for representing each system under study.
|
Mateus Gonçalves; Arlan Gonçalves; Tanos Franca; Mozarte Santana; Elaine da Cunha; Teodorico de Ramalho
|
Physical Chemistry; Quantum Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631b72c949042af13dd19f67/original/an-improved-protocol-for-the-selection-of-structures-from-molecular-dynamics-of-organic-systems-in-solution-the-value-of-investigating-different-wavelet-families.pdf
|
6583142be9ebbb4db95c9dc7
|
10.26434/chemrxiv-2023-5jxq7-v2
|
Implementation of FAIR Practices in Computational Metabolomics Workflows - A Case Study
|
Scientific workflows facilitate the automation of data analysis tasks by integrating various software and tools executed in a particular order. To enable transparency and reusability in workflows, it is essential to implement the FAIR principles. Here, we describe our experiences implementing the FAIR principles for metabolomics workflows using Metabolome Annotation Workflow (MAW) as a case study. MAW is specified using the Common Workflow Language (CWL), allowing for the subsequent execution of the workflow on different workflow engines. MAW is registered using CWL description on WorkflowHub with the DOI https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.510.2. During the submission process on WorkflowHub, a CWL description is used for packaging MAW using the Workflow RO-Crate profile, which includes metadata in Bioschemas. Researchers can use the instructions presented in this snapshot as a base template to adopt FAIR practices for their bioinformatics or cheminformatics workflows while incorporating necessary amendments specific to their research area.
|
Mahnoor Zulfiqar; Michael R. Crusoe; Birgitta König-Ries; Christoph Steinbeck; Kristian Peters; Luiz Gadelha
|
Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-12-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6583142be9ebbb4db95c9dc7/original/implementation-of-fair-practices-in-computational-metabolomics-workflows-a-case-study.pdf
|
614b8a8e6fc3a89d92a9b35b
|
10.26434/chemrxiv-2021-jxxbh-v2
|
EHreact: Extended Hasse Diagrams for the Extraction and Scoring of Enzymatic Reaction Templates
|
Data-driven computer-aided synthesis planning utilizing organic or biocatalyzed reactions from large databases has gained increasing interest in the last decade, sparking the development of numerous tools to extract, apply and score general reaction templates. The generation of reaction rules for enzymatic reactions is especially challenging, since substrate promiscuity varies between enzymes, causing the optimal levels of rule specificity and optimal number of included atoms to differ between enzymes. This complicates an automated extraction from databases and has promoted the creation of manually curated reaction rule sets. Here we present EHreact, a purely data-driven open-source software tool to extract and score reaction rules from sets of reactions known to be catalyzed by an enzyme at appropriate levels of specificity without expert knowledge. EHreact extracts and groups reaction rules into tree-like structures, Hasse diagrams, based on common substructures in the imaginary transition structures. Each diagram can be utilized to output a single or a set of reaction rules, as well as calculate the probability of a new substrate to be processed by the given enzyme by inferring information about the reactive site of the enzyme from the known reactions and their grouping in the template tree. EHreact heuristically predicts the activity of a given enzyme on a new substrate, outperforming current approaches in accuracy and functionality.
|
Esther Heid; Samuel Goldman; Karthik Sankaranarayanan; Connor W. Coley; Christoph Flamm; William H. Green
|
Theoretical and Computational Chemistry; Catalysis; Chemoinformatics - Computational Chemistry; Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-09-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614b8a8e6fc3a89d92a9b35b/original/e-hreact-extended-hasse-diagrams-for-the-extraction-and-scoring-of-enzymatic-reaction-templates.pdf
|
6476241a4f8b1884b78ce44c
|
10.26434/chemrxiv-2023-xvqfx
|
Effects of pH/Nicotine, Refill Fluid, Cigarette Type, and Storage on Element/Metal Concentrations in Electronic Cigarette Fluids and Aerosols
|
The concentrations of metals, acids, nicotine, and flavor chemicals were analyzed in four refill fluids before and after vaping in third-and-fourth-generation electronic cigarettes (ECs), and the effect of storing fluids in ECs on element/metal concentrations was determined. Metals and organic chemicals were analyzed using inductively coupled plasma optical emission spectroscopy, HPLC, and GC/MS. Maleic, benzoic, propionic, and citric acid were the refill fluid (0.032 to 5.498 mg/mL). Nickel, zinc, tin, selenium, silicon, copper, and lead were often in refill fluids before and after heating and in aerosols. Third generation ECs and low pH fluids generally had the highest concentrations of metals in their fluids and aerosols. Thirty flavor chemicals were in at least one refill fluid. During storage, metal concentrations in EC fluids increased significantly by 28 days and increased exponentially over 387 days. After storage, EC fluids with the lowest pH often had the highest concentrations of nickel, zinc, lead, and tin. The acids and increase in metals after heating and storage are a health concern that could contribute to respiratory diseases. These data support the need for providing date-of-manufacture on packaging, regulating acids/metals in ECs, and better understanding of the effects of EC metals/acids on human health.
|
Monique Williams; Wentai Luo; Kevin McWhirter; Krassimir Bozhilov ; Prue Talbot
|
Organic Chemistry; Inorganic Chemistry; Minerals
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-06-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6476241a4f8b1884b78ce44c/original/effects-of-p-h-nicotine-refill-fluid-cigarette-type-and-storage-on-element-metal-concentrations-in-electronic-cigarette-fluids-and-aerosols.pdf
|
624f3c55505f63929e6e74f1
|
10.26434/chemrxiv-2022-3r6jj
|
Solvent-free Synthesis of polymethoxy and dichloro p-nitrophenyl hydrazones
|
A solvent-free method for the synthesis of novel p-nitrophenyl hydrazones was successfully developed. The condensation of the p-nitrophenyl hydrazine with aromatic aldehydes through this mechanochemical technique furnished three products (3a-c) with moderate to high yield. The developed method is eco-friendly, efficient, simple, and convenient and indicated high reproducibility, short reaction time, catalyst-free, simple workup, and afforded pure and unsolvated products.
|
Sodeeq Babalola; Abdullah Idris; Yeken Sani; Asmau Hamza; Nosakhare Igie; Hayatudeen Muhammad; Gowin Erumiseli; Lateef Bakare
|
Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-04-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624f3c55505f63929e6e74f1/original/solvent-free-synthesis-of-polymethoxy-and-dichloro-p-nitrophenyl-hydrazones.pdf
|
62723e99bdc9c29f4ced4dd6
|
10.26434/chemrxiv-2022-sqnl1-v3
|
Thioester Mediated Biocatalytic Amide Bond Synthesis with In Situ Thiol Recycling
|
The conversion of carboxylic acids to thioesters is a key step in the biosynthesis of natural products, resulting in activation of the acyl groups for a broad range of subsequent biochemical reactions, such as acylations and alkylations. In particular, the thioesters of Coenzyme A (CoA-SH) play disproportionate roles in many metabolic pathways, from fatty acids, polyketides and peptides to epigenetic post-translational modifications, such as N-, O- and S-acylations of proteins. However, lack of access to a broad range of structurally diverse thioesters and the structural complexity of CoA-SH have limited the wider exploitation of thioesters in biochemistry, cell biology and biotechnology. Here we report an in-situ recycling system of thioesters from free carboxylic acids that aims to address these challenges. We show that the adenylation domain of the carboxylic acid reductase from Segniliparus rugosus (CARsr-A) can function as an efficient and robust acyl-S-CoA synthetase, accepting a wide range of carboxylic acids as substrates. In addition, CARsr-A was able to generate thioesters from structurally simpler thiols such as pantetheine. The resulting thioesters were shown to be substrates for acyltransferases leading to diverse amides, including more challenging targets such as pharmaceutically relevant aryl amides. Importantly, CoA-SH is regenerated in situ and can be used in sub-stoichiometric quantities. In a further application, the histone-derived peptide H4-20 was successfully acylated via thioester activation with a range of natural and unnatural ‘clickable’ carboxylic acids, by combination with the epigenetic ‘writer’ lysine acetyltransferase HATp300. Overall, this broad-spectrum biocatalyst for thioester synthesis, allowing in-situ CoA-SH recycling in combination with a range of thioester-dependent enzymes, provides a generic platform for thioester-dependent cell-free biosynthesis, with potential to open up applications beyond amide bond formation.
|
Christian Schnepel; Laura Rodriguez-Perez; Yuqi Yu; Antonio Angelastro; Rachel S. Heath; Max Lubberink; Francesco Falcioni; Keith Mulholland; Martin A. Hayes; Nicholas J. Turner; Sabine L. Flitsch
|
Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Bioorganic Chemistry; Chemical Biology; Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-05-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62723e99bdc9c29f4ced4dd6/original/thioester-mediated-biocatalytic-amide-bond-synthesis-with-in-situ-thiol-recycling.pdf
|
60c743f5ee301c9b50c790a6
|
10.26434/chemrxiv.9715955.v1
|
A Simple Nickel Catalyst Enables Broad E-Selective Alkyne Semihydrogenation
|
A simple and commercially available nickel catalyst for E-selective alkyne semihydrogenation is presented. The protocol is practical and encompasses a wide variety of internal alkynes, with aryl and alkyl substituents tolerated alike.
|
Niklas O. Thiel; Benyapa Kaewmee; Trung Tran Ngoc; Johannes F. Teichert
|
Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-08-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743f5ee301c9b50c790a6/original/a-simple-nickel-catalyst-enables-broad-e-selective-alkyne-semihydrogenation.pdf
|
6746af8d7be152b1d0ffc5ce
|
10.26434/chemrxiv-2024-hpqb7-v2
|
Proton first: rationalizing a proton transfer in a protein-fragment complex
|
We present a combination of experimental and theoretical approaches to decipher the molecular recognition event of benzoic acid complexed with Protein Kinase A. The publicy known crystal structure suggests the protonated form of benzoic acid to be complexed with Protein Kinase A. Such a protonation pattern of is unlikely for benzoic acid in aqueous enviromnent and must be induced by complexation to Protein Kinase. Unfortunately, isothermal titration calorimetry does not reveal any binding event which might be caused by the low affinity. However, Poisson Boltzmann calculations and molecular dynamics simulations strengthen the initial hypothesis.
|
Helge Vatheuer; Lisa Johannknecht; Rebecca Maria Ziora; Gerald Keller; Jonas Paulus; Lukas Stelzl; Paul Czodrowski
|
Biological and Medicinal Chemistry; Biochemistry; Drug Discovery and Drug Delivery Systems
|
CC BY 4.0
|
CHEMRXIV
|
2024-11-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6746af8d7be152b1d0ffc5ce/original/proton-first-rationalizing-a-proton-transfer-in-a-protein-fragment-complex.pdf
|
622f93612d837498ac81e3b5
|
10.26434/chemrxiv-2022-4glgt
|
Selective and Reversible Polysulfide-macrocycle Binding at Modified Membranes Suppress Shuttling in Lithium Sulfur Batteries
|
Lithium sulfur (LiS) batteries are among the next generation of rechargeable batteries offering high energy densities. Obstacles remain for their practical application, such as capacity fading and low Coulombic efficiency resulting from shuttling and reaction of polysulfides with the Li anode. A new supramolecular approach to suppress shuttling using reversible binding of anionic polysulfides, e.g., S3•–, S62–, S72–, S82–, by anion-selective receptors, called cyanostar (CS) macrocycles is reported. Standard separators were coated with the macrocycles and formed chemically selective membranes. Unlike adsorption materials and non-selective supramolecular approaches, cyanostar provides a well-defined molecule-to-molecule mechanism to capture polysulfides as host-guest complexes like (CS)2•S3•– and (CS)4•S72–. Permselectivity emerges from reversibly binding polysulfides inside the membrane to prevent anions passing while allowing cations to pass. Controls using macrocycles that are not selective for anions do not stop shuttling. Cyanostar-coated membranes turn on charging, reduce capacity fading from 0.51 to 0.36% per cycle and improve Columbic efficiency to 85%. These improvements occur even without addition of lithium nitrate used almost universally to inhibit reactions with the Li anode. This new strategy showcases the benefits of using selective receptors to manage movement of ions in sulfur-based batteries.
|
Christopher Benson; Yi Cui; Wei Guo; Wei Zhao; Jonathan Karty; Likun Zhu; Yongzhu Fu; Amar Flood
|
Energy; Energy Storage; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622f93612d837498ac81e3b5/original/selective-and-reversible-polysulfide-macrocycle-binding-at-modified-membranes-suppress-shuttling-in-lithium-sulfur-batteries.pdf
|
63ea0e2a1d2d18406369d2e8
|
10.26434/chemrxiv-2023-13q43
|
Exploring Temperature Effects in All-Vanadium Redox Flow
Batteries through a Validated Unit-Cell Model
|
Redox flow batteries are a promising electrochemical technology for large-scale stationary energy storage.
Continuous macroscopic models address the design and operational challenges required to increase their
profitability and energy market penetration. Controlling the battery operating temperature and avoiding
cell overheating are two primary ways to ensure optimal overall efficiency. This work presents a nonisothermal
two-dimensional steady-state model of a unit-cell all-vanadium redox flow battery. The model
is validated using polarization and open circuit voltage measurements at different temperatures and states
of charge. After calibration, a parametric study is used to explore the role of operating temperature on cell
performance, deconvoluting the different contributions to cell heating, and providing practical guidance
about the thermal effects of operating conditions. The results reveal that increasing the operating
temperature improves species mass transfer but negatively affects activation losses; the cell suffers higher
overheating during charge than during discharge; and cell length has a proportional effect on cell heating.
Lastly, we propose the use of asymmetric electrolyte temperatures as a performance improvement strategy
for electrochemical storage systems hybridized with thermal energy storage. The results show that nonisothermal
models are a powerful tool for optimizing advanced electrochemical flow reactors in energy
storage devices.
|
Vanesa Muñoz-Perales; Santiago E. Ibáñez; Enrique García-Quismondo; Sabrina Berling; Marcos Vera
|
Energy; Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-02-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ea0e2a1d2d18406369d2e8/original/exploring-temperature-effects-in-all-vanadium-redox-flow-batteries-through-a-validated-unit-cell-model.pdf
|
60c74b8df96a003f1b28761e
|
10.26434/chemrxiv.12339317.v1
|
Data-driven analysis of the number of Lennard-Jones types needed in a force field
|
<p>We optimized force fields with smaller and
larger sets of chemically motivated Lennard-Jones types against the
experimental properties of organic liquids. Surprisingly, we obtained results as good as or
better than those from much more complex typing schemes from exceedingly
simple sets of LJ types; e.g. a model with only two types of hydrogen and
only one type apiece for carbon, nitrogen and oxygen.</p><p>The results justify sharply limiting the number of
parameters to be optimized in future force field development work, thus
reducing the risks of overfitting and the difficulties of reaching a global
optimum in the multidimensional parameter space. They thus increase our chances of arriving at well-optimized
force fields that will improve predictive accuracy, with applications in
biomolecular modeling and computer-aided drug design. The results also prove the feasibility and value of a
rigorous, data-driven approach to advancing the science of force field
development.</p>
|
Michael Schauperl; Sophie Kantonen; Lee-Ping Wang; Michael Gilson
|
Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b8df96a003f1b28761e/original/data-driven-analysis-of-the-number-of-lennard-jones-types-needed-in-a-force-field.pdf
|
63c13a054fba70226b0416be
|
10.26434/chemrxiv-2023-mf7zd
|
Dynamics of the energy transfer involved in a diarylethene-perylenebisimide dyad: comparison between the molecule and the nanoparticle level
|
Photochromic materials are widely used to achieve fluorescence photoswitching. Understanding the energy transfer processes that occur in these systems would be an advantage for their use and a better optimization of their properties. In this scope, we studied a diarylethene-perylenebisimide (DAE-PBI) dyad that presents a bright red emission and a large ON-OFF contrast, both in solution and in an aqueous suspension of nanoparticles (NPs). Using ultrafast transient absorption spectroscopy, the excited state dynamics and the FRET processes were characterized for this dyad in THF solution and compared to its behavior in NPs state, disclosing an efficient energy transfer (ET) in NPs.
|
Nicolas Fabre; Tsuyoshi Fukaminato; Arnaud Brosseau; Michel SLIWA; Rémi Métivier
|
Physical Chemistry; Nanoscience; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-01-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c13a054fba70226b0416be/original/dynamics-of-the-energy-transfer-involved-in-a-diarylethene-perylenebisimide-dyad-comparison-between-the-molecule-and-the-nanoparticle-level.pdf
|
60c73ecd469df48279f42914
|
10.26434/chemrxiv.6990053.v2
|
Theoretical and Experimental Investigation of the Stability Limits of Quinones in Aqueous Media: Implications for Organic Aqueous Redox Flow Batteries
|
<div>
<div>
<p>Quinone-hydroquinone pairs have been proposed as biologically-inspired, low-cost redox couples for organic electrolytes for electrical energy storage, particularly in aqueous redox flow batteries. In their oxidized form, quinones are electrophiles that can react with the nucleophilic water solvent resulting in loss of active electrolyte. Here we study two mechanisms of nucleophilic addition of water, one reversible and one irreversible, that limit quinone performance in practical flow batteries. Using a combination of density functional theory and semi-empirical calculations, we have quantified the source of the instability of quinones in water, and explored the relationships between chemical structure, electrochemical reduction potential, and decomposition or instability mechanisms. By combining these computational estimates with the experimental study of the aqueous stability of alizarin-derived quinones, quantitative thresholds for chemical stability of oxidized quinones were established. Finally, ∼140,000 prospective quinone pairs (over 1,000,000 calculations including decomposition products) were analyzed in a virtual screening using the learned design principles. Our conclusions suggest that numerous low reduction potential molecules are stable with respect to nucleophilic addition, but promising high reduction potential molecules are much rarer. This latter fact suggests the existence of a stability cliff for this family of quinone-based organic molecules, which challenges the development of all-quinone aqueous redox flow batteries.<br /></p>
</div>
</div>
|
Daniel P. Tabor; Rafael Gomez-Bombarelli; Liuchuan Tong; Roy G. Gordon; Michael J. Aziz; Alan Aspuru-Guzik
|
Physical Organic Chemistry; Computational Chemistry and Modeling; Theory - Computational; Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-08-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ecd469df48279f42914/original/theoretical-and-experimental-investigation-of-the-stability-limits-of-quinones-in-aqueous-media-implications-for-organic-aqueous-redox-flow-batteries.pdf
|
64e32c8a694bf1540cb764c5
|
10.26434/chemrxiv-2023-nm09n-v2
|
Synthetic glycans reveal determinants of antibody functional efficacy against a fungal pathogen
|
Antibodies play a vital role in the immune response to infectious diseases and can be administered passively to protect patients. In the case of Cryptococcus neoformans, a WHO fungal critical priority pathogen, infection results in antibodies targeting capsular glucuronoxylomannan (GXM). These antibodies produce diverse outcomes, however the molecular basis for antigen recognition remain unknown. To address this, we constructed a microarray containing twenty-six glycans representative of those found in highly virulent cryptococcal strains and utilised it to study sixteen monoclonal antibodies with distinct in vivo functions. Notably, protective and non-protective antibodies shared conserved reactivity to the M2 motif of GXM, irrespective of their origin from infection or vaccination. Interestingly, only two antibodies (12A1 and 18B7) exhibited diverse tri-valent GXM motif reactivity. Additionally, IgG subclass antibodies associated with protective responses showed cross-reactivity to at least two GXM motifs. The specificity and affinity of glycan binding were modulated by somatic mutation (12A1) and isotype switching (3E5 and 4H3), subsequently influencing their functional effects. This enhanced understanding of antibody binding epitopes was used to map the antigenic diversity of two Cryptococcus neoformans strains. Our results highlight the exceptional complexity of fungal capsular polysaccharides and underscore the imperative for developing multi-GXM motif vaccines. Such a vaccine holds the potential to elicit a comprehensive and effective immune response capable of neutralising the vast antigenic diversity presented by cryptococcal capsules.
|
Conor J. Crawford; Lorenzo Guazzelli; Scott A. McConnell; Orla McCabe; Clotilde d'Errico; Seth Greengo; Maggie P. Wear; Anne J. Jedlicka; Arturo Casadevall; Stefan Oscarson
|
Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Chemical Biology; Microbiology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e32c8a694bf1540cb764c5/original/synthetic-glycans-reveal-determinants-of-antibody-functional-efficacy-against-a-fungal-pathogen.pdf
|
641866e92bfb3dc251111cc4
|
10.26434/chemrxiv-2023-6r565-v2
|
Electroreductive Desulfurative Transformations with Thioethers as Alkyl Radical Precursors
|
Herein, the use of aryl alkyl thioethers as precursors for C-centered alkyl radicals is demonstrated for desulfurative C-H and C-C bond formation under electroreductive conditions. The transformations occur with complete selectivity for C(sp3)-S bond cleavage, orthogonal to that of transition metal-catalyzed two-electron routes. Experimental and theoretical studies provide mechanistic insights that serve as a steppingstone for future use of thioethers as efficient radical precursors that can outcompete their established sulfone analogues.
|
Julius Kuzmin; Johannes L. Röckl; Nils Schwarz; Jonas Djossou; Guillermo Ahumada; Mårten Ahlquist; Helena Lundberg
|
Organic Chemistry; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641866e92bfb3dc251111cc4/original/electroreductive-desulfurative-transformations-with-thioethers-as-alkyl-radical-precursors.pdf
|
65a3e7f866c13817296b9036
|
10.26434/chemrxiv-2024-2gddb
|
Estribec: Fast, Precise Estimation of Stribeck Curves in Tribology
|
Tribology is the study on friction, wear and lubrication for contacting and moving two solid materials with fluid lubricants. Friction can be found easily in our life and should be reduced, and lubricants are a powerful answer for this purpose. The mechanism behind friction and lubrication has been primarily analyzed by the Stribeck curve, which should be 1) interpretable, 2) non-homogeneous in variances and 3) a mixture of Stribeck curves further. We propose a machine learning approach, Estribec, to estimate the Stribeck curves from observed data in tribology. Estribec is, considering all above three characteristics, a finite mixture model, with a component of a piecewise function, where
each piece is a comprehensible simple (primarily, linear)
function with a unique variance. Entirely our method keeps linear time complexity for all processes, including parameter estimation and prediction. Empirical results with synthetic data showed Estribec achieved favorable predictive performance against Gaussian process regression (GPR) and its tree variant (TGPR). Importantly Estribec ran always around 20 to 150 times faster than GPR and TGPR, which would be a sizable difference for conducting high-throughput experiments. Finally Estribec showed latent properties of real data which would be useful for tribology research.
|
Kei-ichiro Takahashi; Keita Sakakibara; Hiroshi Watanabe; Yoshinobu Tsujii; Hiroshi Mamitsuka
|
Theoretical and Computational Chemistry; Materials Science; Polymer Science; Polymer brushes; Machine Learning; Artificial Intelligence
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a3e7f866c13817296b9036/original/estribec-fast-precise-estimation-of-stribeck-curves-in-tribology.pdf
|
60c750b1567dfebe89ec58ee
|
10.26434/chemrxiv.13070588.v1
|
Automatic Generation of 3D Printed Reactionware for Chemical Synthesis Digitization using ChemSCAD
|
<p>Digital
chemistry aims to define a hard link from the top abstraction layer in
chemistry down to the synthesis, but this is difficult in traditional glassware
since it is not possible to explicitly link the architecture with the unit
operations. By 3D printing the synthesis modules in the precise order to affect
the synthesis, it is possible to create digitally encoded reactors for chemical
synthesis in ‘reactionware’. However, creation of these devices requires a
specific skillset for CAD modelling which few synthetic chemists have. Herein,
we describe an intuitive system, ChemSCAD, for the creation of digital reactor
models based on the chemical operations, physical parameters and synthetic
sequence to produce a given target compound. We demonstrate the ability of the
ChemSCAD system to translate the gram-scale batch synthesis of the anti-viral
compound Ribavirin (yield 43% over three steps), the narcolepsy drug Modafinil
(yield 60% over three steps), and both batch and flow instances of the
synthesis of the anti-cancer agent Lomustine (batch yield 65% over two steps) in
purities ≥96%. The syntheses of compounds developed using the
ChemSCAD system, including reactor designs and analytical data, can be stored
in a single database repository where all the information necessary to
critically evaluate, and improve upon, reactionware syntheses can be easily
shared and versioned.</p>
|
Wenduan Hou; Andrius Bubliauskas; Philip Kitson; Jean-Patrick Francoia; Henry powell-Davies; Juan Manuel ParrillaGutierrez; Przemysław Frei; Sebastian Manzano; Leroy Cronin
|
Computational Chemistry and Modeling; Process Control; Reaction Engineering; Robotics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-10-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750b1567dfebe89ec58ee/original/automatic-generation-of-3d-printed-reactionware-for-chemical-synthesis-digitization-using-chem-scad.pdf
|
61856d6792abe0ba4336367d
|
10.26434/chemrxiv-2021-4g8w7-v3
|
Protein unfolding in freeze frames: intermediate states are revealed by variable temperature ion mobility-mass spectrometry.
|
The gas phase is an idealized laboratory for the study of protein structure, from which it is possible to examine stable and transient forms of mass selected ions in the absence of bulk solvent. With ion mobility-mass spectrometry (IM-MS) apparatus built to operate at both cryogenic and elevated temperatures, we have examined the conformational transitions of the monomeric proteins: ubiquitin, lysozyme and alpha-synuclein as a function of temperature and in source activation. We rationalize the experimental observations with a temperature dependent framework model and comparison to known conformers. Data from ubiquitin shows unfolding transitions that proceed through diverse and highly elongated intermediate states, which converge to more compact structures. These findings contrast with data obtained from lysozyme – a protein where (un)-folding plasticity is restricted by four disulfide linkages, although this is alleviated in its reduced form. For structured proteins, collision activation of the protein ions in- source, enables subsequent “freezing” or thermal annealing of unfolding intermediates whereas disordered proteins restructure substantially at 250 K even without activation, indicating that cold denaturation can occur without solvent. These data are presented in the context of a toy model framework which describes the relative occupancy of the available conformational space.
|
Jakub Ujma; Jacquelyn Jhingree; Emma Norgate; Rosie Upton; Xudong Wang; Florian Benoit; Bruno Bellina; Perdita Barran
|
Physical Chemistry; Analytical Chemistry; Mass Spectrometry; Biophysical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-11-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61856d6792abe0ba4336367d/original/protein-unfolding-in-freeze-frames-intermediate-states-are-revealed-by-variable-temperature-ion-mobility-mass-spectrometry.pdf
|
63b0a85216e9a865273b2fab
|
10.26434/chemrxiv-2023-1pm15
|
Electron and Ion Transport in Semi-Dilute Conjugated
Polyelectrolytes: View from a Quantum-Mechanically
Informed Coarse-Grained Model
|
Conjugated polyelectrolytes (CPEs) are a rising class of organic mixed ionic-electronic conductors,
with applications in bio-interfacing electronics and energy harvesting and storage devices. Here,
we employ a quantum mechanically informed coarse-grained model coupled with semiclassical rate
theory to generate a first view of semidilute CPE morphologies and their corresponding ionic and
electronic transport properties. We observe that the poor solvent quality of CPE backbones drives
the formation of electrostatically repulsive fibers capable of forming percolating networks at semi-
dilute concentrations. The thickness of the fibers and the degree of network connectivity are found to
strongly influence the electronic mobilities of the morphologies. Calculated structure factors reveal
that fiber formation alters the position and scaling of the inter-chain PE peak relative to good
solvent predictions and induces a narrower distribution of interchain spacings. We also observe that
electrostatic interactions play a significant role in determining CPE morphology, but have only a
small impact on the local site energetics. This work presents a significant step forward in the ability
to predict CPE morphology and ion-electron transport properties, and provides insights into how
morphology influences electronic and ionic transport in conjugated materials.
|
David Friday; Nicholas Jackson
|
Theoretical and Computational Chemistry; Polymer Science; Conducting polymers; Polymer chains; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-01-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b0a85216e9a865273b2fab/original/electron-and-ion-transport-in-semi-dilute-conjugated-polyelectrolytes-view-from-a-quantum-mechanically-informed-coarse-grained-model.pdf
|
658a93719138d231618a45a6
|
10.26434/chemrxiv-2023-hch07-v2
|
Stereoselective Hydroxyallylation of Cyclopropenes with Cyclopropanols via NHC Catalysis of Transient Organozinc Species
|
A stereoselective hydroxyallylation reaction of cyclopropenes with cyclopropanols is achieved under zinc-mediated conditions, affording densely functionalized cyclopropanes with excellent diastereocontrol over three contiguous stereocenters within and outside the cyclopropane ring. A racemic variant of the reaction is synergistically promoted by catalytic N-heterocyclic carbene (NHC) and organic base (DBU), whereas chiral amino alcohol-derived bifunctional NHC enables a catalytic enantioselective variant. Mechanistically, the reaction features transient generation of enolized zinc homoenolate via ring-opening of zinc cyclopropoxide and enolization of the resulting homoenolate, followed by its addition to the cyclopropene as a prochiral allylzinc nucleophile.
|
Kento Tsukiji; Arimasa Matsumoto; Kazuya Kanemoto; Naohiko Yoshikai
|
Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Homogeneous Catalysis; Main Group Chemistry (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658a93719138d231618a45a6/original/stereoselective-hydroxyallylation-of-cyclopropenes-with-cyclopropanols-via-nhc-catalysis-of-transient-organozinc-species.pdf
|
62de373b724581459aa65dab
|
10.26434/chemrxiv-2022-q76km-v2
|
One-pot catalysis from renewable resources: A direct route to recyclable camphor-based polycarbonates
|
To solve some of the environmental problems associated with oil extraction and make plastics production sustainable, there is increasing interest in developing selective methods to convert renewable feedstocks into monomers suitable for polymer production. Here we present a catalytic one-pot synthesis of polycarbonates from renewable resources. This approach relies on the use of a commercially available magnesium catalyst that allows the coupling of diethyl carbonate with a rigid camphor-based diol. In combination with a solvent-free polymerization, this sequence can also be extended to different diols , providing direct access to a new library of unique polycarbonates. Additionally, chemical recycling of these polycarbonates could be triggered by magnesium-catalyzed methanolysis.
|
Bo Jiang; Christophe Thomas
|
Polymer Science; Polymerization (Polymers)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-07-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62de373b724581459aa65dab/original/one-pot-catalysis-from-renewable-resources-a-direct-route-to-recyclable-camphor-based-polycarbonates.pdf
|
60c753ebbb8c1a1a9d3dc142
|
10.26434/chemrxiv.13578140.v1
|
GNINA 1.0: Molecular Docking with Deep Learning
|
Molecular docking computationally predicts the conformation of a small molecule when binding to a receptor. Scoring functions are a vital piece of any molecular docking pipeline as they determine the fitness of sampled poses. Here we describe and evaluate the 1.0 release of the Gnina docking software, which utilizes an ensemble of convolutional neural networks (CNNs) as a scoring function. We also explore an array of parameter values for Gnina 1.0 to optimize docking performance and computational cost. Docking performance, as evaluated by the percentage of targets where the top pose is better than 2A root mean square deviation (Top1), is compared to AutoDock Vina scoring when utilizing explicitly defined binding pockets or whole protein docking. Gnina, utilizing a CNN scoring function to rescore the output poses, outperforms AutoDock Vina scoring on redocking and cross-docking tasks when the binding pocket is defined (Top1 increases from 58% to 73% and from 27% to 37%, respectively) and when the whole protein defines the binding pocket (Top1 increases from 31% to 38% and from 12% to 16%, respectively). The derived ensemble of CNNs generalizes to unseen proteins and ligands and produces scores that correlate well with the root mean square deviation to the known binding pose. We provide the 1.0 version of Gnina under and open source license for use as a molecular docking tool at https://github.com/gnina/gnina.
|
Andrew McNutt; Paul Francoeur; Rishal Aggarwal; Tomohide Masuda; Rocco Meli; Matthew Ragoza; Jocelyn Sunseri; David Koes
|
Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-01-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753ebbb8c1a1a9d3dc142/original/gnina-1-0-molecular-docking-with-deep-learning.pdf
|
63ce918d1a1eadaba6b4b3b3
|
10.26434/chemrxiv-2023-62xjd
|
Scaling Supercapacitive Swing Adsorption of CO2 Using Bipolar Electrode Stacks
|
Supercapacitive Swing Adsorption (SSA) modules with bipolar stacks having 2, 4, 8 and 12 electrode pairs made from BPL 4x6 activated carbon were constructed and tested for carbon dioxide capture applications. Tests were performed with simulated flue gas (15%CO2 /85%N2) at 2, 4, 8 and 12 V, respectively. Reversible adsorption with sorption capacities (~58 mmol·kg-1) and adsorption rates (~38 µmol·kg-1·s-1) were measured for all stacks. The productivity scales with the number cells in the module, and increases from 70 to 390 mmol.h-1m-2. Energy efficiency and the energy consumption improved with increasing number of electrodes from 67% to 84%, and 142 to 60 kJ·mol-1, respectively. Overall, the results show that SSA modules with bipolar electrodes can be scaled without reducing the adsorptive performance, and with improvement of energetic performance.
|
Jiajie Li; Muhammad Bilal; Kai Landskron
|
Energy; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science
|
CC BY 4.0
|
CHEMRXIV
|
2023-01-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ce918d1a1eadaba6b4b3b3/original/scaling-supercapacitive-swing-adsorption-of-co2-using-bipolar-electrode-stacks.pdf
|
60c757f3702a9b700018cbcc
|
10.26434/chemrxiv.14474346.v1
|
Quantum Theoretical and Computational Controlling for Corral at Matter Surface
|
In physics and chemistry realms, the exciting quantum
field would play a major role.Particularly, quantum
control area should have significant and powerful development tendency. With a numerous attempts in a variety of fields, the extremely frontier area move forward to
control elementary particles. Lasting effects must boost
the appearing of breakthrough soonerafter. As is well
known, a mount of milestone works lie on the controlling of atomic and molecules dynamics. Naturally, future researches will concentrate in quantum controlling
at nucleus scale.
|
Quan-Fang Wang
|
Physical and Chemical Properties; Quantum Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757f3702a9b700018cbcc/original/quantum-theoretical-and-computational-controlling-for-corral-at-matter-surface.pdf
|
634550e62e6e7cdf6556daac
|
10.26434/chemrxiv-2022-m1wz3
|
3D Printed Electrochemical Multiwell Plate for Monitoring Food Intolerance from Intestinal Organoids
|
Common symptoms of food intolerance are caused by chemical components within food that have a pharmacological activity to alter the motility of the gastrointestinal tract. Food intolerance is difficult to diagnose as it requires a long-term process of eliminating foods that are responsible for gastrointestinal symptoms. Enterochromaffin (EC) cells are key intestinal epithelium cells that respond to luminal chemical stimulants by releasing 5-HT. Changes in 5-HT levels have been shown to directly alter the motility of the intestinal tract. Therefore, a rapid approach for monitoring the impact of chemicals in food components on 5-HT levels can provide a personalised insight into food intolerance and help stratify diets. Within this study we developed a 3D printed electrochemical multiwell plate to determine changes in 5-HT levels from intestinal organoids that were exposed to varying chemical components found in food. The carbon black/poly-lactic acid (CB/PLA) electrodes had a linear range in physiological concentrations of 5-HT (0.1 – 2µM) with a limit of detection of 0.07 µM. The electrodes were stable for monitoring 5-HT overflow from intestinal organoids. Using the electrochemical multiwell plate containing intestinal organoids, increases in 5-HT were observed in the presence of 0.1 mM cinnamaldehyde and 10 mM quercetin but reduction in 5-HT levels was observed in 1 mM sorbitol when compared to control. These changes in the presence of chemicals commonly found in food were verified with ex vivo ileum tissue measurements using chromatography and amperometry with boron-doped diamond electrodes. Overall, our 3D electrochemical multiwell plate measurements with intestinal organoids highlight an approach that can be a high-throughput platform technology for rapid screening of food intolerance to provide personalised nutritional diet.
|
Emily Brooks; Khalil Hussain; Khushboo Kotecha; Aya Abdalla; Bhavik Patel
|
Analytical Chemistry; Biochemical Analysis; Electrochemical Analysis; High-throughput Screening
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634550e62e6e7cdf6556daac/original/3d-printed-electrochemical-multiwell-plate-for-monitoring-food-intolerance-from-intestinal-organoids.pdf
|
60c755fb9abda2bd6df8e475
|
10.26434/chemrxiv.14178755.v1
|
Photoinduced Nickel-Catalyzed Deaminative Cross-Electrophile Coupling
|
<div>The construction of carbon-carbon bonds through cross-coupling between two electrophiles in the absence of excess metallic reducing agents is a desirable objective in chemistry. Here, we show that <i>N</i>-alkylpyridinium salts can be efficiently merged with aryl or alkyl halides in an intermolecular fashion, affording products in up to 90%</div><div>yield at ambient temperature. These reactions harness the ability of <i>N</i>-alkylpyridinium salts to form electron donor-acceptor complexes with Hantzsch esters, enabling photoinduced single-electron transfer and fragmentation to afford alkyl radicals that are subsequently trapped by a Ni-based catalytic species to promote C(sp<sup>2</sup>)-C(sp<sup>3</sup>) and</div><div>C(sp<sup>3</sup>)-C(sp<sup>3</sup>) bond formation. The operationally simple protocol is applicable to site-selective cross-coupling and tolerates diverse functional groups, including those that are sensitive towards metal reductants.</div>
|
Tao Yang; Yi Wei; Ming Joo Koh
|
Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755fb9abda2bd6df8e475/original/photoinduced-nickel-catalyzed-deaminative-cross-electrophile-coupling.pdf
|
60c7495ebb8c1a3a823dae1c
|
10.26434/chemrxiv.12056127.v1
|
Synthesis of an Oxathiolane Drug Substance Intermediate Guided by Constraint Driven Innovation
|
A new route was developed for construction of the
oxathiolane intermediate used in the synthesis of lamivudine (3TC) and
emtricitabine (FTC). We developed the presented route by constraining ourselves
to low cost, widely available starting materials – we refer to this as supply
centered synthesis. Sulfenyl chloride chemistry was used to construct the
framework for the oxathiolane from acyclic precurors. This bond construction
choice enabled the use of chloroacetic acid, vinyl acetate, sodium thiosulfate
and water to produce the oxathiolane.
|
Komirishetty Kashinath; David Snead; Justina Burns; Rodger W. Stringham; B. Frank Gupton; D. Tyler McQuade
|
Organic Synthesis and Reactions; Process Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7495ebb8c1a3a823dae1c/original/synthesis-of-an-oxathiolane-drug-substance-intermediate-guided-by-constraint-driven-innovation.pdf
|
67d16c3dfa469535b9f817cf
|
10.26434/chemrxiv-2025-24d4d
|
Stable Ferrocenium Molecular Wires
|
Open-shell molecular wires offer prospects for achieving enhanced transport, additional functionality, efficient thermoelectric conversion, and they attract attention for future applications as spin qubits. The synthesis of such compounds as bench-stable species is however inherently challenging due to their high reactivity, and their integration into electronic/spintronic devices is complicated by charge transfer phenomena that can erase the open-shell state. Ferrocenium cations can be isolated as bench-stable species in combination with a variety of anions, and we demonstrate here that they can also be integrated in single-molecule devices with preservation of their unique electronic structure, by using molecular designs that prevent strong electronic coupling to the electrodes. The open-shell character grants significantly more efficient charge transport than their close-shell counterparts, along with non-linear current-voltage behaviour even at relatively low biases. Quantum transport calculations show that additional resonances appear in the transmission spectra upon oxidation at energies closer to the Fermi level of the electrodes, leading to increased conductance. These findings present further prospects for the applications of these materials in molecular spintronics and quantum thermoelectrics.
|
Linlin Hou; Varshini Kumar; Munirah Alsaqer; Adam Larbi; Abdalghani Daaoub; Amit Sil; Stephen Moggach; Sara Sangtarash; Richard Nichols; Hatef Sadeghi; Paul Low; Andrea Vezzoli
|
Physical Chemistry; Nanoscience; Nanodevices; Physical and Chemical Properties; Transport phenomena (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d16c3dfa469535b9f817cf/original/stable-ferrocenium-molecular-wires.pdf
|
6514a2750065940912012b39
|
10.26434/chemrxiv-2023-96bfp
|
Single electron-controlled motions of single molecules
|
In the domain of single-molecule dynamics, we investigate the impact of electrostatic forces on molecular motion. Our study delves into the interplay between quantum mechanics and electrostatic interactions, resulting in trajectories reminiscent of planetary motion and gravity-assisted acceleration. By employing state-dependent diffusion and Green's functions, we establish a robust theoretical foundation that explains quantum control over molecules. We find that surface charge density critically influences diffusion coefficients, following linear scaling similar to Coulombic forces. Our research extends the range of observed diffusion coefficients, reaching up to 6000 µm2ms-1. These findings have practical applications in materials science and molecular engineering. This study advances our understanding of molecular motion and highlights the potential for precise control over single-molecule dynamics through quantum manipulation—an exploration at the nanoscale.
|
Divyam Neer Verma; KV Chinmaya; Moumita Ghosh; Jan R. Heck; G Mohan Rao; Sonia Contera; Siddharth Ghosh
|
Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Nanofluidics; Electrochemistry - Mechanisms, Theory & Study; Interfaces
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-09-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6514a2750065940912012b39/original/single-electron-controlled-motions-of-single-molecules.pdf
|
60c757fd9abda25306f8e81d
|
10.26434/chemrxiv.14483517.v1
|
Uncovering the Release of Micro/nanoplastics from Disposable Face Masks at Times of COVID-19
|
<p>This study aims to assess the
environmental impact of discarded
face masks, that are a source of emerging concern as indicated by most recent
literature, although still little investigated. Herein we evaluated micro- and
nanoplastic particles that can be released from face mask once subject to
environmental conditions. Exposure to simulated-low shear forces demonstrated
to be effective in breaking and fragmenting face mask tissue into smaller
debris. Even at low shear
energy densities, a single mask could release in water thousands of microplastic
fibers and up to 10^11 submicrometric particles. The latter were
quantified using flow cytometry that was proven to be a promising technique for nanoplastic
counting, thus improving our understanding on distribution and fate of NPs
still representing a great analytical challenge in plastic pollution research. </p>
|
Silvia Morgana; Barbara Casentini; Stefano Amalfitano
|
Environmental Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757fd9abda25306f8e81d/original/uncovering-the-release-of-micro-nanoplastics-from-disposable-face-masks-at-times-of-covid-19.pdf
|
66f6b4e651558a15ef51db4e
|
10.26434/chemrxiv-2024-q9l5z
|
Accelerating Fragment Based Drug Discovery using Grand Canonical Nonequilibrium Candidate Monte Carlo
|
Fragment-based drug discovery is a popular approach in academia and industry for the early stages of drug development. Computational tools have become integral to these campaigns and provide a route to library design, virtual screening, the identification of putative small molecule binding sites, the elucidation of binding geometries, and the prediction of accurate binding affinities. Molecular dynamics-based simulations have become increasingly popular, but are often limited by sampling issues related to the simulation timescales obtainable. Here, we expand the use of grand canonical nonequilibrium candidate Monte Carlo (GCNCMC) to overcome these limitations and accurately predict the binding sites, modes, and affinities of fragment-like molecules. GCNCMC has been used previously to accurately predict the location of water molecules in protein-ligand systems, by attempting the insertion and deletion of water to, or from, a region of interest; each proposed move is subject to a rigorous acceptance test based on the thermodynamic properties of the system. Here, we demonstrate the ability of fragment-based GCNCMC to rapidly and reliably find occluded experimental fragment binding sites. We also show that the method can accurately sample multiple fragment binding modes without any prior knowledge of their existence. Finally, we calculate the binding affinities for fragment molecules to three systems. We find that our results are in agreement with a more established method, namely absolute binding free energy calculations. Notably, GCNCMC does not require the use of complex restraints, the handling of multiple binding modes, or post-hoc symmetry corrections. Rather, binding sites, geometries and affinities all arise naturally from a series of GCNCMC simulations.
|
William Poole; Marley Samways; Davide Branduardi; Richard Taylor; Marcel Verdonk; Jonathan Essex
|
Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Statistical Mechanics
|
CC BY 4.0
|
CHEMRXIV
|
2024-09-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f6b4e651558a15ef51db4e/original/accelerating-fragment-based-drug-discovery-using-grand-canonical-nonequilibrium-candidate-monte-carlo.pdf
|
6331ea3fe665bd2ec8139e52
|
10.26434/chemrxiv-2022-z39qc
|
Physics-Guided Curve Fitting for ab Initio Diatomic Spectroscopy
|
When using ab initio calculations to predict the spectra of diatomic molecules, discrete ab initio data must be converted to continuous form. As in other applications of interpolation throughout science and engineering, high-resolution (i.e., fine-mesh) data are desirable so that the method of interpolation does not affect the final results. However, high-resolution data are seldom available, because of their high cost. Current practice to is use splines, polynomials, or Morse-like fitting functions for interpolation and even for extrapolation. The choice is arbitrary and affects the spectroscopic results more than is generally recognized. Here we suggest an alternative procedure, in which the physics of the problem is leveraged to provide more robust results. A high-resolution data set, from a less costly ab initio model of the system of interest, is used as a guiding function. The residuals must still be fitted using splines or polynomials, but the smaller magnitude and weaker structure of the residuals leads to improved stability and accuracy of the spectroscopic results. When two or more guiding potentials are available, they can be used to guide the selection of geometries to be computed at high level, thus improving computational efficiency.
|
Karl Irikura
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY 4.0
|
CHEMRXIV
|
2022-09-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6331ea3fe665bd2ec8139e52/original/physics-guided-curve-fitting-for-ab-initio-diatomic-spectroscopy.pdf
|
60c7410a337d6c3cf3e267e8
|
10.26434/chemrxiv.7916270.v1
|
Specific Ion Effects on Hydrogen-Bond Rearrangements in the Halide–Dihydrate Complexes
|
<div>
<div>
<div>
<p>Small aqueous ionic clusters represent ideal systems to investigate the microscopic hydrogen-bonding structure and dynamics in ion hydration shells. In this context, halide-dihydrate complexes are the smallest systems where the interplay between halide–water and water–water
interactions can be studied simultaneously. Here, quantum molecular dynamics simulations
unravel specific ion effects on the temperature-dependent structural transition in X<sup>-</sup>(H<sub>2</sub>O)<sub>2</sub> complexes (X = Cl, Br and I) which is induced by the breaking of the water–water hydrogen
bond. A systematic analysis of the hydrogen-bonding rearrangements at low temperature provides fundamental insights into the competition between halide–water and water–water interactions depending on the properties of the halide ion. While the halide–water hydrogen-bond
strength decreases going from Cl<sup>-</sup>(H<sub>2</sub>O)<sub>2</sub> to I<sup>-</sup>(H<sub>2</sub>O)<sub>2</sub>, the opposite trend in observed in the
strength of the water–water hydrogen-bond, suggesting that non-trivial many-body effects may
also be at play in the hydration shells of halide ions in solution, especially in frustrated systems
(e.g., interfaces) where the water molecules can have dangling OH bonds.</p>
</div>
</div>
</div>
|
Pushp Bajaj; Debbie Zhuang; Paesani Lab
|
Computational Chemistry and Modeling; Theory - Computational; Clusters; Solution Chemistry; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-04-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7410a337d6c3cf3e267e8/original/specific-ion-effects-on-hydrogen-bond-rearrangements-in-the-halide-dihydrate-complexes.pdf
|
62887f8687d01f2eb4ecc368
|
10.26434/chemrxiv-2022-3gk9x
|
City’s infectious disease treatment with antimicrobial agents – a longitudinal one year study of antimicrobials in two cities via wastewater-based epidemiology
|
Antimicrobial resistance (AMR) is one of the most significant global health threats. Inappropriate and over-usage of antimicrobial agents (AAs) is a major driver for AMR. Wastewater-based epidemiology (WBE) is a promising tool for monitoring AA usage in communities. Two urban catchment areas have been investigated in this study, one city and one small town in the Southwest of the UK over a 13-month period in 2018-2019. Population normalised loads (PNDLs) of 17 AAs and metabolites have been calculated and compared to catchment specific prescription data. Correction factors (CFs) have been applied to several AAs and metabolites in order to back-calculate consumption at the community level and compare to the corresponding catchment prescription data. Results have demonstrated positive correlations for all quantifiable parent AAs and metabolites in wastewater, and spatial variability in AA usage was observed even in neighbouring urban areas. The application of correction factors demonstrated good agreement for several of the studied AAs, including clarithromycin, oxytetracycline, trimethoprim, hydroxy metronidazole, and acetyl sulfamethoxazole. It was noted that in general, the larger population city gave closer agreement to estimated prescription intake than the smaller town. Differences in wastewater and between prescription data could be due to variable prescribing patterns and potential lack of compliance of AAs at the community level. This study has demonstrated that data triangulation, of both prescription data and wastewater data, provides the most comprehensive approach to understanding AA usage in communities.
|
Natalie Sims; Elizabeth Holton; Kishore Jagadeersan; Richard Standerwick; Ruth Barden; Barbara Kasprzyk-Hordern
|
Biological and Medicinal Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Hydrology and Water Chemistry; Wastes; Environmental Analysis
|
CC BY 4.0
|
CHEMRXIV
|
2022-05-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62887f8687d01f2eb4ecc368/original/city-s-infectious-disease-treatment-with-antimicrobial-agents-a-longitudinal-one-year-study-of-antimicrobials-in-two-cities-via-wastewater-based-epidemiology.pdf
|
65baa4409138d23161251797
|
10.26434/chemrxiv-2024-b59sd
|
Which Interfaces Matter Most? A Non-monotonic Relationship between Grain Boundary Defect Chemistry and Ionic Conductivity in a Concentrated Solid Electrolyte
|
High-conductivity solid electrolytes are critical components of solid oxide fuel/electrolysis cells, solid-state batteries, information storage devices, and other electrochemical systems. Like many electrolytes, polycrystalline GdxCe1-xO2-δ (GCO) can suffer from low grain boundary (GB) conductivity relative to grain interiors, attributed to local nanoscale oxygen vacancy ("V" _"O" ^"••" ) depletion which diminishes cross-GB ionic conductivity. To improve conductivity, microscopic analyses of GB structure and chemistry along with multiscale computational models are needed to accurately relate nanoscopic point defect concentrations to macroscopic ionic conductivity. Here, we present an experimental-computational framework that predicts which GBs in a polycrystalline electrolyte likely facilitate ionic conductivity. We developed a thermodynamic phase-field modeling framework and applied it to a model high-solute-content oxygen electrolyte Gd0.25Ce0.75O2-δ, wherein the microscopically measured GB-to-GB variability in defect concentrations was used to predict the GB-to-GB variability in cross-GB ionic conduction. Uniquely, our model prioritizes reproducing microscopically observed GB defect distributions and considers defect-defect interactions in highly concentrated solid solutions, making the framework applicable to most technologically relevant solid electrolytes. Across the GBs studied, we revealed a non-monotonic relationship between "V" _"O" ^"••" depletion and GB conductivity, with the highest conductivity predicted for intermediate "V" _"O" ^"••" depletion amount.
|
HASTI VAHIDI; Alejandro Mejia; Shengquan Xuan; Angelo Cassiadoro; Abednego Abdi; David Mebane; william bowman
|
Theoretical and Computational Chemistry; Materials Science; Energy; Ceramics; Energy Storage; Fuel Cells
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-02-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65baa4409138d23161251797/original/which-interfaces-matter-most-a-non-monotonic-relationship-between-grain-boundary-defect-chemistry-and-ionic-conductivity-in-a-concentrated-solid-electrolyte.pdf
|
67a6d5126dde43c908039e70
|
10.26434/chemrxiv-2025-drwgp
|
Obtaining (BN)4C10 with excellent optoelectronic properties by screening boron-nitrogen analogues of cyclo[18]carbon, (BN)nC(18-2n) (n = 1–9)
|
The geometric structures as well as electronic, nonlinear optical, and photophysical properties of boron-nitrogen (B-N) analogues of cyclo[18]carbon (C18), (BN)nC(18-2n) (n = 1–9), were comprehensively studied using density functional theory (DFT) and time-dependent DFT (TD-DFT) for screening the ring with excellent optoelectronic performances. As the C-C units in the molecules are continuously replaced by B-N units, almost all geometric parameters change monotonically, while almost all electronic properties undergo a turning point at (BN)4C10, suggesting that (BN)4C10 may have special optoelectronic properties. The isotropic polarizabilities of (BN)nC(18-2n) (n = 1–9) decrease sequentially with an increase in the number of B-N units in the molecule, while the total first hyperpolarizabilities as well as the values corresponding to second harmonic generation (SHG) and hyper-Rayleigh scattering (HRS) experiments first increase and then decrease, reaching their respective maximum at (BN)4C10. Taking (BN)4C10 as an example, the anisotropic feature, spatial contribution, and structural origin of (hyper)polarizability were revealed thoroughly by analyzing (hyper)polarizability tensor, (hyper)polarizability density, and (hyper)polarizability decomposition, respectively. The frequency dispersion effect has a positive impact on increasing the response properties of (BN)nC(18-2n) (n = 1–9), and the higher the incident frequency of the applied field, the greater its effect on improving the molecular (hyper)polarizability. The absorption bands of (BN)nC(18-2n) (n = 1–9) lie in the ultraviolet range of 125–400 nm, indicating the transparency of these molecules in the visible light region. The hole-electron analysis of (BN)4C10 graphically and numerically illustrated that the maximum absorption of the molecule comes from localized electron excitation on the C-C moiety, which should also be a common characteristic of all (BN)nC(18-2n) (n = 1–9). The two-level model was used to rationalize the observed variation of the total first hyperpolarizability with replacement of groups from the perspective of electron excitation.
|
Xiaohui Chen; Zhibo Xie; Jiaojiao Wang; Wenwen Zhao; Xiufen Yan; Zeyu Liu; Cai Ning; Tian Lu
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY 4.0
|
CHEMRXIV
|
2025-02-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a6d5126dde43c908039e70/original/obtaining-bn-4c10-with-excellent-optoelectronic-properties-by-screening-boron-nitrogen-analogues-of-cyclo-18-carbon-bn-n-c-18-2n-n-1-9.pdf
|
645a6f35fb40f6b3ee4c8652
|
10.26434/chemrxiv-2023-z877v-v2
|
ESAMP: Event-Sourced Architecture for Materials Provenance Management and Application to Accelerated Materials Discovery
|
While the vision of accelerating materials discovery using data
driven methods is well-founded, practical realization has been
throttled due to challenges in data generation, ingestion, and
materials state-aware machine learning. High-throughput experiments and automated computational workflows are addressing
the challenge of data generation, and capitalizing on these emerging data resources requires ingestion of data into an architecture
that captures the complex provenance of experiments and simulations. In this manuscript, we describe an event-sourced architecture for materials provenance (ESAMP) that encodes the sequence
and interrelationships among events occurring in a simulation or
experiment. We use this architecture to ingest a large and varied dataset (MEAD) that contains raw data and metadata from
millions of materials synthesis and characterization experiments
performed using various modalities such as serial, parallel, multimodal experimentation. Our data architecture tracks the evolution of a material’s state, enabling a demonstration of how stateequivalency rules can be used to generate datasets that significantly enhance data-driven materials discovery. Specifically, using state-equivalency rules and parameters associated with statechanging processes in addition to the typically used composition
data, we demonstrated marked reduction of uncertainty in prediction of overpotential for oxygen evolution reaction (OER) catalysts. Finally, we discuss the importance of ESAMP architecture in
enabling several aspects of accelerated materials discovery such
as dynamic workflow design, generation of knowledge graphs,
and efficient integration of theory and experiment.
|
Michael Statt; Brian A. Rohr; Kris S. Brown; Dan Guevarra; Jens Strabo Hummelshøj; Linda Hung; abraham anapolsky; John Gregoire; Santosh Suram
|
Materials Science; Analytical Chemistry; Energy; Fuels - Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645a6f35fb40f6b3ee4c8652/original/esamp-event-sourced-architecture-for-materials-provenance-management-and-application-to-accelerated-materials-discovery.pdf
|
6654913491aefa6ce11d28a1
|
10.26434/chemrxiv-2024-36wbl-v2
|
The pseudo-ternary phases Eu0.28Yb0.72MnPt and YbCd0.13Mn0.87Pt as TiNiSi type derivatives of the elusive or non-existent “YbMnPt”
|
The ternary RE-Mn-Pt systems (RE = rare-earth metal) have remained surprisingly vacant. Our attempts to stabilize hypo-thetical equiatomic “REMnPt” phases that are isovalent to RECdPt were found to be extremely challenging. However, using metal fluxes synthesis approaches, two quasi-ternary phases Eu0.28Yb0.72MnPt and YbCd0.13Mn0.87Pt, with stoichiometries in the vicinity of the elusive “YbMnPt” phase, were obtained by reacting mixtures of the elements at high temperature with large excess of Eu and Cd, respectively. The two title compounds crystallize in the orthorhombic TiNiSi type structure (space group, Pnma), according to single crystal X-ray diffraction data, with Eu/Yb or Cd/Mn atomic mixing at the corresponding atomic sites. Noteworthy, the two phases feature Mn (3d5) linear zigzag chains with very similar Mn–Mn distances of 2.97 Å, longer than the sum of Mn covalent radii (2.74 Å), but non-negligeable. The Mn chains also interact strongly with the surrounding Pt atoms to form the polyanionic {MnPt} framework. The rare-earth metals Yb and Eu are arguably divalent and, we could surmise that the apparent non-existence of the pristine “YbMnPt” phase can be ascribed to geometric frustrations as they can result from packing mismatched between the cationic and anionic sublat-tices. Hence, partial isovalent substitutions at either Yb position by larger Eu atom or at Mn position by larger Cd atom may be necessarily to optimize the atomic packing. Our findings further demonstrate that chemical heterogeneity can be vital for the stability of certain classes of elusive materials in general.
|
Simeon Ponou; Anja-Verena Mudring; Benedikt Friedrich
|
Physical Chemistry; Inorganic Chemistry; Lanthanides and Actinides; Magnetism; Materials Chemistry; Crystallography – Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6654913491aefa6ce11d28a1/original/the-pseudo-ternary-phases-eu0-28yb0-72mn-pt-and-yb-cd0-13mn0-87pt-as-ti-ni-si-type-derivatives-of-the-elusive-or-non-existent-yb-mn-pt.pdf
|
60c74060337d6c7827e266a8
|
10.26434/chemrxiv.7613042.v2
|
On the Nature of Halide-Water Interactions: Insights from Many-Body Representations and Density Functional Theory
|
<div>
<div>
<div>
<p>Interaction energies of halide-water dimers, X<sup>-</sup>(H<sub>2</sub>O), and trimers, X<sup>-</sup>(H<sub>2</sub>O)<sub>2</sub>, with X = F, Cl, Br, and I,
are investigated using various many-body models and exchange-correlation functionals selected across the hierarchy of density functional theory (DFT) approximations.
Analysis of the results obtained with the many-body models demonstrates the need to
capture important short-range interactions in the regime of large inter-molecular orbital
overlap, such as charge transfer and charge penetration. Failure to reproduce these
effects can lead to large deviations relative to reference data calculated at the coupled
cluster level of theory. Decompositions of interaction energies carried out with the absolutely localized molecular orbital energy decomposition analysis (ALMO-EDA) method demonstrate that permanent and inductive electrostatic energies are accurately reproduced by all classes of XC functionals (from generalized gradient corrected (GGA) to
hybrid and range-separated functionals), while significant variance is found for charge
transfer energies predicted by different XC functionals. Since GGA and hybrid XC
functionals predict the most and least attractive charge transfer energies, respectively,
the large variance is likely due to the delocalization error. In this scenario, the hybrid
XC functionals are then expected to provide the most accurate charge transfer energies.
The sum of Pauli repulsion and dispersion energies are the most varied among the XC
functionals, but it is found that a correspondence between the interaction energy and
the ALMO EDA total frozen energy may be used to determine accurate estimates for
these contributions. </p>
</div>
</div>
</div>
|
Brandon B. Bizzarro; Colin K. Egan; Paesani Lab
|
Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Processes; Physical and Chemical Properties; Quantum Mechanics; Solution Chemistry; Structure
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-01-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74060337d6c7827e266a8/original/on-the-nature-of-halide-water-interactions-insights-from-many-body-representations-and-density-functional-theory.pdf
|
61cae4425b23d455210cc963
|
10.26434/chemrxiv-2022-3gjqx
|
Molecular Modelling of Ionic Liquids: Force-Field Validation and Thermodynamic Perspective from Large-Scale Fast-Growth Solvation Free Energy Calculations
|
Molecular simulations are becoming a common tool for the investigation of dynamic and thermodynamic properties of novel solvents such as ionic liquids and the more recent deep eutectic solvents. As the electrostatics derived from ab initio calculations often fail to reproduce the experimental behaviors of these functionalized solvents, a common treatment is scaling the atomic charges to improve the accord between experimental and computational results for some selected properties, e.g., the density of the liquids. Although there are many computational benchmarks on structural properties of bulk ionic liquids, the choice of the best scaling parameter remains an open question. As these liquids are designed to solvate solutes, whether the solvation thermodynamics could be correctly described is of utmost importance in practical situations. Therefore, in the current work, we provide a thermodynamic perspective of this charge scaling issue directly from solute-solvent interactions. We present a comprehensive large-scale calculation of solvation free energies via nonequilibrium fast-switching simulations for a spectrum of molecules in ionic liquids, the atomic charges of which derived from ab initio calculations are scaled to find the best scaling factor that maximizes the prediction-experiment correlation. The density-derived choice of the scaling parameter as the estimate from bulk properties is compared with the solvation-free-energy-derived one. We observed that when the scaling factor is decreased from 1.0 to 0.5, the mass density exhibits a monotonically decreasing behavior, which is caused by weaker inter-molecular interactions produced by the scaled atomic charges. However, the solvation free energies of external agents do not show consistent monotonic behaviors like the bulk property, the underlying physics of which are elucidated to be the competing electrostatic and vdW responses to the scaling-parameter variation. More intriguingly, although the recommended value for charge scaling from bulk properties falls in the neighborhood of 0.6~0.7, solvation free energies calculated at this value are not in good agreement with the experimental reference. By modestly increasing the scaling parameter (e.g., by 0.1) to avoid over-scaling of atomic charges, the solute-solvent interaction free energy approaches the reference value and the quality of calculated solvation thermodynamics approaches the hydration case. According to this phenomenon, we propose a feasible way to obtain the best scaling parameter that produces balanced solute-solvent and solvent-solvent interactions, i.e., first scanning the density-scaling-factor profile and then adding ~0.1 to that solution. We further calculate the partition coefficient or transfer free energy of solutes from water to ionic liquids to provide another thermodynamic perspective of the charge scaling benchmark. Another central result of the current work is about the widely used force fields to describe bonded and vdW terms for ionic liquids derivatives. These pre-fitted transferable parameters are evaluated and refitted in a system-specific manner to provide a detailed assessment of the reliability and accuracy of these commonly used parameters. Component-specific refitting procedures unveil that the bond-stretching term is the most problematic part of the GAFF derivatives and the angle-bending term in some cases is also not accurate enough. Astonishingly, the torsional potential defined in these pre-fitted force fields performs extremely well.
|
Zhaoxi Sun; Mao Wang; Qiaole He; Zhirong Liu
|
Theoretical and Computational Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-01-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61cae4425b23d455210cc963/original/molecular-modelling-of-ionic-liquids-force-field-validation-and-thermodynamic-perspective-from-large-scale-fast-growth-solvation-free-energy-calculations.pdf
|
635a7e14aa27841ac64ee3cd
|
10.26434/chemrxiv-2022-28vp0-v2
|
Construction of Carbon Dots with Wavelength-tunable Electrochemiluminescence and Enhanced Efficiency
|
While highly efficient electrochemiluminescence (ECL) emitters with finely tunable emission wavelengths are crucial for practical applications, the simultaneous modulation of ECL efficiency and emission wavelength, along with the deep understanding of the mechanism in the molecular level, remain elusive. Herein, we reported carbon dots (CDs) with both fine-tuned ECL efficiency and emission wavelength were achieved by phosphorus (P) doping, e.g., the ECL emission was finely tuned from 425 nm to 645 nm, and the efficiency (relative to the Ru(bpy)32+/K2S2O8 system) was promoted from 10.6% to 57.4%. Experimental and theoretical studies revealed the P dopants in the form of P-C and P-O groups not only imported shallow trapping states but also promoted a significant intramolecular charge transfer (ICT), which jointly induced the redshift and boosted the ECL performance of CDs. This work would provide a clue for the rational design of CDs to tune the ECL properties for advanced biomedical applications finely.
|
Yanfei Shen; Erli Yang; Hong Yang; Zhenqiang Ning; Yanfeng Fang; Mengyuan Chen; Yongjun Zheng; Guoqiu Wu; Wenhua Xu; Yuanjian Zhang
|
Analytical Chemistry; Nanoscience; Electrochemical Analysis; Nanostructured Materials - Nanoscience; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-10-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635a7e14aa27841ac64ee3cd/original/construction-of-carbon-dots-with-wavelength-tunable-electrochemiluminescence-and-enhanced-efficiency.pdf
|
6410d986b5d5dbe9e84245bf
|
10.26434/chemrxiv-2023-24gfx
|
Highly Efficient Polyolefin Hydrogenolysis Enabled by a Single-Site Organo-Tantalum Catalyst on a Super-Acidic Support
|
The novel electrophilic organo-tantalum catalyst AlS/TaNp () (Np = neopentyl) is prepared by chemisorption of the alkylidene Ta(CHtBu)Np onto highly Brønsted acidic sulfated alumina (AlS). The proposed catalyst structure is supported by EXAFS, XANES, ICP, DRIFTS, and SSNMR measurements and is in good agreement with DFT analysis. Adsorbate is a highly effective catalyst for the hydrogenolysis of linear and branched hydrocarbons, ranging from C2 to polyolefins. To the best of our knowledge, 𝟏 exhibits the highest polyolefin hydrogenolysis activity (9,200 (CH₂ units)·mol(Ta)⁻¹·h⁻¹ at 200 °C/17 atm H₂) reported to date in the peer-reviewed literature. Unlike the AlS/ZrNp₂ analog, the Ta catalyst is more thermally stable and has multiple potential reaction pathways for C-C bond activation. For hydrogenolysis, AlS/TaNp₃ is effective for a wide variety of pre- and post-consumer polyolefin plastics and is not significantly deactivated in the presence of standard polyolefin additives.
|
Qingheng Lai; Alexander H. Mason; Amol Agarwal; Wilson C. Edenfield; Xinrui Zhang; Takeshi Kobayashi; Yosi Kratish; Tobin J. Marks
|
Catalysis; Organometallic Chemistry; Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6410d986b5d5dbe9e84245bf/original/highly-efficient-polyolefin-hydrogenolysis-enabled-by-a-single-site-organo-tantalum-catalyst-on-a-super-acidic-support.pdf
|
64e7306779853bbd7851a25a
|
10.26434/chemrxiv-2023-151jq
|
"On-the-fly" synthesis of self-supported LDH hollow structures through controlled microfluidic reaction-diffusion conditions
|
Layered double hydroxides (LDHs) are a class of functional materials that exhibit exceptional properties for diverse applications in areas such as heterogeneous catalysis, energy storage and conversion, and bio-medical applications, among others. Efforts have been devoted to produce millimeter-scale LDH structures for direct integration into functional devices. However, the controlled synthesis of self-supported continuous LDH materials with hierarchical structuring up to the millimeter scale through a straightforward one-pot reaction method remains unaddressed. Herein, we show that millimeter-scale self-supported LDH structures can be produced by means of a continuous flow microfluidic device in a rapid and reproducible one-pot process. Additionally, our microfluidic approach not only allows for an ‘on-the-fly’ formation of unprecedented LDH composite structures, but also for the seamless integration of millimeter-scale LDH structures into functional devices. Our method holds the potential to unlock the integrability of these materials, maintaining their performance and functionality, while diverging from conventional techniques like pelletization and densification that often compromise these aspects. Our strategy will enable exciting advancements in LDH performance and functionality.
|
Michele Mattera; Alessandro Sorrenti; Lidia De Gregorio Perpiñá; Víctor Oestreicher; Semih Sevim; Xiang Zhong Chen; Salvador Pané; Gonzalo Abellán; Josep Puigmarti-Luis
|
Inorganic Chemistry; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e7306779853bbd7851a25a/original/on-the-fly-synthesis-of-self-supported-ldh-hollow-structures-through-controlled-microfluidic-reaction-diffusion-conditions.pdf
|
621de03657a9d2733b6f0a5d
|
10.26434/chemrxiv-2022-ksvbx
|
Efficient pretreatment using dimethyl isosorbide as a biobased solvent for potential complete biomass valorization
|
An efficient and sustainable pretreatment, such as organosolv pretreatment that produces high-quality lignin and highly digestible carbohydrates, could enable the potential complete utilization of lignocellulosic biomass. Demand for bio-based solvents with a high boiling point, low viscosity, and negligible toxicity is increasing. Herein, we report the use of dimethyl isosorbide (DMI) as a solvent to fractionate lignocellulosic biomass into its main components for the first time. High lignin removal efficiency (91.2%) with good cellulose retention (around 80%) could be achieved during the pretreatment of Eucalyptus by DMI/H2O co-solvents under a mild condition. A near-complete cellulose conversion to its monosaccharide could be realized at a relatively low enzyme loading of 20 FPU g−1 glucan. The addition of water could suppress the condensation of lignin, yielding high-quality lignin with a good fraction of β-O-4 linkages reserved (24.8%) and homogeneous molecular weight (Đ<2) suitable for depolymerization to mono-aromatic chemicals. Besides its highly digestible nature, the high quality of the cellulose-rich residue is also demonstrated from a material perspective. A more efficient fibrillation of obtained pulp to nanocellulose was developed, leading to a promising potential of energy saving compared to the traditional bleaching pathway. Overall, this work developed a mild pretreatment technology as a potential basis for a green and closed-loop biorefinery concept for converting lignocellulosic biomass to multiple products (high-quality lignin, fermentable sugars, or functional materials).
|
Shuang Yang; Xianpeng Yang; Xianzhi Meng; Lei Wang
|
Chemical Engineering and Industrial Chemistry; Natural Resource Recovery
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621de03657a9d2733b6f0a5d/original/efficient-pretreatment-using-dimethyl-isosorbide-as-a-biobased-solvent-for-potential-complete-biomass-valorization.pdf
|
60c74a89ee301c340ec79c85
|
10.26434/chemrxiv.12209744.v1
|
The Structural Landscape of SARS-CoV-2 Main Protease: Hints for Inhibitor Search.
|
In 2019, an outbreak occurred which resulted in a global pandemic. The causative agent of this serious global health threat was a coronavirus similar to the agent of SARS, referred to as SARS-CoV-2. In this work an analysis of the available structures of the SARS-CoV-2 main protease has been performed. From a data set of crystallographic structures the dynamics of the protease has been obtained. Furthermore, a comparative analysis of the structures of SARS-CoV-2 with those of the main protease of the coronavirus responsible of SARS (SARS-CoV) was carried out. The results of these studies suggest that, although main proteases of SARS-CoV and SARS-CoV-2 are similar at the backbone level, some plasticity at the substrate binding site can be observed. The consequences of these structural aspects on the search for effective inhibitors of these enzymes are discussed, with a focus on already known compounds. The results obtained show that compounds containing an oxirane ring could be considered as inhibitors of the main protease of SARS-CoV-2.
|
Luigi Leonardo Palese
|
Biochemistry; Bioinformatics and Computational Biology; Biophysics; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a89ee301c340ec79c85/original/the-structural-landscape-of-sars-co-v-2-main-protease-hints-for-inhibitor-search.pdf
|
64e978b9dd1a73847f89f67d
|
10.26434/chemrxiv-2023-brmfm
|
Comment on ``Applicability of perturbed matrix method for charge transfer studies at bio/metallic interfaces: a case of azurin'' by O. Kontkanen, D. Biriukov and Z. Futera, Phys. Chem. Chem. Phys., 2023, 25, DOI: 10.1039/D3CP00197K
|
Polarizability is a fundamental property of all molecular systems describing the deformation of the molecular electronic density in response to an applied electric field. The question of whether polarizability of the active site needs to be included in theories of enzymatic activity remains open. Hybrid quantum mechanical/molecular mechanical calculations are hampered by difficulties faced by many quantum-chemistry algorithms to provide sufficiently accurate estimates of the anisotropic second-rank tensor of molecular polarizability. In this Comment, we provide general theoretical arguments for the values of polarizability of the quantum region or a molecule which have to be reproduced by electronic structure calculations.
|
Setare Sarhangi; Dmitry Matyushov
|
Theoretical and Computational Chemistry; Physical Chemistry; Biophysical Chemistry; Electrochemistry - Mechanisms, Theory & Study
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-09-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e978b9dd1a73847f89f67d/original/comment-on-applicability-of-perturbed-matrix-method-for-charge-transfer-studies-at-bio-metallic-interfaces-a-case-of-azurin-by-o-kontkanen-d-biriukov-and-z-futera-phys-chem-chem-phys-2023-25-doi-10-1039-d3cp00197k.pdf
|
675f0698085116a1337f1a3a
|
10.26434/chemrxiv-2024-v1sc1
|
Large library docking and biophysical analysis of small molecule TMPRSS2 inhibitors
|
Transmembrane protease, serine -2 (TMPRSS2) is an essential host entry factor in human airways for SARS-CoV-2 and influenza A/B and has presented as a target for antiviral drug development; however, no clinically viable, oral small molecule TMPRSS2 inhibitors have been developed to date. Here we perform two large-scale docking campaigns to identify covalent and noncovalent TMPRSS2 small molecule inhibitors from a homology model and crystal structure. We establish a pipeline to rapidly screen TMPRSS2 inhibitors, then interrogate the potency, specificity and biophysical properties of covalent and noncovalent inhibition using enzyme kinetics on synthetic peptide and protein substrates and differential scanning fluorimetry. Furthermore, we established a readily crystallizable form of TMPRSS2 protein that produced high resolution crystal structures with nafamostat, ‘157, and 6-amidino-2-naphthol. A novel noncovalent inhibitor scaffold is biochemically and biophysically validated as a potential avenue to develop TMPRSS2-selective inhibitors.
|
Bryan Fraser; Nicholas Young; Brian Bender; Stefan Gahbauer; Olzhas Ilyassov; Ryan Wilson; Yanjun Li; Almagul Seitova; André Luiz Lourenço; Dong-Hee Chung; Conner Bardine; François Bénard; Brian Shoichet; Charles Craik; Cheryl Arrowsmith
|
Biological and Medicinal Chemistry; Biochemistry; Drug Discovery and Drug Delivery Systems
|
CC BY 4.0
|
CHEMRXIV
|
2024-12-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675f0698085116a1337f1a3a/original/large-library-docking-and-biophysical-analysis-of-small-molecule-tmprss2-inhibitors.pdf
|
6469e7c3a32ceeff2dff842e
|
10.26434/chemrxiv-2023-s1g30
|
Molecular grafting can generate bioactivities within the cyclic peptide PDP-23
|
The stability of cyclic peptides, coupled with their structural diversity and ability to host an extensive range of bioactivities, make them promising leads for the development of new drugs. PawS-Derived Peptide-23 (PDP-23) is a head-to-tail macrocyclic peptide with two disulfide bonds produced in plant seeds. Its unusual fold comprises two -hairpins connected by hinges that allow the structure to adapt to different environments. In water two PDP-23 molecules form a compact intertwined dimer that buries hydrophobic residues, whereas in membrane mimicking conditions it adopts an open monomeric form that expose them. Here we investigate PDP-23 as a novel scaffold for the grafting of bioactive epitopes and conjugation of small molecules. To explore the plasticity of PDP-23 we introduced the bioactive loop of sunflower trypsin inhbitor-1 (SFTI-1) or an integrin binding RGD motif into either of the -hairpins. Solution NMR spectroscopy revealed that although the variants were unable to dimerise, the structural features of both the graft and scaffold were retained. SFTI-1 hybrid variants showed trypsin inhibitory activity. PDP-23 has previously been used as a cell permeable drug scaffold targeting drug-resistant cancer cells by inhibiting the drug efflux pump P-glycoprotein and restoring their sensitivity to chemotherapeutic. Introducing the RGD motif into such PDP-23 conjugates significantly improve their potency, suggesting that the RGD sequence targets the peptide to the membrane of cancer cells and improve cell uptake. In conclusion, this study highlights PDP-23 as a stable and versatile scaffold for molecular grafting of bioactivities and targeted delivery of pharmaceutical payloads.
|
Fatemeh Hajiaghaalipour; Angela Song; Grishma Vadlamani; Jingjing Zhang; Joshua Mylne; Richard Clark; K. Johan Rosengren
|
Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6469e7c3a32ceeff2dff842e/original/molecular-grafting-can-generate-bioactivities-within-the-cyclic-peptide-pdp-23.pdf
|
60c748c0f96a0042f8287109
|
10.26434/chemrxiv.11962524.v1
|
Sodium Bis(oxalato)borate (NaBOB) in Trimethyl Phosphate: A Fire-Extinguishing, Fluorine-Free, and Low-Cost Electrolyte for Full-Cell Sodium-Ion Batteries
|
Sodium-ion batteries based on all-naturally-abundant elements, in which no cobalt, nickel, copper, and fluorine is used, can lead to a major breakthrough in making batteries more sustainable. Safety aspects -in particular flammability of electrolytes- in the state-of-theart battery technology is another important concern, especially for applications in which large numbers of cells are employed. Non-flammable battery electrolytes studied so far are based on highly fluorinated compounds or high salt concentrations, which suffer from high cost and toxicity. We here propose an electrolyte based on a single solvent and lowcost and fluorine-free salt at the lower range of “standard” concentrations. Our results show -for the first time- that sodium bis(oxalato)borate (NaBOB) is soluble in the nonflammable solvent trimethyl phosphate (TMP). This finding enables a non-flammable electrolyte with high ionic conductivity and promising electrochemical performance in fullcell sodium-ion batteries. An electrolyte of 0.5 M NaBOB in TMP provides ionic conductivity of 5 mS cm-1 at room temperature, which is comparable to commonly used electrolytes based on sodium hexafluorophosphate (NaPF6) and organic carbonate solvents. The proposed electrolyte shows the Coulombic efficiency of above 80% in the first cycle, which increased to about 97% from the second cycle in sodium-ion battery fullcells consisting of a hard carbon anode and Prussian white cathode. This work opens up new opportunities to design safe electrolytes which can further be optimized with electrolyte additives such as vinylene carbonate for industrial applications.<br />
|
Ronnie Mogensen; Simon Colbin; Ashok Menon; Erik Björklund; Reza Younesi
|
Electrochemical Analysis; Electrochemistry; Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-03-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748c0f96a0042f8287109/original/sodium-bis-oxalato-borate-na-bob-in-trimethyl-phosphate-a-fire-extinguishing-fluorine-free-and-low-cost-electrolyte-for-full-cell-sodium-ion-batteries.pdf
|
647d260d4f8b1884b7d9271d
|
10.26434/chemrxiv-2023-0sjpl
|
Turnover and Catalytic cycle frequency Determination based on Molar mass-dependent Model equations
|
There were conflicting definitions and misrepresentations of turnover frequency (TOF), catalytic cycle frequency (CCF), and catalytic first-order rate constant (kcat) in the literature. Based on the Benfield and Lineweaver-Burk methods, data were generated. The results showed that the CCF for the forward (3.63 exp. (+7)/s) and reverse (1.196 exp. (+9)/s) and the TOF (8.294 exp. (−4)/s) were respectively the highest and lowest for the highest concentration [E0] of the enzyme. The number of fragments per molecule of an enzyme was = f([ET]), where [ET] was in molar units and it was ≫ [ST] (in molar units), and where [ST] ≫ [ET], it was = f([ST]. In conclusion, TOF and CCF were different, and in particular, the former was not the same as kcat, while the latter was a constant. TOF and CCF vary. Strictly speaking, TOF was = f(M3). This can be verified with sucrase in a future study.
|
IKECHUKWU UDEMA
|
Theoretical and Computational Chemistry; Catalysis; Theory - Computational; Biocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2023-06-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647d260d4f8b1884b7d9271d/original/turnover-and-catalytic-cycle-frequency-determination-based-on-molar-mass-dependent-model-equations.pdf
|
67bde179fa469535b9e17b10
|
10.26434/chemrxiv-2025-qfmvh
|
Nano-Fanowmen: Fano-Resonant Plasmonic Nanoparticles
|
Fano resonance stands as a significant driving force in the advancement of cutting-edge sensors, ultrasensitive spectroscopy, and microdevices with superior optical properties1–9. Although Fano resonant structures have been extensively studied within the resolution range achievable by state-of-the-art photolithography techniques (tens of nm), exploring Fano resonance at the nanoscale—where strong quantum confinement prevails—remains a challenge. Here, we report colloidal Fano-resonant snowman nanoparticles (nano-Fanowman) in the liquid phase, exhibiting a clear characteristic Fano dip in the ensemble spectrum. We demonstrate precise tuning of an 80-nm nano-Fanowman structure featuring a secondary ~1-nm intragap through a DNA-nanointerfacial modulation strategy. Probed using dyes located within this intragap, these nanoparticles exhibited a surface-enhanced Raman scattering (SERS) signal approximately 100-fold stronger than that of non-Fano-resonant counterparts, owing to efficient energy transfer from a bright mode to a dark mode. Enabled by the Fano resonance effect, detectable SERS signals were achievable at laser powers as low as ~1 nW.
|
Gyeong-Hwan Kim; Mouhong Lin; Jeong-Wook Oh; Jae-Myoung Kim; Hohsuk Noh; Dongha Shin; Jung-Hoon Lee; Jwa-Min Nam
|
Nanoscience; Plasmonic and Photonic Structures and Devices
|
CC BY 4.0
|
CHEMRXIV
|
2025-02-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bde179fa469535b9e17b10/original/nano-fanowmen-fano-resonant-plasmonic-nanoparticles.pdf
|
67c4188efa469535b99168dc
|
10.26434/chemrxiv-2025-hhj0t
|
Advances in the Physics and Computation of Compressible Liquid Transients
|
Accurate modeling of compressible liquid transients requires robust modeling of compressibility effects in a liquid, such as density variations and acoustic velocities. Efficient and case-adaptive friction models are crucial for the simulation accuracy of liquid transients. The paper reviews different mathematical models and their numerical implementation for compressible liquid transient simulations. Different aspects of compressible liquid transient modeling and simulation are profoundly explored with the help of relevant literature. The major aspects reviewed are the high-pressure applications of liquids, compressible modeling of liquids, gas shock tube simulation and its extension to liquid shock cases, the importance of numerical techniques such as Riemann solvers in simulation, the need for the development of benchmark results in compressible liquid flows, the evolution of unsteady friction modeling and limitations of models, and scope for improvement of valve-induced surge modeling. Almost every application where liquid compressibility effects are significant is covered under this review. A range of liquid equations of state for different liquids are discussed, and the compressible modeling of liquid water is profoundly analyzed by evaluating the performance of different state equations for the fluid. The significance of the gas shock tube problem in the branch of compressible flows is discussed, and the ways in which it could be extended to compressible liquid shock cases are elaborated through the conceptual problem of the water shock tube. The numerical techniques, especially the Riemann solvers, and the evolution of their different variants are explained with the help of relevant literature. Different formulations for steady and unsteady friction that are generally employed in mathematical models are analyzed, and their limitations for complex transient cases are discussed. Recent advancements in the unsteady friction formulation, such as the variable damping technique, are discussed, and its application to surge modeling is demonstrated. The experimental and numerical studies on valve-induced surges, their mathematical modeling, and the flow characteristics at the upstream and downstream locations of the valve are discussed in detail with the help of published literature. This review can serve as a single sufficient source for understanding the different aspects of compressible liquid transient modeling and to know the state-of-the-art in each aspect. The review also suggests the major directions in which future study is required based on the existing models' limitations and gaps in the literature.
|
Jishnu Chandran; Ashish Garg; Arun Govind Neelan; Risha Raju
|
Chemical Engineering and Industrial Chemistry; Fluid Mechanics; Thermodynamics (Chem. Eng.); Transport Phenomena (Chem. Eng.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c4188efa469535b99168dc/original/advances-in-the-physics-and-computation-of-compressible-liquid-transients.pdf
|
62fee9c1eadd9ab6f67904b2
|
10.26434/chemrxiv-2022-27z1j-v2
|
Facilitating Hydrogen Dissociation over Dilute Nanoporous Ti-Cu Catalysts
|
The dissociation of H2 is an essential elementary step in many industrial chemical transformations, typically requiring precious metals. Here, we report a hierarchical nanoporous Cu catalyst doped with small amounts of Ti (npTiCu) that increases the rate of H2-D2 exchange by approximately one order of magnitude compared to the undoped nanoporous Cu (npCu) catalyst. The promotional effect of Ti was measured via steady-state H2-D2 exchange reaction experiments under atmospheric pressure flow conditions in the temperature range of 300─523 K. Pretreatment with flowing H2 is required for stable catalytic performance and two temperatures, 523 K and 673 K, were investigated. The experimentally-determined H2-D2 exchange rate is 5-7 times greater for npTiCu vs. the undoped Cu material under optimized pretreatment and reaction temperatures. The H2 pretreatment leads to full reduction of Cu oxide and partial reduction of surface Ti oxide species present in the as-prepared catalyst as demonstrated using in-situ ambient pressure X-ray photoelectron spectroscopy and X-ray absorption spectroscopy. The apparent activation energy and pre-exponential factors measured for H2-D2 exchange are substantially different for Ti-doped vs. undoped npCu catalysts. DFT calculations suggest that isolated, metallic Ti atoms on the surface of the Cu host can act as the active surface sites for hydrogen recombination. The increase in the rate of exchange above that of pure Cu is caused primarily by a shift in the rate-determining step from dissociative adsorption on Cu to H/D atom recombination on Ti-doped Cu, with the corresponding decrease in activation entropy that it produces.
|
Jennifer Lee; Zhen Qi; Alexandre Foucher; Hio Tong Ngan; Kevin Dennis; Jun Cui; Ilia Sadykov; Ethan Crumlin; Philippe Sautet; Eric Stach; Cynthia Friend; Robert Madix; Juergen Biener
|
Materials Science; Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-08-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fee9c1eadd9ab6f67904b2/original/facilitating-hydrogen-dissociation-over-dilute-nanoporous-ti-cu-catalysts.pdf
|
639796d4836cebb5487f13fe
|
10.26434/chemrxiv-2022-sx77x
|
Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities
|
Macromolecular recognition and ligand binding are at the core of biological function and drug discovery efforts. Water molecules play a significant role in mediating the protein-ligand interaction, acting as more than just the surrounding medium by affecting the thermodynamics and thus the outcome of the binding process. As individual water contributions are impossible to be measured experimentally, a range of computational methods have emerged to identify hydration sites in protein pockets and characterize their energetic contributions for drug discovery applications. Even though several methods model solvation effects explicitly, they focus on determining the stability of specific water sites and neglect solvation correlation effects upon replacement of clusters of water molecules, which typically happens in hit-to-lead optimization. In this work, we rigorously determine the conjoint effects of replacing all combinations of water molecules in protein binding pockets through the use of the RE-EDS multistate free-energy method, which combines Hamiltonian replica exchange (RE) and enveloping distribution sampling (EDS). Applications on BPTI and four proteins of the bromodomain family illustrate the extent of solvation correlation effects on water thermodynamics and their influence on ligand binding and selectivity.
|
Emilia P. Barros; Benjamin Ries; Candide Champion; Salomé R. Rieder; Sereina Riniker
|
Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Biophysical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-12-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639796d4836cebb5487f13fe/original/accounting-for-solvation-correlation-effects-on-the-thermodynamics-of-water-networks-in-protein-cavities.pdf
|
6733abdd5a82cea2fae99153
|
10.26434/chemrxiv-2024-64r7z-v2
|
Leveraging a separation of states method for relative binding free energy calculations in systems with trapped waters
|
Methods for calculating the relative binding free energy (RBFE) between ligands to a target protein are gaining importance in the structure-based drug discovery domain, especially as methodological advances and automation improve accuracy and ease of use. In an RBFE calculation, the difference between the binding affinities of two ligands to a protein is calculated by transforming one ligand into another, in the protein-ligand complex, and in solvent. Alchemical binding free energy calculations are often used for such ligand transformations. Such calculations are not without challenges, however; for example, it can be challenging to handle interfacial waters when these play a crucial role in mediating protein-ligand binding. In some cases, the exchange of the interfacial waters with solvent water might be very infrequent in the course of typical molecular simulations, and such interfacial waters can be considered trapped on the simulation timescale. In these cases, RBFE calculation between two ligands, where one ligand binds with a trapped water while the other ligand displaces it, can result in inaccuracies if the surrounding water structure is not sampled adequately for both ligands. So far, a popular choice for treating the trapped waters in RBFE calculations is to combine free energy calculations with enhanced sampling methods that insert/delete waters in the binding site. Despite recent developments in the enhanced sampling methods, they can result in hysteresis in the RBFE estimate, depending on whether the simulations were started with or without the trapped waters. In this study, we introduce an alternative method, separation of states, to calculate the RBFE between ligand pairs where the ligands bind to the protein with different numbers/positions of trapped waters. The separation of states approach treats the sampling of the trapped waters separately from the free energy calculation of the ligand transformation. In our method, a trapped water in protein's binding site is decoupled from the system first, and the cavity created by its decoupling is stabilized. We then grow a larger ligand into this cavity-- a ligand that is known to displace the trapped water. In this study, we show that our method results in precise and accurate estimates of RBFEs for ligand pairs involving the rearrangement of trapped water via RBFE calculations for five such ligand pairs. We have optimized our simulation protocol to be suited for large distributed computational resources and have automated our RBFE calculation workflow.
|
Swapnil Wagle; Pascal Merz; Yunhui Ge; Christopher Bayly; David Mobley
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY 4.0
|
CHEMRXIV
|
2024-11-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6733abdd5a82cea2fae99153/original/leveraging-a-separation-of-states-method-for-relative-binding-free-energy-calculations-in-systems-with-trapped-waters.pdf
|
632dd7bb2984c9703f6a59d8
|
10.26434/chemrxiv-2022-pnttw
|
Discovery of Iodinated Polyfluoroalkyl Acids by Nontarget Mass-Spectrometric Analysis
|
Per- and polyfluoroalkyl acids (PFAAs) including polyfluoroalkyl carboxylic acids and polyfluoroalkyl sulfonic acids are a large category of crucial environmental pollutants of global concern. Besides known PFAAs, numerous unknown species may exist in the environment, urgently needing discovery and characterization. This study implemented nontarget analysis for a group of novel PFAA pollutants, viz. iodinated PFAAs (I-PFAAs) in wastewater by liquid chromatography-high-resolution mass spectrometry in combination with an iodine-specific data-processing algorithm. The algorithm took into account of the diagnostic fragment iodine ion (I–) together with carbon and sulfur isotopologue distributions. In total, 21 I-PFAA formulas involving 24 congeners were identified. Semiquantification was conducted, and the total concentrations of I-PFAAs were 1.9-311.9 ng/mL, indicating non-negligible pollution of I-PFAAs in the wastewater. The determined concentrations along with predicted environmental behaviors and toxicities demonstrate that I-PFAAs merit further in-depth investigation. The analytical method including the instrumental analysis and data-processing algorithm can be extended to screening and identification of I-PFAAs in other matrices. Furthermore, the analysis results for the first time provide cognition on the occurrence features and pollution status of I-PFAAs in the environment.
|
Caiming Tang; Yizhe Zhu; Yutao Liang; Yanhong Zeng; Xianzhi Peng; Bixian Mai; Qingguo Huang; Hui Lin
|
Analytical Chemistry; Environmental Analysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632dd7bb2984c9703f6a59d8/original/discovery-of-iodinated-polyfluoroalkyl-acids-by-nontarget-mass-spectrometric-analysis.pdf
|
619a973278db4e947418af24
|
10.26434/chemrxiv-2021-j4prf
|
Aldehyde-Catalyzed Carboxylate Exchange in a-Amino Acids with Isotopically Labeled CO2
|
a-Amino acids are among the essential chemical building blocks of life. These structures are embedded in many small molecule pharmaceuticals and are the primary components of peptide-based therapeutics and biologics. Isotopically labeled a-amino acids and their derivatives have widespread use in structural and mechanistic biochemistry, quantitative proteomics, absorption distribution metabolism and excretion (ADME) profiling, and as imaging agents in positron emission tomography (PET) techniques. The preparation of carbon-labeled a-amino acids remains difficult and time consuming, with established methods involving label incorporation at an early stage of synthesis. This explains the high cost and scarcity of C-labeled products and presents a major challenge in 11C applications (11C t1/2 = 20 min). Here we report that simple aldehydes catalyze the isotopic carboxylate exchange of native a-amino acids with *CO2 (* = 14, 13, 11). Proteinogenic a-amino acids and many non-natural variants containing diverse functional groups undergo labeling. The reaction likely proceeds via the trapping of *CO2 by imine-carboxylate intermediates to generate aminomalonates that are prone to monodecarboxylation. Tempering catalyst electrophilicity was key to preventing irreversible aldehyde consumption. The pre-generation of the imine carboxylate intermediate allows for the rapid and late-stage 11C-radiolabeling of a-amino acids in the presence of 11CO2.
|
Odey Bsharat; Michael Doyle; Maxime Munch; Braeden Mair; Christopher Cooze; Volker Derdau; Armin Bauer; Duanyang Kong; Benjamin Rotstein; Rylan Lundgren
|
Organic Chemistry; Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-11-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619a973278db4e947418af24/original/aldehyde-catalyzed-carboxylate-exchange-in-a-amino-acids-with-isotopically-labeled-co2.pdf
|
614996f34853d206e7acec03
|
10.26434/chemrxiv-2021-djssr-v2
|
A Computational Study on the Ca2+ Solvation, Coordination Environment, and Mobility in Electrolytes for Calcium Ion Batteries
|
Calcium (ion) batteries are promising next-generation energy storage systems, owing to their numerous benefits in terms of performance metrics, low-cost, mineral abundance, and economic sustainability. A central and critical area to the advancement of the technology is the development of suitable eletrolytes that allow for good salt solubility, ion mobility, electrochemical stability, and reversible redox activity. At this time, the study of different solvent-salt combinations is very limited. Here, we present a computational study on the coordination environment, solvation energetics, and diffusivity of calcium ions over a range of pertinent ionic liquids, cyclic and acylic alkyl carbonates, and specific alkyl nitriles and alkyl formamides, using the salts calcium bis(trifluoromethylsulfonyl)imide (Ca(TFSI)2) and calcium perchlorate (Ca(ClO4)2). Key findings are that several solvents from different solvent classes present comparable solvation environments and mobilities. Ca(TFSI)2 is prefered over Ca(ClO4)2 owing to the former’s mix coordination of Ca2+ to O and N atoms. Ionic liquids with alkyl sulfonate anions provide better coordation over TFSI, which leads to greater diffusivity. Binary organic mixtures (carbonates) provide the best solvation of Ca2+, however, single organic solvents also provide good solvation, such as EC, THF and DMF, as well as some acyclic carbonates. Ion pairing with the salt anion is always present, but can be mitigated through solvent selection, which also correlates to greater mobility; however, there are examples in which strong ion pairing is not significantly adverse to diffusivity. The solvent incorporate into the solvation structure with binary organic mixtures correlates well with the solvation capabilities of the individual solvents. Finally, we show that ionic liquids (specifically alkyl imidazole (cation) alkyl sulfonate (anion) ionic liquids) do not decompose when coordinating at a Ca metal interface, which indicates its promising stability. Overall, this study contributes further generalized understanding of the correlation between solvent and salt and the resultant Ca2+ complexes and Ca2+ mobility in a range of electrolytes, and reveals a range of possible solvents suitable for exploration in calcium (ion) batteries.
|
Saeid Biria; Shreyas Pathreeker; Ian D. Hosein
|
Physical Chemistry; Energy; Physical and Chemical Processes; Physical and Chemical Properties; Solution Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-09-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614996f34853d206e7acec03/original/a-computational-study-on-the-ca2-solvation-coordination-environment-and-mobility-in-electrolytes-for-calcium-ion-batteries.pdf
|
658f2829e9ebbb4db90210cc
|
10.26434/chemrxiv-2024-14dr7
|
Observing Long-lived Photogenerated Holes in Cobalt Oxyhydroxide Oxygen Evolution Catalysts
|
Steady-state and time-resolved spectroelectrochemical optical absorption techniques were used to investigate photoexcited states of amorphous cobalt-phosphate oxyhydroxide (CoPi) and cobalt-borate oxyhydroxide (CoBi) oxygen evolution catalysts. These materials revealed concurrent spectroelectrochemical intensity changes in their ground state and photoexcited visible spectra, providing insights into the dynamics of defect states attributable to trapped holes. Notably, long-lived photoexcited states, assignable to hole-based defects persisting beyond 10 ms in H2O, were observed in CoPi and CoBi for the first time. Both thin films exhibited distinct dynamics, however, highlighting differences in their structural and electronic properties despite strong similarities in absorption spectral profiles. These results provide further insight into the differences between the electronic properties and dynamics of CoPi and CoBi, which have been challenging to structurally and electronically characterize due to their amorphous nature.
|
Ruben Mirzoyan; Alec Follmer; Ryan Hadt
|
Materials Science; Inorganic Chemistry; Energy; Catalysts; Thin Films; Spectroscopy (Inorg.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658f2829e9ebbb4db90210cc/original/observing-long-lived-photogenerated-holes-in-cobalt-oxyhydroxide-oxygen-evolution-catalysts.pdf
|
615364ffcea2e936be00fee6
|
10.26434/chemrxiv-2021-w299m
|
Regulating the dynamic folding of a DNA hairpin at the expense of a small, molecular fuel
|
Molecular machines, such as ATPases or motor proteins, couple the catalysis of a chemical reaction, most commonly hydrolysis of nucleotide triphosphates, to their conformational change. In essence, they continuously convert a chemical fuel to drive their motion. An outstanding goal of nanotechnology remains to synthesize a nanomachine with similar functions, precision, and speed. The field of DNA nan- otechnology has given rise to the engineering precision required for such a device. Simultaneously, the field of systems chemistry developed fast chemical reaction cycles that convert fuel to change the function of molecules. In this work, we thus combined a fast, chemical reaction cycle with the precision of DNA nanotechnology to yield kinetic control over the conformational state of a DNA hairpin. Future work on such systems will result in fast and precise DNA nanodevices.
|
Michele Stasi; Alba Monferrer i Sureda; Leon Babl; Sreekar Wunnava; Christina Dirscherl; Dieter Braun; Petra Schwille; Hendrik Dietz; Job Boekhoven
|
Physical Chemistry; Organic Chemistry; Nanoscience; Combinatorial Chemistry; Supramolecular Chemistry (Org.); Self-Assembly
|
CC BY 4.0
|
CHEMRXIV
|
2021-09-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615364ffcea2e936be00fee6/original/regulating-the-dynamic-folding-of-a-dna-hairpin-at-the-expense-of-a-small-molecular-fuel.pdf
|
6239e860658bc09df3b40498
|
10.26434/chemrxiv-2022-9vhsm
|
Inverse Designed Plasmonic Metasurface with ppb Optical Hydrogen Detection
|
Plasmonic sensors rely on optical resonances in metal nanoparticles and are typically limited by their broad spectral features. This constraint is particularly taxing for optical H2 sensors, in which hydrogen is absorbed inside optically-lossy Pd nanoparticles and for which state-of-the-art detection limits are only at the low parts-per-million (ppm) range. Here, we overcome this limitation by inversely designing a plasmonic metasurface based on a periodic array of Pd nanoparticles. Guided by a particle swarm optimization algorithm, we numerically identify and experimentally demonstrate a sensor with an optimal balance between a narrow spectral linewidth and a large field enhancement inside the nanoparticles, enabling a measured hydrogen detection limit of 250 parts-per-billion (ppb). Our work significantly improves current plasmonic hydrogen sensor capabilities and, in a broader context, highlights the power of inverse design of plasmonic metasurfaces for ultrasensitive (gas) detection.
|
Ferry Anggoro Ardy Nugroho; Ping Bai; Iwan Darmadi; Gabriel W. Castellanos; Joachim Fritzsche; Christoph Langhammer; Jaime Gómez Rivas; Andrea Baldi
|
Materials Science; Analytical Chemistry; Nanoscience; Metamaterials; Nanodevices; Plasmonic and Photonic Structures and Devices
|
CC BY 4.0
|
CHEMRXIV
|
2022-03-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6239e860658bc09df3b40498/original/inverse-designed-plasmonic-metasurface-with-ppb-optical-hydrogen-detection.pdf
|
6305d2b411986c7675440472
|
10.26434/chemrxiv-2022-cz7wr-v2
|
Quantum circuit learning as a potential algorithm to predict experimental chemical properties
|
We introduce quantum circuit learning (QCL) as an emerging regression algorithm for chemo- and materials-informatics. The supervised model, functioning on the rule of quantum mechanics, can process linear and smooth non-linear functions from small datasets (< 100 records). Compared with conventional algorithms, such as random forest, support vector machine, and linear regressions, the QCL can offer better predictions with some one-dimensional functions and experimental chemical databases. QCL will potentially help the virtual exploration of new molecules and materials more efficiently through its superior prediction performances.
|
Kan Hatakeyama-Sato; Yasuhiko Igarashi; Takahiro Kashikawa; Koichi Kimura; Kenichi Oyaizu
|
Theoretical and Computational Chemistry; Organic Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-08-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6305d2b411986c7675440472/original/quantum-circuit-learning-as-a-potential-algorithm-to-predict-experimental-chemical-properties.pdf
|
6523b89c8bab5d2055ef04b3
|
10.26434/chemrxiv-2023-d1n9d
|
A Systematic Study of Methyl Carbodithioate Esters as Effective Gold Contact Groups for Single-Molecule Electronics
|
Currently, there is an array of binding groups for use within molecular electronics for anchoring molecules to metal electrodes (e.g., R–SMe, R–NH2, R–CS2−, R–S−). The problem is that some anchoring groups that bind strongly to electrodes have poor/unknown stability, or they have weak electrode coupling. More binding groups are required for molecular design with good stability and strong binding to the electrodes. Here, we present an in-depth investigation into the use of carbodithioate esters as contact groups for single-molecule conductance measurements, using scanning tunnelling microscopy break junction measurements (STM-BJ). We demonstrate using a series of novel molecular wires that the methyl carbodithioate ester acts as an effective contact for gold electrodes in STM-BJ measurements without deprotection. Surface enhanced Raman measurements demonstrate that the C=S functionality remains intact when adsorbed on to gold nanoparticle surfaces. A gold(I) complex was also synthesised showing a C=Sׄ→Au(I) interaction highlighting that the ester remains intact while binding to a gold centre. Comparison with a benzyl thiomethyl ether demonstrates that the C=S significantly contributes to charge transport in single-molecule junctions. The synthetic accessibility and performance of the functional group reported here demonstrates that it should be used more extensively and has strong potential for the fabrication of larger area devices with long-term stability.
|
Jonathan Ward; Andrea Vezzoli; Craig Robertson; Richard Nichols; Simon Higgins
|
Materials Science; Nanoscience; Aggregates and Assemblies; Nanofabrication; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6523b89c8bab5d2055ef04b3/original/a-systematic-study-of-methyl-carbodithioate-esters-as-effective-gold-contact-groups-for-single-molecule-electronics.pdf
|
60c754d44c89194255ad45b1
|
10.26434/chemrxiv.13750414.v1
|
Machine Learning Classification of Disrotatory IRC and Conrotatory Non-IRC Trajectory Motion for Cyclopropyl Radical Ring Opening
|
Transition-state features from trajectories were used for supervised machine learning analysis of the cyclopropyl radical ring opening reaction. Quantitative and qualitative assessment of features controlling disrotatory IRC versus conrotatory non-IRC motion and revealed that there are two key vibrational modes where their directional combination provides prediction of pathway motion. <br />
|
Steven Maley; Jesse Melville; Spencer Yu; Cal Hargis; Reid Hamilton; Benjamin Grant; Matthew Teynor; Daniel Ess
|
Theory - Computational; Machine Learning
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-02-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754d44c89194255ad45b1/original/machine-learning-classification-of-disrotatory-irc-and-conrotatory-non-irc-trajectory-motion-for-cyclopropyl-radical-ring-opening.pdf
|
60c74e539abda24ecaf8d601
|
10.26434/chemrxiv.12735584.v1
|
Enhanced Luminescence and Mechanistic Studies on Mn-doped Double Layered Perovskite Phosphors: Cs4Mn1−xCdxBi2Cl12
|
Halide perovskites offer great promise for optoelectronic applications, but stability issues continue to hinder its
implementation and long-term stability. The stability of all-inorganic halide perovskites and the inherent quantum confinement of
low dimensional perovskites can be harnessed to synthesize materials with high PL efficiency. An example of such materials is the
recently reported new family of layered double perovskites, Cs4Mn1−xCdxBi2Cl12. Herein, we report a new synthetic procedure that
enhances the maximum PLQY of this family materials to up 79.5%, a 20% enhancement from previous reports and the highest
reported for a Mn-doped halide perovskite. Importantly, stability tests demonstrate that these materials are very stable towards
humidity, UV irradiation, and temperature. Finally, we investigated the photophysics, the effects of magnetic coupling and
temperature in the PL efficiency and proposed a mechanism for the emission process. Our results highlight the potential of this family
of materials and related layered all-inorganic perovskites for solid-state lighting and optoelectronic applications<p></p>
|
Brenda Vargas; Diana T. Reyes-Castillo; Eduardo Coutino-Gonzalez; Citlali Sánchez-Aké; Carlos Ramos; Ciro Falcony; Diego Solis-Ibarra
|
Optical Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e539abda24ecaf8d601/original/enhanced-luminescence-and-mechanistic-studies-on-mn-doped-double-layered-perovskite-phosphors-cs4mn1-x-cdx-bi2cl12.pdf
|
660f78e521291e5d1d19c6ba
|
10.26434/chemrxiv-2024-rc6b7
|
Computationally predicting the performance of gas sensor arrays for anomaly detection
|
In many gas sensing tasks, we simply wish to become aware of gas compositions that deviate from normal, "business-as-usual" conditions. We provide a methodology, illustrated by example, to computationally predict the performance of a gas sensor array design for detecting anomalous gas compositions. Specifically, we consider a sensor array of two zeolitic imidazolate frameworks (ZIFs) as gravimetric sensing elements for detecting anomalous gas compositions in a fruit ripening room. First, we define the probability distribution of the concentrations of the key gas species (CO₂, C₂H₄, H₂O) we expect to encounter under normal conditions. Next, we construct a thermodynamic model to predict gas adsorption in the ZIF sensing elements in response to these gas compositions. Then, we generate a synthetic training data set of sensor array responses to "normal" gas compositions. Finally, we train a support vector data description to flag anomalous sensor array responses and test its false alarm and missed-anomaly rates under conceived anomalies. We find the performance of the anomaly detector diminishes with (i) greater variance in humidity, which can mask CO₂ and C₂H₄ anomalies or cause false alarms, (ii) higher levels of noise emanating from the transducers, and (iii) smaller training data sets. Our exploratory study is a step towards computational design of gas sensor arrays for anomaly detection.
|
Paul Morris; Cory Simon
|
Theoretical and Computational Chemistry; Materials Science; Nanostructured Materials - Materials; Machine Learning
|
CC BY 4.0
|
CHEMRXIV
|
2024-04-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660f78e521291e5d1d19c6ba/original/computationally-predicting-the-performance-of-gas-sensor-arrays-for-anomaly-detection.pdf
|
6142b676fc08e32455965b89
|
10.26434/chemrxiv-2021-0gqpg
|
Precise and Long-Term Tracking of Mitochondria in Neurons using a Bioconjugatable and Photostable AIE Luminogen
|
Tracking mitochondrial movement in neurons is an attractive research field as dysregulation of mitochondrial motion is associated with multiple neurological diseases. To attain the precise trajectory of a single mitochondrion and achieve long-term imaging of mitochondria in neurons, specific and photostable fluorescent probes with a long emission lifetime are required. Existing mitochondrial targeting fluorescent dyes suffer from poor photostability, high toxicity, “always-on” behavior, and aggregation-caused quenching effect, which limit their use in studying mitochondria in neurons. To overcome these challenges, we designed and synthesized an aggregation-induced emission (AIE)-active luminogen, TPAP-C5-yne, which consists of an activated alkyne terminus for bioconjugation with amines, and a cationic pyridinium moiety to selectively target mitochondria. For the first time using TPAP-C5-yne, we successfully tracked and analyzed the motion of a single mitochondrion in live primary hippocampal neurons accurately using real-time fluorescence images acquired by a sensitive EMCCD camera. In addition, long-term imaging of mitochondria in live neurons for a week is achieved by TPAP-C5-yne, which was not feasible with a commercially available mitochondrial targeting probe before.
|
Hojeong Park; Guangle Niu; Chao Wu; Chungwon Park; Hyokeun Park; Ryan T. K. Kwok; Benzhao He ; Benzhong Tang
|
Biological and Medicinal Chemistry; Bioengineering and Biotechnology; Chemical Biology; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-09-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6142b676fc08e32455965b89/original/precise-and-long-term-tracking-of-mitochondria-in-neurons-using-a-bioconjugatable-and-photostable-aie-luminogen.pdf
|
61f56f9de59d87f6e14dcedb
|
10.26434/chemrxiv-2022-9xz68
|
Photoelectrocatalytic biosynthesis fueled by microplastics
|
Biocatalytic artificial photosynthesis integrates photocatalysis and redox biocatalysis through inspiration from plants to synthesize value-added chemicals using solar energy. The nature-inspired approach, however, suffers from sluggish rates due to the challenging water oxidation kinetics. Here, we report photoelectrochemical (PEC) biosynthetic reactions that use nonrecyclable real-world PET microplastics as an electron feedstock. A Zr-doped hematite photoanode (i) extracts electrons from hydrolyzed PET solutions obtained from post-consumer PET wastes (e.g., drinking bottles) and (ii) transfers the electrons to the bioelectrocatalytic site. Carbon-based cathodes receive the electrons to (i) activate redox enzymes [e.g., unspecific peroxygenase (UPO), L-glutamate dehydrogenase (GDH), ene-reductase from the old yellow enzyme family (OYE)] and (ii) drive various organic synthetic reactions, such as oxyfunctionalization of C-H bonds, amination of C=O bonds, and asymmetric hydrogenation of C=C bonds. These photoelectrocatalyst/biocatalyst hybrids achieve benchmark total turnover numbers of 362,000 (UPO), 144,000 (GDH), and 1,300 (OYE). This work presents a photoelectrocatalytic approach for integrating environmental remediation and biocatalytic photosynthesis towards sustainable solar-to-chemical synthesis.
|
Jinhyun Kim; Jinha Jang; Thomas Hilberath; Frank Hollmann; Chan Beum Park
|
Catalysis; Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-02-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f56f9de59d87f6e14dcedb/original/photoelectrocatalytic-biosynthesis-fueled-by-microplastics.pdf
|
60c74fc6bdbb894163a39e0e
|
10.26434/chemrxiv.12937691.v1
|
Catalytic Fe-Oxo Clusters Stabilized on the MOF-808 Metal Organicframework for the Degradation of Water Pollutants
|
<p>Stabilizing catalytic iron-oxo-clusters within nanoporous metal-organic
frameworks (MOF) is a powerful strategy to prepare new active materials for the
degradation of toxic chemicals, such as bisphenol A. Herein, we combine pair
distribution function analysis of total X-ray scattering data and X-ray
absorption spectroscopy, with computational modelling to understand the local
structural nature of added redox-active iron-oxo clusters bridging neighbouring zirconia-nodes
within MOF-808.</p>
|
Celia Castillo-Blas; Ignacio Romero-Muñiz; Andreas Mavrandonakis; Laura Simonelli; Ana Eva Platero Prats
|
Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-09-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fc6bdbb894163a39e0e/original/catalytic-fe-oxo-clusters-stabilized-on-the-mof-808-metal-organicframework-for-the-degradation-of-water-pollutants.pdf
|
63b7de9d1f24033ce1183486
|
10.26434/chemrxiv-2023-50tb6
|
Local Water Structures Govern the Mixing Thermodynamics of Glycerol-Water Solutions
|
Glycerol is a major cryoprotective agent and is widely used to promote protein stabilization. Through a combined experimental and theoretical study, we show that global thermodynamic mixing properties of glycerol and water are dictated by local solvation motifs. We identify three water populations, i.e., bulk water, bound water H-bonded to hydrophilic groups of glycerol and wrap water hydrating hydrophobic moieties. Each population provides distinct spectroscopic fingerprints in the THz/FIR spectral range, which allow to quantify their respective abundance and their partial contributions to the mixing enthalpy. We uncover a 1:1 connection between the number of bound waters and the mixing enthalpy, as deduced from experiments as well as from simulations. The balance between local hydrophobic wrap and hydrophilic bound contributions at the molecular level dictates macroscopic thermodynamics of mixing. This offers opportunities to rationally design polyol water mixtures to optimize technological applications by tuning mixing enthalpy and entropy based on spectroscopic screening.
|
Debasish Das Mahanta; Dennis Robinson Brown; Simone Pezzotti; Songi Han; Gerhard Schwaab; M. Scott Shell; Martina Havenith
|
Physical Chemistry; Solution Chemistry; Spectroscopy (Physical Chem.); Thermodynamics (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-01-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b7de9d1f24033ce1183486/original/local-water-structures-govern-the-mixing-thermodynamics-of-glycerol-water-solutions.pdf
|
66fcc8da12ff75c3a11ef338
|
10.26434/chemrxiv-2024-fp1lg
|
Unbiased Dataset for Methane Dry Reforming and Catalyst Design Guidelines Obtained by High-Throughput Experimentation and Machine Learning
|
Traditional solid catalyst design is a highly labor-intensive and post hoc process, involving repeated experimental trials and errors based on hypotheses derived from prior knowledge. Recently, integrating high-throughput experimentation (HTE) with machine learning (ML) aims to achieve a more systematic catalyst design without relying on specific knowledge or assumptions about the target catalysis. As a first step, this study constructs an unbiased HTE dataset for dry reforming of methane (DRM) at 500 °C on 256 γ-Al2O3-supported multi-element catalysts, prepared by randomly combining 17 elements selected from the periodic table without any preconceptions. The obtained data and selected catalysts are analyzed in various ways to gain insights into catalyst design and catalysis. It is found that the inclusion of Ni or platinum group elements does not necessarily lead to DRM activity; rather, careful combinations of elements are crucial. Specifically, the catalysts that exhibit the highest activities are not only based on Ni as the main active element but also frequently contain Li, Al, and Nb, which are hardly regarded as promoters in the literature. Data scientific analyses also reveal that the coexistence of specific elements such as Al, Nb, and Hf with Ni or Rh promotes catalysis. Studying the best-found Ni-based catalyst elucidates individual elements’ roles in improving activity and suppressing carbon deposition. In particular, the ternary combination of Al, Nb, and Hf reduces carbon deposition while enhancing activity. Overall, this study demonstrates the validity of unbiased exploration in providing a foundational dataset for ML and in discovering catalyst design guidelines.
|
Wentao Du; Patchanee Chammingkwan; Keisuke Takahashi; Toshiaki Taniike
|
Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fcc8da12ff75c3a11ef338/original/unbiased-dataset-for-methane-dry-reforming-and-catalyst-design-guidelines-obtained-by-high-throughput-experimentation-and-machine-learning.pdf
|
643d0e3208c86922ff2734e1
|
10.26434/chemrxiv-2023-xg1g4
|
Targeted Discovery of Cryptic Enediyne Natural Products via FRET-coupled High-Throughput Elicitor Screening
|
Enediyne antibiotics are a striking family of DNA-cleaving natural products with high degrees of cytotoxicity and structural complexity. Microbial genome sequences that have recently accumulated point to an untapped trove of ‘cryptic’ enediynes. Most of the cognate biosynthetic gene clusters (BGCs) are sparingly expressed under standard growth conditions, making it difficult to characterize their products. Herein, we report a fluorescence-based DNA cleavage assay coupled to high-throughput elicitor screening for the rapid, targeted discovery of cryptic enediyne metabolites. We applied the approach to Streptomyces clavuligerus, which harbors two such BGCs with unknown products, identified steroids as effective elicitors, and characterized ten cryptic enediyne-derived natural products, termed clavulynes A-J with unusual carbonate and terminal olefin functionalities. Our results contribute to the growing repertoire of enediynes and provide a blueprint for identifying additional ones in the future
|
Esther Han; Seoung Rak Lee; Craig Townsend; Mohammad Seyedsayamdost
|
Biological and Medicinal Chemistry; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643d0e3208c86922ff2734e1/original/targeted-discovery-of-cryptic-enediyne-natural-products-via-fret-coupled-high-throughput-elicitor-screening.pdf
|
640a3b8a6642bf8c8f41ada3
|
10.26434/chemrxiv-2023-zxbfn
|
Sub-second HKUST-1 Synthesis in Continuous Flow Supercritical CO2 Reactor
|
The efficient, reliable, and environmentally friendly synthesis of Metal-Organic Frameworks (MOFs) can trigger their wide adoption in many practical applications. Addressing this challenge, this study focuses on optimizing the continuous flow synthesis of Copper Benzene-1,3,5-Tricarboxylate (HKUST-1) in a supercritical carbon dioxide (scCO2) environment. The effects of the synthesis parameters on the physiochemical characteristics of MOF were investigated over a wide range of CO2 injection temperature Tinj = 50 300 C while maintaining sub-second reactor residence time ~ 650 ms. The X-ray diffraction analysis (XRD) verified a well-defined MOF crystal structure. Analysis of the MOFs' surface area and pore sizes indicated that the optimal properties were obtained at a CO2 injection temperature of 150 C corresponding to an average reactor temperature of ~80 C with the maximum BET-specific surface area ~ 1,550 m2/g and pore size ~ 10.55 . At lower synthesis temperatures, the pore sizes and BET-specific surface area are lower due to insufficient activation, while at temperatures Tinj >250C, BET surface area decreases significantly due to the degradation of organic precursors. The increase in the synthesis temperature results in a fast MOF synthesis and activation due to a single-phase supercritical environment; however, high CO2 injection temperatures may create a high-temperature gradient leading to rapid degradation of organic precursors. This work demonstrates the feasibility of sub-second synthesis of high-quality MOFs and highlights the need to optimize the continuous flow process for HKUST-1 and other MOFs.
|
MOHAMMAD MASRUR HOSSAIN; Conrad Austin ; Igor V. Novosselov
|
Materials Science; Composites; Nanostructured Materials - Materials
|
CC BY 4.0
|
CHEMRXIV
|
2023-03-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640a3b8a6642bf8c8f41ada3/original/sub-second-hkust-1-synthesis-in-continuous-flow-supercritical-co2-reactor.pdf
|
60c75414842e655160db40a9
|
10.26434/chemrxiv.13252544.v2
|
In situ X-ray Diffraction Investigation of the Crystallisation of Perfluorinated Ce(IV)-based Metal-Organic Frameworks with UiO-66 and MIL-140 architectures
|
We report on the results of a thorough <i>in situ</i> synchrotron powder X-ray diffraction study of the crystallisation in aqueous medium of two recently discovered perfluorinated Ce(IV)-based metal-organic frameworks (MOFs), analogues of the already well investigated Zr(IV)-based UiO-66 and MIL-140A, namely, F4_UiO-66(Ce) and F4_MIL-140A(Ce). The two MOFs were originally obtained in pure form in similar conditions, using ammonium cerium nitrate and tetrafluoroterephthalic acid as reagents, and small variations of the reaction parameters were found to yield mixed phases. Here, we investigate the crystallisation of these compounds <i>in situ</i> in a wide range of conditions, varying parameters such as temperature, amount of the protonation modulator nitric acid (HNO<sub>3</sub>) and amount of the coordination modulator acetic acid (AcOH). When only HNO<sub>3</sub> is present in the reaction environment, F4_MIL-140A(Ce) is obtained as a pure phase. Heating preferentially accelerates nucleation, which becomes rate determining below 57 °C, whereas the modulator influences nucleation and crystal growth to a similar extent. Upon addition of AcOH to the system, alongside HNO<sub>3</sub>, mixed-phased products, consisting of F4_MIL-140A(Ce) and F4_UiO-66(Ce), are obtained. In these conditions, F4_UiO-66(Ce) is always formed faster and no interconversion between the two phases occurs. In the case of F4_UiO-66(Ce), crystal growth is always the rate determining step. An increase in the amount of HNO<sub>3</sub> slows down both nucleation and growth rates for F4_MIL-140A(Ce), whereas nucleation is mainly affected for F4_UiO-66(Ce). In addition, a higher amount HNO<sub>3</sub> favours the formation of F4_MIL-140A(Ce). Similarly, increasing the amount of AcOH leads to slowing down of the nucleation and growth rate, but favours the formation of F4_UiO-66(Ce). The pure F4_UiO-66(Ce) phase could also be obtained when using larger amounts of AcOH in the presence of minimal HNO<sub>3</sub>. Based on these <i>in situ</i> results, a new optimised route to achieving a pure, high quality F4_MIL-140A(Ce) phase in mild conditions (60 °C, 1 h) is also identified.
|
Stephen Shearan; Jannick Jacobsen; Ferdinando Costantino; Roberto D’Amato; Dmitri Novikov; Norbert Stock; Enrico Andreoli; Marco Taddei
|
Coordination Chemistry (Inorg.); Reaction (Inorg.); Solid State Chemistry; Chemical Kinetics; Self-Assembly; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-01-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75414842e655160db40a9/original/in-situ-x-ray-diffraction-investigation-of-the-crystallisation-of-perfluorinated-ce-iv-based-metal-organic-frameworks-with-ui-o-66-and-mil-140-architectures.pdf
|
62bcb000e60d988b1af1d4f3
|
10.26434/chemrxiv-2022-p08rn
|
Racemic and Meso Diastereomers of a P-Chirogenic Diboranyldiphosphinoethane
|
Diphosphine ligands have enjoyed great success as sup-porting moieties for transition elements, where modifica-tion of both primary and secondary coordination sphere has been shown to illicit differences in chemical reactivi-ty. This work describes a new family of such ligands con-structed from the previously reported scaffold, (±)-rac/meso-(t-Bu)ClP-CH2CH2-PCl(t-Bu) that bears bulky tert-butyl substituents. Reaction of this precursor with allyl magnesium chloride and subsequent hydroboration using HBCy2 (Cy = cyclohexyl) provides access to a di-boranyldiphosphinoethane – the first in a class of ligands having two electrophilic boranes in their secondary coor-dination sphere. As a testing ground for coordination, these motifs (and their allyl precursor) have been in-stalled at Ni(0) using [Ni(COD)2] (COD = 1,5-cyclooctadiene) in order to determine methods for clean installation. Product stereochemical outcomes are in some cases complicated and have been determined by NMR spectroscopic and crystallographic means. Density func-tional theory optimizations and accurate DLPNO-CCSD(T) energy calculations were also performed to sup-port structural assignment.
|
Brady Austen; Harvey Sharma; Joseph Zurakowski; Marcus Drover
|
Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Organomet.); Ligand Design; Ligands (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-07-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bcb000e60d988b1af1d4f3/original/racemic-and-meso-diastereomers-of-a-p-chirogenic-diboranyldiphosphinoethane.pdf
|
616342f0aa918de65726a4ab
|
10.26434/chemrxiv-2021-fv76p
|
Using Automated Synthesis to Understand the Role of Side Chains on Molecular Charge Transport
|
The development of next-generation organic electronic materials critically relies on understanding structure-function relationships in conjugated polymers. However, unlocking the full potential of organic materials requires access to their vast chemical space while efficiently managing the large synthetic workload to survey new materials. In this work, we use automated synthesis to prepare a library of conjugated oligomers with systematically varied side chain composition followed by single-molecule characterization of charge transport. Our results show that molecular junctions with long alkyl side chains exhibit a concentration-dependent bimodal conductance with an unexpectedly high conductance state that arises due to surface adsorption and backbone planarization, which is supported by a series of control experiments using asymmetric, planarized, and sterically hindered molecules. Density functional theory simulations and experiments using different anchors and alkoxy side chains highlight the role of side chain chemistry on charge transport. Overall, this work opens new avenues for using automated synthesis for the development and understanding of organic electronic materials.
|
Songsong Li; Edward Jira; Nicholas Angello; Jialing Li; Hao Yu; Jeffrey Moore; Ying Diao; Martin Burke; Charles Schroeder
|
Physical Chemistry; Organic Chemistry; Nanoscience; Nanodevices
|
CC BY 4.0
|
CHEMRXIV
|
2021-10-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616342f0aa918de65726a4ab/original/using-automated-synthesis-to-understand-the-role-of-side-chains-on-molecular-charge-transport.pdf
|
670cae9f51558a15efff5afb
|
10.26434/chemrxiv-2024-zvn5k
|
Mini-Review on Sodium Benzoate: Its Uses, Adverse Effects, and Environmental Impact as a Pharmaceutical Product
|
This short overview summarizes sodium benzoate's (SB) dual role as a useful preservative and a possible threat to human and environmental health. This review provides a concise summary of uses, adverse effects, and environmental impact of SB. SB is widely used as a preservative in pharmaceuticals and food products due to its ability to inhibit microbial growth, thus extending the shelf life of various formulations, including syrups and ointments. While generally considered safe, SB can cause allergic reactions and may contribute to conditions like ADHD, particularly in children. It can also disrupt gut microbiota balance. The paper highlights the concerns regarding the environmental persistence of SB. Although it is biodegradable, its degradation rate can vary based on conditions and concentrations. Improper wastewater treatment can lead to its accumulation in aquatic ecosystems, posing risks to both the environment and human health. The review emphasizes the need for awareness regarding the long-term effects of sodium benzoate in ecosystems and suggests that environmentally friendly technologies could mitigate its impact.
|
Dania Mohammed; Hayder Issa
|
Biological and Medicinal Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Wastes; Drug Discovery and Drug Delivery Systems
|
CC BY 4.0
|
CHEMRXIV
|
2024-10-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670cae9f51558a15efff5afb/original/mini-review-on-sodium-benzoate-its-uses-adverse-effects-and-environmental-impact-as-a-pharmaceutical-product.pdf
|
60c7550fbb8c1af6223dc350
|
10.26434/chemrxiv.14035919.v1
|
How Aromatic Are Molecular Nanorings? The Case of a Six-Porphyrin Nanoring
|
<div>
<div>
<div>
<p>Large conjugated rings give rise to novel promising structures that can sustain persistent currents
at low temperatures even in the presence of strong magnetic fields. One of the most interesting
such molecules was recently synthesized [Anderson et al., Nature, 2017, 541, 3512] in the form
of a six-porphyrin nanoring structure, which, according to the authors, in its +6-oxidation state
(c-P66+) sustained an aromatic ring current involving 78π electrons; one of the largest aromatic
rings ever produced. In this paper, we have provided compelling evidence that this molecule is
not aromatic, as it was incorrectly inferred from computational calculations that suffer from large
delocalization errors. A thorough analysis of four oxidation states of the six-porphyrin nanoring re-
veals that the main reason behind the poor aromaticity of these nanorings is the low delocalization
in the transition from the porphyrins to the bridging butadiyne linkers, which disrupts the overall
conjugated circuit. These results highlight the importance of choosing an adequate computational
method to study large conjugated molecules and the appropriate aromaticity descriptors to identify the part of the molecule that is responsible for the loss of aromaticity. We believe the strategy
here employed will be helpful in designing new large aromatic molecular nanorings.
</p>
</div>
</div>
</div>
|
irene casademont-reig; Raúl Guerrero-Avilés; Eloy Ramos-Cordoba; Miquel Torrent-Sucarrat; Eduard Matito
|
Physical Organic Chemistry; Nanostructured Materials - Nanoscience; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-02-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7550fbb8c1af6223dc350/original/how-aromatic-are-molecular-nanorings-the-case-of-a-six-porphyrin-nanoring.pdf
|
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.