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
⌀ |
|---|---|---|---|---|---|---|---|---|---|
651bb371006594091255f0fc
|
10.26434/chemrxiv-2023-wpc4r
|
Pushing Boundaries in Single Molecule Magnets: An Ab Initio Perspective on Harnessing Unusual Oxidation States for Unprecedented Lanthanide SMM Performance
|
The recent breakthrough of attaining blocking temperature near liquid N2 temperature rekindled the interest in lanthanide-based Single Molecule Magnets towards end-user applications. Within this realm, several challenges are present, with a key objective being the further enhancement of the blocking temperature. As the current set of molecules based on Dy(III) has already reached their maximum potential barrier height for magnetization reversal (Ueff), chemical insights-based developments are hampered. In this connection, using DFT and ab initio CASSCF methods, we have explored the possibility of obtaining lanthanide SMMs in unusual oxidation states such as +4 and +5. We are encouraged by the fact that several such complexes are already reported, with some of them found to exhibit performant SMM characteristics. We begin with various small models of [LnO2], [LnO2]−, and [LnO2]+ (Ln varying from Ce to Lu) systems to correlate the nature of the lanthanides to the SMM characteristics. We have also extended our study to include five complexes reported earlier possessing +4 and +5 oxidation states to offer clues to improve the SMM characteristics. Our calculations reveal several advantages in fine-tuning the oxidation state in lanthanide SMMs, and this includes (i) the lanthanide-ligand covalency found to increase as high as 45% compared to the LnIII counterpart (ii) yield barrier height for magnetization reversal as high as 8500 cm-1, an unprecedented tuning up to three times larger compared to the best-in-class LnIII counterpart (iii) among various ways to stabilise such high-oxidation state including encapsulation yield several targets with HoO2@SWCNT(4,4) predicted to yield an impressive energy barrier of ~5400 cm−1 (iv) the stronger lanthanide-ligand bonds also found to help in tuning the spin-phonon relaxation as stronger bonds found to offset the vibrations that cause the relaxation, potentially yield larger blocking temperatures - offering a never-before-seen strategy to new class lanthanide SMMs.
|
Tanu Sharma; Abinash Swain; Gopalan Rajaraman
|
Inorganic Chemistry; Lanthanides and Actinides; Magnetism; Theory - Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651bb371006594091255f0fc/original/pushing-boundaries-in-single-molecule-magnets-an-ab-initio-perspective-on-harnessing-unusual-oxidation-states-for-unprecedented-lanthanide-smm-performance.pdf
|
61862dfaf9f05b2eefee9d9f
|
10.26434/chemrxiv-2021-fmlzp
|
Charge Transfer Landscape Manifesting Structure-Rate Relationship in the Condensed Phase via Machine Learning
|
In this work, we develop a machine learning (ML) strategy to map molecular structure to condensed-phase charge transfer (CT) properties including CT rate constants, energy levels, electronic couplings, energy gaps, reorganization energies, and reaction free energies, which are called CT fingerprints. The CT fingerprints of selected landmark structures covering the conformation space of an organic photovoltaic molecule dissolved in explicit solvent are computed and used to train ML models using kernel ridge regression. The ML models show high predictive power with R2>0.97, and both mean absolute error and root mean square error within chemical accuracy. The CT landscape for millions of molecular dynamics sampled structures is thus constructed, which allows for instant prediction of CT rate properties given any molecular structure. The unprecedented CT landscape will shed light on real-time CT dynamics in nanoscale and mesoscale condensed-phase systems, and the optimal fabrication design for homogeneous and heterogeneous optoelectronic devices.
|
Dominikus Brian; Xiang Sun
|
Theoretical and Computational Chemistry; Theory - Computational; Machine Learning
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-11-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61862dfaf9f05b2eefee9d9f/original/charge-transfer-landscape-manifesting-structure-rate-relationship-in-the-condensed-phase-via-machine-learning.pdf
|
669ebafb01103d79c54a530c
|
10.26434/chemrxiv-2024-77sm0
|
Photothermal Conversion Recycling of Commercial Polystyrene Plastic
|
Photothermal conversion can promote plastic depolymerization (chemical recycling)
through light-to-heat conversion. The highly localized temperature gradient on
photothermal agent surface allows selective heating with spatial controls not observed
with bulk heating. However, identifying practical photothermal agents that are easily
incorporated and reusable can be challenging. Interestingly, the rarely recycled black
plastics containing carbon black is a potential candidate for photothermal conversion
recycling. Herein, we use photothermal conversion to depolymerize commercial
polystyrene plastics back into styrene monomers using the pigment in black plastics.
Synthesized polystyrene-carbon black composites were depolymerized under white LED
light irradiation, producing styrene monomer in up to 60 % yield. We demonstrate the
recyclability of monomer and carbon black for a fully circular plastics economy.
Ultimately, commercial black polystyrene samples are successfully converted to styrene
through photothermal depolymerization without additional additives, with yields up to
70 % under focused solar irradiation in just 5 minutes. Broadly, this sustainable method
holds the potential to actualize a closed-loop economy of black plastics.
|
Sewon Oh; Hanning Jiang; Liat Kugelmass; Erin Stache
|
Organic Chemistry; Materials Science; Polymer Science; Photochemistry (Org.); Carbon-based Materials; Dyes and Chromophores
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669ebafb01103d79c54a530c/original/photothermal-conversion-recycling-of-commercial-polystyrene-plastic.pdf
|
644a80f06ee8e6b5ed2d139b
|
10.26434/chemrxiv-2023-gjj50
|
Highly Sensitive and Selective Electrochemical Detection of Dopamine and Uric Acid Using Sea Urchin-like Tungsten Oxide Nanostructure Modified SPCE
|
Here, screen-printed carbon electrodes (SPCEs) were modified with ultrafine and mainly monodisperse sea urchin-like tungsten oxide (SUWO3) nanostructures synthesized by a simple one-pot hydrothermal method for highly sensitive and selective detection of dopamine (DA) and uric acid (UA). Sea urchin-like nanostructures were clearly observed in scanning electron microscope images and WO3 composition was confirmed with XRD, FTIR and UV-Vis spectrophotometer. Modification SPCEs with SUWO3 nanostructures via the drop-casting method clearly reduced the R𝑐𝑡 value of the electrodes, lowered the ΔEp and enhanced the DA oxidation current due to high electrocatalytic activity. As a result, SUWO3/SPCEs enabled highly sensitive detection of DA (LOD: 51.4 nM and sensitivity: 127 μAmM−1cm−2) and UA (LOD: 253 nM and sensitivity: 55.9 μAmM−1cm−2) at low concentration. Lastly, SUWO3/SPCEs were tested with artificial urine, in which acceptable recoveries for both molecules were obtained. Given the high selectivity, the sensor has the potential to be used for highly sensitive simultaneous detection of DA and UA in real biological samples
|
Merve Oğuz; Ahmet Aykaç; Mustafa Şen
|
Analytical Chemistry; Electrochemical Analysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644a80f06ee8e6b5ed2d139b/original/highly-sensitive-and-selective-electrochemical-detection-of-dopamine-and-uric-acid-using-sea-urchin-like-tungsten-oxide-nanostructure-modified-spce.pdf
|
64272436a029a26b4cb49451
|
10.26434/chemrxiv-2023-7v4sw
|
Optimization of binding affinities in chemical space with generative pretrained transformer and deep reinforcement learning
|
Background: The key challenge in drug discovery is to discover novel compounds with desirable properties. Among the properties, binding affinity to a target is one of the prerequisites and usually evaluated by molecular docking or quantitative structure activity relationship (QSAR) models.
Methods: In this study, we developed Simplified molecular input line entry system Generative Pretrained Transformer with Reinforcement Learning (SGPT-RL), which uses a transformer decoder as the policy network of the reinforcement learning agent to optimize the binding affinity to a target. SGPT-RL was evaluated on the Moses distribution learning benchmark and two goal-directed generation tasks, with Dopamine Receptor D2 (DRD2) and Angiotensin-Converting Enzyme 2 (ACE2) as the targets. Both QSAR model and molecular docking were implemented as the optimization goals in the tasks. The popular Reinvent method was used as the baseline for comparison.
Results: The results on Moses benchmark showed that SGPT-RL learned good property distributions and generated molecules with high validity and novelty. On the two goal-directed generation tasks, both SGPT-RL and Reinvent were able to generate valid molecules with improved target scores. The SGPT-RL method achieved better results than Reinvent on the ACE2 task, where molecular docking was used as the optimization goal. Further analysis shows that SGPT-RL learned conserved scaffold patterns during exploration.
Conclusions: The superior performance of SGPT-RL in the ACE2 task indicates that it can be applied to the virtual screening process where molecular docking is widely used as the criteria. Besides, the scaffold patterns learned by SGPT-RL during the exploration process can assist chemists to better design and discover novel lead candidates.
|
Xiaopeng Xu; Juexiao Zhou; Chen Zhu; Qing Zhan; Zhongxiao Li; Ruochi Zhang; Yu Wang; Xingyu Liao; Xin Gao
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Engineering and Industrial Chemistry; Drug Discovery and Drug Delivery Systems; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-04-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64272436a029a26b4cb49451/original/optimization-of-binding-affinities-in-chemical-space-with-generative-pretrained-transformer-and-deep-reinforcement-learning.pdf
|
60c7421a469df4663ef42f3e
|
10.26434/chemrxiv.8206469.v1
|
Three-Dimensional Printing of Proteinaceous Structures by Aqueous Solvent-Directed Molecular Assembly
|
<p>Hierarchical molecular assembly directed by cell-regulated
aqueous solvent is a fundamental strategy for manufacturing various proteinaceous
structures that are of intense interest for nanotechnology, sustainable
manufacturing and regenerative medicine. However, to translate the natural
strategy into advanced digital manufacturing like three-dimensional (3D)
printing remains a tremendous technical and theoretical challenge. This work
presents a 3D printing technique of a particular protein, silk fibroin, by
rationally designing an<i> de novo </i>aqueous
salt bath capable of directing the hierarchical assembly of the protein
molecules. This technique, conducted under aqueous and ambient conditions,
results in 3D proteinaceous architectures characterized by intrinsic
biocompatibility/biodegradability and remarkable mechanical performance. The
versatility of this method is shown in a diversity of 3D shapes and a range of functional
components integrated into the 3D prints. Exceptional manufacturing capability
and one promising application is exemplified by the single-step construction of
perfusable microfluidic chips, also an analogy of small-diameter vascular grafts,
which eliminates the use of supporting or sacrificial materials owing to optimized
crosslinking dynamics and compartmentalized printing parameters. The 3D shaping
capability of the protein material can benefit a multitude of biomedical devices,
from drug delivery to surgical implants to tissue scaffolds.</p>
|
Xuan Mu; Yu Wang; Chengchen Guo; Yamin Li; Shengjie Ling; Wenwen Huang; Peggy Cebe; Huan-Hsuan Hsu; Fabio De Ferrari; Xiaocheng Jiang; Qiaobing Xu; Alessandra Balduini; Fiorenzo G. Omenetto; David L. Kaplan
|
Biological Materials; Materials Processing; Biopolymers; Hydrogels; Nanostructured Materials - Nanoscience; Bioengineering and Biotechnology; Self-Assembly
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-06-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7421a469df4663ef42f3e/original/three-dimensional-printing-of-proteinaceous-structures-by-aqueous-solvent-directed-molecular-assembly.pdf
|
650c7b9c60c37f4f76356bed
|
10.26434/chemrxiv-2023-dh71k
|
3D Printing of Layered Vanadium Disulfide for Zinc Ion Batteries
|
Aqueous zinc ion batteries are attractive energy storage devices for wearable electronics, owing to their safety and low cost. Among cathode materials, layered vanadium disulfide (VS2) has demonstrated good charge storage capability, as a result of its metallic character and large interlayer spacing. However, VS2 electrodes present fixed shapes and aspect ratios, and they are processed using toxic solvents, which hinders their integration in wearables. It is thus necessary to develop manufacturing methods that can meet the demand for shape customization and do not rely on toxic solvents. Here, we propose a flower-like VS2 architectures using a simple hydrothermal process to formulate an ink for extrusion 3D Printing (Direct Ink Writing). The 3D printing technique enables the fabrication of VS2 electrodes with porous micron-sized struts, high-mass loading of ~ 45 mg cm-2 and good conductivity. Using the 3D printed VS2 cathodes, zinc-ion microbatteries were assembled, achieving a capacity of ~ 1.98 mAh cm-2 and demonstrating a capacity retention of over 55% after 150 cycles. The choice of the electrolyte and processing of the cathode ensured good stability against dissolution, a no-torious challenge for VS2 in aqueous environment. In particular, the dissolution of VS2 cathodes for ZIBs was here prevented by the use of a water-in-salt electrolyte (WISE), enabling a long cycling life with higher capacity. This works paves the way towards form-free manufacturing of aqueous batteries which can be extended to different nanomaterials.
|
Stefano Tagliaferri; Nagaraju Goli; Maria Sokolikova; Rachael Quintin-Baxendale; Cecilia Mattevi
|
Materials Science; Nanoscience; Energy; Energy Storage
|
CC BY 4.0
|
CHEMRXIV
|
2023-09-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650c7b9c60c37f4f76356bed/original/3d-printing-of-layered-vanadium-disulfide-for-zinc-ion-batteries.pdf
|
633da73ae61502562d32c825
|
10.26434/chemrxiv-2022-jpnxq-v2
|
Operando characterization and theoretical modelling of metal|electrolyte interphase growth kinetics in solid-state-batteries - Part I: experiments
|
To harness all the benefits of solid-state battery (SSB) architectures in terms of energy density, their negative electrode should be an alkali metal. However, the high chemical potential of alkali metals makes them prone to reduce most solid electrolytes (SE), resulting in a decomposition layer called an interphase at the metal|SE interface. Quantitative information about the interphase chemical composition and rate of formation are challenging to obtain because the reaction occurs at a buried interface.
In this study, a thin layer of Na metal (Na0) is plated on the surface of a SE of the NaSICON family (Na3.4Zr2Si2.4P0.6O12 or NZSP) inside a commercial XPS system whilst continuously analysing the composition of the interphase operando. We identify the existence of an interphase at the Na0|NZSP interface, and more importantly, we demonstrate for the first time that this protocol can be used to study the kinetics of interphase formation.
A second important outcome of this article is that the surface chemistry of NZSP samples can be tuned to improve their stability against Na0. It is demonstrated by XPS and time-resolved electrochemical impedance spectroscopy (EIS) that a native Na3PO4 layer present on the surface of as-sintered NZSP samples protects their surface against decomposition.
|
Edouard Quérel; Nicholas J. Williams; Ieuan D. Seymour; Stephen J. Skinner; Ainara Aguadero
|
Materials Science; Energy; Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633da73ae61502562d32c825/original/operando-characterization-and-theoretical-modelling-of-metal-electrolyte-interphase-growth-kinetics-in-solid-state-batteries-part-i-experiments.pdf
|
60c73e97702a9ba70f189d99
|
10.26434/chemrxiv.7017482.v1
|
Continuous Synthesis of Doped Layered Double Hydroxides in a Meso-Scale Flow Reactor
|
Detailed characterisation of morphology of doped hydrotalcites as catalysts precursors. Trends of material stability, pore size distribution, particle size as a function of the nature of dopants. Data on the flow synthesis method and reproducibility of materials that can be attained by this method.
|
Polina Yaseneva; Nan An; Matt Finn; Nicholas Tidemann; Nicholas Jose; Adelina Voutchkova-Kostal; Alexei Lapkin
|
Materials Processing; Nanostructured Materials - Materials; Minerals; Physical and Chemical Properties; Structure
|
CC BY 4.0
|
CHEMRXIV
|
2018-08-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e97702a9ba70f189d99/original/continuous-synthesis-of-doped-layered-double-hydroxides-in-a-meso-scale-flow-reactor.pdf
|
60c758b7ee301c12bec7b795
|
10.26434/chemrxiv.14585934.v1
|
A Quantitative Metric for Organic Radical Persistence Using Thermodynamic and Kinetic Features
|
<p>Long-lived organic radicals are promising candidates for the development of high-performance energy solutions such as organic redox batteries, transistors, and light-emitting diodes. However, “stable” organic radicals that remain unreactive for an extended time and that can be stored and handled under ambient conditions are rare<b>. </b>A necessary but not sufficient condition for organic radical stability is the presence of thermodynamic stabilization, such as conjugation with an adjacent p-bond or lone-pair, or hyperconjugation with a s-bond. However, thermodynamic factors alone do not result in radicals with extended lifetimes: many resonance-stabilized radicals are transient species that exist for less than a millisecond. Kinetic stabilization is also necessary for persistence, such as steric effects that inhibit radical dimerization or reaction with solvent molecules. We describe a quantitative approach to map organic radical stability, using molecular descriptors designed to capture thermodynamic and kinetic considerations. The comparison of an extensive dataset of quantum chemical calculations of organic radicals with experimentally-known stable radical species reveals a region of this feature space where long-lived radicals are located. These descriptors, based upon maximum spin density and buried volume are combined into a single metric, the Radical Stability Score, that outperforms thermodynamic scales based on bond dissociation enthalpies in identifying remarkably long-lived radicals. This provides an objective and accessible metric for used in future molecular design and optimization campaigns. </p><p>We demonstrate this approach in identifying Pareto-optimal candidates for stable organic radicals.</p>
|
Shree Sowndarya S. V.; Peter St. John; Robert Paton
|
Physical Organic Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758b7ee301c12bec7b795/original/a-quantitative-metric-for-organic-radical-persistence-using-thermodynamic-and-kinetic-features.pdf
|
60c74808702a9b1f4918aee7
|
10.26434/chemrxiv.11842431.v1
|
Identification of Durable and Non-Durable FeNx Sites in Fe-N-C Materials for Proton Exchange Membrane Fuel Cells
|
While Fe-N-C materials are a promising alternative to platinum for catalyzing oxygen reduction in acidic polymer fuel cells, limited understanding of their operando degradation restricts rational approaches towards improved durability. Here we show that Fe-N-C catalysts initially comprising two distinct FeNx sites (S1 and S2) degrade via the transformation of S1 into iron oxides while the structure and number of S2 were unmodified. Structure-activity correlations drawn from end-of-test 57Fe Mössbauer spectroscopy reveal that both sites initially contribute to the ORR activity but only S2 significantly contributes after 50 h of operation. From in situ 57Fe Mössbauer spectroscopy in inert gas coupled to calculations of the Mössbauer signature of FeNx moieties in different electronic states, we identify S1 to be a high-spin FeN4C12 moiety and S2 a low- or intermediate spin FeN4C10 moiety. These insights lay the ground for rational approaches towards Fe-N-C cathodes with improved durability in acidic fuel cells.<br />
|
Jingkun Li; Moulay-Tahar Sougrati; andrea Zitolo; James Ablett; ismail can oguz; Tzonka Mineva; ivana matanovic; plamen atanassov; andrea di cicco; Kavita Kumar; Laetitia Dubau; frédéric maillard; Frederic Jaouen
|
Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-02-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74808702a9b1f4918aee7/original/identification-of-durable-and-non-durable-fe-nx-sites-in-fe-n-c-materials-for-proton-exchange-membrane-fuel-cells.pdf
|
659d3878e9ebbb4db9c3088f
|
10.26434/chemrxiv-2024-pf4w9
|
Multi-task ADME/PK Prediction at Industrial Scale: Leveraging Large and Diverse Experimental Datasets
|
ADME (Absorption, Distribution, Metabolism, Excretion) properties are key parameters to judge whether a drug candidate exhibits a desired pharmacokinetic (PK) profile. In this study, we tested multi-task machine learning (ML) models to predict ADME and animal PK endpoints trained on in-house data generated at Boehringer Ingelheim. Models were evaluated both at the design stage of a compound (i.e., no experimental data of test compounds available) and at testing stage when a particular assay would be conducted (i.e., experimental data of earlier conducted assays may be available). Using realistic time-splits, we found a clear benefit in performance of multi-task graph-based neural network models over single-task models, which was even stronger when experimental data of earlier assays is available. In an attempt to explain the success of multi-task models, we found that especially endpoints with the largest numbers of data points (physicochemical endpoints, clearance in microsomes) are responsible for increased predictivity in more complex ADME and PK endpoints. In summary, our study provides insight into how data for multiple ADME/PK endpoints in a pharmaceutical company can be best leveraged to optimize predictivity of ML models.
|
Moritz Walter; Jens Markus Borghardt; Lina Humbeck; Miha Skalic
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Machine Learning; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659d3878e9ebbb4db9c3088f/original/multi-task-adme-pk-prediction-at-industrial-scale-leveraging-large-and-diverse-experimental-datasets.pdf
|
639a1a14963bf34c06999218
|
10.26434/chemrxiv-2022-ct450
|
Streamlined Data Processing for Determination of Kd with "Accurate Constant via Transient Incomplete Separation" (ACTIS)
|
The determination of accurate equilibrium dissociation constants Kd of protein–small molecule complexes is important but challenging as all established methods have inherent sources of inaccuracy. ACTIS is a new method for Kd determination using transient incomplete separation of the complex from the unbound small molecule in a pressure-driven flow inside a capillary. ACTIS is accurate and its accuracy is invariant to variations in geometries of both the fluidic system and the flow. Furthermore, ACTIS is implemented using a simple fluidic system supporting its accuracy and providing a simple-to-follow/copy template for instrumentation. Despite the simple and robust instrumentation/acquisition, the current data processing workflow is cumbersome, time-consuming, and prone to hard-to-trace human errors therefore hindering ACTIS’ ability to become a practical reference method for Kd determination. This technical note describes a streamlined workflow for processing ACTIS data; the workflow is implemented as a set of open-source software tools called prACTISed (https://github.com/prACTISedProgram/prACTISed). These tools allow all steps of data processing to be performed in fast and straightforward fashion. These practical software tools complement the simple instrumentation serving both developers and users of ACTIS.
|
Jean-Luc Rukundo; Jessica Latimer; Shiv Jain; Sven Kochmann; Sergey N. Krylov
|
Analytical Chemistry; Analytical Chemistry - General; Biochemical Analysis; Separation Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-12-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639a1a14963bf34c06999218/original/streamlined-data-processing-for-determination-of-kd-with-accurate-constant-via-transient-incomplete-separation-actis.pdf
|
655cad8adbd7c8b54bb4fe85
|
10.26434/chemrxiv-2023-tlwrm
|
Discovery of a novel pseudo-natural product Aurora kinase inhibitor chemotype through morphological profiling
|
The pseudo-natural product (pseudo-NP) concept aims to combine NP fragments in arrangements that are not accessible through known biosynthetic pathways. The resulting compounds retain the biological relevance of NPs but are not yet linked to bioactivities and may therefore be best evaluated by unbiased screening methods resulting in the identification of unexpected or unprecedented bioactivities. Herein, various NP fragments were combined with a tricyclic core connectivity via interrupted Fischer indole and indole dearomatization reactions to provide a collection of highly three-dimensional pseudo-NPs. Target hypothesis generation by morphological profiling via the cell painting assay guided the identification of an unprecedented chemotype for Aurora kinase inhibition with both its relatively highly three-dimensional structure and its physicochemical properties being very different from known inhibitors. Biochemical and cell biological characterization indicated that the phenotype identified by the cell painting assay corresponds to the inhibition of Aurora kinase B.
|
Herbert Waldmann; Lin Wang; Furkan Yilmaz; Okan Yildirim; Beate Schölermann; Sukdev Bag; Luca Greiner; Axel Pahl; Sonja Sievers; Rebecca Scheel; Carsten Strohmann; Daniel Foley; Slava Ziegler; Michael Grigalunas
|
Biological and Medicinal Chemistry; Organic Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-11-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655cad8adbd7c8b54bb4fe85/original/discovery-of-a-novel-pseudo-natural-product-aurora-kinase-inhibitor-chemotype-through-morphological-profiling.pdf
|
6647a78791aefa6ce147b5e6
|
10.26434/chemrxiv-2023-9z6bg-v2
|
Chelate Complexes of 3d Transition Metal Ions – A Challenge for Electronic-Structure Methods?
|
Different electronic-structure methods were assessed for their ability to predict two important properties of the industrially relevant chelating agent nitrilotriacetic acid (NTA): its selectivity with respect to six different first-row transition metal ions and the spin-state energetics of its complex with Fe(III). The investigated methods encompassed density functional theory (DFT), the random phase approximation (RPA), coupled cluster (CC) theory, the auxiliary-field quantum Monte-Carlo (AFQMC) method, as well as the complete active space self-consistent field (CASSCF) method and the respective on-top methods second-order N-electron valence state perturbation theory (NEVPT2) and multiconfiguration pair-density functional theory (MC-PDFT). Different strategies for selecting active spaces were explored and the density matrix renormalization group (DMRG) approach was used to solve the largest active spaces. Despite somewhat ambiguous multi-reference diagnostics, most methods gave relatively good agreement with experimental data for the chemical reactions connected to the selectivity, which only involved transition-metal complexes in their high-spin state. CC methods yielded the highest accuracy followed by range-separated DFT and AFQMC. We discussed in detail that even higher accuracies can be obtained with NEVPT2, under the prerequisite that consistent active spaces along the entire chemical reaction can be selected, which was not the case for reactions involving Fe(III). A bigger challenge for electronic-structure methods was the prediction of the spin-state energetics, which additionally involved lower spin states that exhibited larger multi-reference diagnostics. Conceptually different, typically accurate methods ranging from CC theory via DMRG-NEVPT2 in combination with large active spaces to AFQMC agreed well that the high-spin state is energetically significantly favored over the other spin states. This was in contrast to most DFT functionals and RPA which yielded a smaller stabilization and some common DFT functionals and MC-PDFT even predicting the low-spin state to be energetically most favorable.
|
Lukas Hehn; Peter Deglmann; Michael Kühn
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6647a78791aefa6ce147b5e6/original/chelate-complexes-of-3d-transition-metal-ions-a-challenge-for-electronic-structure-methods.pdf
|
6666b75012188379d8c25a80
|
10.26434/chemrxiv-2024-bbj0n
|
Au(I)-catalysis Enables Regioselective Hydrogen Isotope Labeling of Indoles
|
The gold(I)-catalyzed hydrogen isotope exchange reaction on indoles and related heterocycles is described, under mild conditions and low catalyst loadings, using CD3OD and D2O as readily available deuterium sources. C3-unsubstituted indoles are labeled at the C3 position with an exquisite regioselectivity, while C3-substituted indoles are labeled at the C2 position. The reaction tolerates a number of chemical functions including amines, alcohols, aldehydes, in addition to the most classical functional groups. This method has been applied to the deuterium label-ing of densely functionalized bioactive compounds and to the synthesis of a tritiated analogue of pindolol using tritiated water as isotopic source. Mechanistic study revealed the involvement of aurated indole as key intermediates.
|
Pierre Milcendeau; Pierre Colonna; Mohammed Ramdani; Sebastien Garcia Argote ; Nicolas Glinsky-Olivier; Grégory Pieters; Xavier GUINCHARD
|
Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6666b75012188379d8c25a80/original/au-i-catalysis-enables-regioselective-hydrogen-isotope-labeling-of-indoles.pdf
|
654cc240dbd7c8b54beae480
|
10.26434/chemrxiv-2023-v53qf
|
Magnetic exchange, anisotropy and excitonic fluctuations in a [NiII7] Anderson wheel
|
The solvothermal reaction of Ni(ClO4)2·6H2O with hmpH and picH in a basic MeOH solution affords [Ni7(hmp)7.55(pic)4.45](ClO4)2·6MeOH (1·6MeOH) directly upon cooling the mother liquor. The metallic skeleton of 1 describes a [NiII7] centred hexagon, commonly referred to as an Anderson wheel. Magnetic meaurements reveal ferromagnetic exchange between the central Ni ion and the ring Ni ions, and antiferromagnetic exchange between neighbouring ring Ni ions. They also confirm the presence of easy-plane anisotropy for the central Ni ion, and easy-axis anisotropy for the ring Ni ions, in agreement with DFT calculations and neutron scattering. For the analysis of the latter we apply an excitonic formalism using a Green's function response theory.
|
Euan Brechin; Emily Payne; Mukesh Singh; Gary Nichol; Ross Stewart; Victoria Garcia-Sakai; Russell Ewings; Harry Lane; Juergen Schnack; Chris Stock
|
Inorganic Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-11-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654cc240dbd7c8b54beae480/original/magnetic-exchange-anisotropy-and-excitonic-fluctuations-in-a-ni-ii7-anderson-wheel.pdf
|
66c4b45120ac769e5f2c0f0d
|
10.26434/chemrxiv-2024-24gv6
|
Second Generation Aza-Diarylethene: Photoreversible C=N Bond Formation, Three-State Photoswitching, Thermal Energy Release, and Facile Photoinitiation of Polymerization
|
Diarylethenes are a well-studied and highly optimized class of photoswitches with a wide range of applications, including data storage, smart materials, or photocontrolled catalysis and biological processes. Most recently, aza-diarylethenes have been developed in which carbon-carbon bond connections are replaced by carbon-nitrogen connections. This structural elaboration opens up an entire new structure and property space expanding the versatility and applicability of diarylethenes. In this work, we present the second generation of our zwitterionic aza-diarylethenes, which finally allows for fully reversible photoswitching and precise control over three intrinsic switching states. Fully reversible and high-yielding photoswitching between the neutral open form and a zwitterionic Z isomer is achieved with two different wavelengths of light. The third zwitterionic E isomeric switching state can be reached quantitatively upon irradiation with a third wavelength. Its high energy content of >10 kcal/mol can be released thermally by deliberate solvent change as trigger mechanism, rendering aza-diarylethenes into interesting candidates for molecular solar thermal energy storage (MOST) applications. The third state further serves as locking state, allowing to toggle light-responsiveness reversibly between thermally labile and thermally stable switching. Further, irradiation of the zwitterionic states leads to highly efficient photopolymerization of methyl acrylate (MA), directly harnessing the unleashed chemical reactivity of our aza-diarylethene in a materials application.
|
Maximilian Sacherer; Henry Dube
|
Physical Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Photochemistry (Physical Chem.); Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-08-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c4b45120ac769e5f2c0f0d/original/second-generation-aza-diarylethene-photoreversible-c-n-bond-formation-three-state-photoswitching-thermal-energy-release-and-facile-photoinitiation-of-polymerization.pdf
|
60c741ea469df40f44f42f05
|
10.26434/chemrxiv.8175437.v1
|
Enantio- and Diastereoselective Suzuki-Miyaura Coupling with Racemic Bicycles
|
Herein we describe a rhodium-catalyzed enantio- and
diastereoselective Suzuki-Miyaura cross-coupling between racemic fused bicyclic
allylic chlorides and boronic acids. The highly stereoselective transformation
allows for the coupling of aryl-, heteroaryl- and vinyl boronic acids and gives
access to functionalized bicyclic cyclopentenes which can be converted to other
five-membered ring scaffolds with up to five contiguous stereocenters. Preliminary
mechanistic studies suggest that these reactions occur with overall retention
of the relative stereochemistry and is enantioconvergent for pseudo-symmetric
allylic chloride starting materials. In addition, a bicyclic allylic chloride
starting material without pseudo-symmetry undergoes a highly enantioselective regiodivergent
reaction.
|
Friedrich Wieland Goetzke; Mike Mortimore; Stephen P. Fletcher
|
Organic Synthesis and Reactions; Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-05-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741ea469df40f44f42f05/original/enantio-and-diastereoselective-suzuki-miyaura-coupling-with-racemic-bicycles.pdf
|
6234dde2202c068770d8b351
|
10.26434/chemrxiv-2022-nqjnf-v2
|
A matrix completion algorithm for efficient calculation of quantum and variational effects in chemical reactions
|
This work examines the viability of matrix completion methods as cost-effective alternatives to full nuclear Hessians for calculating quantum and variational effects in chemical reactions. The harmonic variety-based matrix completion (HVMC) algorithm, developed in a previous study (https://doi.org/10.1063/5.0018326), exploits the low-rank character of the polynomial expansion of potential energy to recover, using a small sample, vibrational frequencies (square roots of nuclear Hessian eigenvalues) constituting the reaction path. These frequencies are essential for calculating rate coefficients using variational transition state theory with multidimensional tunneling (VTST-MT). HVMC performance is examined for four SN2 reactions and five hydrogen transfer reactions, with each H-transfer reaction consisting of at least one vibrational mode strongly coupled to the reaction coordinate. HVMC is robust and captures zero-point energies, vibrational free energies, zero-curvature tunneling, and adiabatic ground state and free energy barriers as well as their positions on the reaction coordinate. For medium to large reactions involving H- transfer, with the exception of the most complex Ir catalysis system, less than 35% of total eigenvalue information is necessary for accurate recovery of key VTST-MT observables.
|
Selin Bac; Stephen Jon Quiton; Kareesa J. Kron; Jeongmin Chae; Urbashi Mitra; Shaama Mallikarjun Sharada
|
Theoretical and Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6234dde2202c068770d8b351/original/a-matrix-completion-algorithm-for-efficient-calculation-of-quantum-and-variational-effects-in-chemical-reactions.pdf
|
60c7426cee301c53abc78e2b
|
10.26434/chemrxiv.7609205.v3
|
Small Molecule Isotope Resolved Formula Enumeration: a Methodology for Assigning Isotopologues and Metabolites in Fourier Transform Mass Spectra
|
Improvements in Fourier Transform Mass Spectrometry (FT-MS) enable increasingly more complex experiments in the field of metabolomics. What is directly detected in FT-MS spectra are spectral features (peaks) that correspond to sets of adducted and charged forms of specific molecules in the sample. The robust assignment of these features is an essential step for MS-based metabolomics experiments, but the sheer complexity of what is detected and a variety of analytically-introduced variance, errors, and artifacts has hindered the systematic analysis of complex patterns of observed peaks with respect to isotope content. We have devel-oped a method called SMIRFE that detects small biomolecules and determines their elemental molecular formula (EMF) using de-tected sets of isotopologue peaks sharing the same EMF. SMIRFE does not use a database of known metabolite formulas, instead a nearly comprehensive search space of all isotopologues within a mass range is constructed and used for assignment. This search space can be tailored for different isotope labeling patterns expected in different stable isotope tracing experiments. Using consumer-level computing equipment, a large search space of 2000 daltons was constructed and assignment performance was evaluated and validated using verified assignments on a pair of peak lists derived from spectra containing unlabeled and 15N-labeled versions of amino acids derivatized using ethylchloroformate. SMIRFE identified 18 of 18 predicted derivatized EMFs and each assignment was evaluated statistically and assigned an e-value representing the probability to occur by chance.
|
Hunter Moseley; Joshua Mitchell; Robert M Flight
|
Mass Spectrometry; Bioinformatics and Computational Biology
|
CC BY NC 4.0
|
CHEMRXIV
|
2019-05-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7426cee301c53abc78e2b/original/small-molecule-isotope-resolved-formula-enumeration-a-methodology-for-assigning-isotopologues-and-metabolites-in-fourier-transform-mass-spectra.pdf
|
60c74c74842e6545e9db330b
|
10.26434/chemrxiv.12482435.v1
|
Drug Repurposing for Covid-19: Discovery of Potential Small-Molecule Inhibitors of Spike Protein-ACE2 Receptor Interaction Through Virtual Screening and Consensus Scoring
|
<p><b>Objective</b></p><p> </p><p>There is an increased interest in drug repurposing against Covid-19 (SARS-CoV-2) as its spread has significantly outpaced development of effective therapeutics. Our aim is to identify approved drugs that can inhibit the interaction of SARS-CoV-2 spike protein with human angiotensin-converting enzyme 2 (ACE2) that is critical for coronavirus infection. </p><p> </p><p><b>Methods</b></p><p> </p><p>The published crystal structure of SARS-CoV-2 spike protein-ACE2 receptor interaction was first analyzed for druggable binding pockets. The binding interface was then probed by an integrated virtual screening protocol executed by a high-performance computer cluster, involving docking and consensus scoring using various machine-learning, empirical and knowledge-based scoring functions. The consensus-ranked lists of screened drugs were generated via ‘rank-by-rank’ and ‘rank-by-number’ schemes.</p><p> </p><p><b>Findings</b></p><p> </p><p>Although spike protein and ACE2 lacked druggable pockets in their unbound forms, they presented a well-defined pocket when bound together. Accordingly, we identified many drugs with high binding potential against this protein-protein interaction pocket. Importantly, several antivirals against two major (+)ssRNA viruses (HCV and HIV) constituted major group of our top hits, of which Atazanavir, Grazoprevir, Saquinavir, Simeprevir, Telaprevir and Tipranavir could be of most importance for immediate experimental/clinical investigations. Additional notable hits included many anti-inflammatory/antioxidant, antibiotic/antifungal, and other relevant compounds with proven activity against respiratory diseases, further emphasizing robustness of our current study. Notably, we also discovered Maraviroc, the only FDA-approved drug capable of targeting virus-host interaction and blocking HIV entry. </p><p> </p><p><b>Conclusion</b></p><p> </p>Our newly identified compounds warrant further experimental investigation against SARS-CoV-2 spike-ACE2 interaction, which if proven effective may present much-needed immediate clinical potential against Covid-19.
|
Sachin Patil; Jeremy Hofer; Pedro J. Ballester; Elena Fattakhova; Juliette DiFlumeri; Autumn Campbell; Michael Oravic
|
Biophysics; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c74842e6545e9db330b/original/drug-repurposing-for-covid-19-discovery-of-potential-small-molecule-inhibitors-of-spike-protein-ace2-receptor-interaction-through-virtual-screening-and-consensus-scoring.pdf
|
6668ed3f409abc0345305c51
|
10.26434/chemrxiv-2024-ncjlp
|
Data-driven analysis of text-mined seed-mediated growth AuNP syntheses
|
Gold nanoparticles (AuNPs) are widely used functional nanomaterials that exhibit adjustable properties based on their shapes and sizes. Creating a comprehensive dataset of AuNP syntheses is useful for understanding control over their shape and size. Here, we employed search-based algorithms and fine-tuned the Llama-2 large language model to extract 492 multi-sourced seed-mediated AuNP synthesis recipes from the literature. With this dataset which we share online, we verified that the seed capping agent type such as CTAB or citrate plays a crucial role in determining the morphology of the AuNPs, aligning with established findings in the field. We also observe a weak correlation between the final AuNR aspect ratio and silver concentration, although a large variance reduces the significance of this relationship. Overall, our work demonstrates the value of literature-based datasets for advancing knowledge in the field of nanomaterial synthesis for further exploration and better reproducibility.
|
Sanghoon Lee; Kevin Cruse; Samuel P. Gleason; A. Paul Alivisatos; Gerbrand Ceder; Anubhav Jain
|
Theoretical and Computational Chemistry; Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Kinetics and Mechanism - Inorganic Reactions; Machine Learning
|
CC BY 4.0
|
CHEMRXIV
|
2024-06-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6668ed3f409abc0345305c51/original/data-driven-analysis-of-text-mined-seed-mediated-growth-au-np-syntheses.pdf
|
63ef9e761d2d184063a63f5f
|
10.26434/chemrxiv-2023-gd1gl
|
Interpretable Molecular Property Predictions Using Marginalized Graph Kernels
|
Marginalized graph kernels have shown competitive performance in molecular machine learning tasks but currently lack measures of interpretability, which are important to improve trust in the models, detect biases, and inform molecular optimization campaigns. We here conceive and implement two interpretability measures for Gaussian process regression using a marginalized graph kernel (GPR-MGK) to quantify (1) the contribution of specific training data to the prediction and (2) the contribution of specific nodes of the graph to the prediction. We demonstrate the applicability of these interpretability measures for molecular property prediction. We compare GPR-MGK to graph neural networks on four logic datasets and find that the atomic attribution of GPR-MGK generally outperforms the atomic attribution of graph neural networks. We also perform a detailed molecular attribution analysis using the FreeSolv dataset, showing how molecules in the training set influence machine learning predictions and why Morgan fingerprints perform poorly on this dataset. This is the first systematic examination of the interpretability of GPR-MGK and thereby an important step in the further maturation of marginalized graph kernel methods for interpretable molecular predictions.
|
Yan Xiang; Yu-Hang Tang; Guang Lin; Daniel Reker
|
Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-02-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ef9e761d2d184063a63f5f/original/interpretable-molecular-property-predictions-using-marginalized-graph-kernels.pdf
|
66217dcd418a5379b021ce3d
|
10.26434/chemrxiv-2024-f69l0
|
Active Site Ensembles on Ni2P Surfaces Tune Electrocatalytic Nitrate Reduction Selectivity
|
Active site ensembles on transition metal phosphides tune the selectivity of the nitrate reduction reaction and mitigate competing hydrogen evolution. Using Ni2P nanocrystals as a case study, we demonstrate evidence of a competitive Langmuir-Hinshelwood reaction mechanism that involves the co-adsorption of both H* and NOx* intermediates and the impact of co-adsorption on intermediate binding energetics and reaction selectivity toward NH3.
|
Emily Nishiwaki; Peter Rice; Ding-Yuan Kuo; Florence Dou; Anthony Pyka; Bryce Reid; Hao Nguyen; Eric Stuve; Simone Raugei; Brandi Cossairt
|
Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Electrocatalysis; Nanocatalysis - Reactions & Mechanisms
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-04-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66217dcd418a5379b021ce3d/original/active-site-ensembles-on-ni2p-surfaces-tune-electrocatalytic-nitrate-reduction-selectivity.pdf
|
60c75100337d6c349ae2845a
|
10.26434/chemrxiv.13106807.v1
|
Hybrid Ionic Liquid/water-in-Salt Electrolytes Enable Stable Cycling of LTO/NMC811 Full Cells
|
Water-in-salt electrolytes have successfully expanded the electrochemical stability window of aqueous electrolytes to up to 3 V. While particularly the reductive stability of water-in-salt electrolytes can be further improved by simply increasing the salt concentration, this approach has its limitations as it leads to very viscous and hence poorly conducting solutions. An alternative strategy is the partial substitution of water by ionic liquids, which boosts the lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) solubility while maintaining adequate transport properties at very high salt concentrations.<br />Here, we study such ternary electrolytes based on LiTFSI, water, and imidazolium-type ionic liquids in terms of their thermal, electrochemical, and transport properties. We find that the LiTFSI solubility increases from 21 mol kg<sup>−1</sup> in water to up to 60 mol kg<sup>−1</sup> in the presence of these ionic liquids. Deconvolution of the different contributions to the LiTFSI solubility shows that particularly the ionic liquid 1-ethyl-3-methylimidazolium trifluoromethanesulfonate acts as solubility enhancer.<br />The increased reductive stability of these ternary electrolytes enables stable cycling of both TiO<sub>2</sub> and Li<sub>4</sub>Ti<sub>5</sub>O<sub>12</sub> anodes. We further show that the low water content of these electrolytes also allows stable cycling of LiNi<sub>0.8</sub>Mn<sub>0.1</sub>Co<sub>0.1</sub>O<sub>2</sub> (NMC811) cathodes. For instance, a TiO<sub>2</sub>/NMC811 full cell based on such a hybrid electrolyte shows an energy density of 121 Wh kg<sup>−1</sup> on the active material level, a Coulombic efficiency of >99.7% at C/2, and retains 80% of its initial capacity after 290 cycles at this rate. Owing to the 300 mV lower redox potential of Li<sub>4</sub>Ti<sub>5</sub>O<sub>12</sub> compared to TiO<sub>2</sub>, Li<sub>4</sub>Ti<sub>5</sub>O<sub>12</sub>/NMC811 full cells reach energy densities of 141 and 150 Wh kg<sup>−1</sup> at a rate of 1C and C/2, respectively. These cells still show Coulombic efficiency of 99.4% and 99.2%, respectively, and maintain 80% of their initial capacity after 230 and 154 cycles, respectively. Considering the large number of potential lithium salt–ionic liquid combinations, we anticipate further improvements in electrolyte properties and subsequently cell performance.<br />
|
Maximilian Becker; David Reber; Abdessalem Aribia; Corsin Battaglia; Ruben-Simon Kühnel
|
Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-10-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75100337d6c349ae2845a/original/hybrid-ionic-liquid-water-in-salt-electrolytes-enable-stable-cycling-of-lto-nmc811-full-cells.pdf
|
60c753e1337d6c4bcfe2891e
|
10.26434/chemrxiv.13232279.v1
|
Self-assembled Dendritic Boronate Micelles as a Promising Delivery Strategy for Gemcitabine
|
<p>A novel
drug delivery system is described based on a PEG-dendritic copolymer functionalized with peripheral boronic acids, that self-assembles in the presence of
catechol to afford nanometric micelles with the ability to encapsulate
GEM. The simplicity of the method, with all equilibria (boronate
esterification, copolymer self-assemble, drug encapsulation) occurring
simultaneously, is compatible with a high tunability of the micelle properties (via
diol structure and the boronic acid-to-diol molar ratio).<br /></p>
|
Muna A. Al-Ni’mat; Samuel Parcero-Bouzas; Sandra P. Amaral; Eduardo Fernandez-Megia
|
Drug delivery systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-01-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753e1337d6c4bcfe2891e/original/self-assembled-dendritic-boronate-micelles-as-a-promising-delivery-strategy-for-gemcitabine.pdf
|
65fb2c4ce9ebbb4db92085fd
|
10.26434/chemrxiv-2024-16sxs
|
Quantitative structure-retention relationships for pyridinium-based ionic liquids used as gas chromatographic stationary phases: convenient software and assessment of reliability of the results
|
Ionic liquids, i.e., organic salts with a low melting point, can be used as gas chromatographic liquid stationary phases. These stationary phases have some advantages such as peculiar selectivity, high polarity, and thermostability. Many previous works are devoted to such stationary phases. However, there are still no large enough retention data sets of structurally diverse compounds for them. Consequently, there are very few works devoted to quantitative structure-retention relationships (QSRR) for ionic liquid-based stationary phases. This work is aimed to close this gap. Three ionic liquids with substituted pyridinium cations are considered. We provide large enough data sets (123 - 158 compounds) that can be used in further works devoted to QSRR and related methods. We provide a QSRR study using this data set and demonstrate the following. The retention index for a polyethylene glycol stationary phase (denoted as RIPEG), predicted using another model, can be used as a molecular descriptor. The use of this descriptor significantly improves the accuracy of the QSRR model. Both deep learning-based and linear models were considered for RIPEG prediction. The ability to predict the retention indices for ionic liquid-based stationary phases with high accuracy is demonstrated. Particular attention is paid to the reproducibility and reliability of the QSRR study. It was demonstrated that adding/removing several compounds, small perturbations of the data set can considerably affect the results such as descriptor importance and model accuracy. These facts have to be considered in order to avoid misleading conclusions. For the QSRR research, we developed a software tool with a graphical user interface, which we called CHERESHNYA. It is intended to select molecular descriptors and construct linear equations connecting molecular descriptors with gas chromatographic retention indices for any stationary phase. The software allows the user to generate several hundred molecular descriptors (one-dimensional and two-dimensional). Among them, predicted retention indices for popular stationary phases such as polydimethylsiloxane and polyethylene glycol are used as molecular descriptors. Various methods for selecting (and assessing the importance of) molecular descriptors have been implemented, in particular the Boruta algorithm, partial least squares, genetic algorithms, L1-regularized regression (LASSO) and others. The software is free, open-source and available online.
|
Anastasia Sholokhova; Dmitriy Matyushin; Mikhail Shashkov
|
Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry; Chemoinformatics; Separation Science; Machine Learning
|
CC BY 4.0
|
CHEMRXIV
|
2024-03-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fb2c4ce9ebbb4db92085fd/original/quantitative-structure-retention-relationships-for-pyridinium-based-ionic-liquids-used-as-gas-chromatographic-stationary-phases-convenient-software-and-assessment-of-reliability-of-the-results.pdf
|
668d80145101a2ffa8e358c3
|
10.26434/chemrxiv-2024-bl9lf
|
Isolation and electronic structures of lanthanide(II) bis(trimethylsilyl)phosphide complexes
|
Whilst lanthanide (Ln) silylamide chemistry is mature, the corresponding silylphosphide chemistry is underdeveloped, with [Sm{P(SiMe3)2}{μ-P(SiMe3)2}3Sm(THF)3] being the sole example of a structurally authenticated Ln(II) silylphosphide complex. Here we expand Ln(II) {P(SiMe3)2} chemistry through the synthesis and characterization of nine novel complexes. The dinuclear ‘ate’ salt-occluded complexes [{Ln[P(SiMe3)2]3(THF)}2(μ-I)K3(THF)] (1-Ln; Ln = Sm, Eu) and polymeric ‘ate’ complex [KYb{P(SiMe3)2}3{μ-K[P(SiMe3)2]}2] (2-Yb) were prepared by the respective salt metathesis reactions of parent [LnI2(THF)2] (Ln = Sm, Eu, Yb) with 2 or 3 eq. of K{P(SiMe3)2} in diethyl ether. The separate treatment of these complexes with either pyridine or 18-crown-6 led to the formation of the mononuclear solvated adducts, trans-[Ln{P(SiMe3)2}2(py)4] (3-Ln; Ln = Sm, Eu, Yb) and [Ln{P(SiMe3)2}2(18-crown-6)] (4-Ln; Ln = Sm, Eu, Yb), with concomitant loss of K{P(SiMe3)2}. The complexes were characterized by a combination of NMR, EPR, ATR-IR, electronic absorption and emission spectroscopies, elemental analysis, SQUID magnetometry, and single crystal X-ray diffraction. We find that these complexes exhibit electronic structures that contrast with those of related Ln(II) bis(trimethylsilyl)amide complexes due to differences in ligand donor atom hardness and ligand steric requirements from Ln–P bonds being longer than Ln–N bonds.
|
Jack Baldwin; Adam Brookfield; George Whitehead; Louise Natrajan; Eric McInnes; Meagan Oakley; David Mills
|
Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Coordination Chemistry (Organomet.)
|
CC BY 4.0
|
CHEMRXIV
|
2024-07-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668d80145101a2ffa8e358c3/original/isolation-and-electronic-structures-of-lanthanide-ii-bis-trimethylsilyl-phosphide-complexes.pdf
|
60dd25227d46cd5c68fadcd7
|
10.26434/chemrxiv-2021-l4mcq
|
Red-to-NIR Emissive Radical Cations Derived from Simple Pyrroles for Bio-Imaging
|
Red-to-near-infrared (NIR) fluorophores are highly desirable for bio-imaging with advantages of excellent tissue penetration ability and less interference from auto-fluorescence, but their synthesis usually require tedious procedures and it’s thus highly desirable for red-to-NIR fluorophores directly generated from easily available substrates. Compared with the conventional closed-shell fluorophores, radical cations are featured with a large red-shift absorption, but most of them are not fluorescent due to the fast internal conversion between excited and ground state with a small energy gap. Moreover, radical cations suffer from instability because they can easily undergo radical coupling or nucleophilic addition reactions. Herein, we found that 2,5-dimethylpyrroles can rapidly generate red-to-NIR emissive radical cations, which can be stabilized by adsorption on thin layer chromatography (TLC) plate or being encapsulated in cucurbit[7]uril (CB[7]). The NIR-emissive radical cations derived from pyrroles were verified by electron paramagnetic resonance (EPR) spectroscopy and theoretical calculations. Importantly, the pyrrole-derived radical cations encapsulated in CB[7] can be used for mitochondrial imaging in living cells and tumor imaging in vivo with a high signal-to-noise ratio. The easily available and red-to-NIR emissive radical cations derived from simple pyrroles are promising for applications in biomedical study.
|
Meng Gao; Ben Zhong Tang; Kai Liu; Lihua Zheng; Wenchao Zhu; Zikai Zhou
|
Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-07-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60dd25227d46cd5c68fadcd7/original/red-to-nir-emissive-radical-cations-derived-from-simple-pyrroles-for-bio-imaging.pdf
|
60c7472ef96a00257f286e9d
|
10.26434/chemrxiv.11555814.v1
|
Strain Visualization for Strained Macrocycles
|
Strain has a unique and sometimes unpredictable impact
on the properties and reactivity of molecules. To thoroughly describe strain in
molecules, a computational tool that relates strain to reactivity by localizing
and quantifying strain was developed. Strain is calculated local to every coordinate
in the molecule and areas of higher strain are shown experimentally to be more
reactive. Not only does this tool directly compare strain in parts of the same
molecule, but it also computes total strain to give a full picture of molecular
strain. It is freely available to the public on GitHub under the name StrainViz
and much of the workflow is automated to simplify use for non-experts. Unique
insight into the reactivity of curved aromatic molecules and strained alkyne
bioorthogonal reagents is described within.
|
Curtis Colwell; Tavis Price; Tim Stauch; Ramesh Jasti
|
Physical Organic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-01-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7472ef96a00257f286e9d/original/strain-visualization-for-strained-macrocycles.pdf
|
65952673e9ebbb4db95228f1
|
10.26434/chemrxiv-2023-8003d-v2
|
Machine Learning Interatomic Potentials for Amorphous Zeolitic Imidazolate Frameworks
|
The detailed understanding of the microscopic structure of amorphous phases of metal-organic frameworks (MOFs) remains a widely open question: characterization of these systems is very difficult, both from the experimental and computational point of view. In molecular simulations, approaches have been proposed that rely either on reactive force field, that lack chemical accuracy, or first-principles calculations, that are too computationally expensive. Here, we have found an innovative solution to these problems by training a machine-learnt potential for the description of disordered phases of a zeolitic imidazolate framework (ZIF). We then used it to produce high-quality atomistic models of ZIF glasses, with accuracy close to density functional theory (DFT) but at far lower computational cost in production runs.
|
Nicolas Castel; Dune André; Connor Edwards; Jack D. Evans; François-Xavier Coudert
|
Theoretical and Computational Chemistry; Materials Science
|
CC BY 4.0
|
CHEMRXIV
|
2024-01-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65952673e9ebbb4db95228f1/original/machine-learning-interatomic-potentials-for-amorphous-zeolitic-imidazolate-frameworks.pdf
|
65b619ce66c13817296e962d
|
10.26434/chemrxiv-2024-x4x93
|
Mapping Hydrogen Positions along the Proton Transfer Pathway in an Organic Crystal by Computational X-ray Spectra
|
Understanding the proton transfer dynamics through hydrogen bonds is a fundamental issue in chemistry, especially in condensed phases. While time-resolved X-ray spectroscopy offers a unique probe localized within the hydrogen bonds, accurate interpretation remains a challenge and relies on high-quality theoretical spectral references that map the proton motions. Here, with hybrid quantum mechanical and molecular mechanical (QM/MM) simulations, we computed a two-dimensional (2D) map of the N1s X-ray photoelectron/absorption spectra (XPS/XAS) for an organic crystal, composed of protonated 4,4'-bipyridine (BpyH$^+$, acceptor) and 5-sulfosalicylic acid (Sulfo$^-$, donor), with respect to varying hydrogen positions at nitrogens N1 and N2 of BpyH$^+$. We obtained a continuous picture of each spectrum and the chemical shift, mapping the proton transfer processes from O--H$\cdots$N to O$^{-}\cdots$H$^{+}$--N at N1 and from O$^{-}\cdots$H$^{+}$--N to O--H$\cdots$N at N2. We demonstrate that N1s transient XPS/XAS spectra are sensitive probes for hydrogen positions and proton transfer processes. We observe that reducing the O--H distance at the N1 site by only 0.2 {\AA}, compared to the crystal structure determined from X-ray diffraction (XRD), provides an excellent match between the QM/MM and experimental spectra, consistently in both XPS and XAS. Our calculations also demonstrate that geometry optimizations with periodic boundary conditions are difficult to refine the proton positions in experimental crystal structures, whereas our scaled snapshot protocol offers a more effective way. Our study reveals a nonlinear behavior of the absorption energy for the $\pi_1^*/\pi_2^*$ peak in XAS with increasing N--H distance, exhibiting a distinct barrier at around 0.95 \AA. This study provides a clear mapping of the two correlated proton transfer dynamics into X-ray spectra within a complex crystal, offering insights for future transient experimental studies.
|
Guoyan Ge; Jun-Rong Zhang; Sheng-Yu Wang; Minrui Wei; Yongfei Ji; Sai Duan; Kiyoshi Ueda; Weijie Hua
|
Physical Chemistry; Quantum Mechanics; Spectroscopy (Physical Chem.); Structure
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-02-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b619ce66c13817296e962d/original/mapping-hydrogen-positions-along-the-proton-transfer-pathway-in-an-organic-crystal-by-computational-x-ray-spectra.pdf
|
64b44485ae3d1a7b0dd29526
|
10.26434/chemrxiv-2023-31gbl
|
Quantitative Structure-Property Relationships (QSPR) to Predict Surface Tension and Electrical Conductivity of Ionic Liquid Propellants
|
Quantitative structure property relationships (QSPR) mine data sets of experimentally measured properties to predict different material properties through mathematical regression and machine learning. QSPR have the capability to predict any property, as long as there is a large enough data set of measured values. It is often costly and time-consuming to experimentally test certain properties of ionic liquids, and modern fundamental theoretical (quantum chemical or molecular dynamics) approaches require significant computer resources and may have limited accuracy. On the other hand, QSPR allow for simulations to converge to a result in just a few hours. These simulations are reliable, fast, and accurate, and only require a small number of input parameters. In this work, we predict surface tension and electrical conductivity values of potential ionic liquid propellants via QSPR, and present a detailed discussion on the error analysis performed on the results obtained.
|
Daniel Yos; Steven D. Chambreau; Debasis Sengupta; David A. Newsome; Ghanshyam L. Vaghjiani
|
Theoretical and Computational Chemistry; Physical Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-07-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b44485ae3d1a7b0dd29526/original/quantitative-structure-property-relationships-qspr-to-predict-surface-tension-and-electrical-conductivity-of-ionic-liquid-propellants.pdf
|
64d4f2b5dfabaf06ff0ce579
|
10.26434/chemrxiv-2023-jnl31
|
Solvation Structure and UV-Visible Absorption Spectra of the Nitrate Anion at the Air-Ice Interface by First Principles Molecular Simulations
|
Nitrate is a significant contaminant in Polar snow. Its photolysis in environmental sunlight generates reactive nitrogen, which impacts the oxidative capacity of the atmosphere, influencing the fate and lifetimes of pollutants. The photolysis of nitrate can produce either $\mathrm{NO_2}$ or $\mathrm{NO_2^-}$, with recent experiments suggesting that the process is accelerated at the air-ice interface compared to the bulk solution. In this study, we employed multiscale modeling approaches to investigate the enhanced photoreactivity of nitrate at the ice surface in the presence of two different cations. We characterized the solvation shell of $\mathrm{NO_3^-}$ and explored its pairing with cations in water and ice using {\sl ab initio} molecular dynamics and enhanced sampling. Molecular trajectories were used to calculate light absorption spectra at different solvation conditions and finite temperature. Our analysis revealed that the pairing of nitrate with cations may alter the molar absorption coefficient of nitrate at the air-ice interface affecting the rate of photolysis observed in experiments of ammonium nitrate deposited on snow.
|
Margaret Berrens; Zekun Chen; Kam Tung Chan; Cort Anastasio; Davide Donadio
|
Theoretical and Computational Chemistry; Earth, Space, and Environmental Chemistry; Theory - Computational
|
CC BY 4.0
|
CHEMRXIV
|
2023-08-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d4f2b5dfabaf06ff0ce579/original/solvation-structure-and-uv-visible-absorption-spectra-of-the-nitrate-anion-at-the-air-ice-interface-by-first-principles-molecular-simulations.pdf
|
63e19fb845d4b84aaea4b582
|
10.26434/chemrxiv-2023-f844t
|
Charge "Mis-matched" Hydrogen Bonded Frameworks for Cation Exchange and Dye Sorption
|
Anionic hydrogen bonded frameworks were synthesised from di or tetra-amidinium hydrogen bond donor components and a charge mis-matched tecton possessing a 5 charge but only four hydrogen bond accepting groups. The net negative charge on the framework skeletons necessitates the presence of a cation in the framework channel. In one of the frameworks, the initially incorporated organic cation was rapidly displaced by smaller inorganic cations, or the cationic dye methylene blue. This facilitated the effective and selective removal of this dye from water.
|
Phonlakrit Muang-Non; Adrian Markwell-Heys; Christian Doonan; Nicholas White
|
Organic Chemistry; Inorganic Chemistry; Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-02-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e19fb845d4b84aaea4b582/original/charge-mis-matched-hydrogen-bonded-frameworks-for-cation-exchange-and-dye-sorption.pdf
|
60c74a31ee301cd8dbc79bf1
|
10.26434/chemrxiv.12155235.v1
|
In Search for Effective and Safe Drugs Against SARS-CoV-2: Part I] Simulated Interactions Between Selected Nutraceuticals, ACE2 Enzyme and S Protein Simple Peptide Sequences
|
Coronavirus disease (COVID-19) remains a world pandemic with little treatment options. Nature has provided a plethora of compounds that may offer potential protection and/or treatment choices. Earlier studies have shown a pivotal role of Angiotensin converting enzyme 2 (ACE2) in the pathogenesis of COVID-19. In this context, seven natural compounds were selected and their binding to specific peptide sequences of the coronavirus S-protein: ACE2 interface-drug binding adduct were calculated. Further to the natural drugs, we also similarly examined four well-known antiviral drugs. Moreover, the binding-interface of the isolated coronavirus S-protein and the isolated ACE2 receptor were also individually explored. The identified drug molecules positioned itself achieving geometries of minimum energy resulting in limiting viral recognition of host cells or to disturb host-virus interactions. The frontier orbitals (HOMO-LUMO) play crucial role in the binding interactions of the studied molecules. Most of the drugs act as electron sink whereas the S protein behaves as nucleophile. The results reported pave the way for the identification of small-drug molecule of natural origin with potentially tolerable side effects that can offer protection and/or treatment against coronavirus S-protein COVID-19. Experimental validation is of urgent demand.<br />
|
M. Sabry Abdel-Mottaleb; Yousra Abdel-Mottaleb
|
Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a31ee301cd8dbc79bf1/original/in-search-for-effective-and-safe-drugs-against-sars-co-v-2-part-i-simulated-interactions-between-selected-nutraceuticals-ace2-enzyme-and-s-protein-simple-peptide-sequences.pdf
|
60c754f7bdbb896b8fa3a743
|
10.26434/chemrxiv.13925177.v1
|
Functions of Magnetic Nanoparticles in Selective Laser Sintering (SLS) 3D Printing of Pharmaceutical Dosage Forms
|
<p><a>Selective laser
sintering (SLS) 3D printing (3DP) offers novel opportunities for manufacturing
various pharmaceutical dosage forms with a wide array of drug delivery systems.
The purpose of this research was to introduce ferromagnetic nanoparticles, for
the first time, as a multi-functional magnetic and heat conductive ingredient
for 3DP tablet formulations, and further to analyze its effect on the drug
release of the SLS printed tablets under a specially designed magnetic field. Optimization
of tablet quality was performed by adjusting SLS printing parameters. </a>The independent factors studied were laser scanning speed (2, 50,
100, and 200 mm/s), hatching space (13, 25, 50, 100, 300, and 2000 µm), and
temperature. The responses measured were tablet weight, hardness,
disintegration time (DT), and dissolution kinetics studied within the
first hour. The content uniformity, chemical interaction, drug distribution, and
surface morphology were tested for characterizing the printed dosage forms. It
has been observed, for the drug formulations with carbonyl iron, due to its
inherent heat conductivity, that sintering tablets required low energy input compared
to that of other batches that contained no magnetic particles, to make the
tablets of the same quality attributes. Also, under the magnetic field, printed
tablets with carbonyl iron released 25% more drug as compared to those without.
Therefore, we report for the first time the use of magnetic nanoparticles as a
novel conductive excipient to sinter the particles in an SLS 3D printing
process of pharmaceutical dosage forms and hence this finding opens up numerous
opportunities for magnetically triggerable drug delivery systems.</p>
|
Yu Zhang; Jiaxiang Zhang; Rishi Thakkar; Amit R Pillai; Jiawei Wang; Anqi Lu; Mohammed Maniruzzaman
|
Biocompatible Materials; Biological Materials; Biodegradable Materials; Controlled-Release Systems; Granular Materials; Materials Processing
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-02-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754f7bdbb896b8fa3a743/original/functions-of-magnetic-nanoparticles-in-selective-laser-sintering-sls-3d-printing-of-pharmaceutical-dosage-forms.pdf
|
6774b7cefa469535b969a68b
|
10.26434/chemrxiv-2025-cdp7k
|
The Amplified Hydrogen Bond: A Coupling Pair of Asymmetrical, Flexible, and Polarizable Dipoles
|
Being essential to life on earth, the hydrogen bond and its configuration, performance, and functionality become increasingly inspiring. We humbly share a three-body coupling system involving a pair of asymmetrical, flexible, and polarizable dipoles to amplify the known OH convention.
|
Changqing Sun; Sanmei Wang; Jushan Wang; yong Zhou; Chunyang Nie; Hengxin Fang; Lei Zhang; Biao Wang
|
Physical Chemistry; Physical and Chemical Processes
|
CC BY NC 4.0
|
CHEMRXIV
|
2025-01-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6774b7cefa469535b969a68b/original/the-amplified-hydrogen-bond-a-coupling-pair-of-asymmetrical-flexible-and-polarizable-dipoles.pdf
|
6647cb5191aefa6ce14a5c8b
|
10.26434/chemrxiv-2024-bvwhs
|
Limit theorems for Randić index for Erdos-Rényi graphs
|
We prove that the generalized Randić index over graphs following the Erdos-Rényi model, for both the sparse and dense regimes, is concentrated around its mean when the number of vertices tends to infinity.
|
Laura Eslava; Sayle Sigarreta Ricardo; Arno Siri-Jégousse
|
Theoretical and Computational Chemistry; Theory - Computational
|
CC BY 4.0
|
CHEMRXIV
|
2024-05-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6647cb5191aefa6ce14a5c8b/original/limit-theorems-for-randic-index-for-erdos-renyi-graphs.pdf
|
66ddbfc8cec5d6c1428341bc
|
10.26434/chemrxiv-2024-cnp4g
|
Role of metal coordinated auxiliary residues in catalysis: A structural and mechanistic study.
|
Metal ions are integral to the structure and function of nearly half of all known proteins, with approximately one-quarter to one-third of proteins directly dependent on these ions for their biological activity. While, catalytic and co-catalytic contributions in them have predominantly been attributed to the metal centre and active site residues, The significance of auxiliary residues coordinated to the metal ion has often been underemphasized, and traditionally viewed as passive elements confined to the role of stabilizing the metal ion. Herein, we present the detailed reaction mechanism of Terephthalate 1,2-cis-dihydrodiol dehydrogenase (TphB), the only known Zinc-dependent oxidative decarboxylase and the role of zinc coordinated histidine residues in catalysis. Over 30 X-ray crystallographic structures of active site variants revealed a notable trend in the Nε-Zn-Nε angles during the course of catalytic transitions. Initially the H159Nε2-Zn-Nε2H203, H255Nε2-Zn-Nε2H203, H159Nε2-Zn-Nε2H255 angles in the native state were 60°, 59.2°, and 55.5°. The angles significantly increased in transition state analogues, by 39.4°, 45.05°, and 42°, then again decrease in the product state by 16.7°, 17.7°, and 17.7°, respectively. This trend aligns with the Jencks "Circe effect," where these angular adjustments introduce a conformational restriction, thereby elevating the system's free energy through entropic loss. These fluxional changes, akin to Berry pseudorotation and the Bartell mechanism, accompanied by continuous cycles of entropic loss and gain, facilitate substrate accommodation, catalytic transitions, transition state stabilization/destabilization, product release, and ultimately, reversion to the enzyme’s initial state. This nuanced understanding could inform the design of effective metal-organic frameworks (MOFs) and (de)carboxylase catalysts with industrial and pharmacological implications, while offering a promising avenue for CO2 capture and plastic upcycling, thereby aligning with the sustainability goals.
|
Amith Kamble; Dhruv Pahwa; Pravindra kumar
|
Catalysis; Chemical Engineering and Industrial Chemistry; Chemical Education; Chemical Education - General; Biocatalysis; Nanocatalysis - Reactions & Mechanisms
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-09-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ddbfc8cec5d6c1428341bc/original/role-of-metal-coordinated-auxiliary-residues-in-catalysis-a-structural-and-mechanistic-study.pdf
|
6549a382c573f893f1f64b0b
|
10.26434/chemrxiv-2023-1rd9v
|
Quantum Chemical Modeling of Hydrogen Binding in Metal--Organic Frameworks: Validation, Insight, Predictions and Challenges.
|
A detailed chemical understanding of \ce{H2} interactions with binding sites in the nanoporous crystalline structure of metal--organic frameworks (MOFs) can lay a sound basis for the design of new sorbent materials. Computational quantum chemical calculations can aid in this quest. To set the stage, we review general thermodynamic considerations that control the usable storage capacity of a sorbent. We then discuss cluster modeling of \ce{H2} ligation at MOF binding sites using state-of-the-art density functional theory (DFT) calculations, and how the binding can be understood using energy decomposition analysis (EDA). Employing these tools, we illustrate the connections between the character of the MOF binding site and the associated adsorption thermodynamics using four experimentally characterized MOFs, highlighting the role of open metal sites (OMSs) in accessing binding strengths relevant to room temperature storage. The sorbents are MOF-5, with no open metal sites, \ce{Ni2}(\textit{m}-dobdc), containing Lewis acidic Ni(II) sites, Cu(I)-MFU-4\textit{l}, containing $\pi$ basic Cu(I) sites and V\textsubscript{2}Cl\textsubscript{2.8}(btdd), also containing $\pi$-basic V(II) sites. We next explore the potential for binding multiple \ce{H2} molecules at a single metal site, with thermodynamics useful for storage at ambient temperature; a materials design goal which has not yet been experimentally demonstrated. Computations on Ca$^{2+}$ or Mg$^{2+}$ bound to catecholate or Ca$^{2+}$ bound to porphyrin show the potential for binding up to 4 \ce{H2}; there is precedent for the inclusion of both catecholate and porphyrin motifs in MOFs. Turning to transition metals, we discuss the prediction that two \ce{H2} molecules can bind at V(II)-MFU-4\textit{l}, a material that has been synthesized with solvent coordinated to the V(II) site. Additional calculations demonstrate binding three equivalents of hydrogen per OMS in Sc(I) or Ti(I)-exchanged MFU-4\textit{l}. Overall, the results suggest promising prospects for experimentally realizing higher capacity hydrogen storage MOFs, if nontrivial synthetic and desolvation challenges can be overcome. Coupled with the unbounded chemical diversity of MOFs, there is ample scope for additional exploration and discovery.
|
Romit Chakraborty; Justin Talbot; Hengyuan Shen; Yuto Yabuuchi; Kurtis Carsch; Henry Z. H. Jiang; Hiroyasu Furukawa; Jeffrey R. Long; Martin Head-Gordon
|
Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Theory - Computational; Fuels - Energy Science; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-11-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6549a382c573f893f1f64b0b/original/quantum-chemical-modeling-of-hydrogen-binding-in-metal-organic-frameworks-validation-insight-predictions-and-challenges.pdf
|
60c752c39abda27263f8de81
|
10.26434/chemrxiv.13335941.v1
|
The Passive Permeability Landscape Around Geometrically Diverse Hexa- and Heptapeptide Macrocycles
|
Recent advances in DNA and mRNA encoding technologies have enabled the discovery of high-affinity macrocyclic peptides and peptide-like ligands against virtually any protein target of interest. Unfortunately, even the most potent biochemical leads from these screening technologies often have weak cellular activity due to poor absorption. Biasing such libraries towards passive cell permeability in the design phase would facilitate development of leads against intracellular targets. We set out to empirically evaluate the intrinsic permeability of thousands of geometrically diverse hexa- and heptapeptide scaffolds by permuting backbone stereochemistry and N-methylation, and by including peptoid and β-amino acid residues at select positions, with the goals of providing a resource for biasing library-based screening efforts toward passive membrane permeability and studying the effects of the backbone elements introduced on a large number of compounds. Libraries were synthesized via standard split-pool solid phase peptide synthesis, and passive permeability was measured in pools of 150 compounds using a highly multiplexed version of the parallel artificial mem-brane permeability assay (PAMPA) under sink conditions. Compounds were identified using CycLS, a high-resolution mass spectrometry-based method that uses stable isotopes to encode stereochemistry and matches MSMS data to virtual fragment libraries based on the expected macrocyclic products. From the compounds that were identified with high confidence, 823 hexameric and 1330 heptameric scaffolds had PAMPA permeability coefficients greater than 1x10-6 cm/s. The prevalence of high permeability compounds in these two libraries suggests that passive permeability is achievable for hexa- and heptapeptides with highly diverse backbone geometries.
|
Chad Townsend; Eva Jason; Matthew R. Naylor; Cameron R. Pye; Joshua A. Schwochert; Quinn Edmondson; R. Scott Lokey
|
Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-12-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752c39abda27263f8de81/original/the-passive-permeability-landscape-around-geometrically-diverse-hexa-and-heptapeptide-macrocycles.pdf
|
641dd3a2647e3dca997293ce
|
10.26434/chemrxiv-2023-t26wg
|
Is there any correlation between impedance shapes and electrocatalytic activity?
|
Though electrochemical impedance spectroscopy (EIS) has been widely used in mechanistic investigations of electrocatalytic reactions, the correlation between the shape of an EIS diagram and electrocatalytic activity is largely unclear; the rich complexity of electrocatalytic reactions casts an air of pessimism over the existence and stability of such a correlation. Understanding the correlation can help select reaction mechanisms and electrical circuit models in data analysis, use EIS shape as a descriptor of electrocatalytic activity, and detect side reactions. Herein, the problem is tackled by a systematic mathematical analysis of firstly single-adsorbate reactions and then more complicated reactions. A complete regime diagram of all possible EIS shapes of single-adsorbate reactions is provided, navigating the analysis in the multi-dimensional parametric space. For single-adsorbate reactions involving two steps with identical transfer coefficients of 0.5 in the absence of lateral adsorbate interactions, several rigorous corollaries are derived. Most of them fail miserably when different transfer coefficients and lateral interactions are considered. Nevertheless, several trends in EIS shapes are robust against complexities of reaction mechanisms and variations in reaction parameters, which also receive experimental evidence collected from the literature.
|
Jun Huang
|
Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Electrocatalysis; Heterogeneous Catalysis; Electrochemistry - Mechanisms, Theory & Study
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641dd3a2647e3dca997293ce/original/is-there-any-correlation-between-impedance-shapes-and-electrocatalytic-activity.pdf
|
653b86a3c573f893f13697cf
|
10.26434/chemrxiv-2023-c2kq2
|
Organic Chemicals from Wood: Selective Depolymerization and Dearomatization of Lignin via Aqueous Electrocatalysis
|
Replacing crude oil as the primary industrial source of carbon-based chemicals has become crucial for both environmental and resource sustainability reasons. In this scenario, wood arises as an excellent candidate, whilst depolymerization approaches have emerged as promising strategies to unlock the lignin potential as a resource in the production of high-value organic chemicals. However, many drawbacks, such as toxic solvents, expensive catalysts, high energy inputs, and poor product selectivity have represented major challenges to this task. Herein, we present an unprecedented approach using electrocatalysis for the simultaneous depolymerization and dearomatization of lignin in aqueous medium under ambient conditions. By employing water/sodium carbonate as a solvent system, we demonstrated a pathway for selectively depolymerizing lignin under reductive electrochemical conditions using carbon as an electrocatalyst. After reductive electrocatalysis, the presence of aromatic compounds was no longer detected via nuclear magnetic resonance (NMR) spectroscopy. Further characterization by NMR, FTIR spectroscopy, and mass spectrometry revealed the major presences of sodium levulinate, sodium 4-hydroxyvalerate, sodium formate, and sodium acetate as products. By achieving a complete dearomatization, valuable aliphatic intermediates with enhanced reactivity were selectively obtained, opening new avenues for further synthesis of many different organic chemicals, and contributing to a more sustainable and circular economy.
|
Lucie Lindenbeck; Vanessa Barra; Sira Dahlhaus; Luca Wende; Björn Beele; Nils Schebb; Bruno Rodrigues; Adam Slabon
|
Materials Science; Catalysis; Polymer Science; Carbon-based Materials; Biopolymers; Electrocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653b86a3c573f893f13697cf/original/organic-chemicals-from-wood-selective-depolymerization-and-dearomatization-of-lignin-via-aqueous-electrocatalysis.pdf
|
66ce99b220ac769e5f0f071b
|
10.26434/chemrxiv-2024-gzgqj
|
Quinone-Based Acceptor Engineering of Donor-Acceptor Cycloparaphenylenes via Post-Synthesis for Achieving White-Light Emission in Single-Molecule
|
Developing donor-acceptor [n]cycloparaphenylenes (D-A [n]CPPs) with multiple emissions from different emissive states remains challenging yet crucial for achieving white-light emission in single-molecule. Here, we report our exploration into acceptor engineering of quinone-based D-A [10]CPPs (Nq/Aq/Tq[10]CPPs) via a post-lateral annulation using Diels-Alder reactions of oxTh[10]CPP. X-ray analysis revealed that Nq[10]CPP display a side by side packing via naphthoquione stacking while Aq[10]CPP adopts an intercalated conformation through anthraquinone interaction. Fluorescence investigations revealed that the quinone-based [10]CPPs display distinctive acceptor-dependent dual-emission from both the locally excited state and charge transfer state after single-wavelength excitation in organic solvents, consequently leading to multicolor emissions, in particular, white-light emission in CHCl3 for Aq[10]CPP. In THF/water mixture, quinone-based [10]CPPs and oxTh[10]CPP display a wide range of fluorescence emissions including white-light emission as increasing the fraction of water, accompanying by the formation of nanoparticles as demonstrated by Tyndall effect and SEM. Interestingly, the fluorescence of Aq[10]CPP can be switched from white to blue in CHCl3 upon redox. Our investigations demonstrate that acceptor engineering not only endows quinone-based [10]CPPs with two distint emissive states for achieving white-light emission but also highlights an effective post-synthetic strategy for functionlizing CPP nanohoops with disirable property.
|
Xiaonan Li; Lin Liu; Luyang Jia; Zhe Lian; Jing He; Shengzhu Guo; Ying Wang; Xuebo Chen; Hua Jiang
|
Organic Chemistry; Supramolecular Chemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ce99b220ac769e5f0f071b/original/quinone-based-acceptor-engineering-of-donor-acceptor-cycloparaphenylenes-via-post-synthesis-for-achieving-white-light-emission-in-single-molecule.pdf
|
6176f83f0c0480b47f44a889
|
10.26434/chemrxiv-2021-zbgbj
|
A response surface model to predict and experimentally tune the chemical, magnetic and optoelectronic properties of oxygen-doped boron nitride
|
A new material platform for boron nitride (BN) as a heterogeneous photocatalyst for solar fuels synthesis has recently emerged. One of the bottlenecks of this material is the lack of photoactivity under visible light, which hinders its rate performance. Theoretical studies have predicted that tuning the oxygen content in oxygen-doped BN (BNO) might be used to lower and vary the band gap. However, this is yet to be verified experimentally. We present herein a systematic experimental route facilitating simultaneous tuning of the chemical, magnetic and optoelectronic properties of BNO using a multivariate synthesis parameter space. Deep visible range band gaps (1.50 – 2.90 eV) were experimentally achieved and tuned over an oxygen composition of 2 – 14 at. %, and specific paramagnetic OB3 content of 7 – 294 a.u. g-1, thus supporting theoretical predictions. Through designing a response surface via a design of experiments (DOE) process, the key synthesis parameters influencing the chemical, magnetic and optoelectronic properties of BNO were identified. In addition, model prediction equations relating the aforementioned properties to the synthesis parameter space are presented. Accurate model predictions for the oxygen content and band gap were conducted and validated experimentally. Such a methodology is valuable for further advances in tailoring and optimising BN materials for heterogeneous photocatalytic reactions.
|
Ravi Shankar; Elan Mistry; Daphne Lubert-Perquel; Irena Nevjestic; Sandrine Heutz; Camille Petit
|
Materials Science; Catalysts
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-10-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6176f83f0c0480b47f44a889/original/a-response-surface-model-to-predict-and-experimentally-tune-the-chemical-magnetic-and-optoelectronic-properties-of-oxygen-doped-boron-nitride.pdf
|
66f1a98f12ff75c3a1400a56
|
10.26434/chemrxiv-2024-s1mhh
|
Anomeric Nitroamide Enabled, Cobalt Catalyzed Alkene Hydronitration
|
Tertiary nitroalkanes, as well as its reduced products, α-tertiary amines, play an essential role in drug discovery either as key synthetic precursors or final incorporation in targeted molecules. Existing methods to prepare tertiary nitro compounds generally rely on polar-bond disconnections, in which strong bases or highly active electrophiles are needed. Here, we report the development of an anomeric nitroamide-based reagent that enables exquisitely selective MHAT-based Co-catalyzed alkene hydronitration for the preparation of valuable tertiary nitro compounds. This mild, scalable reaction shows broad functional group tolerance, is applied to a variety of structures. Late-stage nitration of complex contexts (9 examples) derived from drugs and natural products is also pursued. Its high prowess is further highlighted in simplifying the synthesis of a rare naturally occurring nitro sugar. Simple access to isotopically labeled 15N-containing nitro compounds is also disclosed. The anomeric nitroamide reagent was deemed safe by energetic measurements and its unique reactivity rationalized based on X-ray crystallographic analysis.
|
Yu Wang; Marcell Bogner; Jake Bailey; Lauren Grant; Milan Gembicky; Paul Richardson; Phil Baran
|
Organic Chemistry; Organic Synthesis and Reactions
|
CC BY 4.0
|
CHEMRXIV
|
2024-09-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f1a98f12ff75c3a1400a56/original/anomeric-nitroamide-enabled-cobalt-catalyzed-alkene-hydronitration.pdf
|
64f7a5643fdae147fa921f18
|
10.26434/chemrxiv-2023-h4czl-v2
|
A coming of age for many-body methods: Achieving consensus with experiments for CO on MgO
|
The adsorption energy of a molecule onto the surface of a material underpins a wide array of applications, spanning heterogeneous catalysis, gas storage and many more. It is the key quantity where experimental measurements and theoretical calculations meet, with agreement being necessary for reliable predictions of reaction rates and mechanisms. The prototypical molecule-surface system is CO adsorbed on MgO, but despite intense scrutiny from theory and experiment, there is still no consensus on its adsorption energy. In particular, the large cost of accurate many-body methods makes reaching converged theoretical estimates difficult, generating a wide range of values. In this work, we address this challenge, leveraging the latest advances in diffusion Monte Carlo (DMC) and coupled cluster theory [CCSD(T)], to obtain accurate predictions for CO on MgO. These reliable theoretical estimates allow us to evaluate the inconsistencies in published temperature programmed desorption experiments, revealing that they arise from variations in employed pre-exponential factors. Utilizing this insight, we derive new experimental estimates of the (electronic) adsorption energy with a (more) precise pre-exponential factor. As a culmination of all this effort, we are able to reach consensus between multiple theoretical calculations and multiple experiments for the first time. In addition, we show that our recently developed cluster-based CCSD(T) approach provides a low cost route towards achieving accurate adsorption energies. This sets the stage for affordable and reliable theoretical predictions of reaction mechanisms and rates to guide the realization of new catalysts and gas storage materials.
|
Benjamin X. Shi; Andrea Zen; Venkat Kapil; Péter R. Nagy; Andreas Grüneis; Angelos Michaelides
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-09-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f7a5643fdae147fa921f18/original/a-coming-of-age-for-many-body-methods-achieving-consensus-with-experiments-for-co-on-mg-o.pdf
|
66e4b455cec5d6c142fbf180
|
10.26434/chemrxiv-2024-fb7hr
|
Quantitative Elucidation of Catalytic Reaction of Truncated Aldehyde Dehydrogenase Based on Linear Free Energy Relationship
|
Some oxidoreductases can communicate directly and electrically with electrodes; this process is called direct electron transfer (DET)-type bioelectrocatalysis. Understanding its detailed mechanisms is essential for developing and improving DET-based bioelectrochemical devices. In this study, we investigated the pH dependence of kinetic and thermodynamic characteristics of a variant of an aldehyde dehydrogenase (ALDH) without the cytochrome c subunit (ΔC_ALDH) and compared it with that of a wild-type recombinant ALDH (rALDH). Owing to the pronounced DET activity of ΔC_ALDH at multi-walled carbon nanotubes, the voltammograms were analyzed to obtain the enzymatic parameters. The potential difference between the electrode-active site of the enzyme and electron donor (EE – ED) and the limiting catalytic current density (jcat) exhibited an ideal linear free energy relationship (LFER), suggesting that the catalytic reaction of ΔC_ALDH was controlled by the thermodynamic driving force without any specific interactions. We also measured the ferricyanide reductase activity in solution (ksol) to investigate the effect of electron acceptors (electrode and ferricyanide) on the enzymatic properties. The ksol of ΔC_ALDH has a pH dependence similar to that of jcat; therefore, the experimental data were kinetically analyzed based on the LFER by considering the potential difference between the electron acceptor and electrode-active site of the enzyme (EA – EE). By integrating the analytical results obtained from the DET-type acetaldehyde oxidation using an electrode and ferricyanide reduction in solution, the catalytic constant for the DET-type bioelectrocatalysis (kDET) and the surface concentration of the effective enzyme immobilized on the electrode (ΓE,eff) of ΔC_ALDH were calculated to be 5000 ± 2000 s–1 and 13 ± 7 pmol cm–2, respectively. This study achieved a detailed evaluation of the multi-step catalytic reactions of redox enzymes and can help elucidate the reaction mechanisms of DET-type bioelectrocatalysis.
|
Konatsu Ichikawa; Taiki Adachi; Yuki Kitazumi; Osamu Shirai; Keisei Sowa
|
Catalysis; Biocatalysis; Electrocatalysis; Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-09-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e4b455cec5d6c142fbf180/original/quantitative-elucidation-of-catalytic-reaction-of-truncated-aldehyde-dehydrogenase-based-on-linear-free-energy-relationship.pdf
|
63d8e3fb89c04b6693c48fef
|
10.26434/chemrxiv-2023-msrdw
|
Horner-Wadsworth-Emmons Olefination of Proteins and Glycoproteins
|
Chemo-selective and site-specific modifications of proteins are fundamental to the advancement of biological and pharmaceutical sciences, from understanding the basis of cellular biology to development of biotherapeutics. Recent successes in bioconjugation chemistry have inspired the search for more biocompatible chemical reactions, which has prompted us to investigate Horner-Wadsworth-Emmons (HWE) olefinations, iconic reactions used widely in organic synthesis that would give rise to new selective protein olefinations. Our choice of HWE olefinations was inspired by the growing number of methods for the generation of aldehydes as transient reactive groups in proteins and the potential for mild and simple reaction conditions. Here we show that HWE on aldehydes produced by both chemical and enzymatic methods is fully compatible with physiological conditions and highly selective in small and large proteins, including therapeutic antibodies. By exploiting the wide range of easily accessible HWE reagents provided by organic chemistry, we show that the reaction kinetics can be fine-tuned over orders of magnitude by judicious use of substituents. The electrophilic nature of the HWE products can be tuned to allow for subsequent nucleophilic additions, including thiol- and phospha-Michael additions, enabling two-step dual labelling strategies. Our results demonstrate that HWE olefination of aldehydes in proteins provide efficient and selective bioconjugation chemistries that are orthogonal to existing methods.
|
Antonio Angelastro; Alexey Barkhanskiy; William R. F. Goundry; Perdita Barran; Sabine L. Flitsch
|
Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions; Bioengineering and Biotechnology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-01-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d8e3fb89c04b6693c48fef/original/horner-wadsworth-emmons-olefination-of-proteins-and-glycoproteins.pdf
|
662166d591aefa6ce1d6ecfe
|
10.26434/chemrxiv-2024-q05hb-v2
|
Accuracy of projected atomic virtual orbital space in embedding applications
|
The performance of the recently suggested projected atomic orbitals (PAO) approach as the virtual space in excited state projection-based embedding applications is analyzed. The role of the parameters in the PAO generation is discussed and the impact of different choices is evaluated on the ground state of the stacked formaldehyde and pyrrole dimers. A comparison of excitation energies obtained with PAOs and localized virtual orbitals is given and the role of diffuse basis functions is discussed using a benchmark set from previous studies.
|
Ádám B. Szirmai; Bónis Barcza; Attila Tajti; Péter G. Szalay
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-04-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662166d591aefa6ce1d6ecfe/original/accuracy-of-projected-atomic-virtual-orbital-space-in-embedding-applications.pdf
|
60c755cbbdbb89ea0ea3a8e3
|
10.26434/chemrxiv.14161403.v1
|
Crystal Engineering with Copper and Melamine
|
Coordination complex and polymer are central in inorganic and material chemistry
as a variety of both metal centers and coordination geometries lead to a diverse range of
interesting properties. Here, size and structure control of gems-like quality monocrystals
are demonstrated at room temperature. From the same set of precursors, but the
copper-to-melamine molar ratio is adjusted to synthesize either a novel coordination
complex of dinuclear copper and melamine (Cu2M1) or a barely-studied coordination
polymer of zigzag copper-chlorine chains (Cu4M1). Crystals of the former are dark
green and squared with the size up to 350 µm across. The latter is light green and
octagonal as large as 5 mm across. The magnetic properties of both crystals reflect their low-dimensional arrangements of copper. The magnetic susceptibility of Cu2M1 is well
modelled with a spin-1/2 dimer and that of Cu4M1 with a spin-1/2 one-dimensional
Ising chain. Controlled synthesis of such quality magnetic crystals is a prerequisite for
various magnetic and magneto-optical applications<br />
|
Ignacio Bernabé Vírseda; Shiraz Ahmed Siddiqui; Alexander Prado-Roller; Michael Eisterer; Hidetsugu Shiozawa
|
Hybrid Organic-Inorganic Materials; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755cbbdbb89ea0ea3a8e3/original/crystal-engineering-with-copper-and-melamine.pdf
|
60c7550d0f50db7e95397e20
|
10.26434/chemrxiv.14035691.v1
|
Screening Tagged Proteins Using Tandem Affinity-Buffer Exchange Chromatography Online with Native Mass Spectrometry
|
Protein overexpression and purification are critical for in vitro structure-function characterization studies. However, some proteins are difficult to express robustly in heterologous systems due to host-related (e.g., codon usage, translation rate) and/or protein specific (e.g., toxicity, aggregation) challenges. Therefore, it is often necessary to screen<br />multiple overexpression and purification conditions to maximize the yield of functional protein, particularly for resource-heavy downstream applications (e.g., biocatalysts, tertiary structure determination, biotherapeutics). Here, we describe an automatable liquid chromatography–mass spectrometry-based method for rapid, direct analysis of target proteins in cell lysates. This online approach is facilitated by coupling immobilized metal affinity chromatography (IMAC), which leverages engineered poly-histidine tags in proteins of interest, with size exclusion-based buffer exchange (OBE) and native mass spectrometry (nMS). The use of IMAC-OBE-nMS to optimize conditions for large-scale protein production should expedite structural biology and biotherapeutic initiatives.<br />
|
Florian Busch; Zachary VanAernum; Stella M. Lai; Venkat Gopalan; Vicki Wysocki
|
Biochemical Analysis; Mass Spectrometry; Separation Science; Biochemistry; Cell and Molecular Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-02-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7550d0f50db7e95397e20/original/screening-tagged-proteins-using-tandem-affinity-buffer-exchange-chromatography-online-with-native-mass-spectrometry.pdf
|
60c75284469df418cbf44ba6
|
10.26434/chemrxiv.13252610.v1
|
Influence of Bound Water on the Interaction of the Same-Nature and Different-Nature Chemical Groups of Drugs and Receptors
|
Role of water in thermodynamic of molecular recognition processes in the binding of a ligand to a receptor is extremely important. However, there is still a significant lack of specific knowledge to the extent of water influence on the process.
|
Felix S. Dukhovich; Mikhail Darkhovskii
|
Chemical Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-12-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75284469df418cbf44ba6/original/influence-of-bound-water-on-the-interaction-of-the-same-nature-and-different-nature-chemical-groups-of-drugs-and-receptors.pdf
|
60c75127bb8c1a21ba3dbc1f
|
10.26434/chemrxiv.13128836.v1
|
Interaction of Synthetic Cannabinoid Receptor Agonists with Cannabinoid Receptor I: Insights into Activation Molecular Mechanism
|
The manuscript of a paper entitled "Interaction of Synthetic Cannabinoid Receptor Agonists with Cannabinoid Receptor I: Insights into Activation Molecular Mechanism". The work describes computer simulations of activation of the Cannabinoid Receptor I at binding of its agonist ligands. The molecular mechanism of the receptor-ligand interactions and receptor's activation is explored. The study includes theoretical models construction, intense molecular dynamics simulations, comparison with experimentally-known data. Some conclusions allow for better understanding of G-protein-copupled receptor mechanism of transmembrane allosteric modulation.
|
Sergei Gavryushov; Anton Bashilov; Konstantin Cherashev-Tumanov; Nikolay Kuzmich; Tatyana Burykina; Boris Izotov
|
Biochemistry; Bioinformatics and Computational Biology; Biophysics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-10-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75127bb8c1a21ba3dbc1f/original/interaction-of-synthetic-cannabinoid-receptor-agonists-with-cannabinoid-receptor-i-insights-into-activation-molecular-mechanism.pdf
|
67b4894bfa469535b9db7fa5
|
10.26434/chemrxiv-2025-k6v82
|
Iodine in the Atmosphere II: Cluster Formation Potential of Iodine Oxyacids and Iodine Oxides
|
Iodine-driven nucleation is thought to be a significant source of new particle formation, especially in marine and polar regions. Despite numerous studies, the mechanism is still not fully understood. To shed further light on this, we apply ZORA-DLPNO-CCSD(T_0)/TZVPP//ωB97X-D3BJ/aug-cc-pVTZ-PP to calculate the thermochemistry of iodine-containing clusters up to tetramers, and simulate the cluster formation potential for several nucleation paths using the atmospheric cluster dynamics code (ACDC).
We find that iodine oxyacid--amine nucleation can be competitive with sulfuric acid--amine nucleation if iodic acid is present in a 10:1 ratio compared to sulfuric acid. Therefore, the importance of the iodine-driven pathway is regionally dependent. Likewise, we find that increasing the relative humidity from 34% to 73% only changes the cluster formation potential by a factor of 2.
Nucleation pathways consisting of only iodic and iodous acid are unable to explain the relative nucleation rates previously observed in experiments. In contrast, the simultaneous nucleation of iodine oxides, assisted by iodine oxyacids, is better able to describe the trend.
This indicates that a nucleation pathway starting with iodine oxides is more likely to be able to explain observed particle numbers. However, this current model does not include all the hydrates of the clusters and does not account for the hydrolysis reactions of the iodine oxides. This would need to be incorporated in future studies.
|
Morten Engsvang; Jonas Elm
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational
|
CC BY 4.0
|
CHEMRXIV
|
2025-02-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b4894bfa469535b9db7fa5/original/iodine-in-the-atmosphere-ii-cluster-formation-potential-of-iodine-oxyacids-and-iodine-oxides.pdf
|
64c29140ce23211b20a787bb
|
10.26434/chemrxiv-2023-lm42x
|
On the Possibility of p-type Doping in Barium Stannate
|
The combination of optical transparency and bipolar dopability in a single material would revolutionise modern opto-electronics. Of the materials known to be both p- and n-type dopable (such as \ce{SnO} and \ce{CuInO2}), none can satisfy the requirements for both p- and n-type transparent conducting applications. In the present work, perovskite \ce{BaSnO3} is investigated as a candidate material: its n-type properties are well characterised, with La-doping yielding degenerate conductivity and record electron mobility, while it has been suggested on a handful of occasions to be p-type dopable. Herein, group 1 metals Li, Na and K and group 13 metals Al, Ga and In are assessed as p-type acceptor defects in \ce{BaSnO3} using hybrid density functional theory. It is found that while K and In can induce hole concentrations up to \SI{e16}{\per\centi\meter\cubed}, the low energy oxygen vacancy pins the Fermi level in the band gap and ultimately prevents metallic p-type conductivity being achieved in \ce{BaSnO3}. Nevertheless, the predicted hole concentrations exceed experimentally reported values for K-doped \ce{BaSnO3}, suggesting that the performance of a transparent p-n homo-junction made from this material could be significantly improved.
|
Joe Willis; Kieran B. Spooner; David O. Scanlon
|
Theoretical and Computational Chemistry; Materials Science; Optical Materials; Computational Chemistry and Modeling; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-08-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c29140ce23211b20a787bb/original/on-the-possibility-of-p-type-doping-in-barium-stannate.pdf
|
67126463cec5d6c142842e2d
|
10.26434/chemrxiv-2024-h5hbb
|
Quaternary biopesticides and disinfectants derived from quinine and amino acids – environmental prospects and risks
|
The numerous risks associated with the toxicity of conventional quaternary ammonium salts (QASs) to various groups of living organisms have prompted the search for new, safer biologically active compounds synthesized in a sustainable manner from renewable raw materials. Here, we describe new QASs of natural origin containing quinine-based cation and anions derived from amino acids comprising proteins – L-asparagine and L-alanine. The quinine-derived QASs were thoroughly characterized in terms of correctness of chemical structure, physicochemical properties, and biological activity. It was discovered that due to quinine activity, the new salts exhibit strong antifeedant activity toward stored products pests, and in the case of elongation of the alkyl substituent in the 1-alkylquininium cation, they also become potent disinfectants. The performed analyses also allowed to assess the environmental risk by determining toxicity to monocotyledonous (Sorghum bicolor) and dicotyledonous (Sinapis alba) terrestial plants, freshwater algae (Chlorella vulgaris) and crustaceans (Daphnia magna) at various concentrations of the test substance. None of the QASs of natural origin showed phytotoxicity, and salts containing short alkyl substituents in quinine-based cations were noticeably less toxic to aquatic organisms than the other tested compounds. The results indicate that although a trade-off between antimicrobial activity and aquatic toxicity must be made when designing new quinine-based antiseptics, it is entirely possible to obtain potent, naturally-derived and low-toxic biopesticides based on quinine and amino acids.
|
Tomasz Rzemieniecki; Krzysztof Juś; Tomasz Klejdysz; Daniela Gwiazdowska
|
Organic Chemistry; Earth, Space, and Environmental Chemistry; Agriculture and Food Chemistry; Bioorganic Chemistry; Natural Products; Environmental Science
|
CC BY 4.0
|
CHEMRXIV
|
2024-10-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67126463cec5d6c142842e2d/original/quaternary-biopesticides-and-disinfectants-derived-from-quinine-and-amino-acids-environmental-prospects-and-risks.pdf
|
60c741204c89199101ad2236
|
10.26434/chemrxiv.7942628.v1
|
Synthetic Variation and Structural Trends in Layered Two-Dimensional Alkylammonium Lead Halide Perovskites
|
We report the cooling-induced crystallization of layered two-dimensional
lead halide perovskites with controllable inorganic quantum-well thickness (<i>n</i> = 1, 2, 3, 4)<i>,</i> organic spacer chain length (butyl-, pentyl-, hexylammonium),
A-site cation (methylammonium, formamidinium), and halide anion (iodide,
bromide). We report crystal structures for the iodide family as a function of
these compositional parameters, and across their temperature dependent phase
transitions. In general, lower symmetry crystal structures, increasing extents
of organic-spacer interdigitation, and increasing organic-spacer corrugation
tilts are observed at low temperature. In addition, greater structural
distortions are seen in lead halide octahedra closest to the organic spacer
layer, and larger-<i>n </i>structures
exhibit periodic variation in Pb-I bond lengths. We also provide detailed
guidance regarding the combination of synthetic parameters needed to achieve
phase-pure crystals of each composition, and discuss difficulties encountered
when trying to synthesize particular members of the 2D perovskite family
containing formamidinium or cesium as the A-site cation. These results provide
a foundation for understanding structural trends in 2D lead halide perovskites
and the effect these trends have on their thermal, electrical, and optical
properties.
|
Watcharaphol Paritmongkol; Nabeel Dahod; Nannan Mao; Shao-Liang Zheng; William Tisdale
|
Hybrid Organic-Inorganic Materials; Physical and Chemical Properties; Structure
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-04-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741204c89199101ad2236/original/synthetic-variation-and-structural-trends-in-layered-two-dimensional-alkylammonium-lead-halide-perovskites.pdf
|
6261b02f742e9f0be166b973
|
10.26434/chemrxiv-2022-81pdc
|
Entanglement of electrons and nuclei during ultrafast excitation: A most compact representation of the molecular wave function
|
Ultrafast pumping displaces both electrons and nuclei from equilibrium so that the wave function is a double sum of separable terms for the dynamics of the electrons and nuclei. We convert the double sum into a single one by a matricization of the wave function, that is equivalent to the Schmidt decomposition. If more than one term needs to be included in this sum, the wave functions exhibit entanglement of electrons and nuclei. We discuss generating the best exact separable expression for the entangled molecular wave function. Then an approximation with a minimum number of single terms is obtained via Singular Value Decomposition, SVD. Two contrasting examples, LiH and N2, are used as an illustration. In the energy range accessible by a UV excitation, the two differ in their adiabatic electronic dynamics. During the nuclear motion the singlet states of N2 remain bound while the states of LiH are dissociative.
|
Francoise Remacle; Martin Blavier; Natalia Gelfand; Raphael D. Levine
|
Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Photochemistry (Physical Chem.); Quantum Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-04-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6261b02f742e9f0be166b973/original/entanglement-of-electrons-and-nuclei-during-ultrafast-excitation-a-most-compact-representation-of-the-molecular-wave-function.pdf
|
60c751d2567dfe1636ec5b19
|
10.26434/chemrxiv.13214582.v1
|
Effect of Unwanted Guest Molecules on the Stacking Configuration of Covalent Organic Frameworks: A Periodic Energy Decomposition Analysis
|
Elucidating the precise stacking configuration of a covalent organic framework, COF, is critical to fully understand their various applications. Unfortunately, most COFs form powder crystals whose atomic characterisations are possible only through powder X-ray diffraction (PXRD) analysis.
However, this analysis has to be coupled with computational simulations,
wherein computed PXRD patterns for different stacking configurations are
compared with experimental patterns to predict the precise stacking configuration. This task is often computationally challenging firstly because,
computation of these systems mostly rely on the use of semi-empirical methods that need to be adequately parametrised for the system being studied
and secondly because some of these compounds possess guest molecules,
which are not often taken into account during computation. COF-1 is an
extreme case in which the presence of the guest molecule plays a critical role
in predicting the precise stacking configuration. Using this as a case study,
we mapped out a full PES for the stacking configuration in the guest free
and guest containing system using the GFN-xTB semi-empirical method followed by a periodic energy decomposition analysis using first principle DFT.
Our results showed that the presence of the guest molecule leads to multiple
low energy stacking configurations with significantly different lateral offsets.
Also, the semi-empirical method does not precisely predict DFT low energy configurations, however, it accurately accounts for dispersion. Finally, our quantum-mechanical analysis demonstrates that electrostatic-dispersion
model suggested Hunter and Sanders accurately describe the stacking in 2D
COFs as oppose to the newly suggested Pauli-dispersion model.
|
A.D. Dinga Wonanke; Mathew Addicoat
|
Computational Chemistry and Modeling; Quantum Mechanics; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-11-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751d2567dfe1636ec5b19/original/effect-of-unwanted-guest-molecules-on-the-stacking-configuration-of-covalent-organic-frameworks-a-periodic-energy-decomposition-analysis.pdf
|
60c74a16842e6530acdb2e7e
|
10.26434/chemrxiv.12153339.v1
|
Mechanochemical Reactions of Cocrystals: Comparing Theory with Experiment in Making and Breaking Halogen Bonds in Solid State
|
Mechanochemical re-investigation of the halogen-bonded cocrystallization of 1,4-diazabicyclo[2.2.2]octane and 1,2-diiodotetraflurobenzene revealed an unexpectedly complex system, with three distinct cocrystal compositions, one of which also exhibits temperature-dependent polymorphism. This provided an opportunity to experimentally test the ability of dispersion-corrected periodic density functional theory (DFT) not only to explain the formation, but also predict the interconversion between halogen-bonded cocrystals of different stoichiometries,<br />
|
Filip Topic; Mihails Arhangelskis; Poppy Hindle; Ricky Tran; Andrew Morris; Dominik Cincic; Tomislav Friscic
|
Physical Organic Chemistry; Supramolecular Chemistry (Org.); Crystallography – Organic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a16842e6530acdb2e7e/original/mechanochemical-reactions-of-cocrystals-comparing-theory-with-experiment-in-making-and-breaking-halogen-bonds-in-solid-state.pdf
|
6542db4548dad23120e3ea65
|
10.26434/chemrxiv-2023-3818h
|
Synthesizing Amorphous Precursors Through Control of Local Composition
|
Synthesizing compounds predicted to have exceptional properties that are close to or below the ground state convex hull has proven to be very challenging, as avoiding the formation of more thermodynamically or kinetically stable mixtures of known compounds is often required. A homogenous amorphous phase has been suggested as a very general reaction intermediate. However, the preparation of amorphous phases of controlled composition is also very challenging. We postulated that amorphous intermediates with controlled composition can be made by avoiding the formation of regions with compositions close to that of the known compounds. Specifically, we demonstrated that we
could avoid the formation of PbSe and MoSe2 by sequentially depositing nonstoichiometric ultrathin sub-monolayer thickness layers on a nominally room temperature substrate. The substrate temperature needs to be low enough to minimize surface diffusion, preventing agglomeration of elements and resultant concentration gradients. The amount of diffusion required to form nucleation embryos can be controlled by changing the difference between the composition of the film and the stoichiometry of the compound in question. Large enough differences should result in amorphous intermediates in most systems. The presence of more than two elements will further suppress the nucleation of binary compounds,
making this approach particularly useful to prepare amorphous precursors for the synthesis of metastable ternary and quaternary compounds.
|
Hannah Blackwood; Annalise Walker; David Johnson
|
Inorganic Chemistry; Nanoscience; Reaction (Inorg.); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-11-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6542db4548dad23120e3ea65/original/synthesizing-amorphous-precursors-through-control-of-local-composition.pdf
|
62a790eba784d100517d7c75
|
10.26434/chemrxiv-2022-f3lks-v3
|
Calibrate Ligand-ligand Interaction on Nanocrystals via the Dynamic Volume of Chain Segments
|
The intermolecular ligand-ligand interaction is crucial for the surface chemistry, solution properties, and self-assembly processes of colloidal nanocrystals (NCs). The studies on the ligand-ligand interaction are hampered by the disordered and dynamic nature of the surface, the low electron contrast of organic moieties, and the non-characteristic weak intermolecular forces. Solid-state nuclear magnetic resonance (NMR) can provide site-specific information on organic ligands and especially the motional behavior of chain segments. In this work, we develop an advanced solid-state NMR measurement and modelling strategy to quantify the “dynamic volume” of chain segments. The dynamic volume depicts the accessible space of a chain segment under the confinement of neighboring molecules, and is inversely proportional to the intermolecular interaction energy. The ligand-ligand interaction energies have been obtained for NCs with alkanoate ligands of different lengths. We show that the calculated ligand-ligand interaction energy determines solution dispersity and the melting transitions of NCs. This dynamic volume concept can be extended beyond experimental NMR measurements and offer semi-empirical predictions of the interaction energies for arbitrary selections of alkanoate ligands. Our study not only advances the quantitative understanding of ligand-ligand interaction on NCs but also establishes novel tactics to calibrate weak intermolecular interactions.
|
Weicheng Cao; Zhenfeng Pang; Xiaoqi Zhou; Zhenming Cao; Jiachen Li; Qi Wang; Xiaogang Peng; Xueqian Kong
|
Materials Science; Nanoscience; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2022-06-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a790eba784d100517d7c75/original/calibrate-ligand-ligand-interaction-on-nanocrystals-via-the-dynamic-volume-of-chain-segments.pdf
|
60c73d934c89194e5aad1c36
|
10.26434/chemrxiv.5938228.v1
|
Guest-Dependent Stabilization of the Low Spin State in Spin-Crossover Metal-Organic Frameworks
|
<div>
<div>
<div>
<p>Computer simulations are carried out to
characterize the variation of spin crossover (SCO) behavior of the prototypical {Fe(pz)[Pt(CN)4]} metal-organic framework (MOF) upon adsorption of chemically and structurally different guest molecules. A detailed
analysis of both strength and anisotropy of guest molecule-framework interactions reveals direct correlations
between the mobility of the guest molecules inside the
MOF pores, the rotational mobility of the pyrazine rings
of the framework, and the stabilization of the low-spin
state of the material. Based on these correlations, precise
molecular criteria are established for predicting the spin
state of {Fe(pz)[Pt(CN)4]} upon guest adsorption. Finally, predictions of the SCO temperature upon adsorption
of various toxic gases demonstrate that in silico modeling can provide fundamental insights and design principles for the development of spin-crossover MOFs for
applications in gas detection and chemical sensing.
</p>
</div>
</div>
</div>
|
C. Huy Pham; Paesani Lab
|
Hybrid Organic-Inorganic Materials; Magnetism; Sensors; Theory - Inorganic; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-03-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d934c89194e5aad1c36/original/guest-dependent-stabilization-of-the-low-spin-state-in-spin-crossover-metal-organic-frameworks.pdf
|
60c743ecbb8c1a80583da3e5
|
10.26434/chemrxiv.9696044.v1
|
Acid Exfoliation of Imine-linked Covalent Organic Frameworks Enables Solution Processing into Crystalline Thin Films
|
Covalent organic frameworks (COFs) are highly modular, porous, crystalline polymers of interest for charge storage devices, nanofiltration membranes, optoelectronic devices, and more. COFs are typically synthesized as microcrystalline powders, a morphology that limits their performance in these applications, and their limited solubility precludes large-scale processing into more useful morphologies and devices. Here, we report a general, scalable method to exfoliate two-dimensional imine-linked COF powders by temporarily protonating their linkages. The resulting suspensions were cast into continuous, crystalline COF films up to 10 cm in diameter. This strategy was successfully applied to three different COF structures, and excellent film thickness control (50 nm to 20 µm) was achieved by modifying the suspension composition, concentration, and casting protocol. Acid-mediated exfoliation is a promising strategy for solution processing readily accessible imine-linked COF powders into functional devices.
|
David Burke; Chao Sun; Ioannina Castano; Nathan C. Flanders; Austin Evans; Edon Vitaku; David McLeod; Robert H. Lambeth; Lin Chen; Nathan Gianneschi; William Dichtel
|
Materials Processing; Multilayers; Nanostructured Materials - Materials; Thin Films; Organic Polymers; Polymer morphology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-08-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743ecbb8c1a80583da3e5/original/acid-exfoliation-of-imine-linked-covalent-organic-frameworks-enables-solution-processing-into-crystalline-thin-films.pdf
|
6495f47c4821a835f34b8455
|
10.26434/chemrxiv-2023-3dqvx
|
Structural and Chemical Evolution of Highly Fluorinated Li-rich Disordered Rocksalt Oxyfluorides as a Function of Temperature
|
Li-rich disordered rocksalt (DRS) oxyfluorides have emerged as promising high-energy cathode materials for lithium-ion batteries. While a high level of fluorination in DRS materials offers performance advantages, it can only be achieved via mechanochemical synthesis, which poses challenges of reproducibility and scalability. The definition of relationships between fluorination and thermal stability is required to devise alternative methods that overcome these challenges. In this study, we investigated the thermal stability of three highly fluorinated Li2MO2F (M=Mn, Co, and Ni) in inert atmosphere. We utilized diffraction and spectroscopic techniques to examine changes in their electronic and chemical states up until conditions of decomposition. The analysis revealed that the materials phase-separate above 400C, at most. We also observed that heat-treated DRS materials exhibited intricate changes in local coordination and ordering compared to the pristine states. Furthermore, the heat-treated materials displayed a reduced voltage hysteresis on the electrochemical voltage profiles compared to pristine states. These results provide an in-depth understanding of the fundamental crystal chemistry of DRS materials in view of their promising role as next generation of Li-ion cathodes.
|
Neelam Sunariwal; Khagesh Kumar; Fulya Dogan; Indrani Roy; Jordi Cabana
|
Materials Science; Energy; Energy Storage; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-06-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6495f47c4821a835f34b8455/original/structural-and-chemical-evolution-of-highly-fluorinated-li-rich-disordered-rocksalt-oxyfluorides-as-a-function-of-temperature.pdf
|
61dde0eedb4d9f138495717b
|
10.26434/chemrxiv-2022-jktz4
|
Dearomative Michael addition involving enals and 2-nitrobenzofurans realized under NHC-catalysis
|
In the manuscript the first enantioselective dearomative Michael addition between α,β-unsaturated aldehydes and 2-nitrobenzofurans realized under N-heterocyclic carbene activation has been described. The reaction proceeds via addition of homoenolate to Michael acceptors leading to the formation of biologically important heterocycles with high yields and stereoselectivities. Their functionalization potential has been confirmed in selected, diastereoselective transformations.
|
Mateusz Dyguda; Anna Skrzyńska; Lesław Sieroń; Łukasz Albrecht
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Organocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-01-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61dde0eedb4d9f138495717b/original/dearomative-michael-addition-involving-enals-and-2-nitrobenzofurans-realized-under-nhc-catalysis.pdf
|
67b8d0aefa469535b95a32c4
|
10.26434/chemrxiv-2025-wzdgc
|
Magnetic Properties and Large SHG Response of a Chiral Ternary Chalcogenide: Eu2SiSe4
|
Eu(II)-containing chalcogenides are an emerging class of materials that are of high interest due to their high optical activity and intriguing magnetism. Here, we synthesized Eu2SiSe4 as red-colored single crystals and characterized its structure with single crystal X-ray diffraction, confirming the reported chiral monoclinic P21 symmetry at room temperature. The crystal structure of Eu2SiSe4 comprises distorted SiSe4 tetrahedral units and charge-balancing Eu(II) cations. We find the second harmonic generation (SHG) activity (~7x AGS) of polycrystalline Eu2SiSe4 to be among the highest known SHG active chalcogenides. No symmetry lowering is observed down to 100 K in single crystal X-ray diffraction, although an anomalous expansion in the b-axis lattice parameter occurs and may be correlated to lattice vibrations of the SiSe4 tetrahedra. We investigate the physical properties of Eu2SiSe4 and find complex temperature- and field-dependent behavior, including a weak transition at ~145 K as well as multiple magnetic transitions occurring at low temperature, leading to a slightly canted antiferromagnetic or ferrimagnetic ground state. The low-temperature transitions release less entropy than expected, which may be due to complex crystal electric field effects of Eu(II).
|
Shaun O'Donnell; Ian Leahy; Subhendu Jana; Eric Gabilondo; P. Shiv Halasyamani; Paul Maggard; Rebecca Smaha
|
Inorganic Chemistry; Magnetism; Solid State Chemistry; Materials Chemistry; Crystallography – Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-02-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b8d0aefa469535b95a32c4/original/magnetic-properties-and-large-shg-response-of-a-chiral-ternary-chalcogenide-eu2si-se4.pdf
|
6492fdf5853d501c00444f38
|
10.26434/chemrxiv-2023-3c05k-v2
|
Biocatalytic approach to the chemoselective acylation of sesquiterpene lactones from chicory: a pathway to novel ester derivatives
|
In this study, we explore the use of the immobilized lipase Novozym 435 in the selective acylation of chicory sesquiterpene lactones (STLs) - lactucin (Lc), 11β,13-dihydrolactucin (DHLc), lactucopicrin (Lp), and 11β,13-dihydrolactucopicrin (DHLp) - using aliphatic vinyl esters as acyl donors. Despite the scarcity of these STLs due to their challenging extraction process and high cost, our results demonstrate the broad applicability and very high efficiency of this method. Furthermore, this methodology enables the selective acylation of the primary alcohol without transesterifying the existing ester in the substrates (Lp and DHLp). We also describe the enzyme-substrate binding modes in the acylation reactions with STLs, as well as the nature of their interactions with crucial amino acid residues at the active site, providing further insight into the potential of this approach. This study forms a foundation for the tailored functionalization of STLs, offering possibilities for the synthesis of STL derivatives with significant potential applications as pharmaceuticals or biocontrol agents.
|
Juan RODRIGUEZ MOSHEIM; Francesca Ruggieri; Catherine Humeau; Philippe Hance ; Nicolas Willand; Jean-Louis Hilbert; Egon Heuson; Rénato Froidevaux
|
Catalysis; Agriculture and Food Chemistry; Biocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2023-06-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6492fdf5853d501c00444f38/original/biocatalytic-approach-to-the-chemoselective-acylation-of-sesquiterpene-lactones-from-chicory-a-pathway-to-novel-ester-derivatives.pdf
|
60c743ad0f50db1e28395f77
|
10.26434/chemrxiv.9413213.v1
|
Tetrabenzo[5.7]Fulvalene: A Forgotten Aggregation Induced-Emission Luminogen
|
Tetrabenzo[5.7]fulvalene,
one of the first recognized stable members of mixed fulvalenes, has
attracted widespread interest for its remarkable structure. However, little has been
known about its photoactivity, most likely owning to its very weak luminescence
in solution state. Here we show for the first time that this compound exhibits
aggregation-induced emission (AIE) properties. Its photoluminescence and X-ray
crystal structure reveal an interesting mechanism of AIE phenomenon.
|
Reece Crocker; Bolong Zhang; Domenic Pace; Wallace W. H. Wong; Thanh Vinh Nguyen
|
Organic Compounds and Functional Groups; Photochemistry (Org.); Aggregates and Assemblies; Dyes and Chromophores; Optical Materials; Photochemistry (Physical Chem.); Structure; Crystallography – Organic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-08-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743ad0f50db1e28395f77/original/tetrabenzo-5-7-fulvalene-a-forgotten-aggregation-induced-emission-luminogen.pdf
|
6746d6f3f9980725cf1ea159
|
10.26434/chemrxiv-2024-m08b7
|
Large-scale FMO-MP2 calculations of the spike protein droplet model
|
The spike protein of SARS-CoV-2 is a challenging target of theoretical approaches. Here we report a benchmark study of the spike protein droplet model by the fragment molecular orbital (FMO) at the second-order Møller-Plesset perturbation (MP2) level on the Fugaku supercomputer. One hundred structure samples from molecular dynamics (MD) simulations were used for both the closed and open forms of this protein (PDB-IDs 6XLU and 6XM0 respectively). The naive number of total fragments is about 20 thousand, and the job time per structure was about 2 hours with 8 racks of Fugaku.
|
Hideo Doi; Tatsuya Nakano; Kota Sakakura; Kazuki Akisawa; Koji Okuwaki; Yoshinori Hirano; Eiji Yamamoto; Kenji Yasuoka; Satoshi Ohshima; Takahiro Katagiri; Yuji Mochizuki
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6746d6f3f9980725cf1ea159/original/large-scale-fmo-mp2-calculations-of-the-spike-protein-droplet-model.pdf
|
60c7447af96a00c84f2869cf
|
10.26434/chemrxiv.8234021.v2
|
OpenMolcas: From Source Code to Insight
|
In this article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with post calculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory and new electronic and muonic basis sets.
|
Ignacio Fdez. Galván; Morgane Vacher; Ali Alavi; Celestino Angeli; Francesco Aquilante; Jochen Autschbach; Jie J. Bao; Sergey I. Bokarev; Nikolay A. Bogdanov; Rebecca
K. Carlson; Liviu F. Chibotaru; Joel Creutzberg; Nike Dattani; Mickaël G. Delcey; Sijia Dong; Andreas Dreuw; Leon Freitag; Luis Manuel Frutos; Laura Gagliardi; Frédéric Gendron; Angelo Giussani; Leticia Gonzalez; Gilbert Grell; Meiyuan Guo; Chad E. Hoyer; Marcus Johansson; Sebastian Keller; Stefan knecht; Goran Kovačević; Erik Källman; Giovanni Li Manni; Marcus Lundberg; Yingjin Ma; Sebastian Mai; João Pedro Malhado; Per Åke Malmqvist; Philipp Marquetand; Stefanie A. Mewes; Jesper Norell; Massimo Olivucci; Markus Oppel; Quan Manh Phung; Kristine Pierloot; Felix Plasser; Markus Reiher; Andrew M. Sand; Igor Schapiro; Prachi Sharma; Christopher
J. Stein; Lasse Kragh Sørensen; Donald
G. Truhlar; Mihkel Ugandi; Liviu Ungur; Alessio Valentini; Steven Vancoillie; Valera Veryazov; Oskar Weser; Tomasz A. Wesołowski; Per-Olof Widmark; Sebastian Wouters; Alexander Zech; J. Patrick Zobel; Roland Lindh
|
Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry; Physical and Chemical Properties; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-09-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7447af96a00c84f2869cf/original/open-molcas-from-source-code-to-insight.pdf
|
60c74783ee301c14d2c796ee
|
10.26434/chemrxiv.10299062.v2
|
Bridging the Physics and Chemistry of Graphene(s): From Hückel’s Aromaticity to Dirac’s Cones and Topological Insulators
|
By bridging graphene and benzene through a well-defined sequence of polycyclic aromatic hydrocarbons and their inherent shell structure, it is shown that graphene is actually a coherent arrangement of interwoven benzene molecules, coordinated by aromaticity, shell structure, and topology, all interrelated and microscopically realized through dynamical flipping of the atomic pz-orbitals, playing the role of pseudospin or “qubits”. This renders graphene resonance structure, “resonating” between two complementary aromaticity patterns, involving 2k, k→∞ kekulé type of resonances resulting in “robust electronic coherence”, with dual “molecular-crystalline” nature, and two valence-conduction bands of opposite parity, driven by inversion symmetry competition, which is essentially a “molecule-versus-crystal” competition, in accord with topological-insulator and many-body theory. The “average picture” converges to the usual band structure with two aromatic π-electrons per ring, and the fingerprints of inversion-competition at the D3h-symmetric Dirac points, which for rectangular nanographene(s) appear as gapless topological edge states without real spin-polarization, contrary to opposite claims. <br />
|
Aristides Zdetsis
|
Structure
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-01-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74783ee301c14d2c796ee/original/bridging-the-physics-and-chemistry-of-graphene-s-from-huckel-s-aromaticity-to-dirac-s-cones-and-topological-insulators.pdf
|
661cf25491aefa6ce19803b9
|
10.26434/chemrxiv-2024-nwm7n
|
Molecular analysis and design using multimodal generative artificial intelligence via multi-agent modeling
|
We report the use of a multimodal generative artificial intelligence framework, the X-LoRA-Gemma large language model (LLM), to analyze, design and test molecular design. The X-LoRA-Gemma model, inspired by biological principles and featuring ~7 billion parameters, dynamically reconfigures its structure through a dual-pass inference strategy to enhance its problem-solving abilities across diverse scientific domains. The model is used to first identify molecular engineering targets through a systematic human-AI and AI-AI self-driving multi-agent approach to elucidate key targets for molecular optimization to improve interactions between molecules. Next, a multi-agent generative design process is used that includes rational steps, reasoning and autonomous knowledge extraction. Target properties of the molecule are identified either using a Principal Component Analysis (PCA) of key molecular properties or sampling from the distribution of known molecular properties. The model is then used to generate a large set of candidate molecules, which are analyzed via their molecular structure, charge distribution, and other features. We validate that as predicted, increased dipole moment and polarizability is indeed achieved in the designed molecules. We anticipate an increasing integration of these techniques into the molecular engineering workflow, ultimately enabling the development of innovative solutions to address a wide range of societal challenges. We conclude with a critical discussion of challenges and opportunities of the use of multimodal generative AI for molecular engineering, analysis and design.
|
Isabella Stewart; Markus Buehler
|
Theoretical and Computational Chemistry; Materials Science; Nanoscience; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-04-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661cf25491aefa6ce19803b9/original/molecular-analysis-and-design-using-multimodal-generative-artificial-intelligence-via-multi-agent-modeling.pdf
|
60c74505f96a005b1c286b17
|
10.26434/chemrxiv.9937754.v1
|
Metal-Free Click Synthesis of Functional 1-Substituted-1,2,3-Triazoles
|
The 1,2,3-triazole group is one of the most important
connective linkers and functional aromatic heterocycles in modern chemistry.
The boom in growth of, in particular, 1,4-disubstituted triazole products since
the early 2000’s, can be largely attributed to the birth of click chemistry and
the discovery of the Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC). Yet
the synthesis of relatively simple, albeit important,
1-substituted-1,2,3-triazoles, has been surprisingly more challenging. We
report a straightforward and scalable click-protocol for the synthesis of
1-substituted-1,2,3-triazoles from organic azides and the bench stable
acetylene-surrogate, ethenesulfonyl fluoride (ESF). The transformation proceeds
through a thermal 1,3-dipolar cycloaddition of the azide and ESF to give a
sulfonyl fluoride substituted triazoline, that itself spontaneously aromatizes
through formal loss of HF/SO<sub>2 </sub>to give the stable triazole products
with excellent fidelity. The new click reaction tolerates a wide selection of
substrates and proceeds smoothly under metal-free conditions to give the
products in excellent yield, and without need for additives or chromatographic
purification. Further, under controlled conditions, the
1-substituted-1,2,3-triazole products undergo Michael reaction with a second
equivalent of ESF to give the unprecedented 1-substituted triazolium sulfonyl
fluoride salts, demonstrating the versatility and orthogonal reactivity of ESF.
The importance of this novel method is evidenced through the late-stage
modification of several drugs and drug fragments, including the synthesis of a
new improved derivative of the famous antibiotic, chloramphenicol.
|
Marie-Claire Giel; Christopher J. Smedley; Emily R. R. Mackie; Taijie Guo; Jiajia Dong; Tatiana P. Soares da Costa; John E. Moses
|
Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-10-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74505f96a005b1c286b17/original/metal-free-click-synthesis-of-functional-1-substituted-1-2-3-triazoles.pdf
|
60c743b5842e655f66db2313
|
10.26434/chemrxiv.9611909.v1
|
Muconic Acid Esters as Bio-Based Acrylate Mimics
|
The synthesis of polymers from radical polymerization of dialkyl muconates, a renewable monomer that is readily available from biofermentation, is described. Polymuconates are scarcly described in literature, and were previously believed to polymerize only sluggishly. In here we demonstrate the optimized polymerization that yields materials that are analoguous to classical oil-based polyacrylates. Thermal properties of the polymers are explored, and the abaility to control the polymerization via reversible deactivation radical polymerization is showcased.
|
Greg Qunitens; Jeroen Vrijsen; Peter Adriaensens; Dirk Vanderzande; Tanja Junkers
|
Biopolymers; Polymerization (Polymers)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-08-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743b5842e655f66db2313/original/muconic-acid-esters-as-bio-based-acrylate-mimics.pdf
|
6662c6c321291e5d1d457f8e
|
10.26434/chemrxiv-2024-x7r91
|
Photosensitizer-Free Singlet Oxygen Generation via Charge Transfer Transition involving Molecular O2 toward Highly Efficient Oxidative Coupling of Arylamines to Azoaromatics
|
Photosensitizer (PS)‐mediated generation of singlet oxygen, O2 (a1Δg) is a well‐explored phenomenon in chemistry and biology. However, the requirement of appropriate PS with optimum excited state properties is a prerequisite of this approach which limits its widespread application. Herein, we report the generation of O2 (a1Δg) via direct charge-transfer (CT) excitation of solvent‐O2 (X3Σ_g^-) collision complex without any PS and utilize it for the catalyst-free oxidative coupling of arylamines to azoaromatics under ambient conditions in aqueous medium. The electron paramagnetic resonance (EPR) spectroscopy revealed the formation of O2 (a1Δg) upon direct excitation with 370 nm light. The present approach shows broad substrate scope, fast reaction kinetics (90 min), high selectivity (100%), excellent yields (up to 100%), and works well for both homo‐ and hetero‐coupling of arylamines. The oxidative coupling of arylamines was found to proceed through the generation of amine radicals via electron transfer (ET) from amines to O2 (a1Δg). Notably, electron‐rich amines show higher yields of azo products compared to electron‐deficient amines. Detailed mechanistic investigations using various spectroscopic tools revealed the formation of hydrazobenzene as an intermediate along with superoxide radicals which subsequently transform to hydrogen peroxide. The present study is unique in a way that molecular O2 simultaneously acts as a light absorbing chromophore (solvent‐O2 complex) as well as an efficient oxidant (O2 (a1Δg)) in the same reaction. This is the first report for the efficient, selective, and sustainable synthesis of azo compounds in aqueous medium under an ambient atmosphere without any PCs/PSs and paves the way for further in-depth understanding of the chemical reactivity of O2 (a1Δg) generated directly via CT excitation of solvent‐O2 complex toward various photochemical and photobiological transformations.
|
Shivendra Singh; Tushar Kanti Mukherjee
|
Physical Chemistry; Catalysis; Energy; Homogeneous Catalysis; Photocatalysis; Photochemistry (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6662c6c321291e5d1d457f8e/original/photosensitizer-free-singlet-oxygen-generation-via-charge-transfer-transition-involving-molecular-o2-toward-highly-efficient-oxidative-coupling-of-arylamines-to-azoaromatics.pdf
|
66d7ff4b51558a15effe9384
|
10.26434/chemrxiv-2024-wn1m8
|
A microfluidic system for cultivation of cyanobacteria with precise light intensity and CO2 control: Enabling growth data acquisition at single-cell resolution.
|
Quantification of cell growth is central to any study of photoautotrophic microorganisms. However, cellular self-shading and limited CO2 control in conventional photobioreactors lead to heterogeneous conditions that obscure distinct correlations between the environment and cellular physiology. Here we present a microfluidic cultivation platform that enables precise analysis of cyanobacterial growth with spatio-temporal resolution. Since cyanobacteria are cultivated in monolayers, cellular self-shading does not occur, allowing homogeneous illumination and precise knowledge of the photonflux density at single-cell resolution. A single chip contains multiple channels, each connected to several hundred growth chambers. In combination with an externally applied light gradient, this setup enables high-throughput multi-parameter analysis in short time. In addition, the multilayered microfluidic design allows continuous perfusion of defined gas mixtures. Transversal CO2 diffusion across the intermediate polydimethylsiloxane membrane results in homogeneous CO2 supply, with a unique exchange-surface to cultivation-volume ratio. Three cyanobacterial model strains were examined under various, static and dynamic environmental conditions. Phase-contrast and chlorophyllfluorescence images were recorded by automated time-lapse microscopy. Deep-learning trained cell segmentation was used to efficiently analyse large image stacks, thereby generating statistically reliable data. Cell division was highly synchronized, and growth was robust under continuous illumination but stopped rapidly upon initiating dark phases. CO2-limitation, often a limiting factor in photobioreactors, was only observed when the device was operated under reduced CO2 between 50 and 0 ppm. Here we provide comprehensive and precise data on cyanobacterial growth at single-cell resolution, accessible for further growth studies and modeling.
|
Lennart Witting; Johannes Seiffarth; Birgit Stute; Tim Schulze; Jan Matthis Hofer; Katharina Nöh; Marion Eisenhut; Andreas Weber; Eric von Lieres; Dietrich Kohlheyer
|
Biological and Medicinal Chemistry; Bioengineering and Biotechnology; Microbiology; Plant Biology
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-09-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d7ff4b51558a15effe9384/original/a-microfluidic-system-for-cultivation-of-cyanobacteria-with-precise-light-intensity-and-co2-control-enabling-growth-data-acquisition-at-single-cell-resolution.pdf
|
60c741e3bdbb893c8ea383d3
|
10.26434/chemrxiv.8145671.v1
|
Similarities and Differences for Atomic and Diatomic Molecule Adsorption on the B-5 type sites of the HCP(1016) surfaces of Co, Os, and Ru from DFT Calculation
|
DFT study of effects of step-edge type on HCP surfaces for catalysis using Co, Os, and Ru on the adsorption energies of small mono-atomic and di-atomic adsorbates. <br />
|
Rees Rankin
|
Catalysts; Nanostructured Materials - Materials; Computational Chemistry and Modeling; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-05-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741e3bdbb893c8ea383d3/original/similarities-and-differences-for-atomic-and-diatomic-molecule-adsorption-on-the-b-5-type-sites-of-the-hcp-1016-surfaces-of-co-os-and-ru-from-dft-calculation.pdf
|
64998d6d4821a835f36bdeef
|
10.26434/chemrxiv-2023-n79rz
|
A simple, efficient and universal energy decomposition analysis method based on dispersion-corrected density functional theory
|
Energy decomposition analysis (EDA) is an important method to explore the nature of interaction between fragments in a chemical system. It can decompose the interaction energy into different physical components to understand the factors that play key roles in the interaction. This work proposes an energy decomposition analysis strategy based on dispersion-corrected density functional theory (DFT), called sobEDA. This method is fairly easy to implement and very universal. It can be used to study weak interactions, chemical bond interactions, open-shell systems, and interactions between multiple fragments. The total time consumption of sobEDA is only about twice that of conventional DFT calculation for the entire system. This work also proposes a variant of the sobEDA method named sobEDAw, which is designed specifically for decomposing weak interaction energies. Through a proper combination of DFT correlation energy and dispersion correction term, sobEDAw gives a ratio between dispersion energy and electrostatic energy that is highly consistent with the symmetry-adapted perturbation theory (SAPT), which is quite popular and robust in studying weak interactions but expensive. We present a shell script sobEDA.sh to implement the methods proposed in this work based on the very popular Gaussian quantum chemistry program and Multiwfn wavefunction analysis code. Via the script, theoretical chemists can use the sobEDA and sobEDAw methods very conveniently in their study. Through a series of examples, the rationality of the new methods and their implementation are verified, and their great practical values in the study of various chemical systems are demonstrated.
|
Tian Lu; Qinxue Chen
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational
|
CC BY 4.0
|
CHEMRXIV
|
2023-06-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64998d6d4821a835f36bdeef/original/a-simple-efficient-and-universal-energy-decomposition-analysis-method-based-on-dispersion-corrected-density-functional-theory.pdf
|
60c7533ebdbb89bfbda3a416
|
10.26434/chemrxiv.13465682.v1
|
Synthesis of Ruthenium Bipyridyl Linked with Steroidal Oxidative Quencher for Photo Redox Studies
|
<p><b>Abstract:</b>
Synthesis of ruthenium bipyridyl linked with steroid having oxidative quencher,
viologens for study of photo redox properties were described.</p>
|
Sudershan Reddy Gondi
|
Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2020-12-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7533ebdbb89bfbda3a416/original/synthesis-of-ruthenium-bipyridyl-linked-with-steroidal-oxidative-quencher-for-photo-redox-studies.pdf
|
64f09d7579853bbd78cc3782
|
10.26434/chemrxiv-2023-4t8g2
|
Vibration spectra of benzene-like models with Hooke’s law interactions
|
The harmonic oscillations of a spring-ball model of benzene-like nanosystems with Hooke’s law interactions between nearest, second, and third neighbors are explored. We show that in the cylindrical coordinates the dynamics of this cyclic hexagonal system is described by the Lagrange equations similar to those of the one-dimensional two-component crystal model. We expose that the vibration frequencies of the hexagonal model lie on the branches of the dispersion law of the associated lattice model, and their positions are determined by the cyclic Born-Von Karman condition. The hexagonal model is generalized to one describing the benzene molecule and the fully deuterated and halogenated benzenes. The effect of hybridization of vibration modes and pushing apart of spectral branches in the crossover situation is revealed. All the discrete frequency spectrum and normal modes of oscillations and their explicit dependencies on all the constants of elastic interactions are exactly found.
|
Mikhail M. Bogdan; Oksana V. Charkina; Artem Y. Holovashchenko
|
Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Elastic Materials; Spectroscopy (Physical Chem.); Crystallography
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-09-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f09d7579853bbd78cc3782/original/vibration-spectra-of-benzene-like-models-with-hooke-s-law-interactions.pdf
|
62017c5949bd324dab48919f
|
10.26434/chemrxiv-2022-87dpv
|
Novel inorganic crystal structures predicted using autonomous simulation agents
|
We report a dataset of 96,962 new crystal structures discovered and computed using our previously published autonomous, density functional theory (DFT) based, active-learning workflow named CAMD (Computational Autonomy for Materials Discovery). Of these, 931 are within 1 meV/atom of the convex hull and 27,075 are within 200 meV/atom of the convex hull. The dataset contains DFT-optimized pymatgen crystal structure objects, DFT-computed formation energies and phase stability calculations from the convex hull. It contains a variety of spacegroups and symmetries derived from crystal prototypes derived from known experimental compounds, and was generated from active learning campaigns of various chemical systems. This dataset can be used to benchmark future active-learning or generative efforts for structure prediction, to seed new efforts of experimental crystal structure discovery, or to construct new models of structure-property relationships.
|
Xiangyun Lei; Weike Ye; Muratahan Aykol; Joseph Montoya
|
Theoretical and Computational Chemistry; Materials Science; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-02-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62017c5949bd324dab48919f/original/novel-inorganic-crystal-structures-predicted-using-autonomous-simulation-agents.pdf
|
60c74a90bdbb899f2da393ce
|
10.26434/chemrxiv.12218450.v1
|
Responsible Science, Engineering and Education for Water Resource Recovery and Circularity
|
<p>Water resource recovery is central to the circular economy
framework. It underlies the transition of environmental engineering from
pollution prevention to responsible innovation for sustainable systems
engineering. In order to speed this transition, resource recovery and
circularity need integration into new higher education curricula to train the
next generation of young professionals. However, training of new concepts
requires the development of new course materials and books, while integrating
substantial illustrations and problems on circularity and resource recovery in
new editions of existing textbooks in environmental science and engineering.
Moreover, university-utility-industry partnerships are important mechanisms to
bridge theoretical fundamentals to concepts for engineering practice, and to
promote knowledge exchange and technology adoption between practitioners and
academics. Interactive platforms should be designed to facilitate the
integration and development of resource recovery and circularity concepts from
science and practice into education. This paper gives actionable roadmaps to (<i>i</i>) apprehend how new science and
technological findings need to get integrated to sustain resource recovery and
circularity in practice. It highlights that (<i>ii</i>) skills sets can be engineered with relatively minor changes to
existing lecture material that will have maximal impact on the scope of the
thought material. It lays out (<i>iii</i>)
how partnership with engineering practitioners can make a lecture more vivid by
giving students reasoning for why the learned material is important. It drives
(<i>iv</i>) a platform for an integrated
science, education and practice to deliver them with concrete tools for
practical implementation for benefits at community level. </p>
|
David G. Weissbrodt; Mari K. H. Winkler; George F. Wells
|
Biodegradable Materials; Materials Processing; Biopolymers; Inorganic Polymers; Chemical Education - General; Environmental Science; Wastes; Food; Bioengineering and Biotechnology; Environmental biology; Industrial Manufacturing; Natural Resource Recovery; Water Purification; Power
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a90bdbb899f2da393ce/original/responsible-science-engineering-and-education-for-water-resource-recovery-and-circularity.pdf
|
64144484aad2a62ca1e8c4eb
|
10.26434/chemrxiv-2022-chw73-v3
|
Unraveling the Nature of Pressure-Induced Phases of MAPbBr3 by ab initio Molecular Dynamics
|
Pressure-induced phases of hybrid perovskite MAPbBr3 are investigated at room temperature in a pressure range 0-2.8 GPa by ab initio molecular dynamics. We find two structural transitions at 0.7 and 1.1 GPa involving confinement of MA orientational fluctuations to a crystal plane - one (cubic to cubic) involving dynamic disordering over the plane and another (cubic to tetragonal) corresponding to a static disordering of MA dipoles along two crystal axes on the same plane. This is similar to isotropic to isotropic and isotropic to oblate transition from the perspective of nematic transitions of liquid crystal. In the latter phase,
both local anti-polar and polar domains, consisting of at least two units, are formed. The two transitions are primarily driven by octahedral tilting modes of the host lattice involving a displacive character in the first and an ordering of layer-wise tilts in the second transition. Coupling between the MA (guest) orientations/translations and octahedral tilting/lattice scissoring in the inorganic host are also altered along the transitions. H-bonding interactions, which primarily mediate host/guest coupling, facilitate the static disordering of MA dipoles along two crystal axes. Unlike
temperature-driven transitions in the system, high pressures suppress CH3 torsional motion emphasizing the role of C-H· · · Br bonds in driving the transitions.
|
Sayan Maity; Suraj Verma; Lavanya M. Ramaniah; Varadharajan Srinivasan
|
Theoretical and Computational Chemistry; Materials Science; Energy; Hybrid Organic-Inorganic Materials; Liquid Crystals; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64144484aad2a62ca1e8c4eb/original/unraveling-the-nature-of-pressure-induced-phases-of-ma-pb-br3-by-ab-initio-molecular-dynamics.pdf
|
60c75617f96a0017122889d8
|
10.26434/chemrxiv.13720888.v2
|
Ab Initio Molecular Dynamics Investigations of the Speciation and Reactivity of Deep Eutectic Electrolytes in Aluminum Batteries
|
Deep eutectic solvents (DES) have emerged as an alternative for conventional ionic<br />liquids in aluminum batteries. Elucidating DES composition is fundamental to<br />understand aluminum electrodeposition in the battery anode. Despite numerous<br />experiemental efforts, the speciation of these DES remains elusive. This work shows<br />how \textit{Ab initio} molecular dynamics (AIMD) simulations can shed light on the<br />molecular composition of DES. For the particular example of AlCl$_{3}$:urea, one of<br />the most popular DES, we carried out a systematic AIMD study, showing how an<br />excess of AlCl$_{3}$ in the AlCl$_{3}$:urea mixture promotes the stability of ionic<br />species vs neutral ones and also favors the reactivity in the system. These two facts<br />explain the experimentally observed enhanced electrochemical activity in salt-rich<br />DES. We also observe the transfer of simple $[$AlCl$_{x}$(urea)$_{y}]$ clusters<br />between different species in the liquid, giving rise to free $[$AlCl$_{4}]^{-}$ units. The<br />small size of these $[$AlCl$_{4}]^{-}$ units favors the transport of ionic species towards<br />the anode, facilitating the electrodeposition of aluminum.
|
David Carrasco-Busturia; Steen Lysgaard; Piotr Jankowski; Tejs Vegge; Arghya Bhowmik; Juan Maria García Lastra
|
Computational Chemistry and Modeling; Energy Storage; Electrochemistry - Mechanisms, Theory & Study
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75617f96a0017122889d8/original/ab-initio-molecular-dynamics-investigations-of-the-speciation-and-reactivity-of-deep-eutectic-electrolytes-in-aluminum-batteries.pdf
|
665e051f418a5379b001be3f
|
10.26434/chemrxiv-2024-dsfj3
|
Interplay between Anion-Receptor and Anion-Solvent Interactions in Halide Receptor Complexes Characterized with Ultrafast Infrared Spectroscopies
|
The competition between host-guest binding and solvent interactions is a crucial factor in determining the binding affinities and selectivity of molecular receptor species. The interplay between these competing interactions, however, have been difficult to disentangle. In particular, the development of molecular-level descriptions of solute-solvent interactions remains a grand experimental challenge. Herein, we investigate the prototypical halide receptor meso Octamethylcalix[4]pyrrole (OMCP) complexed with either chloride or bromide anions in both dichloromethane (DCM) and chloroform (trichloromethane, TCM) solvent using ultrafast infrared transient absorption and 2D IR spectroscopies. OMCP∙Br‒ complexes in both solvents display slower vibrational relaxation dynamics of the OMCP pyrrole NH stretches, consistent with weaker H bonding interactions with OMCP compared to chloride and less efficient intermolecular relaxation to the solvent. Further, OMCP∙Br‒ complexes show nearly static spectral diffusion dynamics compared to OMCP∙Cl‒, indicating larger structural fluctuations occur within chloride complexes. Importantly, distinct differences in the vibrational spectra and dynamics are observed between DCM and TCM solutions. The data are consistent with stronger and more perturbative solvent effects in TCM compared to DCM, despite DCM’s larger dielectric constant and smaller reported OMCB∙X‒ binding affinities. These differences are attributed to the presence of weak H bond interactions between halides and TCM, in addition to competing interactions from the bulky tetrabutylammonium countercation. The data provide important experimental benchmarks for quantifying the role of solvent and countercation interactions in anion host-guest complexes.
|
Jessika Dean; Caroline Cramer; Joseph Fournier
|
Physical Chemistry; Solution Chemistry; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665e051f418a5379b001be3f/original/interplay-between-anion-receptor-and-anion-solvent-interactions-in-halide-receptor-complexes-characterized-with-ultrafast-infrared-spectroscopies.pdf
|
66cecc6aa4e53c4876dcaa7a
|
10.26434/chemrxiv-2024-5bh40-v2
|
BattProDeep: A Deep Learning-Based Tool for Probabilistic Battery Aging Prediction
|
Profitability, reliability, and efficiency of battery systems across a broad spectrum of applications, including both stationary energy storage and automobile sectors, are critically dependent on accurate battery lifespan predic-tions. Traditional deterministic models for estimating battery longevity are inadequate, as they do not fully cap-ture the complex and stochastic nature of battery degradation. In this contribution BattProDeep is introduced as a groundbreaking tool that employs a deep learning-based framework to offer probabilistic predictions of battery aging, thereby addressing the uncertainties according to the experimental dataset. BattProDeep sets itself apart with its innovative features. It adopts an open-source approach, enhancing transparency and fostering collabora-tion across the global research community. This not only enriches the tool with a diverse range of insights but al-so accelerates advancements in the field. Utilizing cutting-edge TensorFlow and TensorFlow probability libraries, BattProDeep offers a data-driven method for battery aging prediction, improving accuracy and applicability across different battery types and conditions. Furthermore, its probabilistic predictions include confidence inter-vals, providing crucial information about prediction uncertainty, which is invaluable for risk management and decision-making in critical sectors. The validation results show that the mean prediction error for our approach stays within ±0.2 % for high-cyclic applications, with all true measured capacity loss values falling within the 95 % confidence interval, affirming its reliability for risk management. These qualities, coupled with the bench-marking of BattProDeep according to the literature, make BattProDeep a key instrument for advancing battery health management, leading to more dependable and sustainable battery-powered solutions.
|
Houman Heidarabadi; Melina Graner; Holger Hesse
|
Energy; Energy Storage
|
CC BY 4.0
|
CHEMRXIV
|
2024-08-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cecc6aa4e53c4876dcaa7a/original/batt-pro-deep-a-deep-learning-based-tool-for-probabilistic-battery-aging-prediction.pdf
|
60c7563d0f50db5c8f398050
|
10.26434/chemrxiv.14219228.v1
|
Probing Electrosynthetic Reactions with Furfural on Copper Surfaces
|
This work entails the integrated use of electrochemistry and
operando Raman spectroscopy to probe the reduction of a biomass
platform, furfural, to value-added chemicals on Cu electrodes. The
results reveal key strutural differences of the Cu that dictate
selectivity for furfural alcohol or 2-methylfuran.
|
Junnan Li; Nikolay Kornienko
|
Electrocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7563d0f50db5c8f398050/original/probing-electrosynthetic-reactions-with-furfural-on-copper-surfaces.pdf
|
632b94abe665bde6960d987b
|
10.26434/chemrxiv-2022-64bzw
|
Aqueous PFCA Destruction by Hydroxyl Radical at Low pH: A Putative H-atom Abstraction Mechanism
|
Hydroxyl radical is a potent oxidant invoked in numerous advanced oxidation processes as a species responsible for destroying recalcitrant organic contaminants. However, there has been little direct evidence for the reaction between hydroxyl radical and perfluoroalkyl carboxylic acids in the aqueous phase. Nevertheless, we discovered that at low pH, perfluoroalkyl carboxylic acids are degraded by hydroxyl radical. When perfluorobutanoic acid was treated with H2O2 under steady-state 254 nm irradiation in 1 M HClO4, it was transformed to shorter-chain perfluoroalkyl carboxylic acid homologues and F–/HF. Empirical and computational mechanistic studies suggested an H-atom abstraction mechanism. Namely, more perfluorobutanoic acid was removed as the pH was decreased, which corresponds to a larger fraction of protonated perfluorobutanoic acid vs. conjugate base. Meanwhile, density functional theory calculations indicated that single electron transfer oxidation of protonated perfluoroalkyl carboxylic acids has a much larger free energy of activation relative to single electron transfer oxidation of the conjugate base anion, suggesting that single electron transfer is unfavorable at low pH. This is the first clear description of aqueous perfluoroalkyl carboxylic acid destruction by hydroxyl radical under simple reaction conditions.
|
Asa Carre-Burritt; Camille Amador; Shubham Vyas
|
Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632b94abe665bde6960d987b/original/aqueous-pfca-destruction-by-hydroxyl-radical-at-low-p-h-a-putative-h-atom-abstraction-mechanism.pdf
|
60c754d0f96a00fc1d28871a
|
10.26434/chemrxiv.13739692.v1
|
Determining Performance Limits for Non-Aqueous Redox Flow Batteries
|
<p>In this work, we explore the limits of performance and energy density of a non-aqueous redox flow battery under ideal conditions. We compared the performance of an organic redox couple in a symmetric cell to that of a vanadium redox flow cell. Based on cycling performance, we expect that – when losses from separators and poor ionic conductivity are minimized – a non-aqueous flow cell operating at 3.5 V should have a 35% higher energy density than V<sup>4/5+</sup> couple in aqueous system at 100 mA∙cm<sup>-2</sup> current density for a system that could operate at 3.5 V.</p>
|
Zhijiang Tang; Aman Preet Kaur; Alan Pezeshki; Subrahmanyam Modekrutti; Frank Delnick; Thomas Zawodzinski; Gabriel Veith; Susan Odom
|
Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-02-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754d0f96a00fc1d28871a/original/determining-performance-limits-for-non-aqueous-redox-flow-batteries.pdf
|
678a49d26dde43c908ef3ab0
|
10.26434/chemrxiv-2025-jqql1
|
Simple surface treatment of conjugated polymers for enhanced cell adhesion using UV-Ozone
|
Aligning the material properties of organic semiconducting polymers to effectively interface with biological matter is critical for their use in bioelectronic devices. Synthetic modification and advanced processing techniques have typically been employed to promote cell adhesion and growth. In this study we apply UV-Ozone (UVO) treatment as a simple and accessible alternative for modifying pDPP3T films. Exposure to UVO increases polarity of the semiconductor surface, as confirmed by contact angle and XPS analysis. Surface treatment at and above the optimized time (t ≥ 30 s) consequently led to enhanced Schwann cell growth, with comparable behaviour to standard tissue culture plastic (TCP). Simultaneously, prolonged exposure begins to cause significant changes to the polymer's optical properties, with gradual photobleaching leading to the reduction in semiconducting behavior above 30 s. Leveraging the optimal biointerfacing properties of the UVO-treated pDPP3T, the validity of the technique in supporting cell viability and proliferation upon a semiconducting polymer was tested using electrical impedance spectroscopy. This work demonstrates the potential to more easily integrate conjugated polymers with biological environments, widening the opportunity to explore the interplay between ion diffusion and semiconductor electroactivity in the presence of biological cells.
|
Megan M. Westwood; Peter A. Gilhooly-Finn; Ryan P. Trueman; Aisha Mumtaz; Holly Gregory; Joshua P. A. Daoud; Avishek Dey; Robert Palgrave; Christopher A. R. Chapman; James B. Phillips; Bob C. Schroeder
|
Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2025-01-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678a49d26dde43c908ef3ab0/original/simple-surface-treatment-of-conjugated-polymers-for-enhanced-cell-adhesion-using-uv-ozone.pdf
|
66a0aea0c9c6a5c07ab8dac2
|
10.26434/chemrxiv-2024-m2896
|
Synthesis of Silver Nanoparticles using Narcissus Leaf Extract: A Green and Rapid Approach
|
This article presents a simple, rapid, and eco-friendly method for synthesizing silver nanoparticles using Narcissus (daffodils) aqueous leaf extract. The plant extract acts as both a capping and a reducing agent, converting AgNO3 solution into stable silver nanoparticles. The optimal conditions for the synthesis are 5 ml of extract, 45 ml of AgNO3, and 60°C-70°C of temperature. The particle size can be controlled by varying these parameters. The synthesis is confirmed by the color change from colorless to brown and the UV-visible spectrophotometry analysis, which shows an absorbance peak at 430 nm after 10 days. The article also compares the results of this method with other conventional and green methods of silver nanoparticle synthesis and highlights the benefits and challenges of each method. The article concludes with some suggestions for future research and improvement of this method.
|
Umme Salma; Saria Nasir
|
Analytical Chemistry; Nanoscience; Analytical Chemistry - General; Nanostructured Materials - Nanoscience; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a0aea0c9c6a5c07ab8dac2/original/synthesis-of-silver-nanoparticles-using-narcissus-leaf-extract-a-green-and-rapid-approach.pdf
|
679a60da81d2151a0271d924
|
10.26434/chemrxiv-2025-0qk09
|
CRISPR in therapeutics and diagnostics: Perspectives from landscape analysis
|
In this report, we examine the extensive research landscape of CRISPR with an emphasis on CRISPR therapeutics and showcase our results from an in-depth analysis of the most up-to-date scientific information consisting of more than 53,000 publications encompassing academic journal articles and patents, spanning nearly three decades, extracted from the CAS Content Collection. Our analysis indicates that cancer and infectious diseases are the most explored in the context of CRISPR. Identified gene targets associated with CRISPR-related publications are led by TP53, c-myc, and hemoglobin beta subunit (HBB). Among the many delivery methods, adeno-associated vectors (AAVs) appear to be highly explored. With >140 CRISPR-based therapeutics in the clinical development pipeline and billions of dollars in investment, the field of CRISPR continues to evolve rapidly. We also briefly discuss the ethical implications of CRISPR technology. While some fundamental challenges persist, the future of CRISPR is undoubtedly bright.
|
Kavita Iyer; Rumiana Tenchov; Leilani Lotti Diaz; Preeti Jain; Trupti Thite; Yi Deng; Qiongqiong Zhou
|
Biological and Medicinal Chemistry; Cell and Molecular Biology
|
CC BY 4.0
|
CHEMRXIV
|
2025-01-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679a60da81d2151a0271d924/original/crispr-in-therapeutics-and-diagnostics-perspectives-from-landscape-analysis.pdf
|
66ee974612ff75c3a1ffe5f6
|
10.26434/chemrxiv-2024-jpmfq
|
Imidazolium-based ionic liquid electrolytes for fluoride ion batteries
|
The fluoride ion battery (FIB) is a post-lithium anionic battery that utilizes the fluoride-ion shuttle, achieving high theoretical energy densities of up to 1393 Wh/L while eliminating the reliance on critical minerals. However, developing liquid elec- trolytes for FIBs has proven arduous due to a combination of low solubility of flu- oride salts and the chemical reactivity of the fluoride ion. By introducing a novel and chemically stable fluoride electrolyte based on 1,3-dimethylimidazolium [MMIm] bis(trifluoromethanesulfonyl)imide[TFSI]andtetramethylammoniumfluoride(TMAF), we achieve electrochemical stability window (ESW) of 4.65 V, ionic conductivity of 9.53 1 mS cm−1, and a TMAF solubility of 0.67 m. The origin of this high salt solubility and the solvation structure were investigated using both NMR spectroscopy and neutron total scattering, showing a fluoride solvation driven by strong electrostatic interactions and weak hydrogen bonding with no covalent H—F character. This indicates the chemical stability of 1,3-dimethylimidazolium towards the fluoride ion and its potential as an electrolyte for high-voltage FIBs.
|
Omar Alshangiti; Giulia Galatolo; Camilla Di Mino; Thomas Headen; Jacob Christianson; Simone Merotto; Gregory Rees; Yoan Delavoux; Małgorzata Swadźba-Kwaśny; Mauro Pasta
|
Physical Chemistry; Organic Chemistry; Energy; Energy Storage; Solution Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-09-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ee974612ff75c3a1ffe5f6/original/imidazolium-based-ionic-liquid-electrolytes-for-fluoride-ion-batteries.pdf
|
652d588abda59ceb9ab3fbd4
|
10.26434/chemrxiv-2023-bb9b0
|
Flash upcycling of waste glass fiber-reinforced plastics to phase-controllable silicon carbide
|
The increasing use of fiber-reinforced plastic has triggered an urgent demand for its recycling once it reaches its end-of-life. Currently, landfilling and incineration are major disposal methods of fiber-reinforced plastic, which lead to undesirable waste of resources and environmental contamination. To address this issue, we disclose a solvent-free and energy-efficient flash upcycling method to convert the mixture of glass fiber-reinforced plastic and carbon fiber-reinforced plastic into SiC powders within seconds and in yields of >90%. By modulating input pulse voltages and flash times, SiC with two different phases, 3C-SiC and 6H-SiC, can be selectively synthesized, each with phase purity of 90-99%. Theoretical simulations reveal that the increasing content of Si vacancy during flash process dominates the phase transformation from 3C-SiC to 6H-SiC. The SiC powders are further used as the anode material for lithium-ion batteries, which yields a phase-dependent performance. The 3C-SiC anode exhibits superior reversible capacity (741 mAh·g-1 at 0.2 C) and rate performance over the 6H-SiC anode (626 mAh·g-1 at 0.2 C), while both show excellent cycling stability (~95% capacity retention after 200 cycles). Life cycle assessment reveals the flash upcycling process greatly reduces the energy demand, greenhouse gas emission and water consumption over other recycling processes.
|
Yi Cheng; Jinhang Chen; Bing Deng; Weiyin Chen; Karla Silva; Lucas Eddy; Gang Wu; Ying Chen; Bowen Li; Carter Kittrell; Shichen Xu; Tengda Si; Angel Martí; Boris Yakobson; Yufeng Zhao; James Tour
|
Inorganic Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Wastes; Polymers; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652d588abda59ceb9ab3fbd4/original/flash-upcycling-of-waste-glass-fiber-reinforced-plastics-to-phase-controllable-silicon-carbide.pdf
|
60c7407e842e655f8edb1cde
|
10.26434/chemrxiv.7755479.v1
|
The Parmodulin NRD-21 is an Allosteric Inhibitor of PAR1 Gq Signaling with Improved Anti-Inflammatory Activity and Stability
|
Novel analogs of the allosteric, biased PAR1 ligand ML161 (parmodulin 2, PM2) were prepared in order to identify potential anti-thrombotic and anti-inflammatory compounds of the parmodulin class with improved properties. Investigations of structure-activity relationships of the western portion of the 1,3-diaminobenzene scaffold were performed using an intracellular calcium mobilization assay with endothelial cells, and several heterocycles were identified that inhibited PAR1 at sub-micromolar concentrations. The oxazole NRD-21 was profiled in additional detail, and it was confirmed to act as a selective negative allosteric modulator of PAR1 that inhibits human platelet aggregation. It showed superior anti-inflammatory activity to ML161 in a qPCR assay measuring the expression of tissue factor in response to the cytokine TNF-alpha in endothelial cells. Additionally, NRD-21 is much more plasma stable than ML161, and is a promising lead compound for the parmodulin class for anti-thrombotic and anti-inflammatory indications.
|
Disha Gandhi; Ricardo Rosas, Jr.; Eric Greve; Kaitlin Kentala; N'Guessan Diby; Vladyslava Snyder; Allison Stephans; Teresa Yeung; Saravanan Subramaniam; Khia Kurtenbach; Elliot DiMilo; Leggy Arnold; Hartmut Weiler; Chris Dockendorff
|
Bioorganic Chemistry; Organic Compounds and Functional Groups; Chemical Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-02-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7407e842e655f8edb1cde/original/the-parmodulin-nrd-21-is-an-allosteric-inhibitor-of-par1-gq-signaling-with-improved-anti-inflammatory-activity-and-stability.pdf
|
60c75361702a9b546618c354
|
10.26434/chemrxiv.13483335.v1
|
Machine Learning-Based Model Selection and Parameter Estimation from Kinetic Data of Complex First-Order Reaction Systems
|
<a>Dealing with a system of first-order reactions is a recurrent problem in chemometrics, especially
in the analysis of data obtained by spectroscopic methods. Here we argue that global
multiexponential fitting, the still common way to solve this kind of problems has serious
weaknesses, in contrast to the available contemporary methods of sparse modeling. Combining the
advantages of group-lasso and elastic net – the statistical methods proven to be very powerful in
other areas – we obtained an optimization problem tunable to result in from very sparse to very
dense distribution over a large pre-defined grid of time constants, fitting both simulated and
experimental multiwavelength spectroscopic data with very high performance. Moreover, it was
found that the optimal values of the tuning hyperparameters can be selected by a machine-learning
algorithm based on a Bayesian optimization procedure, utilizing a widely used and a novel version
of cross-validation. The applied algorithm recovered very exactly the true sparse kinetic
parameters of an extremely complex simulated model of the bacteriorhodopsin photocycle, as well
as the wide peak of hypothetical distributed kinetics in the presence of different levels of noise. It
also performed well in the analysis of the ultrafast experimental fluorescence kinetics data detected
on the coenzyme FAD in a very wide logarithmic time window.</a>
|
László Zimányi; Áron Sipos; Ferenc Sarlós; Rita Nagypál; Géza Groma
|
Computational Chemistry and Modeling; Machine Learning; Biophysical Chemistry; Chemical Kinetics; Physical and Chemical Processes
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-12-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75361702a9b546618c354/original/machine-learning-based-model-selection-and-parameter-estimation-from-kinetic-data-of-complex-first-order-reaction-systems.pdf
|
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.