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60c741240f50db3147395a6e
|
10.26434/chemrxiv.7952063.v1
|
Electronic Structures of Bent, Formally Two-Coordinate Lanthanide(III) Cations
|
<p>Synthesis of bent, formally two-coordinate lanthanide(III) cations. Characterization by multinuclear NMR, EPR, UV/Vis/NIR and ATR-IR spectroscopy, single crystal XRD, magnetic measurements, elemental analysis and ab initio calculations. <b></b></p>
|
David Mills; Hannah Nicholas; Michele Vonci; Conrad Goodwin; Richard Winpenny; Eric J. L. McInnes; Nicholas Chilton; Siobhan Murphy; Song Loo Wei; Daniel Cassim
|
Coordination Chemistry (Inorg.); Lanthanides and Actinides; Ligands (Inorg.); Magnetism; Organometallic Compounds; Spectroscopy (Inorg.); Theory - Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-04-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741240f50db3147395a6e/original/electronic-structures-of-bent-formally-two-coordinate-lanthanide-iii-cations.pdf
|
60c73d0dee301c1861c784d0
|
10.26434/chemrxiv.5336125.v1
|
Development and application of a highly α2,6-selective pseudosialidase
|
<p>In this manuscript we address an important gap in our
current carbohydrate active enzyme toolbox, by developing a highly a2,6-selective (over a2,3-selective) de facto sialidase that is necessary
both for glycan analysis and glycoconjugate remodeling. Both glycosidic linkages
are commonly found in animal biology and each has been shown to have distinct
biological function.</p>
<p>Our approach is novel in that it harnesses the high
selectivity of known glycosyltransferases ‘in reverse’ for effective hydrolysis,
converting transferases to hydrolases by reaction engineering. </p>
<p>More specifically, we demonstrate that the a2,6-specific
pseudosialidase activity of <i>Photobacterium
</i>sp. JT-ISH-224 a2,6-sialyltransferase
can be used effectively for highly a2,6 selective hydrolysis on a broad range of analytes:
small synthetic probes, isolated complex glycans and complex mixtures of
glycoproteins. </p>
|
Peter Both; Michel Riese; Christopher J. Gray; Kun Huang; Edward G. Pallister; Iaroslav Kosov; Louis P. Conway; Josef Voglmeir; Sabine L. Flitsch
|
Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2017-09-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0dee301c1861c784d0/original/development-and-application-of-a-highly-2-6-selective-pseudosialidase.pdf
|
66b8a0fcc9c6a5c07ae4a901
|
10.26434/chemrxiv-2024-6b3cq
|
Advancements in Thermochemical Predictions: A Multi-Output Thermodynamics-Informed Neural Network Approach
|
The Gibbs free energy of an inorganic material represents its maximum reversible work potential under constant temperature and pressure. Its calculation is crucial for understanding material stability, phase transitions, and chemical reactions, thus guiding optimization for diverse applications like catalysis and energy storage. In this study, we have developed a Physics-Informed Neural Network model that leverages the Gibbs free energy equation. The overall loss function is adjusted to allow the model to simultaneously predict all three thermodynamic quantities, including Gibbs free energy, total energy, and entropy, thus transforming it into a multi-output model. In recent literature, there is a growing emphasis on evaluating machine learning models under challenging conditions, such as small datasets and out-of-distribution predictions. Reflecting this trend, we have rigorously benchmarked our model across these scenarios, demonstrating its robustness and adaptability. It turns out that our model demonstrates a 43% improvement for normal scenario and even more in out-of-distribution regime compared to the next-best model.
|
Raheel Hammad; Sownyak Mondal
|
Physical Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-08-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b8a0fcc9c6a5c07ae4a901/original/advancements-in-thermochemical-predictions-a-multi-output-thermodynamics-informed-neural-network-approach.pdf
|
62b21919486c986b34adbc45
|
10.26434/chemrxiv-2022-134z8
|
Preparation and application of cellulose-based hydrogels derived from bamboo
|
Hydrogels have outstanding research and application prospects in various fields. Among them, the design and preparation of cellulose-based functional hydrogels derived from bamboo have attracted increasing research interest. Cellulose-based hydrogels not only have the skeleton function of hydrogels, but also retain excellent specificity, smart structural design, precise molecular recognition ability, and superior biocompatibility. Cellulose-based hydrogels show important application prospects in various fields such as environmental protection, biomedicine, energy, food packaging and plant agriculture. Recently, researchers have extracted cellulose from bamboo and generated a variety of cellulose-based functional hydrogels with excellent properties by various cross-linking methods. In addition, a variety of multifunctional hybrid cellulose-based hydrogels have been constructed by introducing functional components or combining them with other functional materials, expanding the breadth and depth of their applications. Herein, we elaborate advances in the field of cellulose-based hydrogels and highlight their applications in various fields. Meanwhile, the existing problems and prospects are summarized. The review provides a reference for further development of cellulose-based hydrogels.
|
Xiaobing Cao; Fei Li; Yanjun Li; Siyu Chen; Xin Li; Yi Lu
|
Materials Science; Polymer Science; Chemical Engineering and Industrial Chemistry; Cellulosic materials; Hydrogels; Polymer chains
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-06-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b21919486c986b34adbc45/original/preparation-and-application-of-cellulose-based-hydrogels-derived-from-bamboo.pdf
|
6286b0ed43d1f01722324bdc
|
10.26434/chemrxiv-2022-fs1kk
|
Modelling the effect of defects and disorder in amorphous metal−organic frameworks
|
Amorphous metal−organic frameworks (aMOFs) are a class of disordered framework materials with a defined local order given by the connectivity between inorganic nodes and organic linkers, but absent longer-range order. The rational development of function for aMOFs is hindered by our limited understanding of the underlying structure-property relationships in these systems, a consequence of the absence of long-range order, which makes experimental characterization particularly challenging. Here, we use a versatile modelling approach to generate in-silico structural models for an aMOF based on Fe trimers and 1,3,5-benzenetricarboxylate (BTC) linkers, Fe-BTC. We build a phase space for this material that includes nine amorphous phases with different degrees of defects and local order. These models are analyzed through a combination of structural analysis, pore analysis and pair distribution functions. Therefore, we are able to systematically explore the effects of the variation of each of these features, both in isolation and combined, for a disordered MOF system, something that would not be possible through experiment alone. We find that the degree of local order has a greater impact on structure and properties than the degree of defects. The approach presented here is versatile and allows for the study of different structural features and MOF chemistries, enabling the development of design rules for the rational design of aMOFs.
|
Irene Bechis; Adam Sapnik; Andrew Tarzia; Emma Wolpert; Matthew Addicoat; David Keen; Thomas Bennett; Kim Jelfs
|
Theoretical and Computational Chemistry; Materials Science; Hybrid Organic-Inorganic Materials; Computational Chemistry and Modeling; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-05-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6286b0ed43d1f01722324bdc/original/modelling-the-effect-of-defects-and-disorder-in-amorphous-metal-organic-frameworks.pdf
|
638b08a9b103af697c08f4ed
|
10.26434/chemrxiv-2022-52z0l
|
Catalytic disproportionation via carbonate redox tags – a unified strategy for mild hydrogenolysis and oxidations of C–O bonds
|
Oxygenated molecules are omnipresent in natural as well as artificial settings making the chemical modification of C–O bonds a central tool for their processing. The catalytic hydrogenolysis and oxidation of C–O bonds are particularly important reactions in this context. However, the required (super)stoichiometric terminal redox equivalents which traditionally include highly reactive and hazardous reagents pose multiple practical challenges including process safety hazards, functional group incompatibilities and special waste management requirements. Here, we report a mild Ni-catalyzed disproportionation strategy based on carbonate redox tags for redox transformations of various oxygenated hydrocarbons in the absence of any external redox equivalents or other additives. The purely catalytic process enables the hydrogenolysis of strong C(sp2)–O bonds including that of enol carbonates as well as the catalytic oxidation of C–O bonds at room temperature, underscoring the unusually efficiency of this strategically distinct reactivity. In addition, we investigated the underlying mechanism and provided key insights about such underexplored processes. Further, we show that the studied carbonates have potential as redox active protecting groups. Finally, due to their complete homogeneity, the reactions can be readily downscaled without any adjustments and are compatible with a fluorescence-based reactivity assay. More broadly, the work herein demonstrates the untapped potential of redox tags in organic synthesis and provides the necessary mechanistic understanding for future advancements in this emerging research area.
|
Georgios Toupalas; Loélie Ribadeau-Dumas; Bill Morandi
|
Catalysis; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-12-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638b08a9b103af697c08f4ed/original/catalytic-disproportionation-via-carbonate-redox-tags-a-unified-strategy-for-mild-hydrogenolysis-and-oxidations-of-c-o-bonds.pdf
|
60c744379abda2c05ff8c331
|
10.26434/chemrxiv.9729494.v1
|
Self-Recognizing π-π Stacking Interactions Designed for the Generation of Ultrastable Mesoporous Hydrogen-Bonded Organic Frameworks
|
Creating crystalline porous materials with large pores is typically challenging due to undesired interpen-etration, staggered stacking, or weakened framework stability. Here, we report a pore size expansion strategy by self-recognizing π-π stacking interactions in a series of two-dimensional (2D) hydrogen–bonded organic frameworks (HOFs), HOF-10x (x=0,1,2), self-assembled from pyrene-based tectons with systematic elongation of π-conjugated molecular arms. This strategy successfully avoids interpene-tration or staggered stacking and expands the pore size of HOF materials to access mesoporous HOF-102, which features a surface area of ~ 2,500 m2/g and the largest pore volume (1.3 cm3/g) to date among all reported HOFs. More importantly, HOF-102 shows significantly enhanced thermal and chemical stability as evidenced by powder x-ray diffraction and N2 isotherms after treatments in chal-lenging conditions. Such stability enables the adsorption of dyes and cytochrome c from aqueous media by HOF-102 and affords a processible HOF-102/fiber composite for the efficient photochemical detox-ification of a mustard gas simulant.
|
KAIKAI MA; Peng Li; John Xin; Yongwei Chen; Zhijie Chen; Subhadip Goswami; Xiaofeng Liu; Satoshi Kato; Haoyuan Chen; Xuan Zhang; Megan C. Wasson; Rodrigo Maldonado; Randall Q. Snurr; Omar Farha
|
Supramolecular Chemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-09-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744379abda2c05ff8c331/original/self-recognizing-stacking-interactions-designed-for-the-generation-of-ultrastable-mesoporous-hydrogen-bonded-organic-frameworks.pdf
|
61e641886afbefef29682bf3
|
10.26434/chemrxiv-2022-mwjvk
|
Poisoning density functional theory with benchmark
sets of difficult systems
|
Large benchmark sets like GMTKN55 [Goerigk et al., Phys.
Chem. Chem. Phys., 2017, 19, 32184] let us analyse the
performance of density functional theory over a diverse
range of systems and bonding types. However, assessing over a large and diverse set can miss cases where
approaches fail badly, and can give a misleading sense
of security. To this end we introduce a series of ‘poison’
benchmark sets, P30-5, P30-10 and P30-20, comprising
systems with up to 5, 10 and 20 atoms, respectively. These
sets represent the most difficult-to-model systems in
GMTKN55. We expect them to be useful in developing new
approximations, identifying weak points in existing ones,
and to aid in selecting appropriate DFAs for computational
studies involving difficult physics, e.g. catalysis.
|
Tim Gould; Stephen Dale
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-01-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e641886afbefef29682bf3/original/poisoning-density-functional-theory-with-benchmark-sets-of-difficult-systems.pdf
|
6231dd8a13d478a66690ae89
|
10.26434/chemrxiv-2022-k808c
|
Visible-Light-Promoted Nickel-Catalyzed Cross-Coupling of Al-kyltitanium Alkoxides with Aryl and Alkenyl Halides
|
A light-promoted photocatalyst-free nickel-catalyzed cross-coupling of alkyltitanium alkoxides with aryl and alkynyl halides is reported. The organotitanium reagents were generated in situ from titanium(IV) isopropoxide and Grignard reagents.
|
Andrei Leushukou; Anastasiya Krech; Alaksiej Hurski
|
Organic Chemistry; Photochemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6231dd8a13d478a66690ae89/original/visible-light-promoted-nickel-catalyzed-cross-coupling-of-al-kyltitanium-alkoxides-with-aryl-and-alkenyl-halides.pdf
|
61147eb618911db4cadeb6a8
|
10.26434/chemrxiv-2021-7z76q
|
Mechanism of Ammonia Oxidation to Dinitrogen, Nitrite, and
Nitrate on 𝛽-Ni(OH)2 from First-Principles Simulations
|
The electrocatalyzed ammonia oxidation reaction (AOR) is a potential pathway toward waste ammonia remediation, energy generation, and the synthesis of value- added products. To date, mechanistic studies have focused on elucidating the progress of AOR on Pt-based catalysts with an established pathway for N2 only. In this work, density functional theory was applied to determine the lowest energy intermediates towards nitrogen gas, nitrite, and nitrate formation on 𝛽-Ni(OH)2, a promising electrocatalyst material for AOR. It was found that dinitrogen formation progresses via NH-NH coupling while nitrite and nitrate formation occurs via deprotonation to adsorbed N and subsequent hydroxylation to form oxygenated intermediates. This work is the first to report a mechanism for nitrite and nitrate formation and will also serve as a benchmark for future studies on Ni-based materials.
|
Rachelle M. Choueiri; Stephen W. Tatarchuk; Anna Klinkova; Leanne D. Chen
|
Theoretical and Computational Chemistry; Catalysis; Energy; Computational Chemistry and Modeling; Electrocatalysis; Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-08-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61147eb618911db4cadeb6a8/original/mechanism-of-ammonia-oxidation-to-dinitrogen-nitrite-and-nitrate-on-ni-oh-2-from-first-principles-simulations.pdf
|
669fbb395101a2ffa8b9b996
|
10.26434/chemrxiv-2024-t4qhs
|
Metal doping of halide perovskite nanocrystals under ambient conditions
|
Halide perovskite nanocrystals are promising materials for optoelectronic applications. Metal doping provides an avenue to boost their performance further, e.g., by enhancing light emission, or to provide additional functionalities, such as nano-scale magnetism and polarisation control. However, the synthesis of widely size-tuneable nanocrystals with controlled doping levels has been inaccessible using traditional hot injection synthesis, preventing systematic studies on dopant effects device application.
Here, we report a versatile synthesis method for metal-doped perovskite nanocrystals with precise control over size and doping concentration under ambient conditions. Our room temperature approach results in fully size-tuneable isovalent doping of CsPbX3 nanocrystals (X = Br, Cl) with various transition metals M2+ tested (M = Mn, Ni, Zn). This gives for the first time access to small, yet precisely doped quantum dots beyond the weak confinement regime reported so far. It also enables a comparative study of the photophysics across multiple size and dopant regimes, where we show dopant-induced localisation to dominate over quantum confinement effects. This generalisable, facile synthesis method thus provides a toolbox for engineering perovskite nanocrystals toward light-emitting technologies under industrially relevant conditions.
|
Zachary A. VanOrman; Mateo Cárdenes Wuttig; Antti-Pekka M. Reponen; Taek-Seung Kim; Claire E. Casaday; Dongtao Cui; Christian Reece; Sascha Feldmann
|
Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Solution Chemistry; Spectroscopy (Physical Chem.); Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-07-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669fbb395101a2ffa8b9b996/original/metal-doping-of-halide-perovskite-nanocrystals-under-ambient-conditions.pdf
|
675ac5157be152b1d0bb7fae
|
10.26434/chemrxiv-2024-nqqbn
|
Indications for a Direct Singlet Fission Mechanism in TIPS-Pentacene Crystals from Hybrid DFT/MRCI and Molecular Mechanics Studies
|
A hybrid quantum mechanics/molecular mechanics setup was used to model the singlet fission (SF) of electronically excited 6,13-bis(triisopropylsilylethynyl)pentacene (TIPS-pentacene) in the crystalline phase. The optically bright S^bright_1 state possesses nearly identical excitation
energies and oscillator strengths in the two nonequivalent dimer units with large and small structural overlap, respectively. A shearing/tilting motion of the two slip-stacked TIPS-pentacene building blocks is the key for stabilizing the singlet-coupled triplet-pair state, ^1(TT),
in the large/small overlap situation. In both dimer models, the S^bright_1 and ^1(TT) states swap energetic order upon geometry relaxation, indicative of strong nonadiabatic coupling between these states and a direct SF mechanism in TIPS-pentacene crystals, at variance with unsubstituted
pentacene. The overall energy balance E(S^bright_1 ) -(E(T_1)+E(T_1)) remains positive at all investigated nuclear arrangements. Charge-transfer states and the ferromagnetically coupled ^5(TT) state lie energetically too high for taking part in the SF mechanism.
|
Timo Schulz; Simon Hédé; Christel Marian
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-12-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675ac5157be152b1d0bb7fae/original/indications-for-a-direct-singlet-fission-mechanism-in-tips-pentacene-crystals-from-hybrid-dft-mrci-and-molecular-mechanics-studies.pdf
|
6751c4f97be152b1d00dfb17
|
10.26434/chemrxiv-2024-mrmjk-v2
|
Electrostatic interaction between SARS-CoV-2
and charged surfaces: Spike protein evolution
changed the game
|
Previous works show a key role of electrostatics for the SARS-CoV-2 virus in aspects such as virus-cell interactions or virus inactivation by ionic surfactants. Electrostatic
interactions depend strongly on the variant since the charge of the Spike protein (responsible for virus - environment interactions) evolved across the variants from the
highly negative Wild Type (WT) to the highly positive Omicron variant. The distribution of the charge also evolved from diffuse to highly localized. These facts suggest
that SARS-CoV-2 should interact strongly with charged surfaces in a way that changed during the virus evolution.
This question is studied here by computing the electrostatic interaction between WT, Delta and Omicron Spike proteins with charged surfaces using a new method (based on Debye-Huckel theory) that provides efficiently general results as a function of the surface charge density σ. We found that the interaction of the WT and Delta variant spikes with charged surfaces is dominated by repulsive image forces proportional to σ2 originated at the protein/water interface. On the contrary, the Omicron variant shows a distinct behaviour, being strongly attracted to negatively charged surfaces and repelled from positively charged ones. Therefore, the SARS-CoV-2 virus has evolved from being repelled by charged surfaces to being efficiently adsorbing to negatively charged ones.
|
Marc Domingo; Horacio Guzman; Matej Kanduc; JORDI FARAUDO
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-12-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6751c4f97be152b1d00dfb17/original/electrostatic-interaction-between-sars-co-v-2-and-charged-surfaces-spike-protein-evolution-changed-the-game.pdf
|
65b0e5c19138d23161a13df8
|
10.26434/chemrxiv-2024-v9znj
|
Pillarquinone-based sodium-ion batteries using a highly concentrated electrolyte
|
Sodium-ion batteries using organic electrode materials are a promising alternative to state-of-the-art lithium-ion batteries. However, their practical viability is hindered by challenges such as a low specific capacity of the organic electrode materials, suboptimal interfacial compatibility, the availability of suitable electrolytes, or intrinsic dissolution issues associated with the organic materials. Previous research primarily addressed dissolution mitigation through electrode or materials engineering, often neglecting the substantial influence of the electrolyte. Herein, we use a highly concentrated electrolyte with a small-molecule organic positive electrode based on pillar[5]quinone (P5Q) with a high theoretical specific capacity of 446 mAh g−1, encapsulated within CMK-3 as mesoporous carbon, achieving record cycling performance with improved cycling stability even at elevated temperature (40 °C). Using 5 M sodium bis(fluorosulfonyl)imide in succinonitrile as electrolyte, the P5Q@CMK-3 composite electrode delivers 430 mAh g−1 specific discharge capacity at 0.2C and retains 90% of this value over 200 cycles. This corresponds to an impressive energy density of 831 Wh kg−1 (based on P5Q mass) and surpasses previous reports based on pillarquinones as electrode material. When operated at 40 °C, the P5Q@CMK-3 composite electrodes deliver a record-specific discharge capacity of 438 mAh g−1 with 88% capacity retention over 500 cycles, which translates to a minimal capacity decay of only 0.02% per cycle, and with ca. 100% Coulombic efficiency. This study underscores the crucial role of the electrolyte in advancing the prospect of organic sodium batteries for large-scale energy storage applications, offering a promising avenue for the future of sustainable energy technologies.
|
Md Adil; Maximilian Schmidt; Julia Vogt; Thomas Diemant; Martin Oschatz; Birgit Esser
|
Physical Chemistry; Organic Chemistry; Energy; Organic Compounds and Functional Groups; Energy Storage; Electrochemistry - Mechanisms, Theory & Study
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-01-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b0e5c19138d23161a13df8/original/pillarquinone-based-sodium-ion-batteries-using-a-highly-concentrated-electrolyte.pdf
|
62c489659c9c6b63162ce94d
|
10.26434/chemrxiv-2022-14g3n
|
Reversible O–O Bond Scission and O2 evolution at MOF-supported Tetramanganese Clusters
|
The scission of the O–O bond in O2 and the formation of O–O bonds during the evolution of O2 in photosynthesis are the engines of aerobic life as we know it. Likewise, the reduction of O2 and its reverse, the oxidation of reduced oxygen species to form O2, are indispensable components of emerging renewable technologies for energy storage and conversion. Storing and unleashing the energy contained within the O2 molecule requires control over the formation or scission of the four-electron double bond between two oxygen atoms. Nature performs these demanding multi-electron transformations by distributing the redox burden among multiple metal ions: evolution created metalloenzymes with polynuclear clusters wherein metal ions act in concert to deliver or accept multiple electrons. Most relevant in this sense are the tetramanganese-calcium (Mn4CaO5) cluster in the oxygen-evolving complex of photosystem II, responsible for O2 formation, and the tricopper clusters in multi-copper oxidases, which mediate O2 reduction. The critical step in both O2 reduction and O2 evolution is the interconversion between multinuclear metal-oxo species, where the O atoms carry formal –2 charges, and O–O bonded species where the oxygen atoms are more oxidized. Attempts to mimic the natural systems with synthetic analogs have led to a number of elegant molecular clusters that shed light on the electron transfer events and stepwise mechanism of O–O bond cleavage and formation. To our knowledge, however, the interconversion between molecular O2 and metal-oxo species in either synthetic or enzymatic discrete systems has not been documented. Here, we report that a tetramangenese cluster formed by self-assembly within a metal–organic framework (MOF) spontaneously cleaves the oxygen-oxygen double bond and reduces O2 by four electrons at room temperature. The ensuing tetranuclear manganese-oxo cluster engages in weak C–H bond activation and, more importantly, is competent for O–O bond formation and O2 evolution at elevated temperature, enabled by the head-to-head orientation of two fully reduced oxo atoms that bridge neighboring Mn pairs. This study demonstrates the viability of four-electron interconversion between molecular O2 and metal-oxo species and highlights the importance of site-isolation for achieving multi-electron chemistry at polynuclear metal clusters.
|
Xin He; Tzuhsiung Yang; Andrei Iliescu; Maxx Arguilla; Tianyang Chen; Heather Kulik; Mircea Dinca
|
Inorganic Chemistry; Bioinorganic Chemistry; Small Molecule Activation (Inorg.); Transition Metal Complexes (Inorg.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-07-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c489659c9c6b63162ce94d/original/reversible-o-o-bond-scission-and-o2-evolution-at-mof-supported-tetramanganese-clusters.pdf
|
66302cef91aefa6ce1c4ce57
|
10.26434/chemrxiv-2024-rmsnj
|
CosolvKit: a versatile tool for cosolvent MD preparation and analysis
|
Cosolvent molecular dynamics (MD) are an increasingly popular form of simulations where small molecule cosolvents are added to water-solvated protein systems. These simulations can perform diverse target characterization tasks, including cryptic and allosteric pocket identification and pharmacophore profiling, and supplement suites of enhanced sampling methods to explore protein conformational landscapes. The behavior of these systems is tied to the cosolvents used, so the ability to define diverse and complex mixtures is critical in dictating the outcome of the simulations. However, existing methods for preparing cosolvent simulations only support a limited number of predefined cosolvents and concentrations. Here we present CosolvKit, a tool for the preparation and analysis of systems composed of user-defined cosolvents and concentrations. This tool is modular and agnostic of the MD engine and force field used, offering access to a variety of generalizable small molecule force fields. To the best of our knowledge, CosolvKit represents the first generalized approach for the construction of these simulations.
|
Niccolo Bruciaferri; Jerome Eberhardt; Manuel A. Llanos; Johannes R. Loeffler; Matthew Holcomb; Monica L. Fernandez-Quintero; Diogo Santos-Martins; Andrew B. Ward; Stefano Forli
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-05-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66302cef91aefa6ce1c4ce57/original/cosolv-kit-a-versatile-tool-for-cosolvent-md-preparation-and-analysis.pdf
|
646f48c24f8b1884b742fe5f
|
10.26434/chemrxiv-2023-mvrnj
|
Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors
|
Predicting the interaction modes and binding affinities of virtual compound libraries is of great interest in drug development. It reduces the cost and time of lead compound identification and selection. Here we apply path-based metadynamics simulations to characterise the binding of potential inhibitors to the Plasmodium falciparum aspartic protease plasmepsin V (plm V), a validated antimalarial drug target that has a highly mobile binding site. The potential plm V binders were identified in a high throughput virtual screening (HTVS) campaign and were experimentally verified in a fluorescence resonance energy transfer (FRET) assay. Our simulations allowed us to estimate compound binding energies and revealed putative transition states along binding/unbinding pathways in atomistic resolution. We believe that the method described allows the prioritisation of compounds for synthesis and enables rational structure-based drug design for targets that undergo considerable conformational changes upon inhibitor binding.
|
Raitis Bobrovs; Laura Drunka; Iveta Kaņepe; Aigars Jirgensons; Amedeo Caflisch; Matteo Salvalaglio; Kristaps Jaudzems
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biophysics; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646f48c24f8b1884b742fe5f/original/exploring-the-binding-pathway-of-novel-non-peptidomimetic-plasmepsin-v-inhibitors.pdf
|
60c73e7f337d6c5b86e2634e
|
10.26434/chemrxiv.6987719.v1
|
The Needle in the Haystack for Theory of High Temperature Superconductivity: Negative Nuclear Magnetic Moments
|
This work outlines a theory for explaining high temperature superconductivity on the basis of relativistic scattering of Cooper pairs via beyond room temperature conditions causing high energy relativistic scattering of Cooper pairs with nuclei having positive and negative nuclear magnetic moments for fractionally reversibly fissing and fusing the nuclei for manifesting in the electronic lattice for altered quantum fields for more tightly binding the Cooper pair beyond the conventional critical temperature 40K limit for superconductivity beyond room temperature.
|
Reginald Little
|
Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-08-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e7f337d6c5b86e2634e/original/the-needle-in-the-haystack-for-theory-of-high-temperature-superconductivity-negative-nuclear-magnetic-moments.pdf
|
6290eef6d50418c0c6c546ca
|
10.26434/chemrxiv-2022-qqp41
|
Oxalate Oxidase for In Situ H2O2-generation in Unspecific Peroxygenase-Catalysed Drug Oxyfunctionalisations
|
H2O2-driven enzymes are of great interest for industrial biotransformations. Herein, we show for the first time that oxalate oxidase (OXO) is an efficient in situsource of H2O2 for one of these biocatalysts, which is known as unspecific peroxygenase (UPO). OXO is reasonably robust, produces only CO2 as a by-product and usesoxalate as a cheap sacrificial electron donor. UPO is a top-rated catalyst for selective C-H oxyfunctionalisations, as we confirm herein by testing a diverse drug panel using miniaturised high-throughput assays and mass spectrometry. 33 out of 64 drugs were converted in 5 μL-scale reactions by the UPO with OXO (conversion >70% for 11drugs). Furthermore, 84% isolated yield was achieved for the drug tolmetin on a larger scale (50 mg, TONUPO 25,664), which was excelled by implementing enzyme immobilization. This one-pot approach ensures adequate H2O2 levels, enabling rapid access to industrially relevant molecules which are difficult to obtain by other routes.
|
Elvira Romero; Magnus Johansson; Jared Cartwright; Gideon Grogan; Martin Hayes
|
Biological and Medicinal Chemistry; Catalysis; Drug Discovery and Drug Delivery Systems; Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-05-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6290eef6d50418c0c6c546ca/original/oxalate-oxidase-for-in-situ-h2o2-generation-in-unspecific-peroxygenase-catalysed-drug-oxyfunctionalisations.pdf
|
658c0f1366c138172924f555
|
10.26434/chemrxiv-2023-sqvhq-v2
|
Active droplets through enzyme-free, dynamic phosphorylation
|
Life continuously transduces energy to perform critical functions using energy stored in reactive molecules like ATP or NADH. ATP dynamically phosphorylates active sites on proteins and thereby regulates their function. Inspired by such machinery, regulating supramolecular functions using energy stored in reactive molecules has gained traction. Enzyme-free, synthetic systems that use dynamic phosphorylation to regulate supramolecular processes do not exist.
We present an enzyme-free reaction cycle that consumes phosphorylating agents by transiently phosphorylating amino acids. The phosphorylated amino acids are labile and deactivate through hydrolysis. The cycle exhibits versatility and tunability, allowing for the dynamic phosphorylation of multiple precursors with a tunable half-life. Notably, we show the resulting phosphorylated products can regulate the peptide’s phase separation, leading to active droplets that require the continuous conversion of fuel to sustain. Our new reaction cycle will be valuable as a model for biological phosphorylation but can also offer insights into protocell formation.
|
Simone Poprawa; Michele Stasi; Monika Wenisch; Brigitte Kriebisch; Judit Sastre; Job Boekhoven
|
Organic Chemistry; Combinatorial Chemistry; Supramolecular Chemistry (Org.)
|
CC BY 4.0
|
CHEMRXIV
|
2023-12-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658c0f1366c138172924f555/original/active-droplets-through-enzyme-free-dynamic-phosphorylation.pdf
|
63bbfeb61f1258550e968d84
|
10.26434/chemrxiv-2023-nspmt
|
Fabrication of 3D Oriented MOF Micropatterns with Anisotropic Fluorescent Properties
|
Micropatterning crystalline materials with oriented pores is necessary for the fabrication of devices with anisotropic properties. Crystalline and porous metal-organic frameworks (MOFs) are ideal materials as their chemical and structural mutability enables precise tuning of functional properties for applications ranging from microelectronics to photonics. Herein, we design a patternable oriented MOF film: by using a photomask under X-ray exposure, the MOF film decomposes in the irradiated areas, remaining intact in the unexposed regions. The MOF film acts simultaneously as a resist and as functional porous material. While the heteroepitaxial growth from aligned Cu(OH)2 nanobelts is used to deposit oriented MOF films, the sensitivity to radiation is achieved by integrating a brominated dicarboxylic ligand (Br2BDC) into a copper-based MOF Cu2L2DABCO (L=BDC/Br2BDC). The lithographed samples act as a diffraction grating upon irradiation with a laser, thus confirming the quality of the extended MOF micropattern. Furthermore, the oriented MOF patterns are functionalized with fluorescent dyes. As a result, by rotating the polarization angle of the laser excitation, we demonstrate the alignment of the dye in the MOF. By controlling the functional response to light, this MOF patterning protocol could be used for the microfabrication of optical components for photonic devices.
|
Miriam de J. Velásquez-Hernández; Mercedes Linares-Moreau; Lea A. Brandner; Benedetta Marmiroli; Mariano Barella; Guillermo P. Acuna; Simone Dal Zilio; Margot F. K. Verstreken; Dmitry E. Kravchenko; Francesco Carraro; Heimo Wolinski; Rob Ameloot; Christian Doonan; Paolo Falcaro
|
Materials Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-01-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bbfeb61f1258550e968d84/original/fabrication-of-3d-oriented-mof-micropatterns-with-anisotropic-fluorescent-properties.pdf
|
637d409a9b5b80a294d20ab9
|
10.26434/chemrxiv-2022-q7rcn
|
Plastic recognition and electrogenic uniport translocation of 1st-, 2nd-, and 3rd-row transition and post-transition metals by primary-active transmembrane P1B-2-type ATPase pumps
|
Transmembrane P1B-type ATPase pumps catalyze the extrusion of transition metal ions across cellular lipid membranes to maintain essential cellular metal homeostasis and detoxify toxic metals. Zn(II)-pumps of the P1B-2-type subclass, in addition to Zn2+, select diverse metals (Pb2+, Cd2+ and Hg2+) at their transmembrane binding site and feature promiscuous metal-dependent ATP hydrolysis in the presence of these metals. Yet, a comprehensive understanding of the transport of these metals, their relative translocation rates, and transport mechanism remains elusive. We developed a platform for the characterization of primary-active Zn(II)-pumps in proteoliposomes to study metal selectivity, translocation events and transport mechanism in real-time, employing a “multi-probe” approach with fluorescent sensors responsive to diverse stimuli (metals, pH and membrane potential). Together with atomic-resolution investigation of cargo selection by X-ray Absorption Spectroscopy (XAS), we demonstrate that Zn(II)-pumps are electrogenic uniporters that preserve the transport mechanism with 1st-, 2nd- and 3rd-row transition metal substrates. Promiscuous coordination plasticity, guarantees diverse, yet defined, cargo selectivity coupled to their translocation.
|
Sameera S. Abeyrathna; Nisansala S. Abeyrathna; Priyanka Basak; Gordon W. Irvine; Limei Zhang; Gabriele Meloni
|
Biological and Medicinal Chemistry; Biochemistry; Biophysics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-11-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637d409a9b5b80a294d20ab9/original/plastic-recognition-and-electrogenic-uniport-translocation-of-1st-2nd-and-3rd-row-transition-and-post-transition-metals-by-primary-active-transmembrane-p1b-2-type-at-pase-pumps.pdf
|
64d3c0d869bfb8925aa7537c
|
10.26434/chemrxiv-2023-vzlb8
|
Addressing Global Water Stress using Desalination and Atmospheric Water Harvesting: A Thermodynamic and Technoeconomic Perspective
|
Freshwater is a critical resource for many sectors of the economy, but excessive withdrawal of natural freshwater reserves has resulted in global water stress that is projected to impact 4 billion people by the end of this decade. Methods of artificially producing freshwater include desalination, which is a well-established technology in which water is extracted from a saline solution (typically seawater). Atmospheric water harvesting (AWH) is an alternate emerging approach in which water vapor is extracted from ambient air and condensed into freshwater. AWH has recently attracted attention for decentralized water production, but a comparative analysis of these different technologies using the same performance (kWh/m3) and cost metrics ($/m3) does not exist. Herein we develop the first thermodynamic and technoeconomic framework for clean water production that considers the population and water risk across all global locations. We find that AWH consumes more energy than practical desalination with subsequent water transport for roughly 90% of the global population, even when AWH operates under reversible (albeit impractical) operation. Furthermore, a practical AWH system is far more expensive (6× – 40× depending on the location and AWH technology used) than seawater desalination on a levelized cost of water (LCOW) basis, even after accounting for the costs associated with transporting desalinated water inland. The one exception is when water transport costs are increased by 5×, resulting in sorbent AWH becoming the lowest cost option for arid locations far from the coast (e.g., Sahara Desert). Our analysis framework informs cost and performance targets (material and system level design tradeoffs) for technology deployment that maximizes global impact.
|
Jordan Kocher; Akanksha Menon
|
Energy
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d3c0d869bfb8925aa7537c/original/addressing-global-water-stress-using-desalination-and-atmospheric-water-harvesting-a-thermodynamic-and-technoeconomic-perspective.pdf
|
66d8da0b51558a15ef10d643
|
10.26434/chemrxiv-2024-hw6dn
|
Adapting Gas Fermenting Bacteria for Light-driven Domino Valorization of CO2
|
We report the adaptive laboratory evolution (ALE) of Clostridium ljungdahlii (Cl) for enhanced syngas fermentation, enabling its integration into a photocatalytic CO₂-to-syngas conversion system for the upcycling of CO₂ to C₂ products, acetate and ethanol. The adapted strain, Cladapt, exhibits a 2.5-fold increase in growth rate and a 120-fold enhancement in C₂ production compared to the wild-type (Clwt). Isotopic labeling confirmed Cladapt's high conversion efficiency, yielding 6:1 and 9:1 ratios of ¹³C:¹²C in acetate and ethanol, respectively. Whole genome sequencing revealed eight unique mutations in Cladapt, whereas RNA-seq identified significant alterations in gene expression, shedding light on its enhanced metabolism. Coupling Cladapt with a CO₂-to-syngas converting semiconductor-molecule hybrid photocatalyst, TiO₂|phosphonated Co(terpyridine)₂, enabled the assembly of a photocatalytic domino system for CO2-to-syngas-to-C2 conversion. This study offers a streamlined approach to improving syngas fermentation in Cl, insights into microbial adaptability, and an ALE-guided pathway for solar-powered CO₂ upcycling using an inorganic-bacterial cascade strategy.
|
Lin Su; Santiago Rodriguez Jimenez; Marion Short; Erwin Reisner
|
Inorganic Chemistry; Catalysis; Energy; Transition Metal Complexes (Inorg.); Biocatalysis; Photocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2024-09-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d8da0b51558a15ef10d643/original/adapting-gas-fermenting-bacteria-for-light-driven-domino-valorization-of-co2.pdf
|
65d46e75e9ebbb4db9c5e2ff
|
10.26434/chemrxiv-2024-gs80k
|
Theoretical investigations on surface stabilities of
CuBi2O4 and CuFeO2
|
CuBi2O4 and CuFeO2 are p-type semiconductors that recently have been suggested as profitable photocathode materials for photo(electro)chemical reactions, such as water splitting or carbon dioxide reduction. There exist a few experimental and theoretical studies, providing a detailed description of the bulk properties of these materials, however, much less is known about the surfaces. In this work, we perform electronic structure simulations using DFT+U to investigate the structures, electronic properties, and thermodynamic stability of CuFeO2 and CuBi2O4 surfaces. The calculations indicate higher stabilities for stoichiometrically terminated (001)–CuBi2O4 and (012)–CuFeO2 surfaces. The density of states and the Bader charge analysis show states above the Fermi level for cation-deficient surface terminations and charge fluctuations among surface atoms, depending on the surface termination. These effects could enable higher absorption efficiency for cation-deficient surfaces. Our results emphasize the importance of surface terminations for a better understanding of electronic properties.
|
Julian Beßner; Stefanie E. Bogenrieder; Robert Neuhoff; Björn Kirchhoff; Timo Jacob
|
Theoretical and Computational Chemistry; Physical Chemistry; Physical and Chemical Properties; Surface; Thermodynamics (Physical Chem.); Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-02-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d46e75e9ebbb4db9c5e2ff/original/theoretical-investigations-on-surface-stabilities-of-cu-bi2o4-and-cu-fe-o2.pdf
|
60c757bd9abda2fff1f8e7bd
|
10.26434/chemrxiv.14454645.v1
|
Vesicle Viewer: Online Analysis of Small Angle Scattering from Lipid Vesicles
|
In this project, we developed an internet-based application, called Vesicle Viewer, to visualize and analyze small angle scattering data generated in the study of lipid bilayers. Vesicle Viewer models SAS data using the EZ-SDP model. In this way, key bilayer structural parameters, such as area per lipid and bilayer thickness, can be easily determined. This application primarily uses Django, a python package specialized for the development of robust web applications. In addition, several other libraries are used to support the more technical aspects of the project – notable examples are MatPlotLib (for graphs) and NumPy (for calculations). Without the barrier of downloading and installing software, the development of this web-based application will allow scientists all over the world to take advantage of this solution, regardless of their preferred operating system.
|
Aislyn Lewis-Laurent; Milka Doktorova; Frederick A. Heberle; Drew Marquardt
|
Biophysics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757bd9abda2fff1f8e7bd/original/vesicle-viewer-online-analysis-of-small-angle-scattering-from-lipid-vesicles.pdf
|
67b7677e6dde43c908bce105
|
10.26434/chemrxiv-2025-f2p26
|
A Fast Neural Network for Isotopic Charge State Assignment
|
Electrospray ionization (ESI) mass spectrometry is an essential technique for chemical analysis in a range of fields. In ESI, analytes can produce multiple charge states, which must be correctly assigned for identification. Existing approaches to charge state assignment can suffer from limited accuracy and/or poor speed. Here, we developed a fast deep learning neural network to perform isotopic cluster charge assignment. The performance of our algorithm, IsoDec, was demonstrated on top-down proteomics spectra collected on diverse instruments. On these highly complex individual spectra, we found that IsoDec produces similar sequence coverage to existing software tools but with improved accuracy. Importantly, this performance enhancement stems directly from the neural network charge assignment approach, not simply improved scoring and filtering of isotopic clusters. Finally, when applied to large top-down proteomics data sets, we discovered that IsoDec produces proteoform-spectrum matches with a better combination of coverage and accuracy. Overall, IsoDec provides a compelling demonstration of the potential of lightweight neural networks in mass spectrometry data analysis for diverse applications.
|
John Pavek; Nicholas Bollis; Josiah Grimes; Michael Shortreed; Lloyd Smith; Michael Marty
|
Analytical Chemistry; Biochemical Analysis; Chemoinformatics; Mass Spectrometry
|
CC BY 4.0
|
CHEMRXIV
|
2025-02-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b7677e6dde43c908bce105/original/a-fast-neural-network-for-isotopic-charge-state-assignment.pdf
|
60cd0fc8e2113325bcdfab0f
|
10.26434/chemrxiv-2021-4g7cz
|
Carbon Clusters: Thermochemistry and Electronic Structure at High Temperatures
|
This paper studies the thermochemistry and electronic structure of small carbon clusters and hydrocarbons which are major constituents of pyrolysis gases released into the boundary layer of ablating heat shields. Our focus lies on clusters of up to four carbon atoms including C3H and C4H. A study of electronically excited states of these molecules computed using the EOM-CCSD method has revealed C4 and C4H to be potential sources of radiation absorption in the boundary layer. We also study the effect of low-lying excited electronic states on the thermodynamics in the high temperature regime and show that neglecting these states records a difference of upto 12% in the computed Cp values. Finally, comparisons of the equilibrium mole fractions obtained using the thermodynamics computed in this paper with the existing state-of-the-art tables used for hypersonic applications (for example JANAF and Gurvich Tables) show an order of magnitude difference in the mixture compositions.
|
Maitreyee Sharma Priyadarshini; Richard Jaffe; Marco Panesi
|
Earth, Space, and Environmental Chemistry; Space Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2021-06-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60cd0fc8e2113325bcdfab0f/original/carbon-clusters-thermochemistry-and-electronic-structure-at-high-temperatures.pdf
|
60c756cabb8c1a16633dc6a5
|
10.26434/chemrxiv.14330405.v1
|
How Many Electrons Holds a Molecular Electride?
|
<div>
<div>
<div>
<p>Electrides are very peculiar ionic compounds where electrons occupy the anionic positions.
In a crystal lattice, these isolated electrons often group forming channels or surfaces, furnishing
electrides with a plethora of traits with promising technological applications. Despite their
huge potential, thus far, only a few stable electrides have been produced because of the intricate
synthesis they entail. Due to the difficulty in assessing the presence of isolated electrons, the
characterization of electrides also poses some serious challenges. In fact, their properties are
expected to depend on the arrangement of these electrons in the molecule. Among the criteria
that we can use to characterize electrides, the presence of a non-nuclear attractor (NNA) of the
electron density is both the rarest and the most salient feature. Therefore, a correct description
of the NNA is crucial to determine the properties of electrides. In this paper, we analyze the NNA and the surrounding region of nine molecular electrides with the goal of determining
the number of isolated electrons that are held in the electride. We have seen that the correct
description of a molecular electride hinges on the electronic structure method employed for the
analyses. In particular, one should employ a basis set with sufficient flexibility to describe the
region close to the NNA and a density functional approximation that does not suffer from large
delocalization errors. Finally, we have classified these nine molecular electrides according to
the most likely number of electrons that we can find in the NNA. We believe this classification
highlights the strength of the electride character and will prove useful in the design of new
electrides.</p>
</div>
</div>
</div>
|
Sebastian Sitkiewicz; Eloy Ramos-Cordoba; Josep M. Luis; Eduard Matito
|
Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756cabb8c1a16633dc6a5/original/how-many-electrons-holds-a-molecular-electride.pdf
|
64b7fc19b605c6803b01fc0d
|
10.26434/chemrxiv-2023-klj7x-v2
|
Nitrene C–H Bond Insertion Approach to Carbazolones and Indolones. Formal Total Synthesis of (–)-Methyl N-Decarbomethoxychanofruticosinate, (–)-Aspidospermidine and (+)-Kopsihainanine A
|
A new, modular platform for access to 1,2,3,9-tetrahydro-4H-carbazol-4-ones (H4-carbazolones) and 3,4-dihydrocyclopenta[b]indol-1(2H)-ones (H2-indolones) is disclosed from readily accessed 2-arylcycloalkane-1,3-diones (6- and 5-membered). These precursors were prepared through a Cu-catalyzed arylation of 1,3-cyclohexanediones with aryl iodides or via a ring-expansion of aryl succinoin derivatives. Activation of a single carbonyl group in the diones, a highly regioselective reaction with unsymmetrical 2-arylcyclohexane-1,3-diones, and subsequent azidation gave 3-azido-2-aryl-cycloalk-2-en-1-ones. The regioselectivity was computationally assessed. Finally, a Rh-catalyzed nitrene/nitrenoid insertion into the ortho-C–H bond of the aryl moiety, gave the H4-carbazolones and H2-indolones, products that are of high synthetic value. One carbazolone synthesized was elaborated to a key intermediate for the formal total synthesis of N-decarbomethoxychanofruticosinate, (–)-aspidospermidine, (+)-kopsihainanine A. With 2-aryl-1,3-cycloheptanedione, prepared from cyclohexanone and benzaldehyde, the azidation reaction was accomplished in a facile manner. However, the Rh-catalyzed reaction led to some unusual observations, with an azirine as a major product. DFT computations were performed in order to understand the differences in reactivities of the 5- and 6-membered -azido enones in comparison to the 7-membered analogue.
|
Mahesh Lakshman; Dellamol Sebastian; Padmanava Pradhan; Michelle Neary; Alexis Piette; Samuel Trzebiatowski; Alexander Henriques; Patrick Willoughby
|
Organic Chemistry; Catalysis; Natural Products; Organic Synthesis and Reactions; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-07-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b7fc19b605c6803b01fc0d/original/nitrene-c-h-bond-insertion-approach-to-carbazolones-and-indolones-formal-total-synthesis-of-methyl-n-decarbomethoxychanofruticosinate-aspidospermidine-and-kopsihainanine-a.pdf
|
62913e8eff2dabc85739b104
|
10.26434/chemrxiv-2022-nwk6n
|
Transforming the science of transformation toward sustainability: the case of ammonia and reactive nitrogen
|
Chemistry has played a central role over the past century in the large-scale anthropogenic transformation of matter into diverse materials that have improved the quality of life for many people on our planet. The lens of chemistry is fundamentally necessary to understand the resulting flux of chemical substances in Earth system processes, the unintended consequences of those transformations, impacts on food supply security, water and energy concerns, ways to mediate and adapt to climate change, loss of biodiversity, and how best to build and maintain resilient ecosystems. Reactive nitrogen compounds (Nr) such as ammonia from the industrial fixation of atmospheric nitrogen exemplify both the central importance of chemistry in providing food and meeting basic human needs for a global population of 7.9 billion people and the sustainability challenges arising from the intended and unintended consequences of large-scale human production and release of Nr. The chemistry profession can use the Planetary Boundaries framework as a systems thinking tool to understand and address challenges facing the entire Earth system resulting from the altered biogeochemical flows of nitrogen. This analysis has compelling priority due to the roles Nr currently plays in global food production and ammonia’s potential role as an energy carrier for large-scale human activities in a future low carbon economy. As this example illustrates, navigating the complex benefits and challenges large-scale human activity imposes on Earth system processes requires the convergence of chemistry research, industrial practice, and education. Since the chemical reactions and processes that transform matter are foundational to sustainability challenges, this perspective maps multiple levels at which chemistry can contribute toward the emergence of sustainability of the Earth system. We conclude with recommendations for steps the profession of chemistry can take to make education relevant and engaging and to connect chemistry research and practice to cross-disciplinary sustainability challenges.
|
J. Marc Whalen; Stephen A. Matlin; Thomas A. Holme; Jaclyn J. Stewart; Peter G. Mahaffy
|
Earth, Space, and Environmental Chemistry; Chemical Education; Agriculture and Food Chemistry; Chemical Education - General; Environmental Science; Food
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-05-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62913e8eff2dabc85739b104/original/transforming-the-science-of-transformation-toward-sustainability-the-case-of-ammonia-and-reactive-nitrogen.pdf
|
60c7406cee301c3ae2c78a96
|
10.26434/chemrxiv.7658372.v2
|
Zero-Field Nuclear Magnetic Resonance of Chemically Exchanging Systems
|
Zero- and ultralow-field (ZULF) nuclear magnetic resonance (NMR) is an emerging tool for precision chemical analysis. Unlike conventional (high-field) NMR, which relies on chemical shifts for molecular identification, zero-field analog reports <i>J</i>-spectra that depend on the nuclear spin-spin coupling topology of molecules under investigation. While chemical shifts are usually a small fraction of the resonance frequencies, <i>J</i>-spectra for various spin systems are completely different from each other. In this work, we use zero-field NMR to study dynamic chemical processes and investigate the influence of chemical exchange on ZULF NMR spectra. We develop a computation approach that allows quantitative calculation of ZULF NMR spectra in the presence of chemical exchange and apply it to study aqueous solutions of [<sup>15</sup>N]ammonium as a model system. In this system, proton exchange rates span more than three orders of magnitude depending on acidity (pH), as monitored by high-field and ZULF NMR. We show that chemical exchange substantially affects the <i>J</i>-coupled NMR spectra and, in some cases, can lead to degradation and complete disappearance of the spectral features. To demonstrate potential applications of ZULF NMR for chemistry and biomedicine, we show a ZULF NMR spectrum of [2-<sup>13</sup>C]pyruvic acid hyperpolarized via dissolution dynamic nuclear polarization (dDNP). The metabolism of pyruvate provides valuable biochemical information and its monitoring by zero-field NMR could give spectral resolution that is hard to achieve at high magnetic fields. We foresee applications of affordable and scalable ZULF NMR coupled with hyperpolarization modalities to study chemical exchange phenomena in vivo and in situations where high-field NMR detection is not possible to implement.<br />
|
Danila Barskiy; Michael C. D. Tayler; Irene Marco-Rius; John Kurhanewicz; Daniel B. Vigneron; Sevil Cikrikci; Ayca Aydogdu; Moritz Reh; Andrey Pravdivtsev; Jan-Bernd Hövener; John W. Blanchard; Teng Wu; Dmitry Budker; Alexander Pines
|
Bioorganic Chemistry; Biophysics; Theory - Computational; Chemical Kinetics; Physical and Chemical Processes; Quantum Mechanics; Spectroscopy (Physical Chem.); Statistical Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-02-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7406cee301c3ae2c78a96/original/zero-field-nuclear-magnetic-resonance-of-chemically-exchanging-systems.pdf
|
6712210812ff75c3a1c5aed2
|
10.26434/chemrxiv-2024-n2xj5
|
A Review of Metal-Organic Frameworks and Polymers in Mixed Matrix Membranes for CO2 Capture
|
Polymeric membranes offer an appealing solution for sustainable CO2 capture, with potential for large-scale deployment. However, balancing high permeability and selectivity is an inherent challenge for pristine membranes. To address this challenge, the development of mixed matrix membranes (MMMs) is a promising strategy. MMMs are obtained by carefully integrating porous nano-fillers into polymeric matrices, enabling the simultaneous enhancement of selectivity and permeability. In particular, metal-organic frameworks (MOFs) have gained recognition as MMM fillers for CO2 capture. Here, a review of the current state, recent advancements, and challenges in the fabrication and engineering of MMMs with MOFs for selective CO2 capture is proposed. Key considerations and promising research directions to fully exploit the gas separation potential of MOF-based MMMs in CO2 capture applications are highlighted.
|
Charlotte Skjold Qvist Christensen; Nicholas Hansen; Mahboubeh Motadayen; Nina Lock; Martin Lahn Henriksen; Jonathan Quinson
|
Materials Science; Inorganic Chemistry; Nanoscience; Composites
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-10-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6712210812ff75c3a1c5aed2/original/a-review-of-metal-organic-frameworks-and-polymers-in-mixed-matrix-membranes-for-co2-capture.pdf
|
660fd95d91aefa6ce1dd3135
|
10.26434/chemrxiv-2024-9n229-v2
|
Bayesian optimization of radical polymerization reactions in a flow synthesis system
|
The proportional amounts of monomers within a copolymer will greatly affect the properties of the material. However, as known as composition drift, the monomer ratio in a copolymer can deviate from the value expected from the raw material ratio due to differences in monomer reactivity. Hence, it is therefore necessary to optimize the polymerization process on the basis that this inevitable composition drift will take place. In the present study, styrene-methyl methacrylate copolymers were generated using a flow synthesis system and the processing variables were tuned employing Bayesian optimization (BO) to obtain a target composition. Initial trials employed BO to produce four candidate points per cycle, completing the optimization within five cycles, and the solvent-to-monomer ratio was identified as the most important variable. Subsequent BO tests employed 40 points per cycle and established that multiple sets of processing conditions could provide the desired composition, but with variations in the physical properties of the copolymers. The role of each variable in the radical polymerization reaction was elucidated by assessing the extensive array of processing conditions while evaluating several broad trends. The proposed model confirms that specific monomer proportions can be produced in a copolymer using machine learning while investigating the reaction mechanism. In the future, the use of multi-objective BO to fine-tune the processing conditions is expected to allow optimization of the copolymer composition together with adjustment of physical properties.
|
Shogo Takasuka; Sho Ito; Shunto Oikawa; Yosuke Harashima; Tomoaki Takayama; Aniruddha Nag; Araki Wakiuchi; Tsuyoshi Ando; Tetsunori Sugawara; Miho Hatanaka; Tomoyuki Miyao; Takamitsu Matsubara; Yu-ya Ohnishi; Hiroharu Ajiro; Mikiya Fujii
|
Materials Science; Polymer Science; Organic Polymers; Polymerization (Polymers); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-04-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660fd95d91aefa6ce1dd3135/original/bayesian-optimization-of-radical-polymerization-reactions-in-a-flow-synthesis-system.pdf
|
64b02bd7b053dad33a2af823
|
10.26434/chemrxiv-2023-cz9k2-v2
|
Indium – Polycarboxylic Acid Ligand Interactions Modify InP Quantum Dot Nucleation and Growth
|
Size control through precursor reactivity in InP quantum dot (QD) synthesis has been difficult due to the presence of kinetically persistent InP clusters when using conventional indium carboxylate and tris(trimethylsilyl)phosphine chemistry. However, the advent of the indium halide/aminophosphine-based synthesis creates new opportunities to harness precursor design to impact nucleation and growth. Driven to further explore indium coordination as a synthetic handle in InP QD synthesis, we have examined the effect of a strongly chelating anion on the nucleation and growth of InP QDs. Increasing the equivalents of metal-chelating aminopolycarboxylic acid EDTA ([CH2N(CH2CO2H)2]2) (0 to 0.75 equivalents per indium) is found to decrease the final diameter of InP QDs from 4.5 to 2.3 nm by lowering the initial InP growth rate. This size trend is rationalized by invoking a continuous nucleation model. Control experiments carried out with substoichiometric equivalents of indium do not exhibit a drastic size decrease, pointing to complex effects of EDTA on indium precursor reactivity. By 1H NMR spectroscopy, EDTA is identified to form an octahedral complex with indium that is less reactive. This competitive decrease in reactivity and in the effective concentration of indium precursor is proposed to suppress the initial InP growth rates and consequently decrease the final size of the nanocrystals.
|
Helen Larson; Brandi Cossairt
|
Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Kinetics and Mechanism - Inorganic Reactions; Ligands (Inorg.); Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-07-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b02bd7b053dad33a2af823/original/indium-polycarboxylic-acid-ligand-interactions-modify-in-p-quantum-dot-nucleation-and-growth.pdf
|
643edb3f71383d0921eb4692
|
10.26434/chemrxiv-2023-d2ccz
|
Thermodynamic Stability and Anion Ordering of Perovskite Oxynitrides
|
Perovskite oxynitrides (PONs) are a promising class of materials for applications ranging from catalysis to photovoltaics. However, the vast space of single PON materials (ABO3–xNx}) has yet to be fully explored. Additionally, the community needs guidelines that relate PON chemistry and anion ordering to stability to better understand how to design PON materials that resist corrosion and decomposition under operating conditions. Screening this materials space requires identifying candidate PON materials that will be stable under operating conditions, which in turn requires methods to evaluate each material's stability. Here we predict the stability of single PON materials using a four-step approach based on density functional theory modeling: (I) enumerate viable cation pairs, (ii) select an energetically favorable prototypical anion ordering, (iii) compute each PON's free energy above the thermodynamic convex hull, and (iv) generate computational Pourbaix diagrams to determine allowable ranges of electrochemical operating conditions. A critical part of our approach is determining a prototypical stable anion ordering for both ABO2N and ABON2 stoichiometries across a variety of A- and B-site cations. We demonstrate a stable anion ordering containing a high degree of cis ordering between B cations and minority-composition anions. We predict 85 stable and 109 metastable PON compounds, with A∈{La, Pb, Nd, Sr, Ba, Ca} and B∈{Re, Os, Nb, Ta} forming cation pairs that lead to stable PONs less than 10 meV/atom above the thermodynamic convex hull. Computational Pourbaix diagrams for two stable candidates, CaReO2N and LaTaON2, suggest that not all compounds with zero energy above the thermodynamic convex hull can be easily synthesized.
|
Samuel Young; Jiadong Chen; Wenhao Sun; Bryan Goldsmith; Ghanshyam Pilania
|
Inorganic Chemistry; Electrochemistry; Theory - Inorganic; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-04-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643edb3f71383d0921eb4692/original/thermodynamic-stability-and-anion-ordering-of-perovskite-oxynitrides.pdf
|
65cf425c66c1381729c85489
|
10.26434/chemrxiv-2024-94b66
|
A Fluorescent Probe for Protein Misfolding and Aggregation Due to Oxidative Stress Based on a 7-Azaindole-BODIPY Derivative
|
The development of new fluorescent probes as molecular sensors is a critical step for the understanding of molecular mechanisms. Probes based on BODIPY offer remarkable versatility in molecular sensing due to their unique properties. BODIPY-based probes exhibit high fluorescence quantum yields, exceptional photostability, and tunable absorption/emission wavelengths. Here, we report the synthesis and evaluation of a novel 7-azaindole-BODIPY derivative to probe hydrophobic proteins as well as protein misfolding and aggregation. In organic solvents, this compound exhibits two emissive excited states efficiently interconverting. In contrast, within aqueous environments, the formation of molecular aggregates induces distinct photophysical properties. The complex photophysics of this 7-azaindole-BODIPY derivate were used as a starting point to explore its sensing applications. In presence of albumin, the monomeric form of the probe is stabilized in the hydrophobic regions of the protein, leading to a significant increase of both the fluorescence emission intensity and lifetime. A similar effect was observed when the probe interacts with protein aggregates. Notably, the fluorescence emission is less sensitive to the presence of other macromolecules such as pepsin, DNA, Ficoll 40, and coconut oil. Fluorescence lifetime imaging microscopy (FLIM) and two-photon fluorescence microscopy performed on breast cancer cells (MCF-7) and lung cancer cells (A549) incubated with this probe revealed longer fluorescence lifetimes and higher emission intensity upon oxidative stress. It is known that cellular stress leads to the accumulation and aggregation of misfolded proteins. Protein misfolding in MCF-7 cells under oxidative stress conditions was confirmed by synchrotron FTIR microspectroscopy. These results show that protein misfolding and aggregation triggered by oxidative stress can be monitored using the probe here developed.
|
Diego Herrera-Ochoa; Iván Llano; Consuelo Ripoll; Pierre Cybulski; Martin Kreuzer; Susana Rocha; Eva M. García-Frutos; Iván Bravo; Andrés Garzón Ruiz
|
Physical Chemistry; Biophysical Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-02-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cf425c66c1381729c85489/original/a-fluorescent-probe-for-protein-misfolding-and-aggregation-due-to-oxidative-stress-based-on-a-7-azaindole-bodipy-derivative.pdf
|
67acb4f06dde43c90896605c
|
10.26434/chemrxiv-2024-tp7rh-v2
|
An Expert-Augmented Deep Learning Approach for Synthesis Route Evaluation
|
Selection of efficient multi-step synthesis routes is a fundamental challenge in organic synthesis. Comparing different routes involves numerous parameters, economic considerations, and integration of nuanced chemical knowledge. While computer-aided synthesis planning (CASP) tools can generate synthetic routes, evaluating their overall feasibility and quality continues to rely heavily on human expertise, which is often lacking consistency and reproducibility. To address this, we have developed a data-driven scoring model augmented with human expert knowledge. Experts select key synthesis aspects to score the multi-step routes and apply them to the modeling. The model produces target-specific scores for synthetic routes, achieving a top-1 ranking accuracy of 60% when benchmarked against experimental data and 90% correspondence to the expert synthesis evaluation. Moreover, by incorporating human experts' assessment of routes based on the final route scores, we refined the score into an expert-augmented assessment standard that categorizes routes as Good, Plausible, or Bad universally and interpretably. We demonstrate that this criterion and the resulting route rankings align with expert judgment and synthesis feasibility, that can be obtained from the published reaction data.
|
Guo Yujia; Mikhail Kabeshov; Tat Hong Duong Le; Samuel Genheden; Giulia Bergonzini; Ola Engkvist; Samuel Kaski
|
Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Machine Learning
|
CC BY 4.0
|
CHEMRXIV
|
2025-02-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67acb4f06dde43c90896605c/original/an-expert-augmented-deep-learning-approach-for-synthesis-route-evaluation.pdf
|
625100ae11b1466b181cf74b
|
10.26434/chemrxiv-2022-jm3bv
|
Facile Generation of Fused Seven-Membered Polycyclic Systems via Ring Expansion and Application to the Total Synthesis of Sesquiterpenoids
|
Seven-Membered polycyclic architectures, widely present in natural products and small molecular drugs, are
challenging synthetic targets. So far, methods for synthesizing fused medium-sized bicyclo[m.n.0] ring systems, including the benzocycloheptane systems, are still surprisingly underdeveloped due to the lack of a general
protocol to access these architectures. Herein we describe a base-induced ring expansion as a general strategy,
which enables rapid and efficient construction of a wide range of fused seven-membered ring systems. The
application of this method was demonstrated by the efficient total syntheses of two sesquiterpenoids
plecarpenene and plecarpenone, both bearing a fused bicyclo[5.3.0]decane skeleton.
|
Zhimin Xing; Bowen Fang; Shangwen Luo; Xingang Xie; Xiaolei wang
|
Organic Chemistry; Natural Products; Organic Synthesis and Reactions
|
CC BY 4.0
|
CHEMRXIV
|
2022-04-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625100ae11b1466b181cf74b/original/facile-generation-of-fused-seven-membered-polycyclic-systems-via-ring-expansion-and-application-to-the-total-synthesis-of-sesquiterpenoids.pdf
|
675732ec7be152b1d06f9d0b
|
10.26434/chemrxiv-2024-wvqjd
|
Microcrystal electron diffraction-guided discovery of fungal metabolites
|
Nature remains a vast repository of complex and functional metabolites whose structural characterization continues to drive innovations in pharmaceuticals, agrochemicals, and materials science. The cryogenic electron microscopy (cryoEM) method, microcrystal electron diffraction (microED, a 3D ED technique) has emerged as a powerful tool to structurally characterize small molecules. Despite this emerging role in structural chemistry, the cost and throughput of microED have limited its application in the discovery of natural products (NPs). While recent advances in sample preparation (e.g. ArrayED) have provided a conceptual framework to address these challenges, they have remained unproven. Herein, we report the ArrayED-driven discovery of a structurally-unprecedented family of NPs (zopalide A-E), a muurolane-type sesquiterpene glycoside (rhytidoside A), aspergillicin analogs (aspergillicin H and aspergillicin I), and four crystal structures of previously reported fungal metabolites. We provide the first examples of absolute stereochemistry determination via microED for newly annotat-ed NPs.
|
David Delgadillo; Lin Wu; Caroline Wang; Yalong Zhang; Jessica Burch; Kunal Jha; Lygia Silva de Moraes; Gerald Bills; Benjamin Tu; Yi Tang; Hosea Nelson
|
Organic Chemistry; Natural Products; Stereochemistry; Crystallography – Organic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-12-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675732ec7be152b1d06f9d0b/original/microcrystal-electron-diffraction-guided-discovery-of-fungal-metabolites.pdf
|
644a7d550d87b493e35c2dcb
|
10.26434/chemrxiv-2023-7qzhw
|
Vision-driven Autocharacterization of Perovskite Semiconductors
|
In materials research, the task of characterizing hundreds of different materials traditionally requires equally many human hours spent measuring samples one by one. We demonstrate that with the integration of computer vision into this material research workflow, many of these tasks can be automated, significantly accelerating the throughput of the workflow for scientists. We present a framework that uses vision to address specific pain points in the characterization of perovskite semiconductors, a group of materials with the potential to form new types of solar cells. With this approach, we automate the measurement and computation of chemical and optoelectronic properties of perovskites. Our framework proposes the following four key contributions: (i) a computer vision tool for scalable segmentation to arbitrarily many material samples, (ii) a tool to extract the chemical composition of all material samples, (iii) an algorithm capable of automatically computing band gap across arbitrarily many unique samples using vision-segmented hyperspectral reflectance data, and (iv) automating the stability measurement of multi-hour perovskite degradation experiments with vision for spatially non-uniform samples. We demonstrate the key contributions of the proposed framework on eighty samples of unique composition from the formamidinium-methylammonium lead tri-iodide perovskite system and validate the accuracy of each method using human evaluation and X-ray diffraction.
|
Alexander E. Siemenn; Eunice Aissi; Fang Sheng; Armi Tiihonen; Hamide Kavak; Basita Das; Tonio Buonassisi
|
Materials Science; Energy; Alloys; Materials Processing; Photovoltaics
|
CC BY 4.0
|
CHEMRXIV
|
2023-04-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644a7d550d87b493e35c2dcb/original/vision-driven-autocharacterization-of-perovskite-semiconductors.pdf
|
60c757b7f96a004a8f288d04
|
10.26434/chemrxiv.14452785.v1
|
Dendron-Polymer Hybrids as Tailorable Coronae of Single-Walled Carbon Nanotube
|
Single-walled carbon nanotubes (SWCNTs), non-covalently functionalized by synthetic polymers, find widespread applications including sensing and imaging. Identifying new amphiphiles with interchangeable building blocks that can form unique coronae around the SWCNT, customized for a specific application, is thus of great interest. We present polymer-dendron hybrids, composed of hydrophobic dendrons and hydrophilic polyethylene glycol (PEG), as amphiphilic macromolecules with high degree of structural freedom, for suspending SWCNTs in aqeous solution. Based on a set of four PEG-dendrons differing in their dendritic end-groups, we show thst differences in the chemical structure of the hydrophobic end-groups control the interactions of the PEG-dendrons with the SWCNT-surface. These interactions led to differences in the intrinsic near-infrared fluorescence emission of the SWCNTs and affected the PEG-dendron susceptibility to enzymatic degradation, which was monitored by the SWCNT fluorescent signal. Our findings open new avenues for rational design of SWCNT functionalization, and optical sensing of enzymatic activity<br />
|
Verena Wulf; Gadi Slor; Parul Rathee; Roey J. Amir; Gili Bisker
|
Nanodevices; Nanostructured Materials - Nanoscience; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757b7f96a004a8f288d04/original/dendron-polymer-hybrids-as-tailorable-coronae-of-single-walled-carbon-nanotube.pdf
|
670f611051558a15ef36dec5
|
10.26434/chemrxiv-2024-9fpkq-v2
|
Unveiling the effect of chloride on the surface modification of Cu(111)
|
Electrochemical oxidation-reduction processes in the presence of anions have been widely explored for surface preparation of tailor-made copper catalysts. Nevertheless, the role of the anion and which sites geometries induce remains elusive. To address this uncertainty, we have assessed the effect of chloride on the surface modification of a well-defined Cu(111) single crystalline electrode using a potential-pulse technique. The morphology analysis revealed the formation of shape hexagonal microstructures homogeneously distributed on the single-facet surface. This shape was nearly similar to a (310) particle growing along the direction of the (111) orientation. Herein, we provide experimental insights supporting the idea that chloride induces the formation of n(100)x(110) domains, whereas the crystal-substrate orientation determines the growth direction of the new crystallographic phase. The present work offers a straightforward approach that enables precise control over the modification of highly ordered surfaces. This strategy is relevant for rationally assessing anion effects on the formation of distinct site geometries.
|
Paula Sebastián Pascual; Vicente Pascual-Llorens; Albert Serrà Ramos
|
Materials Science; Nanoscience; Energy; Catalysts; Nanostructured Materials - Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670f611051558a15ef36dec5/original/unveiling-the-effect-of-chloride-on-the-surface-modification-of-cu-111.pdf
|
62d123be468933a0b759764d
|
10.26434/chemrxiv-2022-73431
|
Photoredox-Mediated Deoxygenative Radical Additions of Aromatic Acids to Vinyl Boronic Esters and gem-Diborylalkenes
|
A new method to access β-keto-gem-diborylalkanes, by direct deoxygenative radical addition of aromatic carboxylic acids to gem-dibortlalkenes, is described. The reaction proceeds under mild photoredox catalysis, and involves a photochemical C–O bond activation of aromatic carboxylic acids in the presence of PPh3 to generate an acyl-radical, which further undergo addition reaction with gem-diborylalkenes to form α-gem-diboryl alkyl radical intermediate, which then reduced to the corresponding anion which after protonation yields the β-keto-gem-diborylalkane product. Moreover, the same scenario has been extended to the vinyl boronic esters e.g., gem-Ar,Bpin-alkenes. Importantly, this protocol provides a general platform for the late-stage functionalization of bio-active and drug molecules containing a carboxylic acid group.
|
Anugula Nagaraju; Tamer Saiaede; Ahmad Masarwa
|
Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2022-07-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d123be468933a0b759764d/original/photoredox-mediated-deoxygenative-radical-additions-of-aromatic-acids-to-vinyl-boronic-esters-and-gem-diborylalkenes.pdf
|
6436cc8d1d262d40ea51fff6
|
10.26434/chemrxiv-2023-mvx5c
|
Revising the formation of β-hematin crystals from hemin in aqueous-acetate medium containing chloroquine: modeling the kinetics of crystallization and characterizing their physico-chemical properties
|
We investigated the kinetics of conversion of hemin to β-hematin in aqueous-acetate medium in absence and in presence of two concentrations of chloroquine by using eleven reported kinetic equations. The two best kinetic equations are the combination of order 1 and Avrami and the combination of second order and logistic equations, based on the statistical parameters variance and overall errors. The best fitted equations are composed of two terms from which we model the formation of β-hematin as the result of two processes: the availability of reactive precursors and the formation of nucleation and growth sites. The crystals exhibit needle-like morphologies of about 760 nm long and 140 nm wide. However, the increment of chloroquine favors the formation of crystal twinning with non-homogenous distribution, crystals with lower sizes of similar heights and widths, and crystals symmetrically tapered at the ends of the needles. The lattice volumes, obtained from Rietveld analysis of powder X-ray diffraction patterns, were not regularly affected by chloroquine. The main IR absorption bands did not appreciably change in positions nor in intensities with varying chloroquine concentration. However, important changes were observed in the 2000-4000 cm-1 region. We used Density Functional Theory calculations to understand these changes.
|
Herrera Leidy J.; Parra Cristian A.; Coronado Daniel; Valentina Perez; Julian A Zapata; Adriana L. Pabón; Olga Lopez-Acevedo; Karen E. García; César A. Barrero
|
Inorganic Chemistry; Bioinorganic Chemistry; Kinetics and Mechanism - Inorganic Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6436cc8d1d262d40ea51fff6/original/revising-the-formation-of-hematin-crystals-from-hemin-in-aqueous-acetate-medium-containing-chloroquine-modeling-the-kinetics-of-crystallization-and-characterizing-their-physico-chemical-properties.pdf
|
6734b3cc7be152b1d0f50015
|
10.26434/chemrxiv-2024-h0b3g
|
Surface States-Induced Light Intensity-Dependent Bipolar Photoelectrodes for Selective Sensing
|
The mechanism behind photocurrent generation is essential for tuning photoelectrochemical properties of semiconductors and fabricating related devices. As a basic parameter, the photocurrent polarity has been exploited for information processing, and could be regulated by selecting suitable types of semiconductors, external biased potential, or photo energy. Nonetheless, the light intensity is generally thought to affect only the photocurrent intensity rather than the photocurrent polarity. Here, we report a universal strategy to modulate the photocurrent polarity by light intensity, which was also verified by four different semiconductors. The photoelectrochemical kinetics measurements disclosed that the surface states and light intensity jointly played a crucial role in the process of photogenerated carriers transfer, thus determining the photocurrent polarity. Base on the different charge transfer pathways produced under different illumination, a highly selective PEC sensing platform was constructed to specifically recognize dopamine without any modification process.
|
Wang Li; Hong Yang; Qiushi Ruan; Yanfei Shen; Songqin Liu; Haibin Zhu; Yuanjian Zhang
|
Physical Chemistry; Analytical Chemistry; Electrochemical Analysis; Electrochemistry - Mechanisms, Theory & Study
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6734b3cc7be152b1d0f50015/original/surface-states-induced-light-intensity-dependent-bipolar-photoelectrodes-for-selective-sensing.pdf
|
631018d811986c618e4dcc19
|
10.26434/chemrxiv-2022-dhj14
|
Bio-inspired heterogeneous Fe4S4 single-cluster catalyst for enhanced electrochemical CO2 reduction to CH4
|
Electrochemical conversion of carbon dioxide promises next-level paradigm shifts in sustainability. Applications will include breakthrough solutions to global crisis threatening our civilization, including energy, food, and climate change. Here, inspired by CO dehydrogenase II from Carboxyothermus hydrogenoformans, we designed a heterogeneous Fe4S4 single-cluster catalyst Ni100-Fe4S4, achieving high performance CO2 electroreduction. Combined with the experimental data and theoretical calculation, Ni100-Fe4S4 and CO dehydrogenase have highly similar catalytic geometric centers and CO2 binding modes. By exploring the origin of catalytic activity of this biomimetic structure, we found the activation of CO2 by Ni100-Fe4S4 theoretically exceeds that of natural CO dehydrogenase. Density functional theory calculations reveal that the dehydrogenase enzyme-liked Fe-Ni active site as an electron enrichment 'electro-bridge', activating CO2 molecules efficiently and stabilizing various intermediates in multistep elementary reactions to produce CH4 in a low overpotential (0.13eV) selectively. The calculated electroreduction pathway can completely consistent with the nickel-based catalytic materials reported in the current experiments. This work demonstrates that it is efficient and feasible to design biomimetic high-performance catalytic materials by using blueprints provide by nature. Combining ideas from modern catalyst design with bio-inspired strategies will lead our catalysts beyond its current limitations.
|
Hengyue Xu; Lan Ma
|
Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational; Electrocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631018d811986c618e4dcc19/original/bio-inspired-heterogeneous-fe4s4-single-cluster-catalyst-for-enhanced-electrochemical-co2-reduction-to-ch4.pdf
|
60c74a3e469df423a9f43ce2
|
10.26434/chemrxiv.12174438.v1
|
Experimental Dataset of Electrochemical Efficiency of a Direct Borohydride Fuel Cell (DBFC) with Pd/C, Pt/C and Pd Decorated Ni–Co/rGO Anode Catalysts
|
<p>Dataset includes Direct Borohydride Fuel Cell (DBFC) impedance and
polarization test in anode with Pd/C, Pt/C and Pd decorated Ni–Co/rGO catalysts. In fact, different
concentration of Sodium Borohydride (SBH), applied voltages and various anode catalysts loading with explanation of experimental details of
electrochemical analysis are considered in data. Voltage, power density and resistance of DBFC change as
a function of weight percent of SBH (%), applied voltage and amount of anode
catalyst loading that are evaluated by polarization and impedance curves with
using appropriate equivalent circuit of fuel cell. Can be stated that
interpretation of electrochemical behavior changes by the data
of related cell is inevitable, which can be useful in simulation, power source investigation
and depth analysis in DB fuel cell researches. </p>
<p> </p>
|
Sarmin Hamidi; Sadra Sabouri; Sepand Haghighi; Kasra Askari
|
Energy Storage; Fuel Cells; Power
|
CC BY 4.0
|
CHEMRXIV
|
2020-04-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a3e469df423a9f43ce2/original/experimental-dataset-of-electrochemical-efficiency-of-a-direct-borohydride-fuel-cell-dbfc-with-pd-c-pt-c-and-pd-decorated-ni-co-r-go-anode-catalysts.pdf
|
676e69b9fa469535b9f5331e
|
10.26434/chemrxiv-2024-1q7ln-v2
|
General Method for Carbon–Heteroatom Cross-Coupling Reactions via Semiheterogeneous Red-Light Metallaphotocatalysis
|
Combining transition-metal catalysis with photocatalysis has emerged as a valuable, complementary approach for achieving carbon–heteroatom cross-coupling reactions. However, the need to use blue or high-energy near-UV light leads to problems with scalability, chemoselectivity, and catalyst deactivation, which have limited the synthetic applications of this combination. Herein, we report a method for red-light-driven nickel-catalyzed cross-coupling reactions of aryl halides with 11 different types of nucleophiles using a polymeric carbon nitride (CN-OA-m) as a photocatalyst. This semihomogeneous catalyst system enabled the formation of four different types of carbon–heteroatom bonds (C–N, C–O, C–S, and C–Se) with a wide range of substrates (more than 200 examples) with yields up to 94%. Moreover, the photocatalysts could be recovered and recycled, which makes it a promising new tool for the development of other reactions involving red-light metallaphotoredox catalysis.
|
Geyang Song; Jiameng Song; Qi Li; Wei Zhang; Tengfei Kang; Jianyang Dong; Gang Li; Juan Fan; Quan Gu; Chao Wang; Dong Xue
|
Organic Chemistry; Catalysis; Organometallic Chemistry; Photochemistry (Org.); Catalysis
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CC BY 4.0
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CHEMRXIV
|
2024-12-27
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676e69b9fa469535b9f5331e/original/general-method-for-carbon-heteroatom-cross-coupling-reactions-via-semiheterogeneous-red-light-metallaphotocatalysis.pdf
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60c750a2f96a0082f8287e98
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10.26434/chemrxiv.13065206.v1
|
In Silico Studies of the Biomolecular Interactions Between Natural Products and SARS-CoV-2 Main Protease
|
The
rapid global spread of SARS-CoV-2, the causative agent of COVID-19, has set off
the alarms of healthcare systems all over the world, the situation is
exacerbated as no effective treatment is available to date. One therapeutic
strategy consists in stopping the replication of the virus by inhibiting
SARS-CoV-2 main protease, an important enzyme in the processing of polyproteins
from viral RNA. Applying techniques like virtual screening, molecular docking
and molecular dynamics simulations, our study evaluated the biomolecular
interactions generated between more than 200 thousand natural products structures
collected from the Universal Natural Product Database and the main protease
active site. Through successive docking filters, we identified 3 molecules with
a good affinity profile for the enzyme. These were subjected to molecular dynamics
simulations and their binding free energies were calculated. Structures of the
best natural products identified could be a starting point for developing novel
antiviral candidates targeting SARS-CoV-2 M<sup>pro</sup>
|
Wilmar Puma-Zamora; Fabian Jimenez; Jesus Antonio Alvarado-Huayhuaz; Gerson Cordova-Serrano; Pierre-Marie Allard; Mariano Prado Acosta; Gustavo E. Olivos-Ramirez; Héctor Condori-Alagón; Ihosvany Camps
|
Natural Products; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
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CHEMRXIV
|
2020-10-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750a2f96a0082f8287e98/original/in-silico-studies-of-the-biomolecular-interactions-between-natural-products-and-sars-co-v-2-main-protease.pdf
|
63ff2366897b18336f526f56
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10.26434/chemrxiv-2023-6xnn8
|
Novel chemical tyrosine functionalization of adeno-associated virus improves gene transfer efficiency in liver and retina
|
Decades of biological and clinical research have led to important advances in recombinant adeno-associated viruses rAAV-based gene therapy gene therapy. However, several challenges must be overcome to fully exploit the potential of rAAV vectors. Innovative approaches to modify viral genome and capsid elements have been used to overcome issues such as unwanted immune responses and off-targeting. While often successful, genetic modification of capsids can drastically reduce vector yield and often fails to produce vectors with properties that translate across species. Here, we describe a chemical bioconjugation strategy to modify tyrosine residues on AAV capsids using specific ligands, thereby circumventing the need to genetically engineer the capsid sequence. Aromatic electrophilic substitution of the phenol ring of tyrosine residues on AAV capsids improved the in vivo transduction efficiency of rAAV2 vectors in both liver and retinal targets. This tyrosine bioconjugation strategy represents an innovative technology for the engineering of rAAV vectors for human gene therapy.
|
Aurelien Leray; Pierre-Alban Lalys; Juliette Varin; Mohammed Bouzelha; Audrey Bourdon; Dimitri Alvarez-Dorta; Karine Pavageau; Sebastien Depienne; Maia Marchand; Anthony Mellet; Joanna Demilly; Jean-Baptiste Ducloyer; Tiphaine Girard; Bodval Fraysse; Mireille Ledevin; Mickael Guilbaud; Sebastien G. Gouin; Eduard Ayuso; Oumeya Adjali; Thibaut Larcher; Therese Cronin; Caroline Le Guiner; David Deniaud; Mathieu Mevel
|
Biological and Medicinal Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ff2366897b18336f526f56/original/novel-chemical-tyrosine-functionalization-of-adeno-associated-virus-improves-gene-transfer-efficiency-in-liver-and-retina.pdf
|
64af4f61ba3e99daef00c178
|
10.26434/chemrxiv-2023-b9x1p-v4
|
Structural and Electrochemical Evolution of Alloy Interfacial Layers in Anode-Free Solid-State Batteries
|
“Anode-free” solid-state batteries feature high energy density since there is no anode active material upon assembly. While beneficial effects of interfacial layers at the anode-solid electrolyte interface have previously been demonstrated, the mechanisms through which they influence lithium plating/stripping are unclear. Here, we reveal the evolution of 100-nm silver and gold interfacial layers during anode-free lithium plating/stripping using electrochemical methods, electron microscopy, synchrotron micro x-ray computed tomography, and modeling. The alloy layers significantly improve Coulombic efficiency and resistance to short circuiting, even though the alloys form solute regions or particulates that detach from the current collector as lithium grows. In-situ electrochemical impedance spectroscopy shows that the alloy layers return to the interface and mitigate contact loss at the end of stripping, avoiding a critical vulnerability of anode-free cells. The enhanced contact retention is driven by uniform Li thickness that promotes spatially uniform stripping, as well as local alloy delithiation in response to current concentrations to homogenize current and diminish voiding.
|
Stephanie Sandoval; John Lewis; Bairav Vishnugopi; Douglas Nelson; Matthew Schneider; Francisco Cortes; Christopher Matthews; John Watt; Mengkun Tian; Pavel Shevchenko; Partha Mukherjee; Matthew McDowell
|
Materials Science; Energy; Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-07-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64af4f61ba3e99daef00c178/original/structural-and-electrochemical-evolution-of-alloy-interfacial-layers-in-anode-free-solid-state-batteries.pdf
|
64cce676dfabaf06ffb19a86
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10.26434/chemrxiv-2023-vb01m-v3
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Polarizable Embedding Potentials through Molecular Fractionation with Conjugate Caps including Hydrogen Bonds
|
Polarizable embedding (PE) refers to classical embedding approaches, such as those used in quantum mechanics/molecular mechanics (QM/MM), that allow mutual polarization between the quantum and classical regions. The quality of the embedding potential is critical to provide accurate results, e.g., for spectroscopic properties and dynamical processes. High-quality embedding-potential parameters can be obtained by dividing the classical region into smaller fragments and deriving the parameters from ab-initio calculations on the fragments. For solvents and other systems composed of small molecules, the fragments can be individual molecules, while a more complicated fragmentation procedure is needed for larger molecules, such as proteins and nucleic acids. One such fragmentation strategy is the molecular fractionation with conjugate caps (MFCC) approach. As is widely known, hydrogen bonds play a key role in many biomolecular systems, e.g., in proteins, where they are responsible for the secondary structure. In this work, we assess the effects of including hydrogen-bond fragmentation in the MFCC procedure (MFCC(HB)) for deriving the embedding-potential parameters. The MFCC(HB) extension is evaluated on several molecular systems, ranging from small model systems to proteins, directly in terms of molecular electrostatic potentials and embedding potentials and indirectly in terms of selected properties of chromophores embedded in water and complex protein environments.
|
David Carrasco-Busturia; Jógvan Magnus Haugaard Olsen
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational
|
CC BY 4.0
|
CHEMRXIV
|
2023-08-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64cce676dfabaf06ffb19a86/original/polarizable-embedding-potentials-through-molecular-fractionation-with-conjugate-caps-including-hydrogen-bonds.pdf
|
65adf0b966c1381729fb4c11
|
10.26434/chemrxiv-2024-r8gjv
|
Exploring Transition States of Protein Conformational Changes via Out-of-Distribution Detection in the Hyperspherical Latent Space
|
Identifying transitional states is crucial for understanding protein conformational changes that underlie numerous fundamental biological processes. Markov state models (MSMs) constructed from Molecular Dynamics (MD) simulations have demonstrated considerable success in studying protein conformational changes, which are often associated with rare events transiting over free energy barriers. However, it remains challenging for MSMs to identify the transition states, as they group MD conformations into discrete metastable states and do not provide information on transition states lying at the top of free energy barriers between metastable states. Inspired by recent advances in trustworthy artificial intelligence (AI) for detecting out-of-distribution (OOD) data, we present Transition State identification via Dispersion and vAriational principle Regularized neural neTworks (TS-DART). This deep learning approach effectively detects the transition states from MD simulations using hyperspherical embeddings in the latent space. The key insight of TS-DART is to treat the transition state structures as OOD data, recognizing that the transition states are less populated and exhibit a distributional shift from metastable states. Our TS-DART method offers an end-to-end pipeline for identifying transition states from MD simulations. By introducing a dispersion loss function to regularize the hyperspherical latent space, TS-DART can discern transition state conformations that separate multiple metastable states in an MSM. Furthermore, TS-DART provides hyperspherical latent representations that preserve all relevant kinetic geometries of the original dynamics. We demonstrate the power of TS-DART by applying it to a 2D-potential, alanine dipeptide and the translocation of a DNA motor protein on DNA. In all these systems, TS-DART outperforms previous methods in identifying transition states. As TS-DART integrates the dimensionality reduction, state decomposition, and transition state identification in a unified framework, we anticipate that it will be applicable for studying transition states of protein conformational changes.
|
Bojun Liu; Jordan G. Boysen; Ilona Christy Unarta; Xuefeng Du; Yixuan Li; Xuhui Huang
|
Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Biophysical Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-01-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65adf0b966c1381729fb4c11/original/exploring-transition-states-of-protein-conformational-changes-via-out-of-distribution-detection-in-the-hyperspherical-latent-space.pdf
|
66289dcb21291e5d1d8daf76
|
10.26434/chemrxiv-2024-dbrr7
|
Tracking Trash to Treasure: In situ monitoring of Single Microbial Cell Oil biosynthesis from Waste Cooking Oil using Raman Reverse Isotope Probing and Imaging
|
Single microbial cell oil (SMCO) plays a fundamental role in maintaining the structure of cellular membranes and as energy reservoirs. Oleaginous microbes are known to have a high content of lipids, which often acts as a microbial factory for the bioremediation of waste cooking oil (WCO)
which is a major pollutant contaminating land and water bodies. The biomass of microbes grown in WCO can be utilized to develop sustainable value-added products such as biodiesel, organic chemicals, bio preservatives, biosurfactants biopolymers. Conventional methods excel in SMCO analysis but lack efficacy for in situ or lysis-free monitoring of nascent SMCO synthesis and its
turnover dynamics. To bridge this knowledge gap, in this study we have employed Raman reverse stable isotope probing (RrSIP) to investigate the time dependent nascent SMCO synthesis and assimilation in Yarrowia lipolytica, a well-known oleaginous yeast. Our finding provides a unique
perspective for utilizing optical spectroscopy methods for lysis-free SMCO analysis which holds potential for utilization as an adjunct tool in bioprocess and biofuels industries.
|
SURYA PRATAP SINGH; Jiro Karlo; Arto Koistinen; Victor Carrasco Navarro
|
Biological and Medicinal Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Analytical Chemistry - General; Spectroscopy (Anal. Chem.); Biophysics
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-04-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66289dcb21291e5d1d8daf76/original/tracking-trash-to-treasure-in-situ-monitoring-of-single-microbial-cell-oil-biosynthesis-from-waste-cooking-oil-using-raman-reverse-isotope-probing-and-imaging.pdf
|
677d609881d2151a0239b4d4
|
10.26434/chemrxiv-2024-bncb0-v2
|
Advances in sulfur fluoride exchange for chemical biology
|
Since their introduction as a new strategy for synthesizing diverse chemotypes, sulfur(VI)–fluoride exchange (SuFEx) transformations have found applications ranging from polymer chemistry and covalent probe development to bioconjugation tools and chemistries for the synthesis of compound libraries. The collection of SuFEx reactions has expanded significantly since their introduction as a concept, comprising functionalities with varying reactivities towards different nucleophiles; thus, enabling the generation of a wide array of sulfur-containing functional groups for the linkage of structural elements in diverse chemotypes. In this review, we focus on the most recent developments in the use of SuFEx chemistry as a means for the preparation of compound libraries for biological screening as well as the introduction of SuFEx hubs into various biomolecules.
|
Tobias N. Hansen; Marcos San Segundo; Annika M. Mergel; Christian Adam Olsen
|
Organic Chemistry; Bioorganic Chemistry; Combinatorial Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677d609881d2151a0239b4d4/original/advances-in-sulfur-fluoride-exchange-for-chemical-biology.pdf
|
60c73cc0bdbb8910a5a37b79
|
10.26434/chemrxiv.14755134.v1
|
Non-Innocent Radical Ion Intermediates in Photoredox Catalysis: Parallel Reduction Modes Enable Coupling of Diverse Aryl Chlorides
|
We describe a photocatalytic system that elicits potent photoreductant activity from conventional photocatalysts by leveraging radical anion intermediates generated <i>in situ</i>. The combination of isophthalonitrile and sodium formate promotes diverse aryl radical coupling reactions from abundant but difficult to reduce aryl chloride substrates. Mechanistic studies reveal two parallel pathways for substrate reduction both enabled by a key terminal reductant byproduct, carbon dioxide radical anion.
|
Alyah Chmiel; Oliver P. Williams; Colleen Chernowsky; Charles Yeung; Zachary Wickens
|
Organic Synthesis and Reactions; Photochemistry (Org.); Homogeneous Catalysis; Organocatalysis; Photocatalysis; Redox Catalysis
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CC BY NC ND 4.0
|
CHEMRXIV
|
2021-06-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc0bdbb8910a5a37b79/original/non-innocent-radical-ion-intermediates-in-photoredox-catalysis-parallel-reduction-modes-enable-coupling-of-diverse-aryl-chlorides.pdf
|
60c73d8f842e65f76adb17a3
|
10.26434/chemrxiv.5850003.v1
|
Workfunction of Al-Doped ZnO Films Deposited by Atomic Layer Deposition
|
Al-doped ZnO (AZO) is a promising earth-abundant alternative to Sn-doped In<sub>2</sub>O<sub>3</sub> (ITO) as an n-type transparent conductor for electronic and photovoltaic devices; AZO is also more straightforward to deposit by atomic layer deposition (ALD). The workfunction of this material is particularly important for the design of optoelectronic devices. We have deposited AZO films with resistivities as low as 1.1 x 10<sup>-3</sup> Ωcm by ALD using the industry-standard precursors trimethylaluminum (TMA), diethylzinc (DEZ), and water at 200<sup>◦</sup>C. These films were transparent and their elemental compositions showed reasonable agreement with the pulse program ratios. The workfunction of these films was measured using a scanning Kelvin Probe (sKP) to investigate the role of aluminum concentration. In addition, the workfunction of AZO films prepared by two different ALD recipes were compared: a “surface” recipe wherein the TMA was pulsed at the top of each repeating AZO stack, and a interlamellar recipe where the TMA pulse was introduced halfway through the stack. As aluminum doping increases, the surface recipe produces films with a consistently higher workfunction as compared to the interlamellar recipe. The resistivity of the surface recipe films show a minimum at a 1:16 Al:Zn atomic ratio and using an interlamellar recipe, minimum resistivity was seen at 1:19. The film thicknesses were characterized by ellipsometry, chemical composition by EDX, and resistivity by four-point probe.<br />
|
Peter George Gordon; Goran Bacic; Gregory P. Lopinski; Sean Thomas Barry
|
Thin Films; Physical and Chemical Processes
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-02-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d8f842e65f76adb17a3/original/workfunction-of-al-doped-zn-o-films-deposited-by-atomic-layer-deposition.pdf
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6661b56b91aefa6ce1eaad8b
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10.26434/chemrxiv-2024-31rs5
|
Membrane-immobilized transaminases for the synthesis of enantiopure amines
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For the manufacture of enantiopure amines, greener synthesis processes are needed. Transaminases (TAs) are able to produce chiral amines with excellent enantioselectivity and in mild conditions, and can be immobilized to target stability, recoverability, and reusability. In the perspective of process intensification, we propose to study TA immobilization onto polymeric membranes. Two main immobilization strategies were investigated, requiring prior membrane surface functionalization. On the one hand, a polyacrylonitrile (PAN) membrane surface was partially hydrolyzed and coated with polyethyleneimine (PEI) to electrostatically trap TAs. On the second hand, a polypropylene (PP) membrane was coated with polydopamine (PDA), which was subsequently modified with glycerol diglycidyl ether (GDE) in order to covalently graft TAs. The successful membranes functionalization was confirmed by surface characterization techniques (infrared spectroscopy, X-ray photoelectron spectroscopy, contact angle measurements, and scanning electron microscopy). Enzyme leaching was observed from the functionalized PAN membrane, highlighting the need to post-treat the reversibly immobilized TAs to improve their anchoring. The covalent coupling of TAs with PEI using glutaraldehyde (GA) was found highly effective to avoid leaching and to increase the enzyme loading, without affecting the specific activity of the biocatalyst. Similarly, the covalent grafting of TA onto functionalized PP membranes yielded very efficient biocatalysts (retaining 85 % specific activity with respect to soluble TA) displaying perfect recyclability throughout successive cycles. Immobilizing either the S-selective HeWT or the R-selective TsRTA resulted in robust heterogeneous biocatalysts with antagonist enantioselectivities. Thus, chiral amine synthesis can be performed effectively with biocatalytic membranes, which paves the way to intensified continuous flow synthesis processes.
|
Hippolyte Meersseman Arango; Xuan Dieu Linh Nguyen; Patricia Luis; Tom Leyssens; David Roura Padrosa; Francesca Paradisi; Damien Debecker
|
Catalysis; Biocatalysis
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CC BY 4.0
|
CHEMRXIV
|
2024-06-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6661b56b91aefa6ce1eaad8b/original/membrane-immobilized-transaminases-for-the-synthesis-of-enantiopure-amines.pdf
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650d8097ed7d0eccc30360c6
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10.26434/chemrxiv-2023-lvvtz
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Multiphoton Imaging of Spatial Distribution, Coordination and Redox Environment of Uranium under Model Biogeochemical Conditions
|
Nuclear power is a sustainable zero-carbon energy source but requires generated radionuclide waste be remediated from contaminated lands. Legacy, mining and disposal activities all engender environmental contamination, particularly for uranium, which is the main component by mass being both radioactive and toxic. Microbial mediated redox transformations have been targeted as bioremediation techniques. Typically studied by bulk quantitative techniques or on fixed (dead) cells, an absence of techniques capable of quantitatively probing the distribution and environment of radionuclides in living cells has impeded repurposing such wastes. Here we demonstrate the use of two-photon luminescence microscopy utilizing the intrinsic optical properties of the uranyl cation (UVIO2 2+) to follow microbial processes at the sub-micron level in vivo. The fundamental multiphoton photophysical properties of key uranyl species have been determined, and two-photon imaging performed. The long-lived uranyl emission and inherent spatial control of two-photon excitation allows high-resolution, label free visualization of uranyl-containing biological material, while fluorescence lifetime mapping demonstrates the ability to visualize the microscopic redox conditions over the surface of uranyl-reducing bacterial cells.
|
Michael Andrews; Debbie Jones; Adam Woodward; Adam Swinburne; Jonathan Lloyd; Steven Magennis; Stanley Botchway; Andrew Ward; Louise Natrajan
|
Physical Chemistry; Inorganic Chemistry; Energy; Lanthanides and Actinides; Photochemistry (Physical Chem.)
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CC BY 4.0
|
CHEMRXIV
|
2023-09-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650d8097ed7d0eccc30360c6/original/multiphoton-imaging-of-spatial-distribution-coordination-and-redox-environment-of-uranium-under-model-biogeochemical-conditions.pdf
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61bb0abe7284d006b2ede549
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10.26434/chemrxiv-2021-hb0cg
|
Dual promotional effect of CuxO clusters grown with atomic layer deposition on TiO2 for photocatalytic hydrogen production
|
The promotional effects on photocatalytic hydrogen production of CuxO clusters deposited using atomic layer deposition (ALD) on P25 TiO2 are presented. The structural and surface chemistry study of CuxO/TiO2 samples, along with first principles Density Functional Theory simulations, reveal the strong interaction of ALD deposited CuxO with TiO2, leading to the stabilization of CuxO clusters on the surface; it also demonstrated substantial reduction of Ti4+ to Ti3+ on the surface of CuxO/TiO2 samples after CuxO ALD. The CuxO/TiO2 photocatalysts showed remarkable improvement in hydrogen productivity, with 11 times greater hydrogen production for the optimum sample compared to unmodified P25. With the combination of the hydrogen production data and characterization of CuxO/TiO2 photocatalysts, we inferred that ALD deposited CuxO clusters have a dual promotional effect: increased charge carrier separation and improved light absorption, consistent with known copper promoted TiO2 photocatalysts and generation of a substantial amount of surface Ti3+ which results in self-doping of TiO2 and improves its photo-activity for hydrogen production. The obtained data were also employed to modify the previously proposed expanding photocatalytic area and overlap model to describe the effect of cocatalyst size and weight loading on photocatalyst activity. Comparing the trend of surface Ti3+ content increase and the photocatalytically promoted area, calculated with our model, suggests that the depletion zone formed around the heterojunction of CuxO-TiO2 is the main active area for hydrogen production, and the hydrogen productivity of the photocatalyst depends on the surface coverage by this active area. However, the overlap of these areas initiates the deactivation of the photocatalyst.
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Saeed Saedy; Nico Hiemstra; Dominik Benz; Hao van Bui; Michael Nolan; J Ruud van Ommen
|
Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Nanocatalysis - Reactions & Mechanisms; Photocatalysis; Materials Chemistry
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CC BY NC 4.0
|
CHEMRXIV
|
2021-12-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61bb0abe7284d006b2ede549/original/dual-promotional-effect-of-cux-o-clusters-grown-with-atomic-layer-deposition-on-ti-o2-for-photocatalytic-hydrogen-production.pdf
|
64e5333e3fdae147faa01202
|
10.26434/chemrxiv-2023-8x112
|
STOPLIGHT: A Hit Scoring Calculator
|
We introduce STOPLIGHT, a web portal to assist medicinal chemists in prioritizing hits from screening campaigns and selection of compounds for optimization. STOPLIGHT incorporates services to assess 6 physiochemical and structural properties, 6 assay liabilities, and 11 pharmacokinetic properties for any small molecule represented by its SMILES string. We briefly describe each service and illustrate the utility of this portal with a case study. The STOPLIGHT portal provides a user-friendly tool to guide hit selection in early drug discovery campaigns, whereby compounds with unfavorable properties can be quickly recognized and eliminated.
Availability and implementation: STOPLIGHT is freely accessible at https://stoplight.mml.unc.edu/.
|
James Wellnitz; Holli-Joi Martin; Mohammad Hossain; Marielle Rath; Colton Fox; Konstantin Popov; Timothy Willson; Eugene Muratov; Alexander Tropsha
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e5333e3fdae147faa01202/original/stoplight-a-hit-scoring-calculator.pdf
|
60c74cb1f96a00b33b287814
|
10.26434/chemrxiv.12517535.v1
|
Deciphering the Binding Mechanism of Dexamethasone Against SARS-CoV-2 Main Protease: Computational Molecular Modelling Approach
|
<p>At present, there are
no proven agents for the treatment of 2019 coronavirus disease (COVID-19). The
available evidence has not allowed guidelines to clearly recommend any drugs
outside the context of clinical trials. One of the most important SARS-CoV-2
protein targets for therapeutics is the 3C-like protease (main protease, Mpro).
Here in this study we utilize the recently published 6W63 crystal structure of
Mpro complexed with a non-covalent inhibitor X77. Various docking methods FRED,
HYBRID, CDOCKER and LEADFINDER tools were benchmark to optimally re-dock the
co-crystal ligand within the active site of SARS-COV-2 Mpro. This study was
restricted to molecular docking without validation by molecular dynamics
simulations. CDOCKER was found to depict the exact binding of co-crystal ligand
having lowest RMSD of less than 2 A.
Interactions with the SARS-COV-2 Mpro may play a key role in fighting
against viruses. Dexamethasone was found to bind with a high affinity to the
same sites of the SARS-COV-2 Mpro than the Remdesivir. Dexamethasone was
forming six hydrogen bonds compared to the three hydrogen bonds formed by
Remdesivir within the active site of SARS-COV-2 Mpro. LEU141, GLY143, HIS163,
GLU166, GLN192 were the key amino acid residue of SAR-COV-2 Mpro involved in
stabilizing the complex between Dexamethasone and SARS-COV-2 Mpro. The results
suggest the effectiveness of Dexamethasone as potent drugs against SARS-CoV-2
since it bind tightly to its Mpro. In addition, the results also suggest that
dexamethasone as top antiviral treatments option than the Remdesivir with high
potential to fight the SARS-CoV-2.</p>
|
Shafi Ullah Khan; Thet.thet Htar
|
Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cb1f96a00b33b287814/original/deciphering-the-binding-mechanism-of-dexamethasone-against-sars-co-v-2-main-protease-computational-molecular-modelling-approach.pdf
|
66b65e99c9c6a5c07aa80cc2
|
10.26434/chemrxiv-2023-b84wl-v2
|
A High-Throughput Workflow to Analyze Sequence-Conformation Relationships and Explore Hydrophobic Patterning in Disordered Peptoids
|
Understanding how a macromolecule’s primary sequence governs its conformational landscape is crucial for elucidating its function, yet these design principles are still emerging for macromolecules with intrinsic disorder. Herein, we introduce a high-throughput workflow that implements a practical colorimetric conformational assay, introduces a semi-automated sequencing protocol using MALDI-MS/MS, and develops a generalizable sequence-structure algorithm. Using a model system of 20mer peptidomimetics containing polar glycine and hydrophobic N-butylglycine residues, we identified nine classifications of conformational disorder and isolated 122 unique sequences across varied compositions and conformations. Conformational distributions of three compositionally identical library sequences were corroborated through atomistic simulations and ion mobility spectrometry coupled with liquid chromatography. A data-driven strategy was developed using existing sequence variables and data-derived ‘motifs’ to inform a machine learning algorithm towards conformation prediction. This multifaceted approach enhances our understanding of sequence-conformation relationships and offers a powerful tool for accelerating the discovery of materials with conformational control.
|
Erin C. Day; Supraja S. Chittari; Keila C. Cunha; Jianhan Zhao; James N. Dodds; Delaney C. Davis; Erin S. Baker; Rebecca B. Berlow; Joan-Emma Shea; Rishikesh U. Kulkarni; Abigail S. Knight
|
Materials Science; Analytical Chemistry; Polymer Science; Polymer chains; Imaging; High-throughput Screening
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b65e99c9c6a5c07aa80cc2/original/a-high-throughput-workflow-to-analyze-sequence-conformation-relationships-and-explore-hydrophobic-patterning-in-disordered-peptoids.pdf
|
60c74cae337d6c9192e27ca7
|
10.26434/chemrxiv.12510038.v1
|
Anti-Selective [3+2] (Hetero)annulation of Non-Conjugated Alkenes via Directed Nucleopalladation
|
2,3-Dihydrobenzofurans and indolines are common substructures in medicines and natural products. Herein, we describe a method that enables direct access to these core structures from non-conjugated alkenyl amides and <i>ortho</i>-iodoanilines/phenols. Under palladium(II) catalysis this [3+2] heteroannulation proceeds in an <i>anti</i>-selective fashion and tolerates a wide variety of functional groups. <i>N</i>-Acetyl, -tosyl, and -alkyl substituted <i>ortho</i>-iodoanilines, as well as free –NH<sub>2</sub> variants, are all effective. Preliminary results with carbon-based coupling partners also demonstrate the viability of forming indane core structures using this approach. Experimental and computational data with phenols support a mechanism involving turnover-limiting, endergonic directed oxypalladation, followed by intramolecular oxidative addition and reductive elimination.
|
Hui-Qi Ni; Ilia Kevlishvili; Pranali Bedekar; Joyann Barber; Shouliang Yang; Michelle Tran-Dubé; Hou-Xiang Lu; Indrawan McAlpine; Peng Liu; Keary Engle
|
Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Computational Chemistry and Modeling; Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cae337d6c9192e27ca7/original/anti-selective-3-2-hetero-annulation-of-non-conjugated-alkenes-via-directed-nucleopalladation.pdf
|
671a58c41fb27ce1246dd1f5
|
10.26434/chemrxiv-2024-0j46r
|
A Bright Red Molecular Marker for Super Resolution Imaging of DNA Nanostructures
|
SEZ-NDEA, a long-range emissive molecular marker, can be used in fluorescence microscopy for super-resolution imaging (SRRF) of DNA nanostructures. The developed probe stains the cell nucleus with minimum cytoplasmic leakage and good contrast. It showed good photostability in cellular medium.
|
Iswar Chandra Mondal; Farhan Anjum; Abdul Salam; Snata Deka; Sayan Mandal; Anirban Karmakar; Chayan K. Nandi ; Subrata Ghosh
|
Biological and Medicinal Chemistry; Organic Chemistry; Biochemistry; Chemical Biology
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-10-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671a58c41fb27ce1246dd1f5/original/a-bright-red-molecular-marker-for-super-resolution-imaging-of-dna-nanostructures.pdf
|
62ba8f717da6cebd712372d8
|
10.26434/chemrxiv-2022-21j55
|
Brushed creation of liquid marbles
|
A method where particulates are transferred via a cosmetic brush onto liquid drops created on a highly non-wetting substrate with a hole to generate talc and graphite liquid marbles (LMs) and talc-graphite Janus liquid marbles is described. van der Waals forces facilitated the attachment of particulates to the dry brush bristles. Subsequently, the surface tension forces arising from particle interaction with water (which were O(102) higher than the van der Waals forces) engendered transfer of the particulates to the liquid-gas interface of the drop. Forces below 1 mN applied by a dangling foil on the LM ensured preservation of the drop shape when the force was removed. During the application of this force, the contact angles at the contact lines behaved differently from sessile drops that are inclined on surfaces. This preparation method portends the ability to automate the creation of LMs and Janus LMs for various applications.
|
Eric Shen Lin; Zhixiong Song; Jian Wern Ong; Hassan Ali Abid; Oi Wah Liew; Tuck Wah Ng
|
Materials Science; Nanoscience; Chemical Engineering and Industrial Chemistry; Aggregates and Assemblies; Granular Materials; Nanofluidics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-06-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ba8f717da6cebd712372d8/original/brushed-creation-of-liquid-marbles.pdf
|
622b0ccb702f04005eb815b2
|
10.26434/chemrxiv-2022-2vd87
|
Structure and Stability of 7-mercapto-4-methylcoumarin SAM on Gold: an Experimental and Computational analysis.
|
Self-assembled monolayers of 7-mercapto 4-methylcoumarin (MMC) on a flat gold surface were studied by Molecular Dynamics (MD) simulations, reference-free grazing incidence X-ray fluorescence (GIXRF) and X-ray photoemission spectroscopy (XPS), to determine the maximum monolayer density and to investigate the nature of the molecule/surface interface. In particular, the protonation state of the sulfur atom upon adsorption was analyzed, since some recent literature presented evidences for physisorbed thiols (preserving the S-H bond), unlike the common picture of chemisorbed thiyls (losing the hydrogen). MD with a specifically tailored force field was used to simulate either thiol or thiyl monolayers with increasing number of molecules, to determine the maximum dynamically stable densities. This result was refined by computing the monolayer chemical potential as a function of the density with the Bennet Acceptance Ratio method, based again on MD simulations. The monolayer density was measured with GIXRF, which provided a quantitative estimate of the number of sulfur atoms on top of flat gold surfaces embedded in a solution of MMC, to allow the formation of a dense monolayer. The sulfur core level binding energies in the same monolayers were measured by XPS, fitting the recorded spectra with the binding energies proposed in the literature for free or adsorbed thiols and thiyls, to get insight on the nature of the molecular species present in the layer.
|
Davide Marchi; Eleonora Cara; Federico Ferrarese Lupi; Philipp Hönicke; Yves Kayser; Burkhard Beckhoff; Micaela Castellino; Alberto Zoccante; Michele Laus; Maurizio Cossi
|
Physical Chemistry; Interfaces
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622b0ccb702f04005eb815b2/original/structure-and-stability-of-7-mercapto-4-methylcoumarin-sam-on-gold-an-experimental-and-computational-analysis.pdf
|
64886f7c4f8b1884b73c3fdc
|
10.26434/chemrxiv-2023-d5w1t
|
Enhancing Photophysical and Photosensitizing Properties of Nanoaggregates of Weakly Emissive Non-Planar Push-Pull Chromophore
|
The development of luminescent dye based on 1,1,4,4-tetracyanobuta-1,3-dienes (TCBDs) is an active research area, to date, only a few examples of designer TCBDs molecules displaying emission properties with quantum yields of 7.8 and 8.5% due to fluorophore conjugation and aggregation have been reported, both in organic, non-polar solvents. Our novel method radically refines weakly emissive 2,3-disubstituted TCBD (phenyl-TCBD 1) (ΦF = 2.3% in CH3CN) into a water-soluble, biocompatible nano-formulation as highly emissive aggregates 1NPsPF-127 with ΦF = 7.9% in H2O and without fluorophore conjugation. Spectroscopic studies including FT-IR revealed that aggregated phenyl-TCBD particles were encapsulated in a non-luminescent tri-block copolymer (PF-127) based nano-micelle. With increasing water fraction, the Phenyl-TCBD nano-aggregates exhibit a 3-fold higher quantum yield, greater lifetime, and redshift (155 nm). Singlet oxygen generation capability was tested to explore future studies as a bio-probe for bio-imaging applications and in photodynamic therapy to selectively target cancer cell lines with singlet oxygen generation (Φ= 0.25) capability. This study has significant implications for developing non-planar push-pull chromophores-based dyes as biosensors and their potential applications beyond bioimaging.
|
Arif Hassan Dar; Anas Ahmad; Ajay Kumar; Vijayendran Gowri; Chandrashekhar Jori; Shaifali Sartaliya; Neethu K M; Rehan Khan; Govindasamy Jayamurugan
|
Organic Chemistry; Nanoscience; Photochemistry (Org.); Physical Organic Chemistry; Nanostructured Materials - Nanoscience; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-06-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64886f7c4f8b1884b73c3fdc/original/enhancing-photophysical-and-photosensitizing-properties-of-nanoaggregates-of-weakly-emissive-non-planar-push-pull-chromophore.pdf
|
64d398b3dfabaf06fffce121
|
10.26434/chemrxiv-2023-1h55c
|
Strain induced reactivity of cyclic iminoboranes: The (2 + 2) cycloaddition of a 1-H-1,3,2-diazaborepine with ethene
|
Iminoboranes have gathered immense attention due to their reactivity and potential applications as isoelectronic and isosteric alkynes. While cyclic alkynes are well investigated and useful reagents, cyclic iminoboranes are underexplored and their existence was inferred only via trapping experiments. We report the first direct spectroscopic evidence of a cyclic seven-membered iminoborane, 1-(tert-butyldimethylsilyl)-1-H-1,3,2-diazaborepine 2, under cryogenic matrix isolation conditions. The amino-iminoborane 2 was photochemically generated in solid argon at 4 K from 1-(tert-butyldimethylsilyl)-2-azido-1,2-dihydro-1,2-azaborine (3) and was characterized using FT-IR, UV-Vis spectroscopy, and computational chemistry. The characteristic BN stretching vibration (1751 cm-1) is shifted by about 240 cm-1 compared to linear amino-iminoboranes indicating a significant weakening of the bond. The Lewis acidity value determined computationally (LAB = 9.1 ± 2.6) is similar to that of boron trichloride, and twelve orders of magnitude lower than that of 1,2-azaborinine (BN-aryne, LAB = 21.5 ± 2.6), a six-membered cyclic iminoborane. In contrast to the latter, the reduced ring strain of 2 precludes nitrogen fixation, but it unexpectedly allows facile (2 + 2) cycloaddition reaction with C2H4 under matrix isolation conditions at 30 K. The reaction of 2 with ethene provides the first example of a (2 + 2) cycloaddition reaction of an iminoborane.
|
Divanshu Gupta; Ralf Einholz; Holger F. Bettinger
|
Organometallic Chemistry; Kinetics and Mechanism - Organometallic Reactions; Main Group Chemistry (Organomet.); Spectroscopy (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d398b3dfabaf06fffce121/original/strain-induced-reactivity-of-cyclic-iminoboranes-the-2-2-cycloaddition-of-a-1-h-1-3-2-diazaborepine-with-ethene.pdf
|
60c73fdf9abda2aa40f8bb85
|
10.26434/chemrxiv.7538747.v1
|
Metallopolymerization as a Strategy to Translate Ligand-Modulated Chemoselectivity to Porous Catalysts
|
<div>
<div>
<div>
<p>Porous catalysts have garnered substantial interest as potential platforms for
group-transfer catalysis due to the ability to site-isolate catalysts and to non-covalently co-
localize substrates in proximity to reactive intermediates. In contrast to soluble molecular
catalysts, the limited synthetic toolbox available to prepare porous catalysts presents a
formidable challenge to controlling the primary coordination sphere of lattice-confined
catalysts and thus modulating the electronic structures of reactive catalyst intermediates.
Here, we utilize Sonogashira cross-coupling chemistry to prepare a family of porous
metallopolymers, in which the primary coordination sphere of Ru2 sites is systematically
varied. The newly synthesized materials are characterized by IR, elemental analysis, gas
sorption, powder X-ray diffraction, thermogravimetric analysis, X-ray absorption
spectroscopy, and diffuse-reflectance UV-vis-NIR spectroscopy. The resulting porous
materials are catalysts for nitrene-transfer chemistry and the chemoselectivty for allylic
amination of olefin aziridination can be tuned by modulating the primary coordination
sphere of the catalyst sites. The demonstration of metallopolymerization as a rational
synthetic strategy allows to translate ligand-modulated chemoselectivity to porous
catalysts, which represents a new opportunity to tailor the functionality of heterogeneous
analogues of molecular complexes.
</p>
</div>
</div>
</div>
|
Wen-Yang Gao; Andrew A. Ezazi; Chen-Hao Wang; Jisue Moon; Carter Abney; Joshua Wright; David Powers
|
Catalysts; Heterogeneous Catalysis; Redox Catalysis; Polymerization (Organomet.); Transition Metal Complexes (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fdf9abda2aa40f8bb85/original/metallopolymerization-as-a-strategy-to-translate-ligand-modulated-chemoselectivity-to-porous-catalysts.pdf
|
6670d4dcc9c6a5c07ab0ceeb
|
10.26434/chemrxiv-2024-jjj4n
|
Burner system for solid sample flame emission spectroscopy
|
We present a burner system to analyze solid inflammable samples utilizing flame emission spectroscopy without requiring any sample preparation procedures. The acetylene-nitrous oxide burner was designed to efficiently introduce solid particles into the flame through active injection, enabling real-time elemental analysis. Computational Fluid Dynamics (CFD) simulations were employed to study particle transport dynamics within the burner system. The emission was characterized through spectral analysis of the flame emission from metal powder mixtures, demonstrating its ability to determine elemental compositions without prior sample treatment. An artificial neural network (ANN) was implemented to analyze spectral data obtained from binary metal mixtures, enabling rapid and reliable identification of constituent elements with an uncertainty of = 2.7 % (mol/mol)
|
Adam Bernicky; Boyd Davis; Hans-Peter Loock
|
Chemical Engineering and Industrial Chemistry; Process Control; Reaction Engineering
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6670d4dcc9c6a5c07ab0ceeb/original/burner-system-for-solid-sample-flame-emission-spectroscopy.pdf
|
6710da0712ff75c3a1aecc05
|
10.26434/chemrxiv-2024-th83z-v2
|
Protein-protein interaction and conformational change in the alpha-helical membrane transporter BtuCD-F in the native cellular envelope
|
Alpha-helical membrane proteins perform numerous critical functions essential for the survival of living organisms. Traditionally, these proteins are extracted from membranes using detergent solubilization and reconstitution into liposomes or nanodiscs. However, these processes often obscure the effects of nanoconfinement and the native environment on the structure and conformational heterogeneity of the target protein. We demonstrate that pulsed dipolar electron spin resonance spectroscopy, combined with the Gd3+-nitroxide spin pair, enables the selective observation of the vitamin B12 importer BtuCD-F in its native cellular envelope. Despite the high levels of non-specific labeling in the envelope, this orthogonal approach combined with the long phase-memory time for the Gd3+ spin enables the observation of the target protein complex at a few micromolar concentrations with high resolution. In the native envelope, vitamin B12 induces a distinct conformational shift at the BtuCD-BtuF interface, which is not observed in the micelles. This approach offers a general strategy for investigating protein-protein and protein-ligand/drug interactions and conformational changes of the alpha-helical membrane proteins in their native envelope context.
|
Benesh Joseph
|
Physical Chemistry; Biological and Medicinal Chemistry; Biochemistry; Biophysics; Biophysical Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-10-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6710da0712ff75c3a1aecc05/original/protein-protein-interaction-and-conformational-change-in-the-alpha-helical-membrane-transporter-btu-cd-f-in-the-native-cellular-envelope.pdf
|
66f4016a12ff75c3a16b28c2
|
10.26434/chemrxiv-2024-ltmj2
|
Computational Methods in Drug Discovery and Development
|
The rapid advancements in computational methods have revolutionized drug discovery and development. These methods, ranging from molecular modelling to machine learning algorithms, have drastically increased in number and sophistication. However, a comprehensive understanding of these diverse approaches is essential for researchers aiming to make significant contributions to this evolving field. This review aims to provide a detailed overview of the most prominent computational methods currently used in drug discovery. It will analyze their underlying principles, discuss their applications, and highlight their potential for future advancements in the field. Through this examination, we aim to equip researchers with the necessary insights to navigate and contribute to the rapidly expanding landscape of computational drug discovery.
|
Sadettin Yavuz Ugurlu
|
Biological and Medicinal Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-09-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f4016a12ff75c3a16b28c2/original/computational-methods-in-drug-discovery-and-development.pdf
|
60c7540e0f50db3740397c86
|
10.26434/chemrxiv.13274732.v2
|
Struct2IUPAC -- Transformer-Based Artificial Neural Network for the Conversion Between Chemical Notations
|
Providing IUPAC chemical names is necessary for chemical information exchange. We developed a Transformer-based artificial neural architecture to translate between SMILES and IUPAC chemical notations: <i>Struct2IUPAC</i> and <i>IUPAC2Struct</i>. Our models demonstrated the performance that is comparable to rule-based solutions. We proved that both accuracy, speed of computations, and the model's robustness allow us to use it in production. Our showcase demonstrates that a neural-based solution can encourage rapid development keeping the same performance. We believe that our findings will inspire other developers to reduce development costs by replacing complex rule-based solutions with neural-based ones. The demonstration of <i>Struct2IUPAC</i> model is available online on <i>Syntelly</i> platform <i>https://app.syntelly.com/smiles2iupac</i>
|
Lev Krasnov; Ivan Khokhlov; Maxim Fedorov; Sergey Sosnin
|
Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-01-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7540e0f50db3740397c86/original/struct2iupac-transformer-based-artificial-neural-network-for-the-conversion-between-chemical-notations.pdf
|
63dc9816805bad91da1160db
|
10.26434/chemrxiv-2023-zgdm3
|
Further cautionary tales on thermostatting in Molecular Dynamics: energy equipartitioning and non-equilibrium processes in gas-phase simulations
|
Molecular dynamics (MD) simulations of gas-phase chemical reactions are typically carried out on a small number of molecules near thermal equilibrium by means of various thermostatting algorithms. Correct equipartitioning of kinetic energy among translations, rotations and vibrations of the simulated reactants is critical for many processes occurring in the gas phase. As thermalizing collisions are infrequent in gas-phase simulations, the thermostat has to efficiently reach equipartitioning in the system during equilibration and maintain it throughout the actual simulation. Furthermore, in non-equilibrium simulations where heat is released locally, the action of the thermostat should not lead to unphysical changes in the overall dynamics of the system. In this study, we explore issues related to both obtaining and maintaining thermal equilibrium in MD simulations of an exemplary ion-molecule dimerization reaction. We first compare the efficiency of Nosé-Hoover, Canonical Sampling through Velocity Rescaling, and Langevin thermostats for equilibrating the system and find that of these three only the Langevin thermostat achieves equipartition in a reasonable simulation time. We also study the effect of unphysical removal of latent heat released during simulations involving multiple dimerization events, when global thermostatting schemes are applied, which effectively cools down the reactants and leads to an overestimation of the dimerization rate. Our findings underscore the importance of thermostatting for the proper thermal initialization of gas-phase systems and the consequences of global thermostatting in non-equilibrium MD simulations.
|
Roope Halonen; Ivo Neefjes; Bernhard Reischl
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-02-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63dc9816805bad91da1160db/original/further-cautionary-tales-on-thermostatting-in-molecular-dynamics-energy-equipartitioning-and-non-equilibrium-processes-in-gas-phase-simulations.pdf
|
669a8035c9c6a5c07adc1ae0
|
10.26434/chemrxiv-2024-jrfxj
|
DFT-Based Permutationally Invariant Polynomial
Potentials Capture the Twists and Turns of
C14H30
|
Hydrocarbons are ubiquitous as fuels, solvents, lubricants, and as the principal components of plastics and fi bers, yet our ability to predict their dynamical properties is
limited to force- eld mechanics. Here, we report two machine-learned potential energy surfaces (PESs) for the linear 44-atom hydrocarbon C14H30, using an extensive data set of roughly 250,000 DFT (B3LYP) energies for a large variety of con figurations, obtained using MM3 direct-dynamics calculations at 500 K, 1000 K and 2500 K. The
surfaces, based on Permutationally Invariant Polynomials (PIPs) and using both a many-body expansion approach and a fragmented-basis approach, produce precise fits for energies and forces and also produce excellent out-of-sample agreement with direct DFT calculations for torsional and dihedral angle potentials. Going beyond precision,
the PESs are used in molecular dynamics calculations that demonstrate the robustness of the PESs for a large range of conformations. The many-body PIPs PES, although
more compute intensive than the fragmented-basis one, is directly transferable for other linear hydrocarbons.
|
Joel Bowman; Chen Qu ; Paul Houston ; Thomas Allison ; Barry Schneider
|
Theoretical and Computational Chemistry; Machine Learning
|
CC BY 4.0
|
CHEMRXIV
|
2024-07-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669a8035c9c6a5c07adc1ae0/original/dft-based-permutationally-invariant-polynomial-potentials-capture-the-twists-and-turns-of-c14h30.pdf
|
60c7545a337d6c5ef7e28a18
|
10.26434/chemrxiv.12758015.v3
|
Massive Pressure Amplification by Stimulated Contraction of Mesoporous Frameworks
|
Negative Gas Adsorption (NGA), discovered in a
series of mesoporous switchable MOFs, was hitherto regarded as a curios
phenomenon occurring only at pressures well below or close to atmospheric
merit. Herein we demonstrate mesoporous frameworks interacting with carbon
dioxide, to show stimulated breathing transitions well above 100 kPa.
Reversible CO<sub>2</sub> adsorption-induced switching was observed in DUT-46
(DUT = Dresden University of Technology), in contrast to irreversible
transitions for DUT-49 and DUT-50, as demonstrated via synchrotron in situ
PXRD/adsorption experiments. Systematic physisorption experiments reveal the
best conditions for high pressure NGA transitions in the pressure range of 350
- 680 kPa. The stimulated framework contraction expells CO<sub>2</sub> in the
range of 1.1 to 2.4 mmol g<sup>-1</sup> leading to autonomous pressure amplification
in a closed system. In a pneumatic demonstrator system we achieved pressure amplification of
90 kPa at a high operating pressure of 340 kPa. According to system level estimations even higher theoretical pressure
amplification may be achieved between 535 kPa and 1011 kPa for DUT-49 using CO<sub>2</sub>
as a non-toxic and non-flammable working gas. Operable pressure ranges
exceeding 100 kPa render pressure amplifying framework materials as
realistic candidates for the integration into energy autonomous responsive
pneumatic systems.
|
Volodymyr Bon; Simon Krause; Irena Senkovska; Nico Grimm; Dirk Wallacher; Daniel D. Többens; Stefan Kaskel
|
Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Physical and Chemical Processes; Physical and Chemical Properties; Structure; Surface; Thermodynamics (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-01-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7545a337d6c5ef7e28a18/original/massive-pressure-amplification-by-stimulated-contraction-of-mesoporous-frameworks.pdf
|
67154a8812ff75c3a1fe3343
|
10.26434/chemrxiv-2024-k0x94
|
Interaction of Light with Gas-Liquid Interfaces: Influence on Photon Absorption in Continuous-Flow Photoreactors
|
Light interacts with gas bubbles in various ways, potentially leading to photon losses in gas-liquid photochemical applications. Given that light is a costly 'reagent', understanding these losses is crucial for optimizing reactor efficiency. In this study, we address the challenge of quantifying these interactions by implementing a method that separately determines the photon flux and utilizes the effective optical path length as a key descriptor of photon absorption. The results reveal an unexpected impact of gas phase introduction in continuous-flow photoreactors. Notably, photon absorption, and consequently the throughput of a photoreactor, can be increased by the introduction of a gas phase. This enhancement arises from the reflection and refraction effects of gas bubbles, which can intensify light intensity in the liquid volume and thereby offset any loss in residence time. The photon absorption losses that were observed were associated with large bubbles and were less significant than anticipated. In contrast, the introduction of small bubbles was found to increase photon absorption, suggesting a potential strategy to optimize photoreactor performance.
|
Jasper Schuurmans; Stefan Zondag; Arnab Chaudhuri; Miguel Claros; John Van der Schaaf; Timothy Noel
|
Organic Chemistry; Chemical Engineering and Industrial Chemistry; Photochemistry (Org.); Reaction Engineering; Transport Phenomena (Chem. Eng.)
|
CC BY 4.0
|
CHEMRXIV
|
2024-10-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67154a8812ff75c3a1fe3343/original/interaction-of-light-with-gas-liquid-interfaces-influence-on-photon-absorption-in-continuous-flow-photoreactors.pdf
|
667249dd01103d79c58a7648
|
10.26434/chemrxiv-2024-6l2r1-v2
|
Copper-Catalyzed Disruption of a Cascade Reaction: Synthesis of γ-Ketoamides from Nitrones and Ynamides
|
A thermal dipolar cycloaddition and rearrangement reaction to form pyrrolines has been redirected towards the synthesis of γ-keto- and γ-aldoamides from nitrones and ynamides with a Cu(II) catalyst. A copper-coordinated iminium intermediate is proposed to initiate a diastereoselective rearrangement for C–C bond formation and a combination of catalyst and nitrone protecting group balance the desired reactivity, diastereoselectivity, and sensitivity to hydrolysis. Reaction optimization is described in addition to scope, mechanistic studies, and conversion of γ-ketoamides to 1,4-diones. This catalytic method showcases distinct copper-catalyzed reactivity of N-alkenylnitrones for the synthesis of 1,4-dicarbonyl compounds.
|
Abdullah Alshreimi; Esther Shim; Donald Wink; Laura Anderson
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667249dd01103d79c58a7648/original/copper-catalyzed-disruption-of-a-cascade-reaction-synthesis-of-ketoamides-from-nitrones-and-ynamides.pdf
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656f51975bc9fcb5c91adb77
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10.26434/chemrxiv-2023-m16q0
|
Direct Synthesis of Partially Ethoxylated Branched Polyethylenimine from Ethanolamine
|
We report here a new method to make a branched and partially ethoxylated polyethyleneimine derivative directly from ethanolamine. The polymerization reaction is catalysed by a pincer complex of Earth-abundant metal, manganese, and produces water as the only byproduct. Industrial processes to produce polyethyleneimines involve the transformation of ethanolamine to a highly toxic chemical, aziridine, by an energy-intensive/waste-generating process followed by the ring-opening polymerization of aziridine. Through bypassing the need to produce a highly toxic feedstock, the reported method herein is greener than the current state-of-the-art. We propose that the polymerization process follows a hydrogen borrowing pathway that involves (a) dehydrogenation of ethanolamine to form 2-aminoacetaldehyde, (b) dehydrative coupling of 2-aminoacetaldehyde with ethanolamine to form an imine derivative, and (c) subsequent hydrogenation of imine derivative to form alkylated amines.
|
Claire Brodie; Alister Goodfellow; Aniekan Owen; Michael Bühl; Amit Kumar
|
Catalysis; Organometallic Chemistry; Polymer Science; Homogeneous Catalysis; Polymerization (Organomet.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-12-06
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656f51975bc9fcb5c91adb77/original/direct-synthesis-of-partially-ethoxylated-branched-polyethylenimine-from-ethanolamine.pdf
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6661acbe418a5379b0363cf0
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10.26434/chemrxiv-2024-t9n2b
|
Chemoselective placement of unsaturated phosphorus
electrophiles into ubiquitin for proximity-induced protein targeting
|
Mildly reactive electrophiles have emerged as powerful functional groups for developing chemical
probes to target pharmacologically important proteins and study key biological mechanisms. With the current
manuscript, we introduce unsaturated N-alkyl-phosphonamidates as a new and powerful class of chemical
warheads that enable proximity-induced labeling and the specific targeting of protein-protein interactions. In
contrast to many other electrophilic warheads, these cysteine-selective electrophiles can be incorporated into
specific amino acid side on the protein level by a chemoselective Staudinger-phosphonite reaction using
unsaturated phosphonites as chemical reactants with azido-containing ubiquitins obtained by auxotrophic
expression. Following this protocol, we prepared several ethynyl-N-alkyl-phosphonamidate-containing ubiquitins,
which undergo proximity-induced labeling with deubiquitinases (DUBs) and other ubiquitin-interacting proteins,
even in the presence of high thiol concentrations and cell lysates. Furthermore, we demonstrate that changing
the position of the electrophile allows selective targeting, enrichment and distinct functional regulation of DUBs
via covalent binding to individual distinct ubiquitin binding pockets as highlighted in the functional regulation of
USP5, a DUB that contains multiple ubiquitin binding sites. Our study highlights the prospect of targeting proteinprotein interactions with electrophilic protein-based probes by simultaneously enlarging the repertoire of
chemical probes beyond purely synthetically derived warheads.
|
Christian Stieger; Sergej Schwagerus; Gillian Dornan; Lee Armstrong; Kristin Kemnitz-Hassanin; Michal Nadler-Holly; Heike Stephanowitz; Fan Liu; Volker Haucke; Yogesh Kulathu; Christian Hackenberger
|
Biological and Medicinal Chemistry; Biochemistry; Bioengineering and Biotechnology; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6661acbe418a5379b0363cf0/original/chemoselective-placement-of-unsaturated-phosphorus-electrophiles-into-ubiquitin-for-proximity-induced-protein-targeting.pdf
|
664ee4c291aefa6ce1c4fc8d
|
10.26434/chemrxiv-2024-c77p4
|
Constrained synthesis planning with disconnection-aware transformer and multi-objective search
|
Designing synthesis routes with shared intermediates for a set of target compounds is a common task in drug discovery. Multistep retrosynthesis tools such as
AiZynthFinder are frequently used by chemists to generate possible routes. Although these tools can find solved routes for a majority of target compounds, they may not generate routes which comply with specific bond constraints. Such bond constraints could be defined in the project to obtain synthesis routes with common intermediates for the set of compounds. Here, we present a novel retrosynthesis approach which aims to generate routes in the feasible region defined by these constraints. The constraints are divided into bonds to break and bonds to freeze. First, we introduce a filter in the search which discards any reaction that violates the frozen bond constraints. Second, we benchmark four possible strategies for breaking selected bonds in the search for synthetic routes. We show that a combination of disconnection-aware transformer and multi-objective search generates routes which satisfy bond constraints for more targets in the PaRoutes dataset compared to the standard search (75.57% vs. 54.80%). Finally, we apply the strategy on a set of drug compounds to exemplify a real-world scenario. Using our novel approach, we can build a short joint synthesis route which satisfies the given bond constraints and covers eight of the ten compounds.
|
Annie M. Westerlund; Lakshidaa Saigiridharan; Samuel Genheden
|
Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-05-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664ee4c291aefa6ce1c4fc8d/original/constrained-synthesis-planning-with-disconnection-aware-transformer-and-multi-objective-search.pdf
|
641dc9d191074bccd038b061
|
10.26434/chemrxiv-2022-twp5d-v2
|
In situ monitoring of block copolymer self-assembly via solvent exchange through controlled dialysis with light and neutron scattering detection
|
Solution self-assembly of amphiphilic block copolymers (BCs) is typically performed by solvent to water exchange. However, BC assemblies are often trapped in metastable states depending on the mixing conditions, such as the magni-tude and rate of water addition. BC self-assembly can be performed under near thermodynamic control by dialysis which accounts for a slow and gradual water addition. In this communication we report the use of a specifically de-signed dialysis cell to continuously monitor by dynamic light scattering and small-angle neutron scattering the mor-phological changes of PDMS-b-PEG BCs during THF to water exchange. The complete phase diagrams of near-equilibrium structures can then be established. Spherical micelles first form before evolving to rod-like micelles and vesicles, decreasing the total developed interfacial area of self-assembled structures in response to increasing interfacial energy as the water content increases. The dialysis kinetics can be tailored to the time scale of BC self-assembly by modifying the membrane pore size, which is of interest to study the interplay between thermodynamics and kinetics in self-assembly pathways.
|
Martin Fauquignon; Lionel Porcar; Annie Brûlet; Jean-Francois Le Meins; Olivier Sandre; Jean-Paul Chapel; Marc Schmutz; Christophe Schatz
|
Physical Chemistry; Polymer Science; Self-Assembly
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641dc9d191074bccd038b061/original/in-situ-monitoring-of-block-copolymer-self-assembly-via-solvent-exchange-through-controlled-dialysis-with-light-and-neutron-scattering-detection.pdf
|
64fe1aff99918fe537b7f108
|
10.26434/chemrxiv-2023-dl4pw
|
The Development and Mechanistic Study of an Iron-Catalyzed Intramolecular Nitroso Ene Reaction of Nitroarenes
|
An intramolecular iron-catalyzed nitroso ene reaction was developed to afford six- or seven-membered N-heterocycles from nitroarenes using an earth abundant iron catalyst and phenylsilane as the terminal reductant. The reaction can be triggered using as little as 3 mol % of iron(II) acetate and 3 mol % of 4,7-dimethoxyphenanthroline as the ligand. The scope of the reaction is broad tolerating a range of electron-releasing or electron-withdrawing substituents on the nitroarene, and the ortho-substituent can be modified to diastereoselectively construct benzoxazines, dihydrobenzothiazines, tetrahydroquinolines, tetrahydroquinoxalines, or tetrahydrobenzooxazepines. Mechanistic investigations indicated that the reaction proceeds via a nitrosoarene intermediate, and kinetic analysis of the reaction revealed a first order rate dependence in catalyst- and nitroarene concentration, and an inverse kinetic order in acetate was observed. The difference in rates between PhSiH3 and PhSiD3 was found to be 1.50 ± 0.09, and investigation of the temperature dependence of the reaction rate revealed that the activation parameters to be ΔH‡ = 13.5 kcal•mol–1 and ΔS‡ = –39.1 cal•mol–1•K–1. These data were interpreted to indicate that the turnover-limiting step to be hydride transfer from iron to the coordinated nitroarene, which occurs through an ordered transition state with little Fe–H bond breaking.
|
Van Vu; Jair Powell; Russell Ford; Pooja Patel; Tom Driver
|
Organic Chemistry; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-09-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64fe1aff99918fe537b7f108/original/the-development-and-mechanistic-study-of-an-iron-catalyzed-intramolecular-nitroso-ene-reaction-of-nitroarenes.pdf
|
62d7f13a724581f5139f775c
|
10.26434/chemrxiv-2022-7vtxs
|
Chemometric Strategies for Fully Automated Interpretive Method Development in Liquid Chromatography
|
The great potential gains in separation power and analysis time that can result from rigorously optimizing LC-MS and 2D-LC-MS methods for routine measurements has prompted many scientists to develop computer-aided method-development tools. The applicability of these has been proven in numerous applications, but their proliferation is still limited. Arguably, the majority of LC methods are still developed in a conventional manner, i.e. by analysts who rely on their knowledge and experience. In this work, a novel, open-source algorithm was developed for automated and interpretive method development of LC separations. A closed-loop workflow was constructed that interacted directly with the LC and ran unsupervised in an automated fashion. The algorithm was tested using two newly designed strategies. The first utilized retention modeling, whereas the second used the Bayesian-optimization machine-learning approach. In both cases, the algorithm could arrive within ten iterations at an optimum of the objective function, which included resolution and measurement time. The design of the algorithm was modular, so as to facilitate compatibility with previous works in literature and its performance thus hinged on each module (e.g., signal processing, choice of retention model, objective function). Key focus areas for further improvement were identified. Bayesian optimization did not require any peak tracking or retention modeling. Accurate prediction of elution profiles was found to be indispensable for the strategy using retention modeling. This is the first interpretive algorithm demonstrated with complex samples. Peak tracking was conducted using UV-Vis absorbance detection, but use of MS detection is expected to significantly broaden the applicability of the workflow.
|
Tijmen Bos; Jim Boelrijk; Stef Molenaar; Brian van 't Veer; Leon Niezen; Denice van Herwerden; Saer Samanipour; Dwight Stoll; Patrick Forré; Bernd Ensing; Govert Somsen; Bob Pirok
|
Analytical Chemistry; Analytical Chemistry - General; Chemoinformatics; Separation Science
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-07-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d7f13a724581f5139f775c/original/chemometric-strategies-for-fully-automated-interpretive-method-development-in-liquid-chromatography.pdf
|
6380970dc56753c4189625aa
|
10.26434/chemrxiv-2022-b0gz4
|
Isolation of Bis(2-Ethylhexyl) Terephthalate and Bis(2-Ethylhexyl) Phthalate from Capparis spinosa L. Leaves
|
Capparis spinosa L., commonly known as the caper bush, is a spiny shrub known for its edible flower buds and its use as a medicinal plant in traditional medicine. While performing bio-guided isolation of active compounds from Capparis spinosa L. leaves and buds, large amounts of bis(2-ethylhexyl) terephthalate (DEHT, a.k.a. dioctyl terephthalate or DOTP) and bis(2-ethylhexyl) phthalate (DEHP) were isolated from a fraction from the leaf extract that showed antifungal activity against Cryptococcus neoformans. The structures of these two compounds were confirmed by NMR and mass spectroscopic data, which matched with those from the standards that were purchased from Sigma-Aldrich. DEHT and DEHP are phthalic and terephthalic acid esters, the main plasticizers that are used to confer elasticity and flexibility to various fiber and plastic products. This is the first time DEHT and DEHP have been isolated from the leaves of a plant that is as commonly used as Capparis spinosa L. This study adds to the increase in the detection of plasticizers in our food and medicine sources and to the alarming concern about the potential effects of these compounds on human health.
|
Ayoub Kdimy; Seong Jong Kim; Zulfiqar Ali; Md Imdadul Khan; Siddharth Tripathi; Souad El Hajjaji; Hoang Le
|
Agriculture and Food Chemistry; Food
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-11-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6380970dc56753c4189625aa/original/isolation-of-bis-2-ethylhexyl-terephthalate-and-bis-2-ethylhexyl-phthalate-from-capparis-spinosa-l-leaves.pdf
|
66f28920cec5d6c1420accd6
|
10.26434/chemrxiv-2024-5dmml
|
The Synthesis of Sulfonyl Fluoride Functionalized 2-Aminothiazoles using a Diversity Oriented Clicking Strategy
|
We present the synthesis of 16 unprecedented sulfonyl fluoride functionalized 2-aminothiazoles in good to excellent yields. The transformation is simple to perform, tolerant of a wide range of functionality and regioselective for a single product. Additionally, we showcase the diversification of the novel 2-aminothiazoles through SuFEx click chemistry. Finally, we propose a plausible stepwise reaction mechanism.
|
Joshua Kop; Carol Hua; Christopher J. Smedley
|
Biological and Medicinal Chemistry; Organic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-09-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f28920cec5d6c1420accd6/original/the-synthesis-of-sulfonyl-fluoride-functionalized-2-aminothiazoles-using-a-diversity-oriented-clicking-strategy.pdf
|
6606793ae9ebbb4db9e02852
|
10.26434/chemrxiv-2024-r0b0v-v2
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Predicting Spin States of Iron Porphyrins with DFT Methods Including Crystal Packing Effects and Thermodynamic Corrections
|
Accurate computational treatment of spin states for transition metal complexes, exemplified by iron porphyrins, lies at the heart of quantum bioinorganic chemistry, but at the same time represents a great challenge for approximate density functional theory (DFT) methods, which are predominantly used. Here, the accuracy of DFT methods for spin–state splittings in iron porphyrin is assessed by probing the ability to correctly predict the ground states for six Fe(III) or Fe(II) complexes experimentally characterized in solid state. For each case, molecular and periodic DFT calculations are employed to quantify the effect of porphyrin side substituents and the crystal packing effect (CPE) on the spin–state splitting. It is proposed to partition the total CPE into additive components, the direct and structural one, the importance of which is shown to significantly vary from case to case. By knowing the substituent effect, the CPE, and the Gibbs free energy thermodynamic correction from calculations, one can employ the experimental ground-state information in order to derive a quantitative constraint on the electronic energy difference for a simplified (porphin) model of the experimentally characterized metalloporphyrin. The constraints derived in such a way—in the form of single or double inequalities—are used to assess the accuracy of dispersion-corrected DFT methods for 6 spin–state splittings of [Fe(III)(P)(2-MeIm)2]+, [Fe(III)(P)(2-MeIm)]+, [Fe(II)(P)(THF)2] and [Fe(II)(P)] models (where P is porphin, 2-MeIm is 2-methylimidazole, THF is tetrahydrofuran). These data constitute the new benchmark set of spin states for crystalline iron porphyrins (SSCIP6). The highest accuracy is obtained in the case of double-hybrid functionals (B2PLYP-D3, DSD-PBEB95-D3), whereas hybrid functionals, especially those with reduced admixture of the exact exchange (B3LYP*-D3, TPSSh-D3), are found to considerably overstabilize the intermediate spin state, leading to incorrect ground-state prediction in Fe(III) porphyrins. The present approach, which can be generalized to other transition metal complexes, is not only useful in method benchmarking, but also sheds light on the interpretations of experimental data for metalloporphyrins, which are important models to understand the electronic properties of heme proteins.
|
Mariusz Radon
|
Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Bioinorganic Chemistry; Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6606793ae9ebbb4db9e02852/original/predicting-spin-states-of-iron-porphyrins-with-dft-methods-including-crystal-packing-effects-and-thermodynamic-corrections.pdf
|
6318aaa803e27d1e54cc51d0
|
10.26434/chemrxiv-2022-jf09w
|
Resolving high potential structural deterioration in Ni-rich layered cathode materials for lithium-ion batteries operando
|
LixNi0.90Co0.05Al0.05O2 (NCA) extracted from an automotive battery cell is studied using a combination of in-house operando techniques to understand the correlation between gas evolution and structural collapse when NCA is cycled to high potentials in a lithium-ion battery configuration. The operando techniques comprise X-ray diffraction (XRD) and online electrochemical mass spectrometry (OEMS), and cycled using intermittent current interruption (ICI). The ICI cycling protocol is used to assess the dynamic change in resistance as well as to provide a validation of the operando setups. Both gas evolution and structural collapse have previously been observed as degradation mechanisms of Ni-rich electrodes including NCA, however, their causal link is still under debate. Here our presented results show a correlation between the decrease of the interlayer distance in NCA with both an increase in CO2 evolution and diffusion resistance above 4.1 V. Additionally, particle cracking, which is a mechanism often correlated with gas evolution, was found to be reversible and visible before gas evolution and Li diffusion resistance increase. The ICI technique is shown to be useful for the correlation of operando experiments on parallel setups and evaluation of mass transport dependent processes.
|
Anastasiia Mikheenkova; Olof Gustafsson; Casimir Misiewicz; William R. Brant; Maria Hahlin; Matthew J. Lacey
|
Energy; Energy Storage; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6318aaa803e27d1e54cc51d0/original/resolving-high-potential-structural-deterioration-in-ni-rich-layered-cathode-materials-for-lithium-ion-batteries-operando.pdf
|
60c74a08842e65df93db2e67
|
10.26434/chemrxiv.12126684.v1
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Enantioselective Partitioning of Polychlorinated Biphenyls in a HepG2 Cell Culture System: Experimental and Modeling Results
|
We investigated the partitioning of chiral PCBs (PCB 91, PCB 95, PCB 132, or PCB 136) in the human hepatoma HepG2 cell line and used a computational model for the in vitro to in vivo extrapolation (IVIVE) of PCB levels. HepG2 cells were incubated with PCBs for 72 h. PCB levels were quantified in cells, media, and cell culture dishes. PCBs were present in cell culture medium > cells > dishes, and displayed atropisomeric enrichment in cells and dishes. The free PCB concentration in media, estimated using polyparameters linear free energy relationships (PP-LFERs) and a composition-based model, was used to extrapolate from the nominal PCB concentration used in vitro to PCB tissue levels and vice versa. This approach allows for an IVIVE but does not account for the atropselective partitioning of chiral PCBs between medium and cells.<br />
|
Chun-Yun Zhang; Susanne Flor; Gabriele Ludewig; Hans-Joachim Lehmler
|
Stereochemistry; Environmental Science; Environmental Analysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a08842e65df93db2e67/original/enantioselective-partitioning-of-polychlorinated-biphenyls-in-a-hep-g2-cell-culture-system-experimental-and-modeling-results.pdf
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66e082d012ff75c3a1f665ab
|
10.26434/chemrxiv-2024-glz1z
|
Cobalt-Hydride Catalyzed Alkene-Carboxylate Transposition (ACT) of Allyl Carboxylates via 1,2-Radical Migration (RaM)
|
The Alkene-Carboxylate Transposition (ACT) of allyl carboxylates is one of the most atom-economic and synthetically reliable transformations in organic chemistry, as allyl carboxylates are versatile synthetic intermediates. Classic ACT trans-formations, including 3,3-sigmatropic rearrangement and transition metal-catalyzed allylic rearrangement, typically yield 1,2-alkene/1,3-acyloxy shifted products through a two-electron process. However, position-altered ACT to produce distinct 1,3-alkene/1,2-acyloxy shifted products has remained elusive. Here, we report the first cobalt-hydride catalyzed ACT of allyl carboxylates, enabling access to these unprecedented 1,3-alkene/1,2-acyloxy shifted products via a 1,2-radical migration (RaM) strategy. This transformation demonstrates broad functional group tolerance, is suitable for late-stage modification of complex molecules, and is amenable to gram-scale synthesis. It also expands the reaction profiles of both allyl carbox-ylates and cobalt catalysis. Preliminary experimental and computational studies suggest a mechanism involving metal-hydride hydrogen atom transfer (MHAT) and 1,2-RaM process. This reaction is expected to serve as the basis for the devel-opment of versatile Co-H catalyzed transformations of allyl carboxylates, generating a wide array of valuable building blocks for synthetic, medicinal, and materials chemistry.
|
Gaoyuan Zhao; Arman Khosravi; Sahil Sharma; Djamaladdin Musaev; Ming-Yu Ngai
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis
|
CC BY 4.0
|
CHEMRXIV
|
2024-09-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e082d012ff75c3a1f665ab/original/cobalt-hydride-catalyzed-alkene-carboxylate-transposition-act-of-allyl-carboxylates-via-1-2-radical-migration-ra-m.pdf
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661e2cd091aefa6ce1aa061d
|
10.26434/chemrxiv-2023-tf1fg-v2
|
Unprecedented selectivity for homologous lectin targets: differential targeting of the viral receptors L-SIGN and DC-SIGN
|
DC-SIGN (CD209) and L-SIGN (CD209L) are two C-type lectin receptors (CLRs) that facilitate SARS-CoV-2 infections as viral co-receptors. SARS-CoV-2 manipulates both DC-SIGN and L-SIGN for enhanced infection, leading to interest in developing receptor antagonists. Despite their structural similarity (82% sequence identity), they function differently. DC-SIGN, found in dendritic cells, shapes the immune response by recognizing pathogen-associated carbohydrate patterns. In contrast, L-SIGN, expressed in airway epithelial endothelial cells, is not directly involved in immunity. COVID-19’s primary threat is the hyperactivation of the immune system, potentially reinforced if DC-SIGN engages with exogenous ligands. Therefore, L-SIGN, co-localized with ACE2-expressing cells in the respiratory tract, is a more suitable target for anti-adhesion therapy. However, designing a selective ligand for L-SIGN is challenging due to the high sequence identity of the Carbohydrate Recognition Domains (CRDs) of the two lectins. We here present Man84, a mannose ring modified with a methylene guanidine triazole at position 2. It binds L-SIGN with a KD of 12.7 μM ± 1 μM (ITC) and is the first known L-SIGN selective ligand, showing 50-fold selectivity over DC-SIGN (SPR). The X-ray structure of the L-SIGN CRD/Man84 complex reveals the guanidinium group’s role in achieving steric and electrostatic complementarity with L-SIGN. This allows us to trace the source of selectivity to a single amino acid difference between the two CRDs. NMR analysis confirms the binding mode in solution, highlighting Man84’s conformational selection upon complex formation. Dimeric versions of Man84 achieve additional selectivity and avidity in the low nanomolar range. These compounds selectively inhibit L-SIGN dependent trans-infection by SARS-CoV-2 and Ebola virus. Man84 and its dimeric constructs display the best affinity and avidity reported to date for low-valency glycomimetics targeting CLRs. They are promising tools for competing with SARS-CoV-2 anchoring in the respiratory tract and have potential for other medical applications.
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Clara Delaunay; Sara Pollastri; Michel Thépaut; Gianluca Cavazzoli; Laura Belvisi; Clémentine Bouchikri; Nuria Labiod; Ana Gimeno; Antonio Franconetti; Jesús Jiménez-Barbero; Ana Ardá; Rafael Delgado; Anna Bernardi; Franck FIESCHI
|
Biological and Medicinal Chemistry; Nanoscience; Biochemistry; Biophysics; Chemical Biology
|
CC BY 4.0
|
CHEMRXIV
|
2024-04-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661e2cd091aefa6ce1aa061d/original/unprecedented-selectivity-for-homologous-lectin-targets-differential-targeting-of-the-viral-receptors-l-sign-and-dc-sign.pdf
|
60c75824567dfe85d9ec67d1
|
10.26434/chemrxiv.12670952.v3
|
Phospholipids dock SARS-CoV-2 spike protein via hydrophobic interactions: a minimal in-silico study of lecithin nasal spray therapy
|
<div><div><div><p>Understanding the physical and chemical properties of viral infections at molecular scales is a major challenge for the scientific community more so with the outbreak of global pandemics. There is currently a lot of effort being placed in identifying molecules that could act as putative drugs or blockers of viral molecules. In this work, we computationally explore the importance in antiviral activity of a less studied class of molecules, namely surfactants. We employ all-atoms molecular dynamics simulations to study the interaction between the receptor-binding domain of the SARS-CoV-2 spike protein and the phospholipid lecithin (POPC), in water. Our microsecond simulations show a preferential binding of lecithin to the receptor-binding motif of SARS-CoV-2 with binding energies significantly larger than kBT. Furthermore, hydrophobic interactions in- volving lecithin non-polar tails dominate these binding events, which are also accompanied by dewetting of the receptor binding motif. Through an analysis of fluctuations in the radius of gyra- tion of the receptor-binding domains, its contact maps with lecithin molecules, and distributions of water molecules near the binding region, we elucidate molecular interactions that may play an important role in interactions involving surfactant-type molecules and viruses. We discuss our minimal computational model in the context of lecithin-based liposomal nasal sprays as putative mitigating therapies for COVID-19.</p></div></div></div>
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Muhammad Nawaz Qaisrani; Jawad Ur Rehman; Roman Belousov; Elham Moharramzadeh Goliaei; Ivan Girotto; Ricardo Franklin; Oriol Güell; Ali Hassanali; Edgar Roldan
|
Physical and Chemical Processes
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-04-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75824567dfe85d9ec67d1/original/phospholipids-dock-sars-co-v-2-spike-protein-via-hydrophobic-interactions-a-minimal-in-silico-study-of-lecithin-nasal-spray-therapy.pdf
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67a5794afa469535b9559535
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10.26434/chemrxiv-2025-kt9ml
|
Gate-tailoring with protons and metal cations in a flexible zeolite for high-efficiency ethylene/ethane separation
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The separation of ethylene (C2H4) from ethane (C2H6) is a critical yet energy-intensive process in the chemical industry, demanding energy-efficient and cost-effective solutions. Here, we report a Li+-exchanged silicoaluminophosphate RHO zeolite (Li-SAPO-RHO) with unprecedented selectivity for C2H4 over C2H6. This exceptional performance is attributed to the synergy between H+ and Li+ ions strategically positioned at the flexible eight-membered ring (8MR) gates of the zeolite. These ions effectively modulate the transport barriers for C2H4 and C2H6, significantly enhancing separation efficiency. Li-SAPO-RHO exhibits an Ideal Adsorbed Solution Theory selectivity exceeding 20,000 and enables the production of polymer-grade C2H4 (>99.9%) from refinery dry gas, with a productivity of up to 238.6 mmol/L. This performance surpasses that of all existing zeolite and metal-organic framework-based benchmark adsorbents. The H+-Li+ synergistic gating effect has been investigated using advanced characterization techniques, such as electron diffraction and neutron powder diffraction, along with ab initio molecular dynamics simulations. In addition to its exceptional selectivity and productivity, Li-SAPO-RHO offers advantages of low-cost synthesis, ultrahigh stability, and excellent cyclic performance, making it a highly promising candidate for industrial-scale light olefin separations.
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Xiaohe Wang; Libo Li; Nana Yan; Lei Wang; Reisel Millán; Puxu Liu; Yueying Chu; Wei Gao; Jun Xu; Yida Zhou; Juping Xu; Wen Yin; Bao Yuan; Zhenduo Wu; Avelino Corma; Shutao Xu; Zhongmin Liu; Wenfu Yan; Peng Guo; Jinping Li; Mercedes Boronat; Jihong Yu
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Physical Chemistry; Inorganic Chemistry; Materials Chemistry; Crystallography; Crystallography – Inorganic
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CC BY 4.0
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CHEMRXIV
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2025-02-10
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a5794afa469535b9559535/original/gate-tailoring-with-protons-and-metal-cations-in-a-flexible-zeolite-for-high-efficiency-ethylene-ethane-separation.pdf
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60c751f9702a9b187f18c038
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10.26434/chemrxiv.13237373.v1
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Computational Modeling Predicts the Stability of Both Pd+ and Pd2+ Ion-Exchanged into H-CHA
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<p>Passive NO<sub>x</sub> adsorbers (PNA) using Pd/zeolites have emerged as a promising solution for the reduction of cold-start emissions from vehicle exhaust. However, the nature of the active sites and the mechanisms underlying NO<sub>x</sub> adsorption in Pd/zeolites remain a subject of ongoing investigation. In this study, we employ quantum chemical simulations to investigate the structure of Pd species in cation-exchange sites at isolated Al and Al pairs in the 6-ring and 8-ring of the CHA framework, before the introduction of NO<sub>x</sub>. Our calculations show that the speciation of Pd in these exchange sites strongly depends on the precise Al arrangement within the framework, as well as the operating conditions. Ionically dispersed Pd is found to be the most favorable species over a wide range of oxidizing and reducing conditions. Small oligomers of PdO and metallic Pd do not appear to be competitive at either isolated Al or Al pairs. Notably, our calculations show that ion exchange sites other than next-next-nearest neighbor Al pairs in the 6-ring will be preferentially occupied by Pd<sup>+</sup> instead of Pd<sup>2+</sup>. The stability of Pd<sup>+</sup> in the zeolite environment is an interesting contrast with its rareness in molecular Pd compounds. Nonetheless, a detailed analysis of the electronic structure shows that predicted Pd oxidation states are consistent with chemical intuition for all complexes investigated in this study. We also discuss the potential ambiguity in Pd characterization provided by typical experimental techniques such as XANES, EXAFS and UV-VIS, and highlight the need for additional EPR spectroscopy studies to further elucidate the initial Pd speciation in zeolites for PNA applications. </p>
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Jeroen Van der Mynsbrugge; Martin Head-Gordon; Alexis T. Bell
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Computational Chemistry and Modeling
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CC BY NC ND 4.0
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CHEMRXIV
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2020-11-16
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751f9702a9b187f18c038/original/computational-modeling-predicts-the-stability-of-both-pd-and-pd2-ion-exchanged-into-h-cha.pdf
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669029525101a2ffa81c504e
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10.26434/chemrxiv-2024-7069c
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PolyUniverse: Generation of a Large-scale Polymer Library Using Rule-Based Polymerization Reactions for Polymer Informatics
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Recent advancements in machine learning have revolutionized polymer research, leading to the swift integration of diverse computational techniques for de novo molecular design. A crucial aspect of these processes is to expand the number of candidate polymer structures, as the currently known real polymer structures are very limited. In contrast, small molecule databases are vast, offering extensive opportunities for the design of new molecules, such as drug discovery. In this study, we collected extensive small molecule compounds from GDB-17, GDB-13, and PubChem, and selected polymerization reaction pathways for eight types of polymers, including polyimide, polyolefin, polyester, polyamide, polyurethane, epoxy, polybenzimidazole (PBI), and vitrimer. These small molecule datasets and polymerization reactions enabled us to generate hundreds of quadrillions of hypothetical polymer structures. For each of the eight polymers, along with one promising copolymer, poly(imide-imine), we randomly generated over one million hypothetical structures, except for PBI, for which we created 10,000 structures. Chemical space visualization using t-distributed stochastic neighbor embedding and synthetic accessibility scores were employed to assess the feasibility of synthesizing these new polymers. Customized feedforward neural network models predicted thermal, mechanical, and gas permeation properties for both real and hypothetical polymers. Results show that many hypothetical polymers, especially polyimides, exhibit significant potential, often surpassing real polymers in performance, particularly for high-temperature applications and gas separation. Our findings highlight the immense potential of large-scale hypothetical polymer libraries for materials discovery and design. These libraries not only aid in identifying promising polymer materials through high-throughput screening but also provide valuable datasets for training advanced machine learning models, such as large language models. This research also demonstrates the power of data-driven approaches in polymer science, paving the way for the development of next-generation polymeric materials with superior properties for diverse industrial applications.
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Tianle Yue; Jianxin He; Ying Li
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Polymer Science
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CC BY NC ND 4.0
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CHEMRXIV
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2024-07-12
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669029525101a2ffa81c504e/original/poly-universe-generation-of-a-large-scale-polymer-library-using-rule-based-polymerization-reactions-for-polymer-informatics.pdf
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664b7b97418a5379b0d137bf
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10.26434/chemrxiv-2023-0m1hb-v4
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Shapeshifting Ligands Mask Lewis Acidity of Dicationic Palladium(II)
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Supporting ligands limit the degree of electrophilic ac-tivation for any substrate because they also reduce the Lewis acidity of the transition metal ion. Here, we tem-porarily mask the Lewis acidity of dicationic Pd(II) by using “shapeshifting” bidentate pyrimidine/olefin lig-ands L1 and L2. These ligands delocalize/relocalize charge via reversible C–N bond formation. So, although ligated dicationic Pd compounds [1]2+ and [2]2+ appear charge separated (distributed across Pd and ligand), they react comparably to a solvated Pd(II) dication. We also observe properties that are atypical of electrophilic cata-lysts (e.g. broader functional group tolerance). We pro-pose these properties originate from the more nucleo-philic (charge separated) state. More broadly, catalysts featuring reversible dynamics may be advantaged rela-tive to structurally static counterparts.
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Karli Sipps; Wyatt Gibbs; Elvira Sayfutyarova; Jonathan Kuo
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Inorganic Chemistry; Catalysis; Organometallic Chemistry; Organometallic Compounds; Kinetics and Mechanism - Organometallic Reactions; Ligand Design
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CC BY NC ND 4.0
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CHEMRXIV
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2024-05-21
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664b7b97418a5379b0d137bf/original/shapeshifting-ligands-mask-lewis-acidity-of-dicationic-palladium-ii.pdf
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60c7542cbb8c1a3aab3dc1b7
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10.26434/chemrxiv.13621220.v1
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Porous Colloidal Hydrogels Formed by Coordination-Driven Self-Assembly of Charged Metal-Organic Polyhedra
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Introduction of porosity into supramolecular gels endows soft materials with functionalities for molecular encapsulation, release, separation and conversion. Metal-organic polyhedra (MOPs), discrete coordination cages containing an internal cavity, have recently been employed as building blocks to construct polymeric gel networks with potential porosity. However, most of the materials can only be synthesized in organic solvents, and the examples of porous, MOP-based hydrogels are scarce. Here, we demonstrate the fabrication of porous hydrogels based on [Rh<sub>2</sub>(OH-bdc)<sub>2</sub>]<sub>12</sub>, a rhodium-based MOP containing hydroxyl groups on its periphery (OH-bdc = 5-hydroxy-1,3-benzenedicarboxylate). By simply deprotonating [Rh<sub>2</sub>(OH-bdc)<sub>2</sub>]<sub>12</sub> with the base NaOH, the supramolecular polymerization between MOPs and organic linkers can be induced in the aqueous solution, leading to the kinetically controllable formation of hydrogels with hierarchical colloidal networks. When heating the deprotonated MOP, Na<sub>x</sub>[Rh<sub>24</sub>(O-bdc)<sub>x</sub>(OH-bdc)<sub>24-x</sub>], to induce gelation, the MOP was found to partially decompose, affecting the mechanical property of the resulting gels. By applying a post-synthetic deprotonation strategy, we show that the deprotonation degree of the MOP can be altered after the gel formation without serious decomposition of the MOPs. Gas sorption measurements confirmed the permanent porosity of the corresponding aerogels obtained from these MOP-based hydrogels, showing potentials for applications in gas sorption and catalysis.
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Zaoming Wang; Gavin Craig; alexandre legrand; Frederik Haase; Saori Minami; Kenji Urayama; Shuhei Furukawa
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Supramolecular Chemistry (Inorg.)
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CC BY NC 4.0
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CHEMRXIV
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2021-01-22
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7542cbb8c1a3aab3dc1b7/original/porous-colloidal-hydrogels-formed-by-coordination-driven-self-assembly-of-charged-metal-organic-polyhedra.pdf
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65e733e8e9ebbb4db9f39e61
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10.26434/chemrxiv-2024-mm272
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Simultaneous multi-resonant thermally activated delayed fluorescence and room temperature phosphorescence from biluminescent nitrogen-containing indolocarbazoles
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Organic biluminescence, the simultaneous emission from both the singlet and triplet excited state manifolds, is a rare and incompletely understood emission process. However, biluminescent compounds have wide-reaching applications, such as in sensing, anti-counterfeiting, and optoelectronics, owing to the complex interplay of excited states having distinct spectral profiles and lifetimes. Herein, we describe the biluminescence of a family of polycyclic aromatic heterocycles known as nitrogen-containing indolocarbazoles (NICz). As 1 wt% doped films in polymethylmethacrylate (PMMA), these compounds exhibit dual fluorescence/room temperature phosphorescence (RTP) with λPL in the near-UV (ca. 375 nm) and green (ca. 500 nm), respectively, and remarkably long phosphorescence lifetimes extending into the multi-second regime. This RTP is shown to persist even at doping concentrations as low as 0.1 wt%. Additionally, two of the emitters exhibit multi-resonant thermally activated delayed fluorescence (MR-TADF)/RTP biluminescence, which, to the best of our knowledge, would be the first examples of such behavior. Finally, we provide insight into the dependence of these competing emission pathways on the temperature and concentration, with supporting wavefunction-based computations.
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Oliver Lee; Aidan McKay; David Cordes; Malte Gather; Eli Zysman-Colman
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Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Spectroscopy (Physical Chem.); Materials Chemistry
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CC BY 4.0
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CHEMRXIV
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2024-03-06
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e733e8e9ebbb4db9f39e61/original/simultaneous-multi-resonant-thermally-activated-delayed-fluorescence-and-room-temperature-phosphorescence-from-biluminescent-nitrogen-containing-indolocarbazoles.pdf
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