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678ded8d6dde43c908472edf
|
10.26434/chemrxiv-2025-4lskc
|
dMSGB-IE: Computational Mutational Scanning for (de)Methylation Thermodynamics
|
The (de)methylation regulates the functional interactions between unstructured N-terminal of histone and other globular proteins. The multistate behavior of the methyl-substitution makes the situation complex, e.g., being mono-methylated, di-methylated, or tri-methylated. As a pivotal epigenetic marker, understanding its thermodynamic impact on protein-protein binding is crucial for the elucidation of the regulation mechanism of epigenetic modifications on target genes. To this aim, in this work we present a cost-effective free energy technique named computational (de)methylation scanning with generalized Born and interaction entropy (dMSGB-IE). Our regime is built on implicit-solvent-based end-point free energy techniques, and provides an efficient route to access the (de)methylation-induced affinity change with a screening power comparable to costlier alchemical free energy calculations. We use a batch of histone-reader recognition protein-protein complexes as illustrative cases, showing the capabilities and reliabilities of dMSGB-IE.
|
Zhendong Li; Lei Zheng; Yuqing Yang; Xiaohui Wang; Zhaoxi Sun; John Zeng Hui Zhang
|
Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Computational Chemistry and Modeling; Thermodynamics (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678ded8d6dde43c908472edf/original/d-msgb-ie-computational-mutational-scanning-for-de-methylation-thermodynamics.pdf
|
61cb1558a53f1b06b9ab3cde
|
10.26434/chemrxiv-2021-rd08s
|
Decoding key transient inter-catalyst interactions in a metallaphotoredox-catalysed cross-electrophile coupling reaction
|
Metallaphotoredox chemistry has recently witnessed a renaissance through the use of abundant first-row transition metals combined with suitable photocatalysts. The intricate details arising from the combination of two (or more) catalytic components during the reaction and specially the inter-catalyst interactions remain poorly understood. As a representative example of a catalytic process featuring such intricacies, we here present a meticulous study of the mechanism of a cobalt-organophotoredox catalysed allylation of aldehydes. Importantly, the commonly proposed elementary steps in reductive metallaphotoredox chemistry are more complex than previously assumed. After initial reductive quenching, a transient charge-transfer complex forms that interacts with both the transition-metal catalyst, as well as the catalytic base. Surprisingly, the former interaction leads to deactivation due to induced charge recombination, while the latter promotes deprotonation of the electron donor, which is a crucial step in order to promote productive catalysis, but is often neglected. Due to the low efficiency of this process, the overall catalytic reaction is photon-limited and the cobalt catalyst remains in a dual resting state awaiting photoinduced reduction. These new insights are of general importance to the synthetic community, as photoredox chemistry has become a powerful tool used in the creation of elusive compounds through carbon-carbon bond formations. Understanding the underlying factors that determine the efficiency of such reactions provides a conceptually stronger reactivity paradigm to empower future approaches to synthetic challenges that rely on dual metallaphotoredox catalysis.
|
Bart Limburg; Àlex Cristòfol; Arjan Kleij
|
Physical Chemistry; Organic Chemistry; Catalysis; Homogeneous Catalysis; Photocatalysis; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-12-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61cb1558a53f1b06b9ab3cde/original/decoding-key-transient-inter-catalyst-interactions-in-a-metallaphotoredox-catalysed-cross-electrophile-coupling-reaction.pdf
|
60c73d989abda2a783f8b749
|
10.26434/chemrxiv.12550523.v4
|
A Computational and Literature-Based Evaluation for a Combination of Chiral Anti-CoV Drugs to Block and Eliminate SARS-CoV-2 Safely
|
<p><a>It has been a great challenge for scientists to
develop an anti-covid drug/vaccine with fewer side effects, since the
coronavirus began. Of course, the prescription of chiral
drugs (chloroquine or hydroxychloroquine) has
been proved wrong because these chiral drugs neither kill the virus nor
eliminate it from the body, but block SARS-CoV-2
from binding to human cells. Another hurdle in front of the world, is
not only the positive test of the patient recovered from coronavirus but also
the second wave of Covid 19. Hence, the word demands such
a drug or drug combination which not only prevents the entry of SARS-CoV-2 in
the human cell but also eliminates it or its material from the body completely.
The presented computational study explains (i) why the prescription of
chiral drugs was not satisfactory (ii) what types of modification can make their
prescription satisfactory (iii) the mechanism of action of chiral drugs (chloroquine and hydroxychloroquine) to block SARS-CoV-2 from binding to human cells, and (iv) the
strength of mefloquine to eliminate SARS-CoV-2. As the main protease (M<b><sup>pro</sup></b>)
of microbes is considered as an effective target for drug design and development,
the binding affinities of mefloquine with the main proteases (M<sup>pros</sup>)
of JC virus and SARS-CoV-2, were calculated,
and then compared to know the eliminating strength of mefloquine against SARS-CoV-2. The main protease (M<sup>pro</sup>) of JC
virus was taken because mefloquine has already shown a
tremendous result of eliminating it from the body. The current study includes the
docking results and literature data in support of the prescription of a combination
of S-(+)-hydroxychloroquine and (+) mefloquine. Besides, the presented
study also confirms that the prescription of only hydroxychloroquine
would not be so effective as in combined form with mefloquine.</a></p>
|
Mohd. Suhail
|
Biochemistry; Chemical Biology; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-06-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d989abda2a783f8b749/original/a-computational-and-literature-based-evaluation-for-a-combination-of-chiral-anti-co-v-drugs-to-block-and-eliminate-sars-co-v-2-safely.pdf
|
61f13ef41916370a0cf4b36e
|
10.26434/chemrxiv-2022-7859b
|
Computer- and NMR-aided design of small-molecule inhibitors of the Hub1 protein
|
Protein-protein interactions play a key role in cell homeostasis and physiological functions of the organisms. Consequently, their malfunction leads to diseases such as cancer, metastasis and neurodegeneration. The Hub1/Snu66 interaction is responsible for controlling alternative splicing through non-covalent binding to the HIND (Hub1-Interacting Domain) domain of the Snu66 spliceosomal protein. To better understand how Hub1 works in living organisms, we conducted a study to find small molecules that have an affinity for the Snu66 binding site of Hub1. The in silico investigation was based on global peptide modeling followed by high-resolution protein-peptide refinement. Docking analysis of nearly 200 molecules in the binding pocket of Hub1 is also described. Finally, Nuclear Magnetic Resonance fragment-based screening was used to confirm our findings.
|
Ewa Surmiak; Katarzyna Kubica; Atilio Reyes Romero; Jacek Plewka; Ismael Rodriguez; Katarzyna Magiera-Mularz; Alexander Domling; Tad Holak
|
Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-01-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f13ef41916370a0cf4b36e/original/computer-and-nmr-aided-design-of-small-molecule-inhibitors-of-the-hub1-protein.pdf
|
60c7455bbdbb890061a389d9
|
10.26434/chemrxiv.10006607.v1
|
Formation of Enamines via Catalytic Dehydrogenation by Pincer-Iridium Complexes
|
Efficient pincer-ligated iridium catalysts are reported for the dehydrogenation of simple tertiary amines to give enamines, and for the dehydrogenation of β-functionalized amines to give the corresponding 1,2-difunctionalized olefins. Experimentally determined kinetic isotope effects in conjunction with DFT-based analysis support a dehydrogenation mechanism involving initial pre-equilibrium oxidative addition of the amine α C-H bond followed by rate-determining elimination of the β-C-H bond.<br />
|
Xiawei Zhang; Santanu Malakar; Karsten Krogh-Jespersen; Faraj Hasanayn; Alan Goldman
|
Catalysis; Small Molecule Activation (Organomet.); Theory - Organometallic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-10-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7455bbdbb890061a389d9/original/formation-of-enamines-via-catalytic-dehydrogenation-by-pincer-iridium-complexes.pdf
|
60c744874c89193ab9ad2819
|
10.26434/chemrxiv.9858500.v1
|
Design and Development of Fe-Catalyzed Intra- and Intermolecular Carbofunctionalization of Vinyl Cyclopropanes
|
Design and implementation of the first (asymmetric) Fe-catalyzed intra- and intermolecular difunctionalization of vinyl cyclopropanes (VCPs) with alkyl halides and aryl Grignard reagents has been realized via a mechanistically driven approach. Mechanistic studies support the diffusion of the alkyl radical intermediates out of the solvent cage to participate in an intra- or -intermolecular radical cascade with the VCP followed by re-entering the Fe radical cross-coupling cycle to undergo selective C(sp2)-C(sp3) bond formation. Overall, we provide new design principles for Fe-mediated radical processes and underscore the potential of using combined computations and experiments to accelerate the development of challenging transformations.
|
Lei Liu; Wes Lee; Mingbin Yuan; Chris Acha; Michael B. Geherty; Brandon Williams; Osvaldo Gutierrez
|
Organic Synthesis and Reactions; Physical Organic Chemistry; Stereochemistry; Computational Chemistry and Modeling; Base Catalysis; Homogeneous Catalysis; Catalysis; Kinetics and Mechanism - Organometallic Reactions; Reaction (Organomet.); Theory - Organometallic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-09-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744874c89193ab9ad2819/original/design-and-development-of-fe-catalyzed-intra-and-intermolecular-carbofunctionalization-of-vinyl-cyclopropanes.pdf
|
6605b0fd66c1381729187cfb
|
10.26434/chemrxiv-2024-r636h
|
Discovery of molecular intermediates and non-classical nanoparticle formation mechanisms by liquid phase electron microscopy and reaction throughput analysis
|
The formation kinetics of metal nanoparticles are generally described via mass transport and thermodynamics-based models, such as diffusion limited growth and classical nucleation theory (CNT). However, metal monomers are commonly assumed as precursors, leaving the identity of molecular intermediates and their contribution to nanoparticle formation unclear. Here we utilize liquid phase transmission electron microscopy (LPTEM) and reaction kinetic modeling to establish the nucleation and growth mechanisms and discover molecular intermediates during silver nanoparticle formation. Quantitative LPTEM measurements showed that their nucleation rate decreased while growth rate was nearly invariant with electron dose rate. Reaction kinetic simulations showed that Ag4 and Ag- followed a statistically similar dose rate dependence as the experimentally determined growth rate. We demonstrate that experimental growth rates are consistent with diffusion limited growth via attachment of these species to nanoparticles. Dose rate dependence of nucleation rate was inconsistent with CNT. We propose a reaction limited nucleation mechanism and demonstrate that experimental nucleation kinetics are consistent with Ag42+ aggregation rates at millisecond time scales. Reaction throughput analysis of the kinetic simulations uncovered formation and decay pathways mediating intermediate concentrations. The work demonstrates the power of quantitative LPTEM combined with kinetic modeling for establishing nanoparticle formation mechanisms and the principal intermediates.
|
Jiayue Sun; Birk Fritsch; Andreas Korner; Mehran Taherkhani; Chiwoo Park; Mei Wang; Andreas Hutzler; Taylor Woehl
|
Materials Science; Nanoscience; Aggregates and Assemblies; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-03-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6605b0fd66c1381729187cfb/original/discovery-of-molecular-intermediates-and-non-classical-nanoparticle-formation-mechanisms-by-liquid-phase-electron-microscopy-and-reaction-throughput-analysis.pdf
|
60c74266702a9b0e9918a426
|
10.26434/chemrxiv.8217326.v2
|
Rational Engineering of Hydratase from Lactobacillus Acidophilus Reveals Critical Residues Directing Substrate Specificity and Regioselectivity
|
<div>Enzymatic conversion of abundant fatty acids (FAs) through fatty acid hydratases (FAHs) presents an environment-friendly and efficient route for production of high-value hydroxy fatty acids (HFAs). However, a limited diversity was achieved among HFAs to date with respect to chain length and hydroxy group position, due to high substrate- and regio-selectivity of hydratases. In this study, we compared two highly similar FAHs from <i>Lactobacillus acidophilus</i>: FA-HY2 has narrow substrate scope and strict regioselectivity, whereas FA-HY1 utilize longer chain substrates and hydrate various double bond positions. We reveal three active-site residues that play remarkable role in directing substrate specificity and regioselectivity of hydration. When these residues on FA-HY2 are mutated to the corresponding residues in FA-HY1, we observe a significant expansion of substrate scope and distinct shift and enhancement in hydration of double bonds towards omega-end of FAs. A three-residue mutant of FA-HY2 (TM-FA-HY2; T391S/H393S/I378P) displayed an impressive reversal of regioselectivity towards linoleic acid, shifting ratio of the HFA product regioisomers (10-OH:13-OH) from 99:1 to 12:88. Although kcat values are still low in comparison to wild-type FA-HY1, TM-FA-HY2 exhibited about 60-fold increase in catalytic efficiency (<i>k</i><sub>cat</sub>/<i>K</i><sub>m</sub>) compared to wild-type FA-HY2. Important changes in regioselectivity were also observed with mutant enzymes for arachidonic acid and C18 PUFAs. In addition, TM-FA-HY2 variant exhibited high conversion rates for <i>cis</i>-5, <i>cis</i>-8, <i>cis</i>-11,<i> cis</i>-14, <i>cis</i>-17-eicosapentaenoic acid (EPA) and <i>cis</i>-8, <i>cis</i>-11, <i>cis</i>-14-eicosatrienoic acid (ETA) at preparative scale and enabled isolation of 12-hydroxy products with moderate yields. Furthermore, we demonstrated the potential of microalgae as a source of diverse FAs for HFA production. Our study paves the way for tailor-made FAH design and for efficient conversion of FA sources into diverse range of HFAs with high potential for various applications from polymer industry to medical field.</div><div><br /></div>
|
Bekir Engin Eser; Michal Poborsky; Rongrong Dai; Shigenobu Kishino; Anita Ljubic; Michiki Takeuchi; Charlotte Jacobsen; Jun Ogawa; Peter Kristensen; Zheng Guo
|
Biochemistry; Bioengineering and Biotechnology; Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74266702a9b0e9918a426/original/rational-engineering-of-hydratase-from-lactobacillus-acidophilus-reveals-critical-residues-directing-substrate-specificity-and-regioselectivity.pdf
|
65c60e4966c138172947d5a7
|
10.26434/chemrxiv-2024-xlst1
|
En Route to a Molecular Terminal Tin Oxide
|
In the pursuit of terminal tin chalcogenides, heteroleptic stannylenes bearing terphenyl and hexamethyldisilazide ligands were reacted with carbodiimides to yield the respective guanidinato complexes. Further supported by quantum chemical calculations, this revealed that the iso-propyl-substituted derivative provides the maximum steric protection achievable. Oxidation with elemental selenium produced monomeric terminal tin selenides with four-coordinate tin centres. In reactions with N2O as oxygen transfer reagent, silyl migration towards putative terminal tin oxide intermediates gave rise to tin complexes with terminal –OSiMe3 functionality. To prevent silyl migration, the silyl groups were substituted for cyclohexyl moieties. This analogue exhibited distinctively different reactivities towards selenium and N2O, yielding a tetraselenastannolane and chalcogenide-bridged dimeric compounds, respectively.
|
Leon Kreßner; Daniel Duvinage; Pim Puylaert; Nico Graw; Regine Herbst-Irmer; Dietmar Stalke; Oliver P. E. Townrow; Malte Fischer
|
Inorganic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-02-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c60e4966c138172947d5a7/original/en-route-to-a-molecular-terminal-tin-oxide.pdf
|
6414e97b2bfb3dc251f12d88
|
10.26434/chemrxiv-2023-dptqs
|
An Isotope Dilution Mass Spectrometry Assay to track Norovirus-Like Particles in Vaccine Process Intermediates by Quantifying Capsid Protein VP1
|
The coronavirus disease (COVID-19) pandemic shows the rapid pace at which vaccine development can occur which highlights the need for more fast and efficient analytical methodologies to track and characterize candidate vaccines during manufacturing and purification processes. The candidate vaccine in this work comprises plant-derived Norovirus-like particles (NVLPs) which are structures that mimic the virus but lack any infectious genetic material. Presented here is a liquid chromatography-tandem mass spectrometry (LC-MS/MS) methodology for the quantification of viral protein VP1, the main component of the NVLPs in this study. It combines isotope dilution mass spectrometry (IDMS) with multiple reaction monitoring (MRM) to quantify targeted peptides in process intermediates. Multiple MRM transitions (precursor/product ion pairs) for VP1 peptides were tested with varying MS source conditions and collision energies. Final parameter selection for quantification includes three peptides with two MRM transitions each offering maximum detection sensitivity under optimized MS conditions. For quantification, a known concentration of the isotopically labeled version of the peptides to be quantified was added into working standard solutions to serve as an internal standard (IS); calibration curves were generated for concentration of native peptide vs. the peak area ratio of native-to-isotope labeled peptide. VP1 peptides in samples were quantified with labeled versions of the peptides added at the same level as that of the standards. Peptides were quantified with limit of detection (LOD) as low as 1.0 fmol/μL and limit of quantitation (LOQ) as low as 2.5 fmol/μL. NVLP preparations spiked with known quantities of either native peptides or drug substance (DS) comprising assembled NVLPs produced recoveries indicative of minimal matrix effects. Overall, we report a fast, specific, selective, and sensitive LC-MS/MS strategy to track NVLPs through the purification steps of the DS of a Norovirus candidate vaccine.
|
Jacquelyn Jhingree; Julie Boisvert; Geneviève Mercier
|
Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry; Separation Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6414e97b2bfb3dc251f12d88/original/an-isotope-dilution-mass-spectrometry-assay-to-track-norovirus-like-particles-in-vaccine-process-intermediates-by-quantifying-capsid-protein-vp1.pdf
|
61082b2f7bf0c92652627a31
|
10.26434/chemrxiv-2021-4pq0b
|
Accounting for Dispersion Effects in DFT Framework of Electrocatalysis: A Case Study of Solvent Mediated Oxygen Reduction Reaction
|
Density functional theory (DFT) is a pivotal tool in the field of computational electrocatalysis. Dispersion effects, which are not incorporated in the regular DFT framework, play a significant role in improving the accuracy of DFT-based catalytic simulations. We perform a calibration study for addressing the effect of different dispersion corrected DFT methods in determining the electrocatalytic properties by conducting a case study of oxygen reduction reaction (ORR). The distinct trends of these methods towards determining the structural, energetic, and electronic properties of catalysis are scrutinized. By systematically incorporating an upgraded solvation model, the importance of the inclusion of dispersion effects for the accurate prediction of chemical and physical properties governing the catalytic activity is illustrated. The combined thermodynamic and kinetic analysis predicts a uniform ORR activity trend, with semi-empirical dispersion corrected DFT methods emerging as optimal choices with comparable or higher accuracy than advanced van der Waal’s methods.
|
Akhil S. Nair; Biswarup Pathak
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY 4.0
|
CHEMRXIV
|
2021-08-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61082b2f7bf0c92652627a31/original/accounting-for-dispersion-effects-in-dft-framework-of-electrocatalysis-a-case-study-of-solvent-mediated-oxygen-reduction-reaction.pdf
|
661d535991aefa6ce19d8715
|
10.26434/chemrxiv-2024-qzcd5
|
Unraveling O-Glycan Diversity of Mucins: Insights from SmE Mucinase and Ultraviolet Photodissociation Mass Spectrometry
|
Deciphering the pattern and abundance of O-glycosylation of mucin domain proteins, glycoproteins heavily implicated in cancer and other diseases, remains an ongoing challenge. Both the macro- and micro-heterogeneity of glycosylation complicates the analysis, motivating the development of new strategies for structural characterization of this diverse class of glycoproteins. Here we combine digestion of mucin domain proteins using a targeted protease, Enhancin from Serratia marcescens (SmE), with ultraviolet photodissociation (UVPD) mass spectrometry to advance glycan mapping and elucidation of O-glycosylation trends of densely glycosylated mucin proteins. UVPD facilitates identification of O-glycoforms of mucin domain proteins TIM-1, MUC-1 and MUC-16. Additionally, UVPD elucidates several glycoforms of MUC-16 and unravels O-glycosylation across tandem repeats of MUC-1.
|
Amanda Helms; Vincent Chang; Stacy Malaker; Jennifer Brodbelt
|
Analytical Chemistry; Mass Spectrometry
|
CC BY 4.0
|
CHEMRXIV
|
2024-04-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661d535991aefa6ce19d8715/original/unraveling-o-glycan-diversity-of-mucins-insights-from-sm-e-mucinase-and-ultraviolet-photodissociation-mass-spectrometry.pdf
|
62bc77679ca5bb77faeb4f5d
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10.26434/chemrxiv-2022-39t56
|
Vinylimidazole–based Polymer Electrolytes with Superior Conductivity and Promising Electrochemical Performance for Calcium Batteries
|
Calcium batteries are next–generation energy storage technologies with promising techno-economic benefits. However, performance bottlenecks associated to conventional electrolytes with oxygen–based coordination chemistries must be overcome to enable faster cation transport. Here, we report an imidazole–based polymer electrolyte with the highest reported conductivity and promising electrochemical properties. The polymerization of vinylimidazole in the presence of calcium bis(trifluoromethanesulfonyl)imide (Ca(TFSI)2) salt creates a gel electrolyte comprising a polyvinyl imidazole (PVIm) host infused with vinylimidazole liquid. Calcium ions effectively coordinate with imidazole groups, and the electrolytes present room temperature conductivities >1 mS/cm. Reversible redox activity in symmetric Ca cells is demonstrated at 2 V overpotentials, stably cycling at 0.1 mA/cm2 and areal capacities of 0.1 mAh/cm2. Softer coordination, polarizability, and closer coordinating site distances of the imidazole groups can explain the enhanced properties. Hence, imidazole is a suitable benchmark chemistry for future design and advancement of polymer electrolytes for calcium batteries.
|
Shreyas Pathreeker; Ian D. Hosein
|
Physical Chemistry; Polymer Science; Energy; Polymerization (Polymers); Energy Storage; Electrochemistry - Mechanisms, Theory & Study
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-06-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bc77679ca5bb77faeb4f5d/original/vinylimidazole-based-polymer-electrolytes-with-superior-conductivity-and-promising-electrochemical-performance-for-calcium-batteries.pdf
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60c73e16bb8c1a983f3d986c
|
10.26434/chemrxiv.6510125.v1
|
From Amines to Alkynes – Lighting the Way
|
We present a metal-free photoredox strategy for the formation of Csp3-Csp bonds from redox-activated primary amine derivatives. The developed reaction of 2,4,6-triphenylpyridiniu salts with alkynyl tosylates, leading to functionalized alkynes , is easily scalable, offers broad substrate scope, high chemoselectivity, and mild conditions. Its potentials also highlighted by diversification of complex molecular scaffolds. Moreover, mechanistic studies contribute to the elucidation of unexpected differences in reactivity of primary, secondary and alkyl pyridinium salts.
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Dorota Gryko; Michał Ociepa; Joanna Turkowska
|
Organic Synthesis and Reactions; Photocatalysis; Redox Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-06-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e16bb8c1a983f3d986c/original/from-amines-to-alkynes-lighting-the-way.pdf
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64f9b258b6ab98a41c023f05
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10.26434/chemrxiv-2023-l3knn
|
Wall-slip effects on the Yield-stress fluid flows in the rigid and deformable channel
|
Yield stress fluids flow through deformable conduits and are prevalent in nature and have numerous technological applications [1-11]. In this paper, we focus on investigating the impact of many factors such as the deformability of the channel-wall, yield stress, shear-thinning, and shear-thickening index in the presence of slip and compared it with flow dynamics with no-slips as predicted by Garg and Prasad [12]. Using lubrication theory, we have derived a model for the velocity profiles and flow rate using the Herschel-Bulkley rheological model in rigid and deformable shallow channels with slip-walls. To model deformable walls, we have utilized small displacement structural mechanics and perturbation theory presented by Gervais et al. [13] and Christov et al. [14], respectively. Our newly developed model encompasses the flow characteristics of Newtonian fluids, power-law fluids, and Bingham fluids, both with and without wall-slip, as observed in previous literature [13-16]. We find that the deformability increases the same effective channel height with and without wall-slip but the flow rate is increased more when slips are present within the channel. We find many scalings for the flow rate under different regimes of applied pressure and the deformability parameter. A threshold inlet pressure is required for the onset of yield-stress fluid flow in the channels unlike in the case of the Newtonian or power-law fluids. Garg and Prasad [12] finds that below this threshold, the flow is choked in the channels with plug height the same as the channel height: we find the same observations in the presence of slips. Although in case of deformable channels an early onset of flow with the pressure is found in comparison to the rigid channel. We observe the back flow due to deformability in the channel when the yield surface is between $H_o/2 < H_p < (H_o+\delta)/2$, where $H_o$ and $H_p$ represents the initial height of the channel without deformability and the yield surface’s height, respectively. $\delta$ is the increase in channel's height due to deformability. Beyond choked flow, the plug height decreases for both the rigid and the deformable channels with the pressure. We also observe that for any given applied pressure and yield stress, the $(H_p)_{\text{deformable}} < (H_p)_{\text{rigid}}$. This suggests that deformable walls decrease the plug region in comparison to the rigid channel. We also find that the wall-slip has no effect on the plug region and the onset of flow. In the presences of wall-slip, we also find that increasing the yield stress leads to a decrease in the velocity in the plug flow as well as in the non-plug flow regions. Increasing yield stress also leads to increasing the yield surface height and the solid plug in the central region due to which there is decrease in the flow rate similar to as found by Garg and Prasad [12]. Further, we also find that the shear thinning/thickening index does not affect the plug height, although as the index increases, the flow rate starts to decrease due to the corresponding increase in shear thickening of the material.
|
Ashish Garg; Pranjal Prasad
|
Polymer Science; Nanoscience; Chemical Engineering and Industrial Chemistry; Nanofluidics; Fluid Mechanics
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CC BY NC ND 4.0
|
CHEMRXIV
|
2023-09-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f9b258b6ab98a41c023f05/original/wall-slip-effects-on-the-yield-stress-fluid-flows-in-the-rigid-and-deformable-channel.pdf
|
60c748ab4c89195347ad2f77
|
10.26434/chemrxiv.11859885.v2
|
Sorption Hysteresis on Soils and Sediments: Obtaining Characteristic Free Energies Using "Single-Point Desorption Isotherms"
|
<p>Sorption-desorption hysteresis (SDH) may control distributions
of chemicals between diverse environmental phases, including soils and
sediments. Formation of metastable states caused
by pore deformation or inelastic swelling of a sorbent and their
persistence during desorption were considered in the literature as one reason
for "true" SDH. Such metastable states persisting during desorption lead
to the lack of closure of sorption-desorption loop at non-zero sorbate concentrations,
which is often observed in soil and environmental literature. Also, SDH was often characterized using single-point desorption isotherms
(DIs) combining sorbed states reached during single desorption steps started
from different points along a sorption isotherm (SI). The objective of this
contribution is to demonstrate how the single-point DIs could be used to
characterize SDH in liquid phase sorption experiments in terms of Gibbs free
energy. This free energy is accumulated in some non-relaxed sorbed states
belonging to DI as compared with the states of the same composition (sorbed
concentration) belonging to SI. Using the literature
data on SIs and single-point DIs of some polycyclic aromatic hydrocarbons and
pesticides on soils and sediments, it is shown how these
extra free energies could be obtained and how they could change in the selected
sorbate-sorbent systems. When the extent of SDH decreases with increasing
solute concentration, these additional free energies decline. They may remain
constant or even increase, suggesting in the latter case that a larger work is
needed to perturb a sorbent structure at higher sorbed concentrations. This paper
proposes a novel approach for quantifying and understanding liquid phase SDH in
the cases when a thermodynamic justification is sought, and, therefore, it advances
the ability to predict the fate and activity of multiple chemicals in typical soil/sediment
environments. </p><p><br /></p>
|
Mikhail Borisover
|
Environmental Science; Geochemistry; Hydrology and Water Chemistry; Soil Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-02-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748ab4c89195347ad2f77/original/sorption-hysteresis-on-soils-and-sediments-obtaining-characteristic-free-energies-using-single-point-desorption-isotherms.pdf
|
60c750c99abda28572f8dac1
|
10.26434/chemrxiv.13050242.v1
|
From Science Student to Scientist
|
Science students are taught that science is a collection of facts and equations when in fact, science is a journey full of false starts, dead ends, and creative detours undertaken by scientists to uncover the truth of reality. A science student seeking to become a scientist must often regress back to a state of childlike wonder and curiosity to prepare for such a journey. We seek to spark this change with hundreds of Quick Takes and Inquiries into specifically chemistry and physics at the introductory level. Each question demands the student to strike out into the wilderness of knowledge---to think deeply, read and ask widely, and model extensively. Upon completion of this curriculum, students should be equipped with the knowledge and mindset to conceive of and execute independent scientific investigations of their own. We also hope that science teachers are inspired to incorporate our open-ended investigations into their own curricula.
|
Derek Wang; David Dai
|
Chemical Education - General
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-10-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750c99abda28572f8dac1/original/from-science-student-to-scientist.pdf
|
62acbd6104a3a911c04a6528
|
10.26434/chemrxiv-2022-hcz2m
|
Appearing as eumelanin or as pheomelanin and the push towards eumelanin by cysteine.
|
This report is a combination of new and former experimental results collected over the past three years. It details our observations and spectroscopic studies of the air-mediated oxidation of a wide variety of catecholic precursors into melanin-like materials. Depending on the precursor involved and the reaction conditions employed, dark-brown to black or yellow to rusty-orange colored reaction mixtures, akin to eumelanin- or pheomelanin-like materials, can be obtained. This report expands and confirms an earlier report that behind the dark colors of eumelanin-like materials, distinct, light-colored, pheomelanin-like materials are hidden. In addition, this report expands and confirms earlier observations regarding the effect of the presence of amino acids on the color of the reaction mixture; particularly the effect of the presence of cysteine. The presence of cysteine delays the onset of color formation and leads to dark-colored reaction mixtures; turning pheomelanin-like reaction mixtures into eumelanin-like mixtures. Visible and infrared spectroscopic analyses were made to evaluate the nature, eumelanin- vs. pheomelanin-like, of the materials generated under the varying reaction conditions. Reactions involving epinephrine as the precursor presented unique results which are detailed in this report.
|
Koen Vercruysse; Venise Govan; Jada Harrison; Tyona Caldwell; Jaila Winford
|
Biological and Medicinal Chemistry; Biochemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-06-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62acbd6104a3a911c04a6528/original/appearing-as-eumelanin-or-as-pheomelanin-and-the-push-towards-eumelanin-by-cysteine.pdf
|
62c9b4588a8b390d3dd62e78
|
10.26434/chemrxiv-2022-jl7rs-v2
|
Scavengome of an Antioxidant
|
The term ‘scavengome’ refers to the chemical space of all the metabolites that may be formed from an antioxidant upon scavenging reactive oxygen or nitrogen species (ROS/RNS). This chemical space is very rich in structures representing an increased chemical complexity as compared to the parent antioxidant: a wide range of unusual heterocyclic structures, new C-C bonds, etc. may be formed. Further, in a biological environment, this increased chemical complexity is directly translated from the localized conditions of oxidative stress that determines the amounts and types of ROS/RNS present. Biomimetic oxidative chemistry provides an excellent tool to model chemical reactions between antioxidants and ROS/RNS. In this chapter, we provide an overview on the known metabolites obtained by biomimetic oxidation of a few selected natural antioxidants, i.e., a stilbene (resveratrol), a pair of hydroxycinnamates (caffeic acid and methyl caffeate), and a flavonol (quercetin), and discuss the drug discovery perspectives of the related chemical space.
|
Attila Hunyadi; Orinamhe Godwin Agbadua; Gergely Takács; György Tibor Balogh
|
Biological and Medicinal Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-07-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c9b4588a8b390d3dd62e78/original/scavengome-of-an-antioxidant.pdf
|
60c74eee469df4e515f4459e
|
10.26434/chemrxiv.12661514.v2
|
Spectroscopic and Electrokinetic Evidence for a Bifunctional Mechanism of the Oxygen Evolution Reaction
|
The oxygen evolution reaction (OER) is an essential anodic reaction in many energy storage processes. OER is most often proposed to occur via a mechanism involving four consecutive proton-coupled electron transfer (PCET) steps, which imposes a performance limit due to the scaling relationship of various oxygen intermediates. A bifunctional OER mechanism, in which the energetically demanding step of the attack of hydroxide on a metal oxo unit is facilitated by a hydrogen atom transfer to a second site, has the potential to circumvent the scaling relationship. However, the bifunctional mechanism has hitherto only been supported by theoretical computations. Here we describe an operando Raman spectroscopic and electrokinetic study of two highly active OER catalysts, FeOOH-NiOOH and NiFe layered double hydroxide (LDH). The data support two distinct mechanisms for the two catalysts: FeOOH-NiOOH operates by a bifunctional mechanism where the rate-determining O-O bond forming step is the OH- attack on a Fe=O coupled with a hydrogen atom transfer to a NiIII-O site, whereas NiFe LDH operates by a conventional mechanism of four consecutive PCET steps. The experimental validation of the bifunctional mechanism enhances the understanding of OER catalysts.<br />
|
Lichen Bai; seunghwa lee; Xile Hu
|
Electrocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74eee469df4e515f4459e/original/spectroscopic-and-electrokinetic-evidence-for-a-bifunctional-mechanism-of-the-oxygen-evolution-reaction.pdf
|
66c8b51c20ac769e5f96dd42
|
10.26434/chemrxiv-2024-tgbjq
|
Nonadiabatic Excited State Molecular Dynamics with explicit solvent: NEXMD-SANDER implementation
|
In this article, the Nonadiabatic Excited-state Molecular dynamics (NEXMD) package is linked with the SANDER package, provided by AMBERTOOLS. The combination of these software packages enables the simulation of photoinduced dynamics of large multichromophoric conjugated molecules involving several coupled electronic excited states embedded in an explicit solvent by using Quantum/Mechanics/Molecular Mechanics (QM/MM) methodology. The fewest switches surface hopping algorithm, as implemented in NEXMD, is used to account for quantum transitions among the adiabatic excited-states Simulations of the photoexcitation and subsequent nonadiabatic electronic transitions and vibrational energy relaxation of a substituted polyphenylene vinylene oligomer (PPV3-NO2) in vacuum and methanol as explicit solvent has been used as a test case. The impact of including specific solvent molecules in the QM region is also analysed. Our NEXMD-SANDER QM/MM implementation provides a useful computational tool to simulate qualitatively solvent-dependent effects, like electron transfer, stabilization of charge separated excited states, the role of solvent reorganization in the molecular optical properties, observed in solution-based spectroscopic experiments.
|
Dustin Tracy; Sebastian Fernandez-Alberti; Johan Fabian Galindo; Sergei Tretiak; Adrian Roitberg
|
Physical Chemistry; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c8b51c20ac769e5f96dd42/original/nonadiabatic-excited-state-molecular-dynamics-with-explicit-solvent-nexmd-sander-implementation.pdf
|
679fb3cd81d2151a02efc29a
|
10.26434/chemrxiv-2024-n8bj6-v2
|
BaNiO3 electrocatalysts for oxygen evolution
reaction: the role of synthetic methods
|
BaNiO3 and other Ba-Ni-O related phases are among the most active non-precious electrocatalysts towards the oxygen evolution reaction (OER) in basic media but the relationships between the synthesis conditions and the electrochemical properties have not been thoroughly investigated, which prevents further optimization of the materials performances. In this work, we compare the electrocatalytic activities of hexagonal perovskite BaNiO3 prepared by three different synthesis methods: sol-gel, metal nitrate decomposition and molten salts. We show by combining atomic-scale imaging and spectroscopic techniques how the choice of the synthesis method influences the chemical, morphological and microstructural features of the materials. We especially demonstrate by Energy Electron Loss Spectroscopy and X-Ray Photoelectron Spectroscopy that previously reported electrocatalytic results concerning BaNiO3 prepared in molten salts are actually related to the presence of an unreported nickel hydroxide shell, which ultimately results in enhanced electrocatalytic activity. These results highlight how the synthesis method can strongly influence oxygen electrocatalysis, which paves the way to further surface engineering of other energy materials.
|
Daniel Gutiérrez-Martín; Áurea Varela; Almudena Torres-Pardo; María Hernando; Emilio Matesanz; José María González-Calbet; David Portehault; Marina Parras
|
Inorganic Chemistry; Catalysis; Solid State Chemistry; Electrocatalysis; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-02-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679fb3cd81d2151a02efc29a/original/ba-ni-o3-electrocatalysts-for-oxygen-evolution-reaction-the-role-of-synthetic-methods.pdf
|
60c7505ef96a0083cd287e03
|
10.26434/chemrxiv.13032428.v1
|
Prevention of UVI Precipitation in Alkaline Aqueous Solutions by the Siderophore Desferrioxamine B
|
<p>In alkaline and saline solutions, uranium
VI (U<sup>VI</sup>)<sup> </sup>forms uranyl salts, limiting its mobility in leachates
released from nuclear waste repositories into groundwater. However, recent experimental
and computational work suggested that natural organic molecules widely present
in groundwater such as siderophores could potentially prevent solid
precipitation because of the formation of stable UVI-siderophore complexes. It
is important we assess the impact of siderophores on aqueous U<sup>VI</sup>
chemistry as they could mobilise U<sup>VI
</sup>from contaminated land and radioactive waste storage and disposal sites. Here we test this hypothesis by combining for
the first time experimental studies on uranium precipitation in alkaline pH in the presence of desferrioxamine
B (DFOB) and electron structure method calculation of uranyl – hydroxamate
complexes to assess their stability. Stirred batch experiments containing 0 to 420
µM DFOB, 42 µM U<sup>VI</sup> and 0.1 M NaCl were
conducted at pH 11.5. DFT was employed to explore the relative stability of
different U<sup>VI</sup>-hydroxamate complexes, representative of the local
binding mode of DFOB. During the stirred batch experiments, 5%, 11-12%, 41-53%,
95-96% and 100% of U<sup>VI</sup> passes through the filter membranes (0.2-1 µm pore diameter) after 24 hours when
0, 4.2, 42, 130 and 420 µM DFOB
was added to solution. The DFT results suggest one hydroxamate functional group
is most likely to complex with U<sup>VI</sup> with ∆<sub>r</sub>G calculated as
+3 kJ/mol and -9 kJ/mol for [UO<sub>2</sub>(OH)<sub>3</sub>(L<sub>mono</sub>)]<sup>2-
</sup>and [UO<sub>2</sub>(OH)<sub>2</sub>(L)]<sup>-</sup> respectively.
Conversion of the experimentally derived log β (-1.2 ± 0.3) through the equation ∆<sub>r</sub>G = -2.303RTlogβ provides
∆<sub>r</sub>G of +7 kJ/mol, similar to the ∆<sub>r</sub>G of these two
complexes. The results of our study confirm that U<sup>VI</sup> precipitation
could be hindered by the formation of a DFOB complex with U<sup>VI</sup> complexation
through a single hydroxamate functional group as a likely mechanism. These
results highlight the mobilising effect siderophores have on U<sup>VI</sup>
from contaminant sources and need to be incorporated in environmental risk
assessment studies.</p>
|
Matthew Kirby; Jason Louis Sonnenberg; Jonathan S. Watson; Dominik Weiss
|
Geochemistry; Wastes; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-10-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7505ef96a0083cd287e03/original/prevention-of-uvi-precipitation-in-alkaline-aqueous-solutions-by-the-siderophore-desferrioxamine-b.pdf
|
60c7453a0f50db42ad396203
|
10.26434/chemrxiv.9981488.v1
|
A Structure-Based Platform for Predicting Chemical Reactivity
|
Despite their enormous potential, machine learning methods
have only found limited application in predicting reaction outcomes, as current
models are often highly complex and, most importantly, are not transferrable to
different problem sets. Herein, we present the direct utilization of Lewis
structures in a machine learning platform for diverse applications in organic
chemistry. Therefore, an input based on multiple fingerprint features (MFF) as
a universal molecular representation was developed and used for problem sets of
increasing complexity: First, molecular properties across a diverse array of
molecules could be predicted accurately. Next, reaction outcomes such as
stereoselectivities and yields were predicted for experimental data sets that
were previously evaluated using (complex) problem-oriented descriptor models. As
a final application, a systematic high-throughput data set showed good
correlation when using the MFF model, which suggests that this approach is
general and ready for immediate adoption by chemists.
|
Frederik Sandfort; Felix Strieth-Kalthoff; Marius Kühnemund; Christian Beecks; Frank Glorius
|
Organic Synthesis and Reactions; Machine Learning; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-10-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7453a0f50db42ad396203/original/a-structure-based-platform-for-predicting-chemical-reactivity.pdf
|
671fe54b98c8527d9ea7647a
|
10.26434/chemrxiv-2024-twmlz
|
Active learning meets metadynamics: Automated workflow for reactive machine learning potentials
|
Atomistic simulations driven by machine learning-based potentials (MLPs) are a cost-effective alternative to ab initio molecular dynamics (AIMD). Yet, their broad applicability in reaction modelling remains hindered, in part, by the need for large training datasets that adequately sample the relevant potential energy surface, including high-energy transition state (TS) regions. To optimise dataset generation and extend the use of MLPs for reaction modelling, we present a workflow that combines automated active learning with well-tempered metadynamics, requiring no prior knowledge of TSs. Using data-efficient architectures, such as the linear Atomic Cluster Expansion, we illustrate the performance of this strategy in various organic reactions where the environment is described at different levels, including the SN2 reaction between fluoride and chloromethane in implicit water, the methyl shift of 2,2-dimethylisoindene in the gas phase, and a glycosylation reaction in explicit dichloromethane solution, where competitive pathways exist. The proposed training strategy yields accurate and stable MLPs for all three cases, highlighting its versatility for modelling reactive processes.
|
Valdas Vitartas; Hanwen Zhang; Veronika Juraskova; Tristan Johnston-Wood; Fernanda Duarte
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning
|
CC BY 4.0
|
CHEMRXIV
|
2024-11-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671fe54b98c8527d9ea7647a/original/active-learning-meets-metadynamics-automated-workflow-for-reactive-machine-learning-potentials.pdf
|
63c5021c4fba70c4160744cd
|
10.26434/chemrxiv-2022-89q4q-v3
|
More Is Better: Acceptor Engineering for Constructing NIR-II AIEgens to Boost Multimodal Phototheranostics
|
The manipulation of electron donor/acceptor (D/A) shows endless impetus for innovating optoelectronic materials. Because of the diversity of electron-donating species, the study on donor engineering has explored systematically, whereas the research on electron acceptor engineering received a snub by contrast. Inspired by the philosophical idea of “more is different”, two systems with D'−D−A−D−D' (1A system) and D'−D−A−A−D−D' (2A system) structures based on the acceptor engineering are ingeniously designed and studied. It is demonstrated that the 1A system presents a weak aggregation-induced emission (AIE) to aggregation-caused quenching (ACQ) phenomenon along with the increased acceptor electrophilicity. Interestingly, the 2A system exhibits an opposite ACQ-to-AIE transformation, manifesting the dual-acceptor tactic could facilitate AIE activity. Thanks to the highest molar absorptivity, near-infrared-II (NIR-II, 1000–1700 nm) emission, superior AIE effect, favorable reactive oxygen species generation and high photothermal conversion efficiency, a representative member of 2A system handily perform in fluorescence-photoacoustic-photothermal multimodal imaging-guided photodynamic-photothermal synergetic therapy for efficient tumor elimination. Meanwhile, NIR-II fluorescence imaging of blood vessels and lymph nodes in living mice are also accomplished. This work provides a fascinating molecular design philosophy for developing versatile phototheranostic agent with a higher molar absorptivity, superb aggregation-intensified NIR-II fluorescent emission, and improved heat generation capacity.
|
Shiping Yang; Jianyu Zhang; Rongyuan Zhang; Xinwen Ou; Xue Li; Zhijun Zhang; Weilin Xu; Miaomiao Kang; Dingyuan Yan; Jianwei Sun; Jacky W. Y. Lam; Dong Wang; Ben Zhong Tang
|
Biological and Medicinal Chemistry; Nanoscience; Biochemistry; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-01-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c5021c4fba70c4160744cd/original/more-is-better-acceptor-engineering-for-constructing-nir-ii-ai-egens-to-boost-multimodal-phototheranostics.pdf
|
65795bd5fd283d7904e383e6
|
10.26434/chemrxiv-2023-4tdtf-v2
|
Multi-Responsive Thermally Activated Delayed Fluorescence Materials: Optical ZnCl2 Sensors and Efficient Green to Deep-red OLEDs
|
Thermally activated delayed fluorescence (TADF) is an emission mechanism whereby both singlet and triplet excitons can be harvested to produce light. Significant attention has been devoted to developing TADF materials for organic light-emitting diodes (OLEDs), while their use in other organic electronics applications such as sensors, has lagged. We have developed and systematically studied a family of TADF emitters, TPAPyAP, TPAPyBP, and TPAPyBPN containing a triphenylamine (TPA) donor and differing nitrogen-containing heterocyclic pyrazine-based acceptors. Depending on the acceptor strength, these three compounds emit with photoluminescence maxima (λPL), of 516 nm, 550 nm, and 575 nm in toluene. Notably, all three compounds showed a strong and selective spectral response to the presence of ZnCl2, making them the first optical TADF sensors for this analyte. We also demonstrate that these three emitters can be used in vacuum-deposited OLEDs, which showed moderate efficiencies. Of note, the device with TPAPyBPN in 2,8-bis(diphenyl-phoshporyl)-dibenzo[b,d]thiophene (PPT) host emitted at 657 nm and showed an EQEmax 12.5%. This electroluminescence was significantly red-shifted yet showing comparable efficiency compared to a device fabricated in 4,4′-bis(N-carbazolyl)-1,1′-biphenyl (CBP) host (λEL= 596 nm, EQEmax = 13.6%).
|
Changfeng Si; Abhishek Kumar Gupta; Biju Basumatary; Aidan McKay; David Cordes; Alexandra Slawin; Ifor Samuel; Eli Zysman-Colman
|
Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Spectroscopy (Physical Chem.); Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-12-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65795bd5fd283d7904e383e6/original/multi-responsive-thermally-activated-delayed-fluorescence-materials-optical-zn-cl2-sensors-and-efficient-green-to-deep-red-ole-ds.pdf
|
65170113ade1178b245daf37
|
10.26434/chemrxiv-2023-zcqnq-v2
|
Methods for spatial extrapolation of methane measurements in constructing regional estimates from sample populations
|
Reporting initiatives for methane emissions from oil and gas operations are broadly shifting towards measurement-informed inventories. Measurement campaigns typically measure a subpopulation of facilities, and these measurements are extrapolated to a larger region or basin. Methane emissions from oil and gas systems are inherently variable and intermittent, which makes it difficult to determine whether a sample population is sufficiently large to be representative of a larger region. This work proposes a framework using a case study of an operator in the Green River Basin that assesses selection of sample populations, extrapolation of measurements to a larger region, and methods for estimating the error associated with extrapolation. This work also identifies a new metric, the capture ratio, which has a strong correlation with extrapolation error (Spearman’s correlation coefficient = -0.75). The strength of this correlation between the capture ratio, which takes into account the skewness of source-level emissions, and extrapolation error suggests that understanding the distributions of source-level emissions distributions is necessary when identifying sample populations and extrapolating measurements. The results from this work can be broadly applied to inform the selection and extrapolation of site measurements when developing methane emission inventories.
|
Colette Schissel; David Allen; Howard Dieter
|
Energy; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65170113ade1178b245daf37/original/methods-for-spatial-extrapolation-of-methane-measurements-in-constructing-regional-estimates-from-sample-populations.pdf
|
6734eb227be152b1d0fa839c
|
10.26434/chemrxiv-2024-tk00d
|
Collective asymmetric synthesis of the Strychnos alkaloids via thiophene S,S-dioxide cycloaddition cascades
|
The Strychnos alkaloids have long been regarded as landmark targets for chemical synthesis due to their captivating architectures and notorious biological properties. The family has fascinated synthetic and medicinal chemists for almost 100 years, since the decades-long debate over the structure of the 'flagship' member strychnine, and its first total synthesis by Woodward. Featuring a dense array of carbo- and heterocyclic rings, and numerous stereochemical challenges, these molecules have inspired many synthetic strategies. In spite of this rich history, the design of approaches that can access multiple family members, in an asymmetric, concise, and atom-economical fashion, remains a significant challenge. Here we show that thiophene S,S-dioxides (TDOs) offer a modular and highly concise entry to the Strychnos natural products. We show how the rapid assembly of a tryptamine-tethered TDO enables the synthesis of family member akuammicine in just three steps from tryptamine, with minimal waste generation. We further demonstrate exceptional levels of stereocontrol in unprecedented asymmetric cycloadditions of chiral thiophene S,S-dioxides; these afford tricyclic indolines that are of interest for medicinal chemistry applications, and also enable highly concise, stereoselective and scalable syntheses of the Strychnos alkaloids by either intra- or intermolecular asymmetric cycloadditions. Our results highlight the potential of TDOs as important building blocks in asymmetric cycloaddition chemistry for the streamlined synthesis of polycyclic organic frameworks; in the case of the Strychnos alkaloids, this means that both natural products and analogues that have previously been inaccessible can now be prepared in a handful of transformations.
|
Kun Ho (Kenny) Park; Jisook Park; Nils Frank; Hanwen Zhang; Fernanda Duarte; Edward Anderson
|
Organic Chemistry; Natural Products; Organic Compounds and Functional Groups; Organic Synthesis and Reactions
|
CC BY 4.0
|
CHEMRXIV
|
2024-11-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6734eb227be152b1d0fa839c/original/collective-asymmetric-synthesis-of-the-strychnos-alkaloids-via-thiophene-s-s-dioxide-cycloaddition-cascades.pdf
|
66f6f7c951558a15ef580fb8
|
10.26434/chemrxiv-2024-jwxww
|
Pressure Induced Rhombohedral Phase in ScF3 shows Enhanced Negative Thermal Expansion
|
Negative thermal expansion (NTE) is a counterintuitive phenomenon, in which materials undergo contraction as they are heated. ScF3, a well-known NTE material has been reported to show NTE coefficients up-to 1000K. At ambient conditions, ScF3 crystallizes in a cubic symmetry (Pm-3m space group) same as that in the ReO3-type structures. Crystal-structure predictions (CSP) show that at P=1 GPa, a phase transition occurs in cubic ScF3 to form the rhombohedral phase (R-3C space-group). Quasi-harmonic approximation (QHA) calculations show that this new phase can show NTE coefficients for temperatures as high as 4500 K due to soft rigid-unit modes (RUM). The stability of this phase persists until 4 GPa. Beyond 4 GPa, the rhombohedral phase further undergoes a phase-transition into an orthorhombic-phase (Immm space group) having a non-corner-shared polyhedron network. This phase shows very poor NTE. On further increasing the pressure to 6 GPa, a trigonal-prismatic arrangement of ScF3 is obtained (R32 space group) which shows a reasonably good NTE phase due to the corner shared framework and remains stable till 9 GPa. Amongst the various pressure generated phases in ScF3, the rhombohedral phase shows the highest NTE behaviour. Ab-inito molecular dynamics (AIMD) simulations show that maximum volume contraction occurs for this R-3C phase due to facile bending of the ∠Sc-F-Sc causing framework softening.
|
Soumya Mondal; Shovan Das; Ayan Datta
|
Theoretical and Computational Chemistry; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f6f7c951558a15ef580fb8/original/pressure-induced-rhombohedral-phase-in-sc-f3-shows-enhanced-negative-thermal-expansion.pdf
|
60c73e160f50dbdd053955c6
|
10.26434/chemrxiv.6446432.v1
|
Microfluidic Quantification of Yeast Surface Adhesion
|
<div>Fungal adhesion is fundamental to processes ranging from</div><div>infection to food production yet, robust, population-scale</div><div>quantification methods for yeast surface adhesion are lacking. We developed a microfluidic assay to distinguish the effects of genetic background and solution conditions on adhesion. This approach will enable the rapid screening of yeast adhesive properties for anti-fouling surfaces and a host of other applications.</div>
|
Kristina Reinmets; Amin Dehkharghani; Jeffrey S. Guasto; Stephen Fuchs
|
Biophysics; Cell and Molecular Biology; Microbiology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-06-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e160f50dbdd053955c6/original/microfluidic-quantification-of-yeast-surface-adhesion.pdf
|
641ef44762fecd2a8369c9ce
|
10.26434/chemrxiv-2023-snwpg
|
Carbazolophane Enhances the Efficiency of Thermally Activated Delayed Fluorescence in Carbene Coinage Metal Amides
|
Carbene coinage metal carbazolates are currently the most efficient organometallic TADF emitters. Herein we report on the photophysical influence of introducing a [2.2]paracyclophane moiety via a carbazolophane ligand instead of carbazolate, which greatly enhances the radiative rate constants by a factor of three to 1-3·106 s-1 for triplet exciton emission.
|
Indranil Sen; Ondřej Mrózek; Mousree Mitra; Andrey Belyaev; Changfeng Si; Eli Zysman-Colman; Jasmin Seibert; Stefan Bräse; Andreas Steffen
|
Physical Chemistry; Organometallic Chemistry; Spectroscopy (Organomet.); Transition Metal Complexes (Organomet.); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641ef44762fecd2a8369c9ce/original/carbazolophane-enhances-the-efficiency-of-thermally-activated-delayed-fluorescence-in-carbene-coinage-metal-amides.pdf
|
65154d57a69febde9ed613ee
|
10.26434/chemrxiv-2023-jpdjd
|
Aromatic ionomers based on 2,8-dioxydibenzofuran as a post-polymerisation, sulfonatable unit: synthesis, fabrication of thin-film membranes and performance evaluation in a direct-methanol fuel cell
|
"ABSTRACT: Linear polycondensation of activated aromatic dihalides including 4,4'-difluoro-diphenylsulfone, 1,3-bis(4-fluorobenzoyl)benzene and 3,3'-bis(4-fluorobenzoyl)biphenyl with a combination of the two bisphenol monomers 4,4'-dihydroxybenzophenone and 2,8- dihydroxydibenzofuran affords a novel series of high molecular weight aromatic polyethers. Post-polymerisation sulfonation of these copolymers in 96% sulfuric acid yields a corresponding series of ionomers in which sulfonation has occurred at the 3- and 7-positions of the dibenzofuran rings. The ion-exchange capacities of these ionomers were in the range 1.3 to 1.8 mmol g-1, and their molecular weights (Mn) by GPC were between 39 and 56 kD with dispersities (Đ) between 2 and 3. All the ionomers were successfully solution-cast into tough, transparent, thin-film membranes (40 - 90 μm) which were evaluated for direct- methanol fuel cell (DMFC) performance in terms of proton conductivity, methanol diffusion coefficient, limiting current density and maximum power density. A dibenzofuran-based ionomer derived specifically from 3,3'-bis(4-fluorobenzoyl)biphenyl showed DMFC performance equivalent to, or even slightly better than, a control membrane produced from the industry-standard fluorocarbon ionomer Nafion 115."
|
Siva Purushothaman; Nadia Permogorov; Howard Colquhoun
|
Polymer Science; Energy; Organic Polymers; Polyelectrolytes - Polymers; Fuel Cells; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-09-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65154d57a69febde9ed613ee/original/aromatic-ionomers-based-on-2-8-dioxydibenzofuran-as-a-post-polymerisation-sulfonatable-unit-synthesis-fabrication-of-thin-film-membranes-and-performance-evaluation-in-a-direct-methanol-fuel-cell.pdf
|
62b63e1a58b3d61abb5e1a8e
|
10.26434/chemrxiv-2022-c4sbr
|
Synergistic Porosity and Charge Effects in a Supramolecular Porphyrin Cage Promote Efficient Photocatalytic CO2 Reduction
|
We present a supramolecular approach to catalyzing photochemical CO2 reduction in confined
spaces through synergistic second-sphere porosity and charge effects. A porous iron porphyrin organic
cage bearing 24 cationic groups, FePB-2(P), was made via post-synthetic modification of a versatile
alkyne-functionalized supramolecular synthon. FePB-2(P) promotes the photochemical CO2 reduction
reaction (CO2RR) with 97% selectivity for CO product, achieving turnover numbers (TON) exceeding
7000 and initial turnover frequencies (TOFmax) reaching 1400 min-1. The cooperativity between second-sphere
porosity and charge effects results in a 41-fold increase in activity relative to the parent FeTPP
catalyst, which is far greater than analogs that augment catalysis through porosity (FePB-3(N), 4-fold
increase) or charge (Fe-p-TMA, 6-fold increase) alone. This work establishes that multiple, synergistic
pendants in the secondary coordination sphere can be leveraged as a design element to augment catalysis
at primary active sites within confined spaces.
|
Lun An; Patricia De La Torre; Peter Smith; Mina Narouz; Christopher Chang
|
Inorganic Chemistry; Catalysis; Supramolecular Chemistry (Inorg.); Electrocatalysis; Photocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-06-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b63e1a58b3d61abb5e1a8e/original/synergistic-porosity-and-charge-effects-in-a-supramolecular-porphyrin-cage-promote-efficient-photocatalytic-co2-reduction.pdf
|
60c742b19abda20a00f8c090
|
10.26434/chemrxiv.8488934.v1
|
Identification of Strategic Molecules for Future Circular Supply Chains Using Large Reaction Networks
|
Networks of chemical reactions represent relationships between molecules within chemical supply chains and promise to enhance planning of multi-step synthesis routes from bio-renewable feedstocks. This study aims to identify <i>strategic molecules</i>in chemical reaction networks that may potentially play a significant role within the future circular economy. We mine a commercially available database in order to assemble a network of chemical reactions. We describe molecules within the network by a portfolio of graph theoretical features, and identify strategic molecules with an isolation forest search algorithm. In this work we have identified a list of potential strategic molecules and indicated possibilities for reaction planning using these. This is exemplified by a potential supply chain of functional molecules from bio-waste streams that could be used as feedstocks without being converted to syngas. This work extends the methodology of analysis of reaction networks to the generic problem of development of new reaction pathways based on novel feedstocks.
|
Jana Weber; Pietro Lio’; Alexei Lapkin
|
Combinatorial Chemistry; Chemoinformatics - Computational Chemistry; Pharmaceutical Industry
|
CC BY 4.0
|
CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742b19abda20a00f8c090/original/identification-of-strategic-molecules-for-future-circular-supply-chains-using-large-reaction-networks.pdf
|
660d76f4418a5379b0fc9be9
|
10.26434/chemrxiv-2024-8twph
|
Surface Tension Manipulation with Visible Light through Sensitized Disequilibration of Photoswitchable Amphiphiles
|
The light-induced N=N double bond isomerization of azoarenes lies at the heart of numerous applications ranging from catalysis, energy storage, or drug release to optogenetics and photopharmacology. While efficient switching between their E and Z states has predominantly relied on direct UV light excitation, a recent study by Klajn and co-workers introduced visible light sensitization of E azoarenes and subsequent isomerization as a tool coined disequilibration by sensitization under confinement (DESC) to obtain high yields of the out-of-equilibrium Z isomer. This host-guest approach is, however, still constrained to small, minimally substituted azoarenes with limited applicability and functionality in advanced multicomponent molecular systems. Herein, we expand the DESC concept to steer the supramolecular assembly of surfactants at the air-water interface. Leveraging our expertise with photoswitchable arylazopyrazole amphiphiles, we induce substantial alterations of the surface tension and surface excess of water through their reversible E-Z isomerization. After studying the binding of positively and negatively charged surfactants to the host, we find that the extent of surface activity differences upon visible light irradiation for both isomer states is comparable to those observed for direct UV light excitation. The method is demonstrated on a large range of concentrations (from µM to mM) and can be equally activated using green or red light, depending on the sensitizer chosen. The straightforward implementation of visible light photoswitch sensitization in a complex molecular network showcases how DESC enables the improvement of existing light-responsive systems and allows for the development of novel applications driven exclusively with visible light.
|
Julius Gemen; Bastian Stövesand; Frank Glorius; Bart Jan Ravoo
|
Organic Chemistry; Photochemistry (Org.); Supramolecular Chemistry (Org.)
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-04-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660d76f4418a5379b0fc9be9/original/surface-tension-manipulation-with-visible-light-through-sensitized-disequilibration-of-photoswitchable-amphiphiles.pdf
|
62449fdd437a06e323ece44e
|
10.26434/chemrxiv-2022-6zqq9-v3
|
Why Do Liquids Mix? The Mixing of Protic Ionic Liquids Sharing the Same Cation is Apparently Driven by Enthalpy, not Entropy
|
We study hydrogen bond (HB) redistribution in mixtures of two protic ionic liquids (PILs) sharing the same cation: triethylammonium-methanesulfonate ([TEA][OMs]) and triethylammonium-trifluoromethanesulfonate ([TEA][OTf]). The mixture is exhibiting large negative energies of mixing. Based on results obtained from atomic detail molecular dynamics (MD) simulations, we derive a lattice model, discriminating between HB and nonspecific intermolecular interactions. We demonstrate that due to the ordered structure of the PILs, mostly the HB interactions contribute to the mixing energy. This allows to us to connect the equilibrium of HBs to each of the two anion species with the corresponding excess energies and entropies. The entropy associated with HB redistribution is shown to be negative, and even overcompensating the positive entropy associated with a statistical distribution of the ions in the mixture. This is strongly suggesting that the mixing process is driven by enthalpy, not entropy.
|
Benjamin Golub; Daniel Ondo; Ralf Ludwig; Dietmar Paschek
|
Physical Chemistry; Statistical Mechanics
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-03-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62449fdd437a06e323ece44e/original/why-do-liquids-mix-the-mixing-of-protic-ionic-liquids-sharing-the-same-cation-is-apparently-driven-by-enthalpy-not-entropy.pdf
|
60c7527a842e65f99fdb3d99
|
10.26434/chemrxiv.13299299.v1
|
Synthesis and Thermal Study of Hexacoordinated Aluminum(III) Triazenides for Use in Atomic Layer Deposition
|
<p>Amidinate and guanidinate ligands have been used extensively to produce volatile and thermally stable precursors for atomic layer deposition. The triazenide ligand is relatively unexplored as an alternative ligand system. Herein, we present six new Al(III) complexes bearing three sets of a 1,3-dialkyltriazenide ligand. These complexes volatilize quantitatively in a single step with onset volatilization temperatures of ~150 °C and 1 Torr vapor pressures of ~134 °C. Differential scanning calorimetry revealed these Al(III) complexes exhibited exothermic events that overlapped with the temperatures of their mass loss events in thermogravimetric analysis. Using quantum chemical density functional theory computations, we found a decomposition pathway transforming the relatively large hexacoordinated Al(III) precursor into a smaller dicoordinated complex. The pathway relies on previously unexplored inter-ligand interactions, in which protons migrate between the triazenide ligands. These new Al(III) triazenides provides a series of alternative precursors with unique thermal properties that could be highly advantageous for vapor deposition processes of Al containing materials.</p>
|
Rouzbeh Samii; David Zanders; Sydney Buttera; Vadim Kessler; Lars Ojamäe; Henrik Pedersen; Nathan O'Brien
|
Main Group Chemistry (Inorg.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-12-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7527a842e65f99fdb3d99/original/synthesis-and-thermal-study-of-hexacoordinated-aluminum-iii-triazenides-for-use-in-atomic-layer-deposition.pdf
|
630aa381eadd9a4db783f87a
|
10.26434/chemrxiv-2022-2jnv2
|
Tuning the rare-earth UiO-66 metal–organic framework platform for white light emission
|
Metal–organic frameworks (MOFs) have received notable attention owing to their structural diversity, permanent porosity, and high surface areas. In addition to these properties, rare-earth (RE) MOFs have the added feature of tunable photoluminescence dictated by the identity of the metal ion and organic linker in the RE-MOF. Herein, we explore the tunable photoluminescent properties of RE-UiO-66 by synthesizing and characterizing mono-, bi- and tri-metal RE-UiO-66 analogues where RE = Tb(III), Gd(III), and Eu(III), to ultimately design a white light emitting MOF. The photophysical properties of this series of MOFs are explored and, as a proof of concept, the tri-metal Tb:Gd:Eu-UiO-66 is used as a surface coating on a UV light emitting diode (LED) to give a white light emitting device.
|
Zvart Ajoyan; Hudson A. Bicalho; P. Rafael Donnarumma; Ashlee J. Howarth
|
Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Materials Chemistry; Crystallography – Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-08-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630aa381eadd9a4db783f87a/original/tuning-the-rare-earth-ui-o-66-metal-organic-framework-platform-for-white-light-emission.pdf
|
65f031ede9ebbb4db98b419b
|
10.26434/chemrxiv-2024-mxmgl
|
Improved Mechanical Properties of Graphene/Carbon Fibre Composites via Silanization
|
Despite their excellent mechanical performance, carbon fibre reinforced polymer (CFRP) composites are limited by the interfacial properties due to the inherent nature of laminated structures. One way to modify the interface is by the inclusion of nanomaterials on the surface of carbon fibres. Here, we use electrochemical exfoliation to produce graphene (EEG) flakes which have hydroxyl and epoxy functional groups on their surface. To further improve the interfacial bonding between the flakes and the epoxy matrix, silanization was carried out on the graphene, with 3-aminopropyl triethoxysilane (APTES) which could react with both oxygen and amino groups, and then EEA flakes achieved. Combing SEM and AFM, lateral size and thickness of both flakes were characterized, which showed comparable values, and thus removed the effect of aspect ratio during the comparison. Both EEG and EEA flakes were dispersed in ethanol and sprayed coated onto carbon fibres, followed by vacuum assisted resin infusion to make hybrid composites. Testing of their mechanical properties showed that EEG flakes tend to act as points of stress concentration which accelerated the delamination; while the EEA flakes improved interfacial properties owing to the covalent bonding. As a result, with only 0.5 wt.% EEA flakes spray coated onto the carbon fibres, the tensile and flexural strength of graphene/carbon fibre composites improved by 17.6% and 5.4% respectively.
|
Xudan Yao; Jason Hui; Ian Kinloch; Mark Bissett
|
Materials Science; Nanoscience; Composites; Nanostructured Materials - Materials; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-03-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f031ede9ebbb4db98b419b/original/improved-mechanical-properties-of-graphene-carbon-fibre-composites-via-silanization.pdf
|
61c02f7e7f367e306759a0fd
|
10.26434/chemrxiv-2021-fz6v7-v2
|
Δ-Quantum machine learning for medicinal chemistry
|
Many molecular design tasks benefit from fast and accurate calculations of quantum-mechanical (QM) properties. However, the computational cost of QM methods applied to drug-like molecules currently renders large-scale applications of quantum chemistry challenging. Aiming to mitigate this problem, we developed DelFTa, an open-source toolbox for the prediction of electronic properties of drug-like molecules at the density functional (DFT) level of theory, using Δ-machine-learning. Δ-Learning corrects the prediction error (Δ) of a fast but inaccurate property calculation. DelFTa employs state-of-the-art three-dimensional message-passing neural networks trained on a large dataset of QM properties. It provides access to a wide array of quantum observables on the molecular, atomic and bond levels by predicting approximations to DFT values from a low-cost semiempirical baseline. Δ-Learning outperformed its direct-learning counterpart for most of the considered QM endpoints. The results suggest that predictions for non-covalent intra- and intermolecular interactions can be extrapolated to larger biomolecular systems. The software is fully open-sourced and features documented command-line and Python APIs.
|
Kenneth Atz; Clemens Isert; Markus N. A. Böcker; José Jiménez-Luna; Gisbert Schneider
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-12-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c02f7e7f367e306759a0fd/original/quantum-machine-learning-for-medicinal-chemistry.pdf
|
673bc74df9980725cfa7071b
|
10.26434/chemrxiv-2024-tr17s
|
Theory of Soft Active Wetting
|
We must address active matter in the context of soft boundaries in order to bridge the gap between our understanding of active matter and the dynamics of the biological systems (that the active matter represent) under natural conditions. However, the physics of such active drops (matter) in contact with a soft and deformable surface has remained elusive. In this letter, we attempt to fill this gap and develop a theory for soft, active wetting. Our theory, which accounts for the various free energies for passive substrate and active drops as well as the active stresses, provides an equilibrium description of (active) particle orientation inside the drop and an equilibrium shape of the drop-soft-solid system. We obtain the equation relating the activity to the internal pressure of an active drop. The equilibrium calculation yields an ordered state of the polarization field inside the drop. The presence of the extensile (contractile) activity is found to make the drop press into the soft surface (come out of the soft surface), while increasing (decreasing) the wetting radius as compared to non-active drops. Finally, the three-phase contact line undergoes a rotation that depends on the strength of activity. These findings shed new light on the manner in which the active stresses interact with surface tension and elasticity at the fundamental level.
|
Ghansham Chandel; Siddhartha Das
|
Materials Science
|
CC BY 4.0
|
CHEMRXIV
|
2024-11-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673bc74df9980725cfa7071b/original/theory-of-soft-active-wetting.pdf
|
63485eba1df688649b8f3051
|
10.26434/chemrxiv-2022-1crdw
|
Improved Characterization of Polyoxazolidinones by Incorporating Solubilizing Side Chains
|
Carbon dioxide-based polyoxazolidinones (POxa) are an emerging subclass of non-isocyanate polyurethanes for high temperature applications. Current POxa with rigid linkers suffer from limited solubility that hinders synthesis and characterization. Herein, we report the addition of alkyl and alkoxy solubilizing groups to rigid spirocyclic POxa and their poly(hydroxyoxazolidinone) (PHO) precursors. The modified polymers were soluble in up to 6 organic solvents, enabling characterization of key properties (i.e., molar mass and polymer structure) using solution-state methods. Dehydration of PHO to POxa changed solubility from highly polar to less polar solvents and improved thermal stability by 76–102 °C. The POxa had relatively high glass transition (85–119 °C) and melting (190–238 °C) temperatures tuned by solubilizing group structure. The improved understanding of factors affecting solubility, structure-property relationships, and degradation pathways gained in this study broadens the scope of soluble POxa and enables more rational design of this promising class of materials.
|
Allison Wong; Melissa Barrera; Arpan Pal; Jessica Lamb
|
Organic Chemistry; Polymer Science; Physical Organic Chemistry; Organic Polymers; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63485eba1df688649b8f3051/original/improved-characterization-of-polyoxazolidinones-by-incorporating-solubilizing-side-chains.pdf
|
65affcbbe9ebbb4db9d07f7e
|
10.26434/chemrxiv-2024-90065
|
Nanocrystal Synthesis with Alkoxy Ligands and Solvents
|
Applications of colloidal nanocrystals in polar solvents often require nanocrystals synthesized in nonpolar solvents. However, solvent transfer processes are problematic and deteriorate nanocrystal quality. Here we report syntheses of nanocrystals with nearly universal solvent dispersibility using ligands and solvents with alkoxy repeating units. Core syntheses shell deposition, and cation exchange proceed similarly to traditional methods while products are more stable in aqueous solution than those generated by solvent transfer. (CdSe)CdZnS nanocrystals retain photoluminescence in cells for single-particle tracking experiments and outperform other nanocrystal classes in diffusion metrics reflecting stability and nonspecific binding. Distinct reaction classes yield nanocrystals with either methoxy or hydroxy ligand terminations, both of which can be purified by aqueous methods that are greener than traditional methods. These reactions can further generate nanocrystals with diverse compositions (oxides, sulfides, and selenides), shapes, and spectral bands with wide dispersibility that may make applications in polar solvents more widely accessible.
|
Suresh Sarkar; Opeyemi Arogundade; Yuxiao Cui; Andrew Smith
|
Materials Science; Nanoscience; Biocompatible Materials; Core-Shell Materials; Imaging Agents; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65affcbbe9ebbb4db9d07f7e/original/nanocrystal-synthesis-with-alkoxy-ligands-and-solvents.pdf
|
60c73dd29abda2d880f8b794
|
10.26434/chemrxiv.6120962.v1
|
SERS Comparison from Au, Ag, and Au-Ag Alloys: Insights by the First Principles
|
<div>Surface enhanced Raman scattering (SERS) is presented via a case study of 2,2’-bipyridyl</div><div>(22BPY) molecules adsorbed on pure Au and Ag as well as on Au-Ag alloy nanodiscs. Experimental</div><div>SERS spectra from Au and Ag nanodics show similar peaks, but those from Au-Ag alloy</div><div>reveal new spectral features. The physical enhancement factors due to surface nano-texture were</div><div>considered by numerical simulations of light intensity distribution for the nano-textured Au, Ag,</div><div>and Au-Ag alloy surfaces, but found to cause only minor differences. For the chemical insights of</div><div>enhancement, the density functional theory (DFT) calculations were performed using Au20, Ag20,</div><div>and Au10Ag10 clusters of a pyramidal structure for SERS modeling. Binding of 22BPY to the clusters</div><div>was simulated by considering possible arrangements of vertex and planar physical as well as</div><div>chemical adsorption models. A qualitative match with experimental SERS results for the pure Au</div><div>and Ag was obtained. DFT models showing spectral shifts of 22BPY SERS on the alloy nanodiscs</div><div>are presented.</div>
|
Masato Takenaka; Yoshikazu Hashimoto; Takeshi Iwasa; Tetsuya Taketsugu; Gediminas Seniutinas; Armandas Balcytis; Saulius Juodkazis; Yoshiaki Nishijima
|
Alloys; Plasmonic and Photonic Structures and Devices; Computational Chemistry and Modeling; Theory - Computational; Surface
|
CC BY NC ND 4.0
|
CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd29abda2d880f8b794/original/sers-comparison-from-au-ag-and-au-ag-alloys-insights-by-the-first-principles.pdf
|
6123c522e65e2d57681e7701
|
10.26434/chemrxiv-2021-zs5qg
|
Prebiotic synthesis of 3′-amino-TNA nucleotide triphosphates
|
Nucleic acid replication is essential to the emergence of life. Unlike canonical ribonucleotides, aminonucleotides have shown great promise in non-enzymatic replication, but are assumed to be prebiotically irrelevant due to perceived difficulties with their selective formation on the early earth. Here we demonstrate that, contrary to expectation, 3′-amino-TNA is formed diastereoselectively and regiospecifically from prebiotic feedstocks in four high-yielding steps. Our results suggest that 3′-amino-TNA may have been present on the early earth. Formation of the amino-sugar moiety by 3-component coupling of glycolaldehyde 1, 2-aminooxazole 3 and an aminonitrile 6 regiospecifically positions both the 3′-amine and glycosidic bond. Phosphate provides an unexpected resolution of the two diastereomers formed, leading to purification of the genetically relevant threo-isomer. Under phosphate catalysis, the inhibitory erythro-isomer rearranges to an unreactive guanidinium salt, whilst the Watson-Crick base paring threo-isomer co-crystalises with phosphate, leading to its spontaneous purification and accumulation. Nucleobase construction on the amino-sugar scaffold is observed upon reaction with cyanoacetylene 8, and subsequent thiolysis and photochemical anomerisation sets up the ideal stereochemistry for Watson-Crick base pairing. The resulting 3′-amino-TNA can be phosphorylated directly in water, under mild conditions with cyclic trimetaphosphate (PO3Na)3, forming a nucleotide triphosphate (NTP) in a manner not feasible for canonical nucleosides. The ease with which these activated NTPs form, and the inherent selectivity for the Watson-Crick base pairing structure, warrants further study of 3′-amino-TNA as a precursor to the genetic material of life.
|
Daniel Whitaker; Matthew Powner
|
Organic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-08-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6123c522e65e2d57681e7701/original/prebiotic-synthesis-of-3-amino-tna-nucleotide-triphosphates.pdf
|
64f48ded79853bbd78ffe7ad
|
10.26434/chemrxiv-2023-b7jql
|
Virtual Screening for Promising Kinetic Stabilizers of Light Chains in Immunoglobulin Light Chain Amyloidosis Through Drug Repurposing
|
In immunoglobulin light chain amyloidosis, unstable immunoglobulin light chains aggregate as amyloid fibrils in organs, leading to organ failure and death in more than 50% of untreated patients. Research by Morgan et al. (Morgan, G. J. et. al., Proceedings of the National Academy of Sciences 2019, 116, 8360–8369) and Yan et al. (Yan, N. L. et. al., Journal of Medicinal Chemistry 2021, 64, 6273–6299) has shown that several classes of small molecules can be used as kinetic stabilizers
of native light chains and potentially slow or stop the disease. Based on their criteria of a clinically successful kinetic stabilizer, this study includes an in-silico virtual screening of drugs approved by the U.S. Food and Drug Administration to find promising candidates of kinetic stabilizers through drug repurposing. Of these candidates, molecular dynamics simulations and subsequent studies of molecular mechanics with generalized Born and surface area solvation suggest that delavirdine and pazopanib can potentially be used as kinetic stabilizers of native light chains.
|
Jonas Jeppesen; Casper Steinmann
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-09-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f48ded79853bbd78ffe7ad/original/virtual-screening-for-promising-kinetic-stabilizers-of-light-chains-in-immunoglobulin-light-chain-amyloidosis-through-drug-repurposing.pdf
|
64cda2b369bfb8925a6394f8
|
10.26434/chemrxiv-2023-b9r1z-v2
|
Diarylethene Photoswitches Undergoing 6π Azaelectrocyclic Reaction: Disrotatory Thermal Cycloreversion of the Closed-Ring Isomer
|
Gaining insight into the dynamics of electrocyclic reactions is very important from both fundamental and application perspectives. In this study, we developed novel diarylethene photoswitches that undergo 6π azaelectrocyclic reaction. We found that they exhibit fast thermally reversible type (T-type) photochromism in contrast to the fact that common diarylethenes exhibit photochemically reversible type (P-type) photochromism. The quantum chemical calculations revealed that the fast T-type photochromism originates from the unprecedented disrotatory thermal cycloreversion of the closed-ring isomer. Our results provide useful information not only for the dynamics of the 6π azaelectrocyclic reaction but also for the further development of diarylethene photoswitches utilizing 6π azaelectrocyclic reaction.
|
Shota Hamatani; Daichi Kitagawa; Seiya Kobatake
|
Physical Chemistry; Organic Chemistry; Photochemistry (Org.); Physical Organic Chemistry; Physical and Chemical Properties; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64cda2b369bfb8925a6394f8/original/diarylethene-photoswitches-undergoing-6-azaelectrocyclic-reaction-disrotatory-thermal-cycloreversion-of-the-closed-ring-isomer.pdf
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62515160742e9f939f58858e
|
10.26434/chemrxiv-2022-59ck4-v3
|
The Oriented and Flux-Weighted Current Density Stagnation Graph of LiH
|
A scheme is introduced to quantitatively analyze the magnetically
induced molecular current density vector field J. After determining the
set of zero points of J, which is called its stagnation graph (SG),
the line integrals -1/mu_0 \int_li B.dl along all edges of
the connected subset of the SG are determined. The edges are oriented such that all
line integrals are non-negative and they are weighted with the resultants. An oriented
flux-weighted (current density) stagnation graph (OFW-SG) is obtained.
Since J is in the exact theoretical limit divergence free and due to the
topological characteristics of such vector fields the flux of all separate vortices
and neighbouring vortex combinations can be determined by adding the weights of cyclic subsets
of edges of the OFW-SG. The procedure is exemplified by the case of LiH for
a perpendicular and weak homogeneous external magnetic field B.
|
Raphael J F Berger; Maria Dimitrova
|
Theoretical and Computational Chemistry; Theory - Computational
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-05-24
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62515160742e9f939f58858e/original/the-oriented-and-flux-weighted-current-density-stagnation-graph-of-li-h.pdf
|
66691213409abc0345322e03
|
10.26434/chemrxiv-2023-j1szt-v2
|
Navigating Materials Space with ML-Generated Electronic Fingerprints
|
Finding materials with good performance in a specific application, especially when the origin of good performance is not well understood or not easily computable, is a major challenge in materials science. Trial-and-error random exploration is prohibitively expensive due to the vastness of the materials space. A more practical approach is to search for new materials within the proximity of known compounds that possess the desired property. In such an approach, assessing materials’ similarity requires deriving some fingerprint relevant for material’s performance. Typically, material’s structure is used as the fingerprint, which often does not translate into similarity in properties. Electronic structure fingerprints, e.g., density of states (DOS) or electronic band structure, were proposed as a better alternative, however, the computational cost of their calculation on the scale of 100,000 materials remains too high for rapid exploration. In this work, we developed a Graph Convolutional Network (GCN) ProDosNet which is trained on orbital-resolved and atom-resolved projected density of states (PDOS) data and is capable of predicting the electronic structure of materials at extremely low computational cost. With this model, we were able to generate PDOS fingerprints for all compounds present in the Materials Projects database and cluster them by similarity of their orbital-resolved PDOS. We demonstrate that these electronic fingerprints allow finding materials with similar electronic properties but drastically different structures for applications in photovoltaics, catalysis, and batteries.
|
Ihor Neporozhnii; Zhibo Wang; Rochan Bajpai; Camilo Gómez; Nirvik Chakraborty; Tony Dong; Isaac Tamblyn; Oleksandr Voznyy
|
Theoretical and Computational Chemistry; Materials Science; Machine Learning; Artificial Intelligence
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66691213409abc0345322e03/original/navigating-materials-space-with-ml-generated-electronic-fingerprints.pdf
|
67682d8481d2151a02968f3b
|
10.26434/chemrxiv-2024-3hgws
|
Reconfigurable Photoflow Reactor for Enhanced Optimization of The Aerobic Oxidative Coupling of 2-phenylbenzoic Acid
|
We tested eight configurations of a flat plate photoflow reactor, each with distinct photonic and mixing properties. The model reaction involved the photocatalytic oxidative cross-coupling of 2-arylbenzoic acid to form 6H-benzo[c]chromen-6-one, using air as an oxidant and visible light. Reactor designs included wide rectangular channels with varying depths and inclinations, two types of static mixers, and three serpentine-like channels with variable depths. All configurations outperformed a stirred batch photoreactor, with the 2 mm deep serpentine channel delivering the highest rate acceleration, reducing reaction time from 6 hours to less than 1.25 hours and increasing the apparent rate constant by over fourfold. The rate constant could not be correlated with the reactor illuminated area, but could be correlated with the the inverse product of flow cross-section and light penetration depth. This correlation aids in optimizing similar reactions, with the optimum range influenced by light intensity and photocatalyst concentration, while the reconfigurable kit enables efficient empirical optimization without prior reaction kinetics knowledge.
|
Florian Sommer; Tobias Freidl; Christian Koller; Malek Ibrahim
|
Organic Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Reaction Engineering; Photocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-12-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67682d8481d2151a02968f3b/original/reconfigurable-photoflow-reactor-for-enhanced-optimization-of-the-aerobic-oxidative-coupling-of-2-phenylbenzoic-acid.pdf
|
645fb4b6a32ceeff2d944af0
|
10.26434/chemrxiv-2023-dzxhc
|
Constructing All-Carbon Quaternary Centers from Ketones via Titanacyclobutanes: Rapid Access to Azaspiro[3.n]alkanes
|
Quaternary carbon centers pose a significant challenge in chemical synthesis. Harnessing the underexplored reactivity of titanacyclobutane intermediates, a strategy to construct functionalized all-carbon quaternary centers from ketones is described. This methodology streamlines access to a wide variety of azaspiro[3.n]alkanes that have emerged as valuable three-dimensional inputs for drug discovery.
|
Tyler Weinhold; James Law; James Frederich
|
Organic Chemistry; Organometallic Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-05-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645fb4b6a32ceeff2d944af0/original/constructing-all-carbon-quaternary-centers-from-ketones-via-titanacyclobutanes-rapid-access-to-azaspiro-3-n-alkanes.pdf
|
6662306b21291e5d1d3c8799
|
10.26434/chemrxiv-2024-5qsnt
|
Transferable Machine Learning Interatomic Potential for Carbon Hydrogen Systems
|
In this study, we developed a machine learning interatomic potential based on artificial neural networks (ANN) to model carbon-hydrogen (C-H) systems. The ANN potential was trained on a dataset of C-H clusters obtained through density functional theory (DFT) calculations. Through comprehensive evaluations against DFT results, including predictions of geometries and formation energies across 0D-3D systems comprising C and C-H, as well as modeling various chemical processes, the ANN potential demonstrated exceptional accuracy and transferability. Its capability to accurately predict lattice dynamics, crucial for stability assessment in crystal structure prediction, was also verified through phonon dispersion analysis. Notably, its accuracy and computational efficiency in calculating force constants facilitated the exploration of complex energy landscapes, leading to the discovery of a novel C polymorph. These results underscore the robustness and versatility of the ANN potential, highlighting its efficacy in advancing computational materials science by conducting precise atomistic simulations on a wide range of C-H materials.
|
Somayeh Faraji; Mingjie Liu
|
Theoretical and Computational Chemistry; Machine Learning
|
CC BY 4.0
|
CHEMRXIV
|
2024-06-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6662306b21291e5d1d3c8799/original/transferable-machine-learning-interatomic-potential-for-carbon-hydrogen-systems.pdf
|
6789f5f36dde43c908e87aab
|
10.26434/chemrxiv-2025-sdmw6
|
Development of a Manufacturing Process for S-892216 Part I: A Novel Method for Constructing a Multi-Substituted Barbiturate Skeleton for Scalable Synthesis
|
S-892216 , a second-generation 3CL protease inhibitor, is currently being developed as a clinical drug candidate for the treatment of SARS-CoV-2 infection. This paper outlines the development process and scaling-up of S-892216 for early phase clinical trials. The developed synthetic route involved a condensation reaction between carboxylic acids and urea with T3P, followed by cyclization in the presence of CDI and DBU to construct a barbiturate core. This novel method facilitated the efficient production of high-quality S-892216 in six steps, with an overall yield of 41.3% from readily available starting materials.
|
Naoto Sahara; Yoichi Hirano; Thien Phuc Le; Katsuya Yamakawa; Eisaku Ohashi; Satoru Shibuya; Kazuo Komano; Kiichiro Hirai; Moriyasu Masui; Go Kato; Takafumi Higuchi; Yuto Shimazaki; Takahiro Kawajiri; Tadashi Oohara; Naoki Tsuno; Takafumi Ohara
|
Organic Chemistry; Organic Synthesis and Reactions; Process Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6789f5f36dde43c908e87aab/original/development-of-a-manufacturing-process-for-s-892216-part-i-a-novel-method-for-constructing-a-multi-substituted-barbiturate-skeleton-for-scalable-synthesis.pdf
|
60c73e16ee301cc305c786af
|
10.26434/chemrxiv.6476510.v1
|
Adsorption and Diffusion of Na+, Cs+ and Ca+2 Ions in C-S-H and C-a-S-H Nanopores
|
Cementitious materials act as a diffusion barrier, immobilizing liquid and solid<br />radioactive waste and preventing their release into the biosphere. The retention capability of hydrated<br />cement paste and its main hydration product, C-S-H gel, has been extensively explored experimentally<br />for many alkali and alkaline earth cations. Nevertheless, the retention mechanisms of these cations at<br />the molecular scale are still unclear. In this paper, we have employed molecular dynamics simulations<br />to study the capacity of C-S-H to retain Cs, Ca and Na, analyzing the number of high-affinity sites on<br />the surface, the type of sorption for each cation and the diffusivity of these ions. We have also explored<br />the impact of aluminum incorporation in C-S-H at a constant concentration of the ions in the gel pore.<br />We found strong competition for surface sorption sites, with notable differences in the retention of the<br />cations under study and a remarkable enhance of the adsorption in C-A-S-H with respect to C-S-H.
|
Eduardo Duque-Redondo; Kazuo Yamada; Iñigo Lopez Arbeloa; Hegoi Manzano
|
Granular Materials; Nanostructured Materials - Materials; Computational Chemistry and Modeling; Physical and Chemical Properties; Transport phenomena (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-06-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e16ee301cc305c786af/original/adsorption-and-diffusion-of-na-cs-and-ca-2-ions-in-c-s-h-and-c-a-s-h-nanopores.pdf
|
673a411af9980725cf821dae
|
10.26434/chemrxiv-2024-wk7jk
|
Ring-Opening Metathesis Polymerization of (Oxa)Norbornenes with Sulfonate, Sulfone, and Sulfoxide Sidechains
|
Sulfur-containing polymers are utilized in applications ranging from vulcanized rubbers to optical materials and proton conducting membranes. Typically, sulfur-containing polymers are synthesized via condensation methods. While ring-openining metathesis polymerization is a useful tool for polymerizing functional monomers, previous reports have shown difficulties incorporating sulfur-containing functional groups due to Ru-S interactions. In this work, we report the synthesis and polymerization of a number of poly(oxa)norobornenes containing sulfonate, sulfone, and sulfoxide sidechains. We demonstrate the effects of the identity of the bridge group, sidechain R groups, and substituent stereochemistry on polymerization rates, molecular weight distrubitons, and thermal properties. Interestingly, while the exo-norbornene phenyl sulfoxide monomer was effectively polymerized, the endo isomer resulted in exclusive single addition to the Ru catalyst due to sulfur chelation to the metal centre. This monomer could however be used for alternating copolymerization with other cyclic olefins.
|
Oliver Clarke; Abdulrahman Bashir; Sophie Wazlowski; Sara Ptaszynska; Brian Northrop; Benjamin Elling
|
Polymer Science; Organic Polymers; Polymerization (Polymers)
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-11-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673a411af9980725cf821dae/original/ring-opening-metathesis-polymerization-of-oxa-norbornenes-with-sulfonate-sulfone-and-sulfoxide-sidechains.pdf
|
657a3d7ebec7913d27890085
|
10.26434/chemrxiv-2023-kgfpg-v3
|
Incorporating Neural Networks into the AMOEBA Polarizable Force Field
|
Neural network potentials (NNPs) offer significant promise to bridge the gap be- tween the accuracy of quantum mechanics and the efficiency of molecular mechanics in molecular simulation. Most NNPs rely on the locality assumption that ensures the model’s transferability and scalability and thus lack the treatment of long-range inter- actions, which are essential for molecular systems in condensed phase. Here we present an integrated hybrid model, AMOEBA+NN, which combines the AMOEBA potential for the short- and long-range non-covalent atomic interactions and an NNP to capture the remaining local covalent contributions. The AMOEBA+NN model was trained on the conformational energy of ANI-1x dataset and tested on several external datasets ranging from small molecules to tetrapeptides.The hybrid model demonstrated sub- stantial improvements over the baseline models in term of accuracy as the molecule size increased, suggesting its potential as a next-generation approach for chemically accurate molecular simulations.
|
Yanxing Wang; Théo Jaffrelot Inizan; Chengwen Liu; Jean-Philip Piquemal; Pengyu Ren
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657a3d7ebec7913d27890085/original/incorporating-neural-networks-into-the-amoeba-polarizable-force-field.pdf
|
6653820a91aefa6ce10ca737
|
10.26434/chemrxiv-2024-8rlk4
|
Cp*Rh(III)-Catalyzed Enantioselective C(sp3)–H Amidation of Azine-Linked Cyclobutanes
|
The highly enantioselective desymmetrizing C(sp3)–H amidation of azine-linked cyclobutanes with dioxazolones, to afford enantioenriched cis-configured amido-cyclobutane scaffolds is described. The reaction is catalyzed by an electron-deficient Cp*Rh(III) complex in combination with a newly designed axially chiral carboxylic acid (CCA) that was found to be key in obtaining high levels of enantiocontrol. Computational studies using DFT uncovered the reaction pathway and revealed the presence of multiple non-covalent interactions including inter- and intramolecular n–π* interactions and CH−π interactions which contributed to the high enantioselectivity. The methodology was found to be broad in scope with respect to the dioxazolone and could be further extended to larger cycloalkyl derivatives as well as bis-amidated cyclobutane derivatives.
|
Xing Xu; Heyao Shi; Phillip Biallas; Alistair J. M. Farley; Christophe Genicot; Ken Yamazaki; Darren J. Dixon
|
Organic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6653820a91aefa6ce10ca737/original/cp-rh-iii-catalyzed-enantioselective-c-sp3-h-amidation-of-azine-linked-cyclobutanes.pdf
|
614acc296fc3a869b9a8e98e
|
10.26434/chemrxiv-2021-7thm1
|
Novel dynamic residue network analysis approaches to study homodimeric allosteric modulation in SARS-CoV-2 Mpro and in its evolutionary mutations
|
The rational search for allosteric modulators and the allosteric mechanisms of these modulators in the presence of evolutionary mutations, including resistant ones, is a relatively unexplored field. Here, we established novel in silico approaches and applied to SARS-CoV-2 main protease (Mpro). First, we identified six potential allosteric modulators (SANC00302, SANC00303, SANC00467, SANC00468, SANC00469, SANC00630) from the South African Natural Compounds Database (SANCDB) bound to the allosteric pocket of Mpro that we determined in our previous work. We also checked the stability of these compounds against Mpro of laboratory strain HCoV-OC43 and identified differences due to residue changes between the two proteins. Next, we focused on understanding the allosteric effects of these modulators on each protomer of the reference Mpro protein, while incorporating the symmetry problem in the functional homodimer. In general, asymmetric behavior of multimeric proteins is not commonly considered in computational analysis. We introduced a novel combinatorial approach and dynamic residue network (DRN) analysis algorithms to examine patterns of change and conservation of critical nodes, according to five independent criteria of network centrality (betweenness centrality (BC), closeness centrality (CC), degree centrality (DC), eigencentrality (EC) and katz centrality (KC)). The relationships and effectiveness of each metric in characterizing allosteric behavior were also investigated. We observed highly conserved network hubs for each averaged DRN metric on the basis of their existence in both protomers in the absence and presence of all ligands, and we called them persistent hubs (residues 17, 111, 112 and 128 for averaged BC; 6, 7, 113, 114, 115, 124, 125, 126, 127 and 128 for averaged CC; 36, 91, 146, 150 and 206 for averaged DC; 7, 115 and 125 for EC; 36, 125 and 146 for KC). We also detected ligand specific signal changes some of which were in or around functional residues (i.e. chameleon switch PHE140). Using EC persistent hubs and ligand introduced hubs we identified a residue communication path between allosteric binding site and catalytic site. Finally, we examined the effects of the mutations on the behavior of the protein in the presence of selected potential allosteric modulators and investigated the ligand stability. The hit compounds showed various levels of stability in the presence of SARS-CoV-2 Mpro mutations, being most stable in A173V, N274D and R279C, and least stable in R60C, N151D V157I, C160S and A255V. SANC00468 was the most stable compound in the 43 mutant protein systems. We further used DRN metric analysis to define cold spots as being those regions that are least impacted, or not impacted, by mutations. One crucial outcome of this study was to show that EC centrality hubs form an allosteric communication path between the allosteric ligand binding site to the active site going through the interface residues of Domain I and II; and this path was either weakened or lost in the presence of some of the mutations. Overall, the results of this study revealed crucial aspects that need to be considered in drug discovery in COVID-19 specifically and in general for rational computational drug design purposes.
|
Olivier Sheik Amamuddy; Rita Afriyie Baoteng; Victor Barozi; Dorothy Wavinya Nyamai ; Ozlem Tastan Bishop
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-09-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614acc296fc3a869b9a8e98e/original/novel-dynamic-residue-network-analysis-approaches-to-study-homodimeric-allosteric-modulation-in-sars-co-v-2-mpro-and-in-its-evolutionary-mutations.pdf
|
6178221164e2af5a0c1567e1
|
10.26434/chemrxiv-2021-70pvw
|
Origin of the high specific capacity in sodium manganese hexacyanomanganate
|
Sodium manganese hexacyanomanganate, NaxMn[Mn(CN)6], is an electrochemically active Prussian blue analog (PBA) that has been studied experimentally as an electrode material in rechargeable sodium-ion batteries. It has a reversible specific capacity of 209 mAh/g, which is substantially higher than the theoretical specific capacity of 172 mAh/g expected for two reduction events conventional in the PBAs. It has been suggested the high specific capacity originates from this compound's unique ability to insert a third sodium ion per formula unit. However, the plausibility of this mechanism has remained ambiguous. Here we use density-functional theory (DFT) with a hybrid functional to calculate the formation energies of various oxidation states and magnetic phases of the NaxMn[Mn(CN)6] system. We confirm that the compound Na3Mn(II)[Mn(I)(CN)6] is, indeed, thermodynamically stable. It contains manganese(I) and the sodium ions occupy the interfacial position of the lattice subcubes. We also provide strong evidence that the phase of the fully oxidized Mn[Mn(CN)6] compound is charge-disproportionated, containing manganese(II) and manganese(IV). We proceed to show that the presence of crystalline water increases the reduction potential of the system and that the hydrated compounds have theoretical crystal geometries and reduction potentials that closely match experiment. This work clarifies the charge-storage mechanism in a well-known but less-understood PBA.
|
Kevin Hurlbutt; Feliciano Giustino; George Volonakis; Mauro Pasta
|
Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-10-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6178221164e2af5a0c1567e1/original/origin-of-the-high-specific-capacity-in-sodium-manganese-hexacyanomanganate.pdf
|
625e5714368ab6c99d851e7e
|
10.26434/chemrxiv-2022-v4dps-v2
|
Deciphering the molecular mechanism of substrate-induced assembling of gold nanocube arrays toward accelerated electrocatalytic effect employing heterogeneous diffusion fields confinement
|
The complex electrocatalytic performance of gold nanocubes (AuNCs) is the focus of the presented paper. The faceted shapes of AuNCs and the individual assembling process at the electrode surfaces define heterogeneous conditions for the purpose of electrocatalytic processes. Topographic and electron imaging demonstrated slightly rounded AuNC (avg. 38 nm) assemblies with sizes up to 1 µm, where the dominating patterns are (111) and (200) crystallographic planes. The AuNCs significantly impact the electrochemical performance of the investigated electrode (ITO, GC, bulk gold) systems driven by surface electrons promoting the catalytic effect. Cyclic voltammetry jointly with scanning electrochemical microscopy (SECM) allowed us to decipher the molecular mechanism of substrate-induced electrostatic assembling of gold nanocube arrays, revealing that the accelerated electrocatalytic effect should be attributed to the confinement of the heterogeneous diffusion fields with tremendous electrochemically active surface area variations. The AuNC drop-casting at ITO, GC, and Au led to various mechanisms of heterogeneous charge transfer, where only in the case of GC, the decoration significantly increased both the electrochemically active surface area (EASA) and ferrocyanide redox kinetics. For ITO and Au substrates, AuNC drop-casting lowers system dimensionality rather than expanding the EASA, where Au-Au self-diffusion was also observed. Interactions between the gold, ITO, and GC surfaces with themselves and with surfactant CTAB and ferrocyanide molecules were investigated by performing density functional theory.
|
Pawel Niedzialkowski; Adrian Koterwa; Adrian Olejnik; Artur Zielinski; Karolina Gornicka; Mateusz Brodowski; Robert Bogdanowicz; Jacek Ryl
|
Catalysis; Analytical Chemistry; Electrochemical Analysis; Electrocatalysis; Nanocatalysis - Reactions & Mechanisms; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-04-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625e5714368ab6c99d851e7e/original/deciphering-the-molecular-mechanism-of-substrate-induced-assembling-of-gold-nanocube-arrays-toward-accelerated-electrocatalytic-effect-employing-heterogeneous-diffusion-fields-confinement.pdf
|
6529019cbda59ceb9a7e598a
|
10.26434/chemrxiv-2023-sbcdx
|
Fixing flavins: hijacking a flavin transferase for equipping flavoproteins with a covalent flavin cofactor
|
Most flavin-dependent enzymes contain a dissociable flavin cofactor. We present a new approach for installing a covalent bond between a flavin cofactor and its hosting protein. By using a flavin transferase and carving a flavinylation motif in target proteins, we demonstrate that ‘dissociable’ flavoproteins can be turned into covalent flavoproteins. Specifically, three different FMN-containing proteins were engineered to undergo covalent flavinylation: a light-oxygen-voltage (LOV) domain protein, a mini singlet-oxygen-generator (miniSOG), and a nitroreductase (BtNR). Optimizing the flavinylation motif and expression conditions led to covalent flavinylation of all three flavoproteins. The engineered covalent flavoproteins retained function and often exhibited improved performance such as higher thermostability or catalytic performance. Crystal structures of all three covalent flavoproteins confirmed the designed threonyl-phosphate linkage. The targeted flavoproteins differ in fold and function, indicating that this method of introducing a covalent flavin-protein bond is a powerful new method to create flavoproteins which cannot lose their cofactor, boosting their performance.
|
Yapei Tong; Saniye Kaya; Sara Russo; Henriette Rozeboom; Hein Wijma; Marco Fraaije
|
Biological and Medicinal Chemistry; Catalysis; Biochemistry; Chemical Biology; Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6529019cbda59ceb9a7e598a/original/fixing-flavins-hijacking-a-flavin-transferase-for-equipping-flavoproteins-with-a-covalent-flavin-cofactor.pdf
|
6525542e45aaa5fdbbb17eb0
|
10.26434/chemrxiv-2023-7r6ks
|
Quorum sensing in emulsion droplet swarms driven by a surfactant competition system.
|
Quorum sensing enables unicellular organisms to probe their population density and perform behaviour that exclusively occurs above a critical density. We establish quorum sensing in emulsion droplet swarms that float at a water surface and cluster above a critical density. Our design involves competition between 1) a surface tension gradient that is generated upon release of a surfactant from the oil droplets, and thereby drives their mutual repulsion, and 2) release of a surfactant precursor from the droplets, that forms a strong imine surfactant which suppresses the surface tension gradient and thereby causes droplet clustering upon capillary attraction. The production of the imine-surfactant depends on the population density of the droplets releasing the precursor, so that the clustering only occurs above a critical population density. We exploit the pH-dependence of the imine-surfactant formation to trigger quorum sensing upon a base stimulus, establish dynamic droplet swarms that cluster and spread upon spatiotemporally varying acid and base conditions, and couple the clustering of two droplet subpopulations to a chemical reaction that generates of a fluorescent signal. We foresee that quorum sensing enables control mechanisms in droplet-based systems that display collective responses in contexts of e.g. sensing, optics or dynamic controlled droplet-reactors.
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Pieter J. de Visser; Dimitrios Karagrigoriou; Anne-Déborah C. Nguindjel; Peter A. Korevaar
|
Physical Chemistry; Interfaces; Self-Assembly; Surface
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6525542e45aaa5fdbbb17eb0/original/quorum-sensing-in-emulsion-droplet-swarms-driven-by-a-surfactant-competition-system.pdf
|
630ef0b4d858fb67b362e9ce
|
10.26434/chemrxiv-2021-r3lqh-v9
|
Dynamic Self-organization in an Open Reaction Network: A Principle for the Emergence of Life
|
The emergence of life on Earth has attracted intense attention but remains unclear. A key problem is that the question of how living organisms can exhibit self-organizing ability that leads to highly ordered structures such as enzymes and DNA and high functions such as adaptive and evolutionary ability remains unanswered. This work reveals, by computer simulation and experiments, that a non-equilibrium steady state of an open reaction network (ORN), which is a good model of primitive life, demonstrates such self-organizing ability. Reaction and diffusion processes in an ORN are irreversible and always forced toward equilibrium and, hence, necessarily reach a steady state in which they have approached equilibrium to the largest extent possible and attained a full balance, if no oscillatory or dispersive behavior emerges. Thus, the steady state is firmly stabilized by the irreversible processes and is kept stable against fluctuation. As an ORN in general incessantly changes with time, this result can be interpreted as indicating that the steady state is produced by dynamic self-organization. The steady state can also exhibit adaptive ability because all the involved processes including inflows and outflows of chemical substances have attained a full balance and are in a harmonious state with the environment. Moreover, the steady state, which is in non-equilibrium, has a property of approaching equilibrium and thus can evolve toward highly ordered structures through interaction with the environment. In fact, we can argue that increases in the rate constants of reactions through the construction of highly ordered structures act as an important factor in an approach of a steady state to equilibrium. Thus, a steady state of an ORN can demonstrate multi-functional self-organizing ability essentially the same as that of living things and therefore dynamic self-organization in it can be regarded as providing a principle for the emergence of life.
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Yoshihiro Nakato
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Physical Chemistry; Biophysical Chemistry; Chemical Kinetics; Physical and Chemical Processes
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CC BY 4.0
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CHEMRXIV
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2022-09-09
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630ef0b4d858fb67b362e9ce/original/dynamic-self-organization-in-an-open-reaction-network-a-principle-for-the-emergence-of-life.pdf
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6617d56321291e5d1d9ef449
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10.26434/chemrxiv-2024-ngqqg
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Transfer learning for Heterocycle Synthesis Prediction
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Heterocycles are important scaffolds in medicinal chemistry that can be used to modulate the binding mode as well as pharmacokinetic properties of drugs. The importance of heterocycles has been exemplified by the publication of numerous datasets containing heterocyclic rings and their properties. However, those datasets lack synthetic routes towards the published heterocycles. Consequently, novel and uncommon heterocycles are not easily synthetically accessible. While retrosynthetic prediction models could usually be used to assist synthetic chemists, their performance is poor for heterocycle formation reactions due to low data availability. In this work, we compare the use of four different transfer learning methods to overcome the low data availability problem and improve the performance of retrosynthesis prediction models for ring-breaking disconnections. The mixed fine-tuned model achieves top-1 accuracy of 36.5% and, moreover, 62.1% of its predictions are chemically valid and ring-breaking. Furthermore, we demonstrate the applicability of the mixed fine-tuned model in drug discovery by recreating synthetic routes towards two drug-like targets published this year. Finally, we introduce a method for further fine-tuning the model as new reaction data becomes available.
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Ewa Wieczorek; Joshua W. Sin; Matthew T. O. Holland; Liam Wilbraham; Victor S. Perez; Anthony Bradley; Dominik Miketa; Paul E. Brennan; Fernanda Duarte
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Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry
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CC BY 4.0
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CHEMRXIV
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2024-05-06
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6617d56321291e5d1d9ef449/original/transfer-learning-for-heterocycle-synthesis-prediction.pdf
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61ae1319dce179bf6802ba58
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10.26434/chemrxiv-2021-9w10v
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Mechanism-Based Strategy for Optimizing HaloTag Protein Labeling
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HaloTag labeling technology has introduced unrivaled potential in protein chemistry, molecular and cellular biology. A wide variety of ligands have been developed to meet the specific needs of diverse applications, but only a single protein tag, DhaAHT, is routinely used for their incorporation. Following a systematic kinetic and computational analysis of different reporters, tetramethylrhodamine and three 4-stilbazolium-based fluorescent ligands, we showed that the mechanism of incorporating different ligands depends both on the binding step and the efficiency of the chemical reaction. By studying the different haloalkane dehalogenases DhaA, LinB, and DmmA, we found that the architecture of the access tunnels is critical for the kinetics of both steps and the ligand specificity. We show that highly efficient labelling with specific ligands is achievable with natural dehalogenases. We propose a simple protocol for selecting the optimal protein tag for a specific ligand from a wide pool of available enzymes with diverse access tunnel architectures. The application of this protocol eliminates a need for expensive and laborious protein engineering.
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Sérgio Marques; Michaela Slanska; Klaudia Chmelova; Radka Chaloupkova; Martin Marek; Spencer Clark; Jiri Damborsky; Eric T. Kool; David Bednar; Zbynek Prokop
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Biological and Medicinal Chemistry; Analytical Chemistry; Imaging; Microscopy; Chemical Biology; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2021-12-07
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ae1319dce179bf6802ba58/original/mechanism-based-strategy-for-optimizing-halo-tag-protein-labeling.pdf
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62220c7a50b621afe6e8f765
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10.26434/chemrxiv-2022-xl12g
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Divide-and-conquer: a flexible deep learning strategy for exploring metabolic heterogeneity from mass spectrometry imaging data
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There is growing awareness that metabolic heterogeneity of organism provides vital insight into the disease with molecular mechanism and personalized therapy. The screening of metabolism-related sub-regions that affect disease development is essential for the more focused exploration how disease progress aberrant phenotypes, even carcinogenesis and metastasis. Mass spectrometry imaging (MSI) technique has distinct advantages to reveal the heterogeneity of organism based on the in situ molecular profiles. The challenge of heterogeneous analysis has been to perform an objective identification among biological tissues with different characteristics. By introducing the divide-and-conquer strategy to architecture design and application, we establish here a flexible unsupervised deep learning model, called divide-and-conquer (dc)-DeepMSI, for metabolic heterogeneity analysis from MSI data without prior knowledge of histology. dc-DeepMSI can be used to identify either spatially contiguous region-of-interest (ROIs) or spatially sporadic ROIs. We demonstrate that the novel learning strategy successfully obtain sub-regions that are statistically linked to invasion status and molecular phenotypes of breast cancer, as well as organizing principles during developmental phase.
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Lei Guo; Jiyang Dong; Xiangnan Xu; Zhichao Wu; Yinbin Zhang; Yongwei Wang; Pengfei Li; Chao Zhao; Zongwei Cai
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Biological and Medicinal Chemistry; Bioinformatics and Computational Biology
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CC BY NC 4.0
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CHEMRXIV
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2022-03-07
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62220c7a50b621afe6e8f765/original/divide-and-conquer-a-flexible-deep-learning-strategy-for-exploring-metabolic-heterogeneity-from-mass-spectrometry-imaging-data.pdf
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60c74fb10f50dbf24539744e
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10.26434/chemrxiv.12931880.v1
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Stage-1 Cationic C60 Intercalated Graphene Oxide Films
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A “stage-1” intercalated film has been made by the ion exchange of “cationic C<sub>60</sub>” (pyrrolidinium-functionalised C<sub>60</sub>, C<sub>60</sub>(Py)<sup>n+</sup>) into centimetre-wide, micrometre-thick air-dried graphene oxide (G-O) films composed of tens of thousands of layers of stacked/overlapping G-O platelets, denoted [C<sub>60</sub>(Py)<sup>n+</sup>]G-O films. Spontaneous intercalation by ion exchange of one layer of cationic C60 between adjacent G-O layers expands the interlayer spacing of the films from 0.74 nm to 1.46 nm. The films remain intact in water and various organic solvents, which is likely due to a strong affinity between C<sub>60</sub>(Py)<sup>n+</sup> and G-O. Membranes made of the films showed a 6.8 times faster water vapour permeation rate (allowing the vapour to transport through the membrane almost freely) and a 10.5 times faster liquid water permeation rate than G-O membranes. Heating the films at 2000 °C under applied pressure or at 2700 °C without physical confinement converted them into highly graphitised structures.
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Xianjue Chen; Karin Ching; Aditya Rawal; Douglas Lawes; Mohammad Tajiki; William Donald; Sun Hwa Lee; Rodney Ruoff
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Carbon-based Materials
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CC BY NC ND 4.0
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CHEMRXIV
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2020-09-09
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fb10f50dbf24539744e/original/stage-1-cationic-c60-intercalated-graphene-oxide-films.pdf
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60c74457337d6c5996e26d96
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10.26434/chemrxiv.9778703.v1
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Iridium Catalyzed Deoxygenation of Epoxides with Carbon Monoxide
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This work describes the selective desoxygenation of epoxides to olefins using carbon monoxide as the reducing agent and an iridium pincer complex as the homogeneous catalyst. A lithium salt additive acts as co-catalyst in various steps of the catalytic cycle. The mechanism is elucidated including the isolation of intermediates.<br />
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Theo Maulbetsch; Eva Jürgens; Doris Kunz
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Bond Activation; Catalysis; Kinetics and Mechanism - Organometallic Reactions; Ligands (Organomet.); Transition Metal Complexes (Organomet.)
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CC BY NC ND 4.0
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CHEMRXIV
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2019-09-09
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74457337d6c5996e26d96/original/iridium-catalyzed-deoxygenation-of-epoxides-with-carbon-monoxide.pdf
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62de9274adb01e9af7aafba1
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10.26434/chemrxiv-2022-hrxvj-v2
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Facile Supramolecular Strategy to Construct Solid Fluorophore@Metal-Organic Framework Composites
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The design and synthesis of a microporous construct based on the entrapment of an emissive fluorescein derivative in a zinc 2-methylimidazolate (ZIF-8) metal-organic framework (MOF) is detailed. Synthesis of the MOF in the presence of a fluorophore enables the capture and dispersal of dye molecules within the ZIF-8 framework. Within the resulting supramolecular assemblies, the fluorophore components show excellent photophysical properties such as high emission and increased fluorescence lifetime, despite the tendency of the dye to undergo aggregation-caused quenching in the solid-state, as well as a 4-fold enhancement of the fluorophore’s photostability. The demonstration that supramolecular events can be invoked to construct solid fluorescent systems from separate components is realized. The encapsulation of the fluorescein in an enclosed subunit of the ZIF-8 framework was modelled using the density-functional tight-binding method. Furthermore, the fluorophore@MOF composite can be internalized by mammalian macrophage cells and transported to lysosomes without disrupting cell viability. In principle, this simple protocol can evolve into a general strategy for intracellular delivery of functional molecular components for targeted bioimaging or theranostic applications.
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Lavinia Trifoi; Gregory Hodgson; Nicholas Dogantzis; Sumaiya Soha; Roya Dayam; Costin Antonescu; Roberto Botelho; Stephen Wylie; Stefania Impellizzeri
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Physical Chemistry; Organic Chemistry; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2022-07-26
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62de9274adb01e9af7aafba1/original/facile-supramolecular-strategy-to-construct-solid-fluorophore-metal-organic-framework-composites.pdf
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6687fcaf01103d79c51c9626
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10.26434/chemrxiv-2024-wnw1k
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Tuning the Electronic Properties of Azophosphines as Ligands and their Application in Base-Free Transfer Hydrogenation Catalysis
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The design and tuning of new ligands is crucial for unlocking new reactivity at transition metal centres. Azophosphines have recently emerged as a new class of 1,3-P,N ligands in ruthenium piano-stool complexes. This work shows that the azophosphine synthesis can tolerate N-aryl substituents with strongly electron-donating and electron-withdrawing para-R groups, and that the nature of this R group can affect the spectroscopic and structural properties of the azophosphines, as measured by NMR spectroscopy, UV-Vis spectroscopy, single crystal X-ray diffraction and DFT studies. Azophosphines are shown to be relatively weak phosphine donors, as shown by analysis of the 1JP–Se coupling constants of the corresponding azophosphine selenides, but the donor properties can be fine-tuned within this area of chemical space. Monodentate and bidentate Ru-azophosphine complexes were prepared, and their first use as catalysts was probed. The Ru-azophosphine complexes were found to promote the transfer hydrogenation of acetophenone to 1-phenylethanol without the requirement of a harsh base additive, and the bidentate complex was more active than the monodentate analogue.
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Emma Jordan; Ethan Calder; Bethan Greene; Holly Adcock; Louise Male; Paul Davies; Andrew Jupp
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Inorganic Chemistry; Coordination Chemistry (Inorg.); Main Group Chemistry (Inorg.); Organometallic Compounds
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CC BY 4.0
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CHEMRXIV
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2024-07-08
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6687fcaf01103d79c51c9626/original/tuning-the-electronic-properties-of-azophosphines-as-ligands-and-their-application-in-base-free-transfer-hydrogenation-catalysis.pdf
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60c74d9f567dfe3cd8ec539a
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10.26434/chemrxiv.12640073.v1
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Supercritical Fluid Extraction Enhances Discovery of Secondary Metabolites from Myxobacteria
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Supercritical fluid extraction (SFE) is widely used for the isolation of natural products from plants, but its application in efforts to identify structurally and physicochemically often dissimilar microbial natural products is limited to date. In this study we evaluated the impact of SFE on the extractability of myxobacterial secondary metabolites aiming to improve the prospects of discovering novel natural products. We investigated the influence of different co-solvents on the extraction efficiency of secondary metabolites from three myxobacterial strains as well as the antimicrobial activity profiles of the corresponding extracts. For each known secondary metabolite we found extraction conditions using SFE leading to superior yields in the extracts compared to conventional solvent extraction. Compounds with a logP higher than 3 showed best extraction efficiency using 20% EtOAc as a co-solvent, whereas compounds with logP values lower than 3 were better extractable using more polar co-solvents like MeOH. Extracts generated with SFE showed increased antimicrobial activities including the presence of activities not explained by known myxobacterial secondary metabolites, highlighting the advantage of SFE for bioactivity-guided isolation. Moreover, non-targeted metabolomics analysis revealed a group of chlorinated metabolites produced by the well-studied model myxobacterium Myxococcus xanthus DK1622 which were not accessible previously due to their low concentration in conventional extracts. The enriched SF extracts were used for isolation and subsequent structure elucidation of chloroxanthic acid A as founding member of a novel secondary metabolite family. Our findings encourage the increased utilization of SFE as part of future microbial natural products screening workflows.
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Chantal Bader; Markus Neuber; Fabian Panter; Daniel Krug; Rolf Müller
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Mass Spectrometry; Separation Science
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CC BY NC ND 4.0
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CHEMRXIV
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2020-07-13
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d9f567dfe3cd8ec539a/original/supercritical-fluid-extraction-enhances-discovery-of-secondary-metabolites-from-myxobacteria.pdf
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60c74443842e65ac0cdb2415
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10.26434/chemrxiv.9775958.v1
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Palladium-Catalyzed 2-(Neopentylsulfinyl)aniline Directed C-H Acetoxylation and Alkenylation of the Arylacetamides
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A directing group that promotes very fast diacetoxylation of the arylacetamides is reported. The auxiliary also promotes alkenylation with vinyl ketones, which were generated in one-pot from the cyclopropanols.
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Maryia V. Barysevich; Marharyta V. Laktsevich-Iskryk; Anastasiya V. Krech; Vladimir N. Zhabinskii; Vladimir A. Khripach; Alaksiej Hurski
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Organic Synthesis and Reactions
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CC BY NC ND 4.0
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CHEMRXIV
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2019-09-09
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74443842e65ac0cdb2415/original/palladium-catalyzed-2-neopentylsulfinyl-aniline-directed-c-h-acetoxylation-and-alkenylation-of-the-arylacetamides.pdf
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60c74166567dfe75ffec3d76
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10.26434/chemrxiv.8038892.v1
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A Marcus-Hush Perspective on Adiabatic Singlet Fission
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<div>Singlet fission is a process whereby a bichromophoric system crosses from an excitonically coupled singlet state to a singlet-coupled triplet pair state. If the electronic structure is described locally, then the process may be described by a formal exchange of electrons. As such, it lends itself to a treatment rooted in the Marcus-Hush description of electron transfer. Here we use ab initio and density functional electronic structure theories to reveal a Marcus-Hush perspective on singlet fission and propose experiments to probe singlet fission in the spirit of photo-induced electron transfer.</div>
|
Timothy Schmidt
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Computational Chemistry and Modeling; Theory - Computational; Photochemistry (Physical Chem.); Physical and Chemical Processes; Quantum Mechanics; Spectroscopy (Physical Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
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2019-04-25
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74166567dfe75ffec3d76/original/a-marcus-hush-perspective-on-adiabatic-singlet-fission.pdf
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62acc09e1fdc344b803d780c
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10.26434/chemrxiv-2022-pzj5p
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Ion Binding Site Structure and the Role of Water in Alkali Earth EDTA Complexes
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The interactions between molecular hosts and ionic guests and how the chemical environment in aqueous solutions changes these interactions are challenging to disentangle from solution data alone. The vibrational spectra of cold complexes of ethylenediaminetetraacetic acid (EDTA) chelating alkaline earth dications in vacuo encode structural characteristics of these complexes and their dependence on the size of the bound ion. The correlation between metal binding geometry and the relative intensities of vibrational bands of the carboxylate groups forming the binding pocket allows us to characterize changes in molecular geometry by interaction with other molecules. The evolution of these structural markers from bare ions to water adducts to aqueous solution illustrates the role of water for the structure of ion binding sites in chelators. The results show that the binding pocket of EDTA opens up in aqueous solution, bringing the bound ion closer to the mouth of the binding site, and leading to an increased exposure of the bound ion to the chemical environment.
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Madison Foreman; J. Mathias WEBER
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Physical Chemistry; Clusters; Spectroscopy (Physical Chem.); Structure
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CC BY NC ND 4.0
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CHEMRXIV
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2022-06-20
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62acc09e1fdc344b803d780c/original/ion-binding-site-structure-and-the-role-of-water-in-alkali-earth-edta-complexes.pdf
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60c7545c469df4c1eff44f23
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10.26434/chemrxiv.13653050.v1
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High Electrical Conductivity in Three-Dimensional Porphyrin-Phosphonate Metal Organic-Frameworks
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<p>Herein, we report the design and synthesis of a highly electrically conductive and microporous three-dimensional zinc-phosphonate metal-organic framework [Zn(Cu-<i>p</i>-H<sub>4</sub>TPPA)] ⋅2 (CH<sub>3</sub>)<sub>2</sub>NH<sub>2</sub><sup>+</sup> (designated as GTUB3), constructed using the 5,10,15,20‐tetrakis [<i>p</i>‐phenylphosphonic acid] porphyrin (<i>p</i>-H<sub>8</sub>TPPA) organic linker. GTUB3 has an indirect band gap of 1.64 eV and a high average electrical conductivity of<b> </b>4 S/m, making it a rare example of an electrically conductive zinc metal-organic framework. The N<sub>2</sub>-accessible geometric surface area of GTUB3, as predicted by molecular simulations, is 671 m<sup>2</sup>/g. Owing to its simple, high-yield synthesis at low temperatures, porosity, and electrical conductivity, GTUB3 may be used as a low-cost electrode material in next generation phosphonate-supercapacitors. </p>
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Yunus Zorlu; Patrik Tholen; Mehmet Menaf Ayhan; Ceyda Bayraktar; Gabriel Hanna; A. Ozgur Yazaydin; Ozgur Yavuzcetin; Gündoğ Yücesan
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Hybrid Organic-Inorganic Materials; Inorganic Polymers; Theory - Inorganic; Crystallography – Inorganic
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CC BY NC ND 4.0
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CHEMRXIV
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2021-01-29
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7545c469df4c1eff44f23/original/high-electrical-conductivity-in-three-dimensional-porphyrin-phosphonate-metal-organic-frameworks.pdf
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667bf8b9c9c6a5c07a6e4c44
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10.26434/chemrxiv-2024-v0h7j
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Docking-Based Computational Analysis of Guava (Psidium guajava) Leaves Derived Bioactive Compounds as Coagulation Factor IXa Inhibitor
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Thrombotic disorders pose a global health threat, emphasizing the urgent need for effective management strategies. This study explores the potential of bioactive compounds from guava leaves in inhibiting coagulation factor IXa (CFIXa) using in-silico methods. Using GC-MS, bioactive compounds were identified from guava leaf extracts obtained through ethanol maceration. Pharmacokinetic properties were elucidated using SwissADME. Molecular docking with AutoDock Vina investigated interactions with CFIXa. CFIXa were modeled with pysimm/LAMMPS and analyzed with CastP for active site identification. The setup with higher solvent concentration and lower surface area yielded the highest percent yield (78.541 g, 39.27%). Among 28 identified bioactive compounds, predominantly terpenoids, only seven exhibited suitable pharmacokinetic properties for oral ingestion and drug development. Docking analysis revealed favorable binding of these compounds to CFIXa (-7.6 : -5.3). This study has shown inhibition of coagulation factor IXa, bridging the ambiguity surrounding the effect of guava leaves in hemostasis. These findings also reveal that guava leaf extract harbors bioactive compounds with potential as coagulation pathway inhibitors, promising novel avenues for thrombotic disorder management.
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Joseph De Luna; Shanahi Chelledie Gonzales; Jimuel Jan Nuqui
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Biological and Medicinal Chemistry; Biochemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems
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CC BY NC 4.0
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CHEMRXIV
|
2024-06-27
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667bf8b9c9c6a5c07a6e4c44/original/docking-based-computational-analysis-of-guava-psidium-guajava-leaves-derived-bioactive-compounds-as-coagulation-factor-i-xa-inhibitor.pdf
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60c749dd469df4d40af43c4d
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10.26434/chemrxiv.12110760.v1
|
Gliptin Repurposing for COVID-19
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<i>De novo</i> drug discovery of any therapeutic modality (e.g.
antibodies, vaccines or small molecules) historically takes years from
idea/preclinic to the market and it is therefore not a short-term
solution for the current SARS-CoV-2 pandemic. Therefore, drug
repurposing – the discovery novel indication areas for already approved
drugs - is perhaps the only approach able to yield a short term
relieve. Here we describe computational screening results suggesting
that certain members of the drug class of gliptins are inhibitors of the
two SARS-CoV-2 proteases 3CLpro and PLpro. The oral bioavailable
antidiabetic drug class of gliptins are safe and have been introduced
clinically since 2006 and used by millions of patients since then. Based
on our repurposing hypothesis the nitrile containing gliptins deserve
further investigation as potential anti-COVID19 drugs.
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Matthew Groves; Alexander Domling; Angel Jonathan Ruiz Moreno; Atilio Reyes Romero; Constantinos Neochoritis; Marco Velasco-Velázquez
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Bioinformatics and Computational Biology
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-04-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749dd469df4d40af43c4d/original/gliptin-repurposing-for-covid-19.pdf
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60c74650702a9b3a0718abb2
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10.26434/chemrxiv.11302397.v1
|
On Protein Preferential Solvation in Water:Glycerol Mixtures
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For proteins in solvent mixtures, the relative abundances of each solvent in their solvation shell have a critical impact on their properties. Preferential solvation of a series of proteins in water-glycerol mixtures is studied here over a broad range of solvent compositions via classical molecular dynamics simulations. Our simulation results reveal that the differences between shell and bulk compositions exhibit dramatic changes with solvent composition, temperature and protein nature. In contrast with the simple and widely used picture where glycerol is completely excluded from the protein interface, we show that for aqueous solutions with less than 50% glycerol in volume, protein solvation shells have approximately the same composition as the bulk solvent and proteins are in direct contact with glycerol. We further demonstrate that at high glycerol concentration, glycerol depletion from the solvation shell is largely due to an entropic factor arising from the reduced accessibility of bulky glycerol molecules in protein cavities. The resulting molecular picture is important to understand protein activity and cryopreservation in mixed aqueous solvents.<br />
|
Nicolas Cheron; Margaux Naepels; Eva Pluharova; Damien Laage
|
Computational Chemistry and Modeling; Theory - Computational
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CC BY NC ND 4.0
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CHEMRXIV
|
2019-12-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74650702a9b3a0718abb2/original/on-protein-preferential-solvation-in-water-glycerol-mixtures.pdf
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60c748f9337d6c50dbe2762c
|
10.26434/chemrxiv.12006270.v1
|
Interface Failure in Nacre-like Alumina
|
<div>
<div>
<div>
<p>Among many bioinspired materials contenders, ceramic-ceramic composites based on alumina platelets have recently emerged as a new class of strong and
damage-resistant materials. These materials are brick-and-mortar composites, where bricks are single-crystal alumina platelets, and a glassy interphase acts as
the mortar. Although several processing approaches have been reported to date, these materials were optimized so far by trial-and-error approaches.
Understanding the fracture properties of nacre-like alumina requires the knowledge of the properties of each of its components. However, only the properties
of alumina platelets have been evaluated so far. Here we characterize at a micro scale the fracture property of an aluminosilicate glass interphase between
alumina platelets. Micro-cantilever specimens prepared by FIB milling are tested under bending in order to characterize the failure of interfaces exhibiting
orientations between 0° and 90° with respect to the beam direction, and thus undergoing different combined shear and tensile stress. Failure appears to be
mainly driven by the interface opening stress that seems to predominate over shear stress. The apparent fracture stresses vary from 0.5 GPa to 3.0 GPa depending
on the interface angle. It results in a maximum opening stress of 0.72 ± 0.18 GPa reached locally at the interface, whereas the apparent tensile fracture stress of
a pack of aligned and perpendicular platelets is approximately 3 GPa. These results should help understand the bulk properties of nacre-like alumina composites
and future similar materials and enable a rational design of their components and microstructures.
</p>
</div>
</div>
</div>
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Ronan Henry; Hassan Saad; Aurélien Doitrand; Sylvain Deville; Sylvain Meille
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Materials Processing; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-03-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748f9337d6c50dbe2762c/original/interface-failure-in-nacre-like-alumina.pdf
|
60c749b34c891966d7ad3107
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10.26434/chemrxiv.12098652.v1
|
In-silico Studies of Antimalarial-agent Artemisinin and Derivatives Portray More Potent Binding to Lys353 and Lys31-Binding Hotspots of SARS-CoV-2 Spike Protein than Hydroxychloroquine: Potential Repurposing of Artenimol for COVID-19.
|
<p>The role of hydroxychloroquine to prevent hACE2 from interacting with SARS-CoV-2 Spike protein is unveiled. Artemisinin & derived compounds entangle better than hydroxychloroquine into Lys353 and Lys31 binding hotspots of the virus Spike protein, therefore preventing infection occurs. Since these molecules are effective antivirals with excellent safety track records, their potential repurposing is recommended for clinical trials of COVID-19 patients.</p>
|
Moussa SEHAILIA; Smain chemat
|
Bioinformatics and Computational Biology; Chemical Biology; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749b34c891966d7ad3107/original/in-silico-studies-of-antimalarial-agent-artemisinin-and-derivatives-portray-more-potent-binding-to-lys353-and-lys31-binding-hotspots-of-sars-co-v-2-spike-protein-than-hydroxychloroquine-potential-repurposing-of-artenimol-for-covid-19.pdf
|
67a0d6176dde43c9087741a6
|
10.26434/chemrxiv-2025-qm64k
|
Guanosine-based supramolecular particles for enhanced drug and gene delivery in cell culture
|
Supramolecular hacky sacks (SHS) are a novel class of self-assembled colloidal particles formed from guanosine (G) derivatives, designed to function as versatile tools for cellular and therapeutic applications. Here, we investigate the structure-dependent cellular uptake, intracellular trafficking, and functional performance of SHS particles. Confocal microscopy and flow cytometry studies reveal that SHS uptake is highly dependent on the composition of the G-derivatives, suggesting selective interactions with cellular pathways. Importantly, we demonstrate that SHS particles serve as a biocompatible platform for drug and gene delivery, effectively encapsulating and releasing doxorubicin for enhanced cytotoxicity, as well as facilitating plasmid transfection with sustained fluorescent protein expression. These results establish SHS particles as a versatile biocompatible platform with tunable bioactivity, offering new opportunities for the application of supramolecular assemblies in drug delivery and gene therapy. The inherent biodegradability, simplicity of synthesis, and versatility of SHS particles underscore their potential as next-generation biomaterials for biomedical applications.
|
Luis M. Negrón; Edwin Vázquez-Rosa; Luxene Belfleur; Tanya L. Díaz; Bismark Madera-Soto; Irving E. Vega; Jose M. Rivera
|
Biological and Medicinal Chemistry; Organic Chemistry; Nanoscience; Supramolecular Chemistry (Org.); Nanodevices; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-02-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a0d6176dde43c9087741a6/original/guanosine-based-supramolecular-particles-for-enhanced-drug-and-gene-delivery-in-cell-culture.pdf
|
648fdfc64f8b1884b780a91b
|
10.26434/chemrxiv-2023-20nmh
|
Revolutions in lipid isomer resolution: application of ultra-high resolution ion mobility to reveal lipid diversity
|
Many families of lipid isomers remain unresolved by contemporary liquid chromatography-mass spectrometry ap-proaches, leading to a significant underestimation of structural diversity within the lipidome. While ion-mobility coupled to mass spectrometry has provided an additional dimension of lipid isomer resolution, some isomers require resolving power beyond the capabilities of conventional platforms. Here we present the application of high-resolution travelling-wave ion mobility for the separation of lipid isomers that differ in (i) the location of a single car-bon-carbon double bond, (ii) the stereochemistry of the double bond (cis or trans) or, for glycerolipids, (iii) the rela-tive substitution of acyl chains on the glycerol backbone (sn-position). Collisional activation following mobility sepa-ration allowed identification of carbon-carbon double bond position and sn-position, enabling confident interpreta-tion of variations in mobility-peak abundance. To demonstrate the applicability of this method, double bond and sn-position isomers of an abundant phosphatidylcholine composition were resolved in extracts from a prostate cancer cell line and identified by comparison to pure isomer reference standards, revealing the presence of six isomers. These findings suggest that ultra-high resolution ion-mobility has broad potential for isomer-resolved lipidomics and is attractive to consider for future integration with other modes of ion-activation, thereby bringing together advanced orthogonal separations and structure elucidation to provide a more complete picture of the lipidome.
|
Berwyck Poad; Lachlan Jekimovs; Reuben Young; Puttandon Wongsomboon; David Marshall; Felicia Hansen; Therese Fulloon; Michael Pfrunder; Tyren Dodgen; Mark Ritchie; Stephen Wong; Stephen Blanksby
|
Analytical Chemistry; Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-06-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648fdfc64f8b1884b780a91b/original/revolutions-in-lipid-isomer-resolution-application-of-ultra-high-resolution-ion-mobility-to-reveal-lipid-diversity.pdf
|
61651e1c8b620dbbf44c99fe
|
10.26434/chemrxiv-2021-66zd8
|
Rapid structural analysis of minute quantities of organic solids by exhausting 1H polarization in solid-state NMR spectroscopy at fast MAS
|
Solid-state nuclear magnetic resonance (NMR) is a powerful and indispensable tool for structural and dynamic studies of various challenging systems. Nevertheless, it often suffers from significant limitations due to the inherent low signal sensitivity when low- nuclei are involved. Herein, we report an efficient solid-state NMR approach for rapid and efficient structural analysis of minute amounts of organic solids. By encoding staggered chemical shift evolution in the indirect dimension and staggered acquisition in 1H dimension, a proton-detected homonuclear 1H/1H and heteronuclear 13C/1H chemical shift correlation (HETCOR) spectrum can be obtained simultaneously in a single experiment at fast magic-angle-spinning (MAS) conditions with barely increasing experimental time, compared to conventional proton-detected HETCOR experiment. We establish that abundant 1H polarization can be efficiently manipulated and fully utilized in proton-detected solid-state NMR spectroscopy for extraction of more critical structural information and thus reduction of total experimental time.
|
Zhiwei Yan; Rongchun Zhang
|
Physical Chemistry; Materials Science; Analytical Chemistry; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Structure
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-10-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61651e1c8b620dbbf44c99fe/original/rapid-structural-analysis-of-minute-quantities-of-organic-solids-by-exhausting-1h-polarization-in-solid-state-nmr-spectroscopy-at-fast-mas.pdf
|
66e9e09451558a15ef482523
|
10.26434/chemrxiv-2024-7gb0p
|
Improved LC-MS detection of opioids, amphetamines, and psychedelics using TrEnDi
|
Substances of misuse are becoming increasingly difficult to analyze as unique methods of smuggling are adopted and due to the rapid emergence of new psychoactive substances, increasing the pool of compounds to characterize and identify. Technologies such as gas chromatography and liquid chromatography coupled to mass spectrometry (MS) represent the gold standard for accurate and robust analysis, with on-site ambient- and portable-MS systems providing rapid methods of drug screening and testing. For many samples containing residual analyte quantities, methods to improve sensitivity through chemical derivatization are critical for accurate determination. Herein, we demonstrate for the first time the use of trimethylation enhancement using diazomethane (TrEnDi) to improve the MS-based sensitivity of 13 different drugs of misuse. All analytes were successfully permethylated, with 11 demonstrating improved analytical characteristics from TrEnDi with MS sensitivity enhancements of 1.2–24.2-fold and increases in reversed-phase chromatographic retention. Derivatization using 13C-isotopically labelled TrEnDi reagents were used to successfully resolve isobaric interference issues between three pairs of controlled substances. The sensitivity of a TrEnDi-modified analyte was increased several orders of magnitude using an unconventional aprotic solvent system for electrospray ionization. Finally, TrEnDi was employed to boost the sensitivity of morphine in a real urine matrix. Our results demonstrate a percent recovery of 103.1% and a sensitivity enhancement of 2.4-fold, demonstrating versatility and applicability of TrEnDi to pre-existing analytical workflows for trace analysis.
|
Christian Rosales; Noah Lepinsky; Wondewossen Gebeyehu; Karl Wasslen; Benjamin Warnes; Jasmine Chihabi; Jeffrey Manthorpe; Jeffrey Smith
|
Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-09-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e9e09451558a15ef482523/original/improved-lc-ms-detection-of-opioids-amphetamines-and-psychedelics-using-tr-en-di.pdf
|
61444ad339ef6a83a01f057f
|
10.26434/chemrxiv-2021-zpfxf
|
Organophotocatalytic Late-stage N-CH3 Oxidation of Trialkylamines with O2 in Continuous Flow
|
We report an organophotocatalytic, N-CH3-selective
oxidation of trialkylamines in continuous flow. Based on the 9,10-dicyanoanthracene (DCA) core, a new catalyst (DCAS) was designed with solubilizing groups for processing in flow which allowed harnessing of O2 as a benign reagent for late-stage photocatalytic N-CH3 oxidation of natural products and active pharmaceutical ingredients. These substrates bear functional groups which are not tolerated by previous methods. The organophotocatalytic process benefited from the flow parameters, affording cleaner reactions in short residence time of 13.5 mins and productivities of up to 0.65 g / day. Mechanistic studies found that catalyst derivatization not only enhanced
solubility of the new catalyst compared to DCA, it profoundly diverted the photocatalytic reaction mechanism from singlet electron transfer (SET) reductive quenching with amines to energy transfer (EnT) with O2.
|
Mark J. P. Mandigma; Jonas Zurauskas; Callum I. MacGregor; Lee J. Edwards; Ahmed Shahin; Ludwig d'Heureuse; Philip Yip; David J. S. Birch; Thomas Gruber; Jörg Heilmann; Matthew P. John; Joshua P. Barham
|
Organic Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Pharmaceutical Industry
|
CC BY 4.0
|
CHEMRXIV
|
2021-09-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61444ad339ef6a83a01f057f/original/organophotocatalytic-late-stage-n-ch3-oxidation-of-trialkylamines-with-o2-in-continuous-flow.pdf
|
60c74b3a702a9b19c118b3c9
|
10.26434/chemrxiv.11968743.v3
|
The intermolecular anthracene-transfer in a regiospecific antipodal C60 difunctionalization
|
We analyze the mechanism of the topochemically controlled difunctionalization of C60 and anthracene, where an anthracene molecule is transferred from one C60 monoadduct to another one under exclusive formation of equal amounts of C60 and the difficult to make antipodal C60 bisadduct. Our herein disclosed dispersion corrected DFT studies show the anthracene transfer to take place in a synchronous retro Diels-Alder/Diels-Alder reaction: an anthracene molecule dissociates from one fullerene under formation of an intermediate, while already undergoing stabilizing interactions with both neighboring fullerenes, facilitating the reaction kinetically. In the intermediate, a planar anthracene molecule is sandwiched between two neighboring fullerenes and forms equally strong "double-decker" type pi-pi stacking interactions with both of these fullerenes. Analysis with the distorsion interaction model shows that the anthracene unit of the intermediate is almost planar with minimal distorsions. This analysis sheds light on the existence of noncovalent interactions engaging both faces of a planar polyunsaturated ring and two convex fullerene surfaces in an unprecedented 'inverted sandwich' structure. Hence, it sheds light on new strategies to design functional fullerene based materials.<br />
|
Radu Talmazan; Klaus R. Liedl; Bernhard Kräutler; Maren Podewitz
|
Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b3a702a9b19c118b3c9/original/the-intermolecular-anthracene-transfer-in-a-regiospecific-antipodal-c60-difunctionalization.pdf
|
67dc60dd6dde43c9089b908b
|
10.26434/chemrxiv-2024-nmm8w-v2
|
Machine learning reveals structural characteristics of stereochemistry-specific interdigitation of synthetic monomycoloyl glycerol analogs
|
Synthetic monomycoloyl glycerol (MMG) analogs possess robust immunostimulatory activity and are investigated as adjuvants for subunit vaccines in preclinical and clinical studies. These synthetic lipids consist of a glycerol moiety attached to a corynomycolic acid. Previous experimental studies have shown that the stereochemistry of the lipid acid moiety affects whether the MMG analogs self-assemble into interdigitated or non-interdigitated structures below the main phase transition temperature (Tm). In this study, we elucidated possible thermodynamic mechanisms governing the phase behavior of MMG analogs by exploring their conformations, interactions, and dynamics using a combination of machine learning (ML) and molecular dynamics (MD) simulations. We compared two analogs, MMG-1 and MMG-6, which differ only by the stereochemistry of the lipid acid moiety; the former has a configuration different from the natural MMG, and the latter displays a native-like stereochemistry. Three different membrane states were simulated: 1) a non-interdigitated single bilayer, 2) a non-interdigitated double bilayer, and 3) a fully interdigitated double bilayer. Our results indicate that the propensity for interdigitation of the MMG analogs in a bilayer is linked to the degree to which their hydrocarbon chains are ordered and oriented. This study demonstrates how combining MD simulations and ML can enhance the molecular understanding of lipid-based pharmaceutical formulations.
|
Suvi Heinonen; Artturi Koivuniemi; Matthew Davies; Mikko Karttunen; Camilla Foged; Alex Bunker
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning
|
CC BY 4.0
|
CHEMRXIV
|
2025-03-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dc60dd6dde43c9089b908b/original/machine-learning-reveals-structural-characteristics-of-stereochemistry-specific-interdigitation-of-synthetic-monomycoloyl-glycerol-analogs.pdf
|
659774eb9138d2316139241f
|
10.26434/chemrxiv-2024-2r1km
|
Characterizing Catalyst Function and Transformations in the Plasma Reduction of CO 2 on Atomic Layer Deposition-Synthesized Catalysts
|
The enhancement of CO2 reduction in atmospheric-pressure, non-thermal plasma has been shown using a variety of catalyst systems with ranging composition, particle sizes, and morphologies. Improvements in CO2 conversion can be attained by choice of catalyst material. However, inhomogeneity in the material distribution arising from the synthesis affects the catalytically active surface area and dielectric environment that modulates the plasma properties near the catalyst. Atomic layer deposition (ALD) can be used to control the composition of ultra- thin layers on support materials. We used ALD to synthesize metal oxide catalyst coatings on high surface area supports. We found that TiO 2 achieved significantly higher yields of CO2 conversion (to CO and O2 ) at low reactor power compared to ZnO or Al2O3 , materials commonly used a support for other catalysts. We also observed an unexpected increase in the catalytic activity on ZnO with increasing power. The results here suggest that ALD can unambiguously isolate the catalytic effects of materials in plasma reactors.
|
Samuel K. Conlin; Hamed Mehrabi; David N. Parette; Eva N. Nichols; Robert H. Coridan
|
Inorganic Chemistry; Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Heterogeneous Catalysis
|
CC BY 4.0
|
CHEMRXIV
|
2024-01-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659774eb9138d2316139241f/original/characterizing-catalyst-function-and-transformations-in-the-plasma-reduction-of-co-2-on-atomic-layer-deposition-synthesized-catalysts.pdf
|
65e774a466c138172943fb87
|
10.26434/chemrxiv-2024-rz914
|
Gold-Thiolate Nanocluster Dynamics and Intercluster Reactions Enabled by a Machine Learned Interatomic Potential
|
Mono-layer protected metal clusters comprise a rich class of molecular systems, and are promising candidate materials for a variety of applications. While a growing number of protected nanoclusters have been synthe- sized and characterized in crystalline forms, their dynamical behavior in solution, including pre-nucleation cluster formation, is not well understood due to limitations both in characterization and first-principles mod- eling techniques. Recent advancements in machine-learned interatomic potentials are rapidly enabling the study of complex interactions such as dynamical behavior and reactivity at the nanoscale. Here, we develop an Au-S-C-H Atomic Cluster Expansion (ACE) interatomic potential for efficient and accurate molecular dynamics simulations of thiolate-protected gold nanoclusters (Aun (SCH3)m ). Trained on more than 30,000 density functional theory calculations of gold nanoclusters, the interatomic potential exhibits ab initio level accuracy in energies and forces, and replicates nanocluster dynamics including thermal vibration and chiral inversion. Long dynamics simulations (up to 0.1 μs time scale) reveal a novel mechanism explaining the ther- mal instability of neutral Au25(SR)18 clusters. Specifically, we observe multiple stages of isomerization of the Au25(SR)18 cluster, including a novel chiral isomer. Additionally we simulate coalescence of two Au25(SR)18 clusters and observe series of new clusters where the formation mechanisms are critically mediated by ligand exchange in the form of [Au–S]n rings.
|
Caitlin McCandler; Antti Pihlajamäki; Sami Malola; Hannu Häkkinen; Kristin Persson
|
Theoretical and Computational Chemistry; Nanoscience; Nanocatalysis - Catalysts & Materials; Computational Chemistry and Modeling; Machine Learning; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e774a466c138172943fb87/original/gold-thiolate-nanocluster-dynamics-and-intercluster-reactions-enabled-by-a-machine-learned-interatomic-potential.pdf
|
6596a4dc9138d231612d6bf1
|
10.26434/chemrxiv-2023-d2ztk-v3
|
Saccharide concentration prediction from proxy sea surface microlayer samples analyzed via infrared spectroscopy and quantitative machine learning
|
Solvated organics in the ocean are present in relatively small concentrations but contribute largely to ocean chemical diversity and complexity. Existing in the ocean as dissolved organic carbon (DOC) and enriched within the sea surface microlayer (SSML), these compounds have large impacts on atmospheric chemistry through their contributions to cloud nucleation, ice formation and other climatological processes. The ability to quantify the concentrations of organics in ocean samples is critical for understanding these marine processes. The work presented herein details an investigation to develop machine learning (ML) methodology utilizing infrared spectroscopy data to accurately estimate saccharide concentrations in complex solutions. We evaluated multivariate linear regression (MLR), K-Nearest-Neighbors (KNN), Decision Trees (DT), Gradient Boosted Regressors (GBR), Multilayer Perceptrons (MLP), and Support Vector Regressors (SVR) toward this goal. SVR models are shown to predict the accurate generalized saccharide concentrations best. Our work presents an application combining fast spectroscopic techniques with ML to analyze organic composition proxy ocean samples to target a generalized method for analyzing field marine samples more efficiently, without sacrificing accuracy or precision.
|
Abigail Enders; Nicole North; Jessica Clark; Heather Allen; Kezia Duah
|
Theoretical and Computational Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Chemoinformatics; Environmental Analysis; Machine Learning
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6596a4dc9138d231612d6bf1/original/saccharide-concentration-prediction-from-proxy-sea-surface-microlayer-samples-analyzed-via-infrared-spectroscopy-and-quantitative-machine-learning.pdf
|
62f5b230d62bc05ed242b5d0
|
10.26434/chemrxiv-2022-vnnc7-v2
|
Theoretical Study on the Mechanism of Hydrogen Evolution Reaction Catalyzed by Platinum Subnanoclusters
|
The smallest subnanocluster models of platinum colloid (Ptn) are supposed to diffuse in aqueous media in order to examine their behaviors when they are subjected to electrocatalytic hydrogen evolution reaction under the zero overpotential condition at pH 0. The DFT approach allows us to clarify the natures of individual proton transfer (PT) and electron transfer (ET) processes together with the importance of relying on concerted proton-electron transfer (CPET) pathways to promote the majority of H* adsorption processes by the Ptn subnanoclusters. Although the CPET processes are closely correlated with the Volmer steps (Pt + H+ + e− --> Pt-H*) described so far in electrochemistry, our study for the first time points out the essential capability of the Ptn clusters to promote the multiple PT steps without the need to transfer any electrons, revealing the fundamentally high basicity of the naked Ptn clusters (pKa = 27-28 for Pt4, Pt5, and Pt6). The discrete cluster models adopted herein avoid the structural constraints forced by the standard slab models and enable us to discuss the drastic alterations in the geometric and electronic structures of the intermediates given by the consecutive promotion of multiple CPET steps. The weakening in the Pt-H* bond strength with the increasing number of CPET steps is well rationalized by carefully examining the changes in the ν(Pt-H*) vibrational frequencies, the hydricity, and the H2 desorption energy. The behaviors are also correlated with the underpotential and overpotential deposited hydrogen atoms (HUPD and HOPD) discussed in the electrochemical studies for many years.
|
Keita Kuge; Kosei Yamauchi; Ken Sakai
|
Theoretical and Computational Chemistry; Inorganic Chemistry; Catalysis; Coordination Chemistry (Inorg.); Computational Chemistry and Modeling; Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-08-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f5b230d62bc05ed242b5d0/original/theoretical-study-on-the-mechanism-of-hydrogen-evolution-reaction-catalyzed-by-platinum-subnanoclusters.pdf
|
621913ac5f1d9a76b5a7d708
|
10.26434/chemrxiv-2022-6b0pc
|
Bending a Photonic Wire into a Ring
|
Natural light harvesting systems absorb sunlight and transfer its energy to the reaction centre, where it is used for photosynthesis. Synthetic chromophore arrays provide useful models for understanding energy migration in these systems. Research has focussed on mimicking rings of chlorophyll molecules found in purple bacteria, known as ‘light-harvesting system 2’. Linear meso-meso linked porphyrin chains mediate rapid energy migration, but until now it has not been possible to bend them into rings. Here we show that oligo-pyridyl templates can be used to bend these rod-like photonic wires, to create covalent nanorings. The macrocycles consist of 24 porphyrin units, with a single butadiyne link. Their elliptical conformations have been probed by scanning tunnelling microscopy (STM). This system exhibits two types of excited state energy transfer processes: (a) from the central template to the peripheral porphyrins and (b) from the 24 light-absorbing porphyrin units to the π-conjugated butadiyne-linked porphyrin dimer segment.
|
Henrik Gotfredsen; Jieren Deng; Jeff Van Raden; Marcello Righetto; Janko Hergenhahn; Michael Clarke; Abigail Bellamy-Carter; Jack Hart; James O’Shea; Tim Claridge; Fernanda Duarte; Alexander Saywell; Laura Herz; Harry Anderson
|
Physical Chemistry; Organic Chemistry; Nanoscience; Supramolecular Chemistry (Org.); Spectroscopy (Physical Chem.); Surface
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-02-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621913ac5f1d9a76b5a7d708/original/bending-a-photonic-wire-into-a-ring.pdf
|
60c74926bdbb8943a2a390f2
|
10.26434/chemrxiv.12037335.v1
|
β-Cyclodextrin-Poly (β-Amino Ester) Nanoparticles Are a Generalizable Strategy for High Loading and Sustained Release of HDAC Inhibitors
|
<p> Here, we
describe a simple, efficient formulation of a novel library of
β-cyclodextrin-poly (β-amino ester) networks (CDN) to achieve this goal. We observed that network
architecture was a critical determinant of CDN encapsulation of candidate
molecules, with a more hydrophobic core enabling effective self-assembly and a
PEGylated surface enabling high loading (up to ~30% w/w), effective self
assembly of the nanoparticle, and slow release of drug into aqueous media (24
days) for the model <i>HDACi</i>
panobinostat. Optimized CDN nanoparticles were taken up by GL261 cells in
culture, and released panobinostat was confirmed to be bioactive.
Pharmacokinetic analyses demonstrated that panobinostat was delivered to the
brainstem, cerebellum, and upper spinal cord following intrathecal
administration via cisterna magna injection in healthy mice. We next constructed
a library of CDNs to encapsulate various small, hydrophobic, ionizable
molecules (panobinostat, quisinostat, dacinostat, givinostat, and bortezomib, camptothecin,
nile red, and cytarabine), which yielded important insights into the structural
requirements for effective drug loading and CDN self-assembly. Taken in sum,
these studies present a novel nanocarrier platform for encapsulation of <i>HDACi</i> via both ionic and hydrophobic
interactions, which is an important step toward better treatment of disease via
<i>HDACi</i> therapy.</p>
|
Sauradip Chaudhuri; Martha Fowler; Afroz S. Mohammad; Wenqui Zhang; Cassandra Baker; Colton Broughton; Brandon Knight; William Elmquist; Sarah Stabenfeldt; Rachael W. Sirianni
|
Biocompatible Materials; Biological Materials; Biodegradable Materials; Controlled-Release Systems; Core-Shell Materials; Oligomers
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-03-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74926bdbb8943a2a390f2/original/cyclodextrin-poly-amino-ester-nanoparticles-are-a-generalizable-strategy-for-high-loading-and-sustained-release-of-hdac-inhibitors.pdf
|
6493db04853d501c004cc312
|
10.26434/chemrxiv-2023-w78g3-v3
|
An Introductory Review on Advanced Multifunctional Materials
|
This review summarizes applications of some of the advanced materials. It included the synthesis of several nanoparticles such as metal oxide nanoparticles (e.g., Fe3O4, ZnO, ZrOSO4, MoO3-x, CuO, AgFeO2, Co3O4, CeO2, SiO2, and CuFeO2); metal hydroxide nanosheets (e.g., Zn5(OH)8(NO3)2·2H2O, Zn(OH)(NO3)·H2O, and Zn5(OH)8(NO3)2); metallic nanoparticles (Ag, Au, Pd, and Pt); carbon-based nanomaterials (graphene, graphene oxide (GO), reduced graphene oxide (rGO), graphitic carbon nitride (g-C3N4), and carbon dots (CDs)); biopolymers (cellulose, nanocellulose, TEMPO-oxidized cellulose nanofibers (TOCNFs), alginate, and chitosan); organic polymers (e.g. covalent-organic frameworks (COFs)); and hybrid materials (e.g. metal-organic frameworks (MOFs)). These materials were applied in several fields such as environmental-based technologies (e.g., water remediation, air purification, gas storage), energy (production of hydrogen, dimethyl ether, solar cells, and supercapacitors), and biomedical sectors (sensing, biosensing, cancer therapy, and drug delivery). They can be used as efficient adsorbents and catalysts to remove emerging contaminants such as metals, dyes, drugs, antibiotics, pesticides, and oils in water via adsorption. They can be also used as catalysts for catalytic degradation, reduction, and oxidation of organic pollutants. They can be used as filters for air purification by capture greenhouse gases such as carbon dioxide (CO2) and volatile organic compounds (VOCs). They can be used for hydrogen production via water splitting, alcohol oxidation, and hydrolysis of NaBH4. Biomedical
2
applications such as antibacterial, drug delivery, and biosensing were also reviewed.
|
Hani Nasser Abdelhamid
|
Materials Science; Catalysis; Energy
|
CC BY 4.0
|
CHEMRXIV
|
2023-06-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6493db04853d501c004cc312/original/an-introductory-review-on-advanced-multifunctional-materials.pdf
|
64f931203fdae147faa71757
|
10.26434/chemrxiv-2023-m8nv4
|
Activity-based sensing reveals elevated labile copper promotes liver aging via hepatic stem cell depletion
|
Oxidative stress is one of the major culprits of aging and age-related disease states. Although the body features numerous antioxidant defense systems to safeguard against this, conditions ranging from neurodegeneration and cancer to organ failure may result once the buffering capacity of these protective mechanisms have been exceeded. While it is known that redox active metal ions such as copper (Cu) can generate reactive oxygen species (ROS), establishing a possible connection between Cu dysregulation and aging, especially in an in vivo context is exceedingly difficult. Through the development of new activity-based imaging probes for Cu(I) exhibiting ultra-sensitivity, we discovered that labile hepatic Cu activity increases during aging, and this results in the depletion of hepatic stem cells (hSCs) as measured by the ALDH1A1 stemness biomarker. Further, the application of a glutathione (GSH)-responsive probe for noninvasive photoacoustic imaging revealed that these findings are linked to an age-dependent decrease of hepatic GSH activity. To delay this phenotype, we designed two longitudinal studies where aged-mice were treated with ATN-224, a Cu-chelating drug. Our results suggest that treatment restores Cu homeostasis which may have a hSC-sparing effect to delay the onset of liver aging.
|
Zhenxiang Zhao; Melissa Lucero; Shengzhang Su; Jiajie Jessica Xu; Jefferson Chan
|
Biological and Medicinal Chemistry; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-09-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f931203fdae147faa71757/original/activity-based-sensing-reveals-elevated-labile-copper-promotes-liver-aging-via-hepatic-stem-cell-depletion.pdf
|
671a87ca83f22e42140c7f02
|
10.26434/chemrxiv-2024-ns2g4
|
Reexamining the Enhanced Solubility of Sodium Laurate/Sodium Oleate Eutectic Mixtures
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Mixtures of multiple surfactants that have superior performance to the individual components are highly sought-after commercially. Mixtures with a reduced Krafft point (TK) are particularly useful as they enable applications at lower temperatures. Such an example is the soap maker’s eutectic: the mixture of sodium laurate (NaL) and sodium oleate (NaOl). A true eutectic implies that the two surfactants do not mix in the solid state but mix readily in the micellar solution above TK, leading to a sharp TK depression at a specific composition. However, the NaL/NaOl mixture shows a broad TK depression of > 15 °C at a NaOl weight fraction (wO) of about 0.5. Our tie-line analysis shows that pure NaL and NaOl do not coexist in the solid phase on either side of the TK minimum. X-ray analysis of the isolated solids with varying wO reveals that a unique intermediate compound (I.C.) forms in the solid state with a NaL-to-NaOl mole ratio of about 4/3. Below the TK minimum, NaL and the I.C. coexist in the solids for wO < 0.5, whereas the I.C. and NaOl coexist in the solids for wO > 0.5. Each pair of solids exhibits eutectic or monotectic solubility behavior, and the congruent I.C. melting point is so close to that of the eutectic point(s) that a broad TK minimum ensues. Thermal analysis and modeling via the freezing-point depression approach support the above interpretation. The fact that surfactants with other headgroups but the same blend of chain lengths do not exhibit similar depressed TK is a topic for further study.
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Jing Hu; Svetoslav E. Anachkov; Teanoosh Moaddel; Joseph O. Carnali
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Physical Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-10-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671a87ca83f22e42140c7f02/original/reexamining-the-enhanced-solubility-of-sodium-laurate-sodium-oleate-eutectic-mixtures.pdf
|
62676123368ab65dea8d7876
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10.26434/chemrxiv-2022-bj274
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Identification and Utilization of a Chemical Probe to Interrogate the Roles of PIKfyve in the Lifecycle of β-Coronaviruses
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From a designed library of indolyl pyrimidinamines we identified a highly potent and cell-active chemical probe (analog 17) that inhibits phosphatidylinositol-3-phosphate 5-kinase (PIKfyve). Comprehensive evaluation of inhibitor selectivity confirmed that this PIKfyve probe demonstrates excellent kinome-wide selectivity. A structurally related indolyl pyrimidinamine (analog 30) was characterized as a suitable negative control analog that lacks PIKfyve inhibitory activity and exhibits exquisite selectivity when profiled against the screenable human kinome. Our chemical probe disrupts multiple phases of the life cycle of β-coronaviruses. We observed potent inhibition of viral replication, reduced viral entry, and impacts on a mediator of viral transmission (lysosomes). Our scaffold is a distinct chemotype versus published PIKfyve inhibitors and lacks the canonical morpholine hinge-binder of classical lipid kinase inhibitors. Our chemical probe set can be used by the community to characterize the role of PIKfyve in virology and beyond.
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David H. Drewry; Frances M. Potjewyd; Jeffrey L. Smith; Rebekah J. Dickmander; Armin Bayati; Stefanie Howell; Sharon A. Taft-Benz; Mohammad Anwar Hossain; Mark T. Heise; Peter S. McPherson; Nathaniel J. Moorman; Alison D. Axtman
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Biological and Medicinal Chemistry
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CC BY NC ND 4.0
|
CHEMRXIV
|
2022-04-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62676123368ab65dea8d7876/original/identification-and-utilization-of-a-chemical-probe-to-interrogate-the-roles-of-pi-kfyve-in-the-lifecycle-of-coronaviruses.pdf
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60c75777702a9b7a8318cabd
|
10.26434/chemrxiv.12657230.v5
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Rapidly Reversible Organic Crystalline Switch for Conversion of Heat into Mechanical Energy
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<div>
<div>
<div>
<p>Solid state thermosalience—a sudden exertion of an expansive or contractive physical force
following a temperature change in a solid state compound—is rare, few are reversible systems,
and most of these are limited to a dozen or so cycles before the crystal degrades or they reverse
slowly over the course of many minutes or even hours. In this work, we show a fully reversible
actuator that is stable at room temperature for multiple years and is capable of actuation for more
than two hundred cycles at near ambient temperature. Specifically, the crystals shrink to 90% of
its original length instantaneously upon heating beyond 45 °C and expands back to its original
length upon cooling below 35 °C. This temperature regime is important because it occurs around
physiologically important temperatures. Furthermore, the phase transition occurs instantaneously,
with little obvious hysteresis, allowing us to create real-time actuating thermal fuses that cycle
between on and off rapidly.
</p>
</div>
</div>
</div>
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Madushani Dharmarwardana; Srimanta Pakhira; Raymond P. Welch; Carlos Caicedo Narvaez; Michael A. Luzuriaga; Bhargav S. Arimilli; Gregory T. McCandless; Babak Fahimi; Jose Mendoza-Cortes; Jeremiah J. Gassensmith
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Carbon-based Materials; Metamaterials; Crystallography – Organic
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CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75777702a9b7a8318cabd/original/rapidly-reversible-organic-crystalline-switch-for-conversion-of-heat-into-mechanical-energy.pdf
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60c755bb469df48119f451ae
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10.26434/chemrxiv.14153408.v1
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Beam Search Sampling for Molecular Design and Intrinsic Prioritization with Machine Intelligence
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Chemical language models enable de novo drug design without the requirement for explicit molecular construction rules. While such models have been applied to generate novel compounds with desired bioactivity, the actual prioritization and selection of the most promising computational designs remains challenging. In this work, we leveraged the probabilities learnt by chemical language models with the beam search algorithm as a model-intrinsic technique for automated molecule design and scoring. Prospective application of this method yielded three novel inverse agonists of retinoic acid receptor-related orphan receptors (RORs). Each design was synthesizable in three reaction steps and presented low-micromolar to nanomolar potency towards RORg. This model-intrinsic sampling technique eliminates the strict need for external compound scoring functions, thereby further extending the applicability of generative artificial intelligence to data-driven drug discovery.<br />
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Michael Moret; Moritz Helmstädter; Francesca Grisoni; Gisbert Schneider; Daniel Merk
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Drug Discovery and Drug Delivery Systems; Machine Learning; Artificial Intelligence
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CC BY 4.0
|
CHEMRXIV
|
2021-03-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755bb469df48119f451ae/original/beam-search-sampling-for-molecular-design-and-intrinsic-prioritization-with-machine-intelligence.pdf
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