id
stringlengths 24
24
| doi
stringlengths 28
32
| title
stringlengths 8
495
| abstract
stringlengths 17
5.7k
| authors
stringlengths 5
2.65k
| categories
stringlengths 4
700
| license
stringclasses 3
values | origin
stringclasses 1
value | date
stringdate 1970-01-01 00:00:00
2025-03-24 00:00:00
| url
stringlengths 119
367
⌀ |
---|---|---|---|---|---|---|---|---|---|
666986b3e7ccf7753a94c3f6
|
10.26434/chemrxiv-2024-0rrg8
|
Manganese-catalyzed [2+2+2] Cycloaddition Reactions
|
We report the cyclotrimerization reactions of triynes using Mn(I) complexes derived from MnBr(CO)5 and phosphine ligands such as 1,1-bis(diphenylphosphino)methane (dppm). These reactions are driven by irradiation under mild conditions (30-80 °C) without the need of additional photoinitiators. Our catalytic screening revealed that counter anions and ligands significantly influence the process. This method accommodates a broad range of functionalities in the substrates, including alkyl, aryl, Bpin, TMS, PPh2, pyridyl, and thienyl moieties, without notable interference in the transformation. Additionally, this method enables reactions with oligoalkynes like (un)substituted hexaynes, producing two-fold cyclization products in excellent yields. Under stoichiometric conditions, the cyclization of diynes with phosphaalkynes results in the first photochemical synthesis of phosphinines. Experimental and theoretical mechanistic studies indicate that the dissociation of the diphosphine ligand precedes the involvement of the Mn-carbonyl species in the catalytic cycle. The ligand plays a crucial role in stabilizing the catalyst during the transformation and preventing the formation of unreactive cluster species.
|
Benedikt N. Baumann; Phong Dam; Jabor Rabeah; Christoph Kubis; Angelika Brückner; Haijun Jiao; Marko Hapke
|
Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Photocatalysis; Transition Metal Complexes (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-09-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666986b3e7ccf7753a94c3f6/original/manganese-catalyzed-2-2-2-cycloaddition-reactions.pdf
|
612058f4d4eb8a764e9e2db8
|
10.26434/chemrxiv-2021-30ggh-v2
|
Water-Accelerated Photo-oxidation of CH3NH3PbI3 Perovskite: Mechanism, rate orders, and rate constants
|
Understanding the chemical reactions that hybrid organic-inorganic halide perovskite (HP) semiconductors undergo in the presence of moisture, oxygen, and light are essential to the commercial development of HP solar cells and optoelectronics. Here we use optical absorbance to study the kinetics of methylammonium lead iodide (MAPbI3) degradation in response to combinations of moisture, oxygen, and illumination over a range of temperatures. We identify two primary reaction pathways that dominate MAPbI3 material degradation in these mixed environmental conditions: (1) dry photooxidation (DPO) due to the combined role of oxygen and photoexcited electrons (with a rate of 2 x 10-9 mol/m2∙s in dry air at 25 C and an effective activation energy of 0.62 eV), and (2) a water-accelerated photooxidation (WPO) process due to the combined role of water, oxygen, and photoexcited electrons (with a rate of 1 x 10-7 mol/m2s in 50% RH air at 25 C and observed effective activation energy of 0.07 eV). Commonly reported humidity-only, blue light, and thermal degradation pathways are demonstrated to have rates that are respectively 100, 1000, and >1000 times slower than predominant photooxidation processes in ambient conditions. Extracting kinetic rate constants from the dynamics of the initial degradation, we calculate that in dry air, photooxidation rate of MAPbI3 follows a f(x)∝x/(1+Kx) relationship with respect to oxygen in the vapor phase (PO2) and excess concentration of photoexcited electrons (n). In humid air, photooxidation of MAPbI3 exhibits first order kinetics with respect to the partial pressure of water in the vapor phase (PH2O). However, with respect to PO2 and n, kinetics follow a f(x)∝x/(1+kx)^2 relationship with respect to rate. We then identify a plausible reaction mechanism for degradation of MAPbI3 material that is consistent with these rate functionalities. The rate determining step for both DPO and WPO is proton abstraction by photogenerated superoxide radicals. However, proton donation by adsorbed water proceeds much more rapidly than donation by methylammonium, resulting in faster degradation rates for WPO at typical ambient conditions (~50% RH). Rate laws derived from this mechanism were fit to the entire dataset to extract rate constants for DPO and WPO processes. Accurate predictions of material degradation rates, with narrow confidence intervals of fit parameters as identified by the Bootstrap algorithm, provide the first experimental estimates of the equilibrium constants of oxygen adsorption on MAPbI3 (Keq ≈ 3 x 10-3 kPa-1) and superoxide generation from adsorbed oxygen and photoexcited electrons in MAPbI3 (Keq ≈ 5 x 10-15 (photons/m2∙s)-0.7). Given that water has been reported as a degradation product of DPO, the results reported here highlight the need for the development of encapsulation schemes that rigorously block oxygen, as over longer time periods, product water (if generated) may accumulate inside the packaging and initiate the much faster WPO process.
|
Timothy Siegler; Wiley Dunlap-Shohl; Yuhuan Meng; Wylie Kau; Preetham Sunkari; Chang-En Tsai; Zachary Armstrong; Yu-Chia Chen; David Beck; Marina Meila; Hugh Hillhouse
|
Materials Science; Hybrid Organic-Inorganic Materials; Thin Films; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2021-08-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612058f4d4eb8a764e9e2db8/original/water-accelerated-photo-oxidation-of-ch3nh3pb-i3-perovskite-mechanism-rate-orders-and-rate-constants.pdf
|
6531fdef87198ede07d89592
|
10.26434/chemrxiv-2023-hnh2d
|
Strongly inhibited spontaneous emission of PbS quantum dots covalently bound to 3D silicon photonic band gap crystals
|
We present an optical study of the spontaneous emission of lead sulfide (PbS) nanocrystal quantum dots in three-dimensional (3D) photonic band gap crystals made from silicon. The nanocrystals emit in the near-infrared (NIR) range to be compatible with the 3D silicon nanophotonics. The nanocrystals are covalently bonded to polymer brush layers that are grafted from the Si-air interfaces inside the nanostructure using surface-initiated atom transfer radical polymerization (SI-ATRP), and their presence and position of the quantum dots was previously characterized by synchrotron X-ray fluorescence tomography. We report both continuous wave (cw) emission spectra and time-resolved time-correlated single photon counting. In time-resolved measurements, we observe that the total emission rate greatly increases when the quantum dots are transferred from suspension to the silicon nanostructures, likely due to quenching (or increased non-radiative decay) that is tentatively attributed to the presence of Cu-catalyst during the synthesis. In this regime, continuous wave emission spectra are known to be proportional to the radiative rate and thus to the local density of states. In spectra normalized to those taken on flat silicon outside the crystals, we observe a broad and deep stop band that we attribute to a 3D photonic band gap with a relative bandwidth up to 26%. The shapes of the relative emission spectra match well with the theoretical density of states spectra calculated with the plane wave expansion. The observed inhibition is 5 to 30 times, similar to previously reported record inhibitions, yet for completely coincidental reasons. Our results are relevant to applications in photochemistry, sensing, photovoltaics, and to efficient miniature light sources.
|
Andreas S. Schulz; Marek Kozoň; G. Julius Vancso; Jurriaan Huskens; Willem L. Vos
|
Physical Chemistry; Materials Science; Nanoscience; Nanostructured Materials - Materials; Optics; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6531fdef87198ede07d89592/original/strongly-inhibited-spontaneous-emission-of-pb-s-quantum-dots-covalently-bound-to-3d-silicon-photonic-band-gap-crystals.pdf
|
60c73e9b702a9b2921189dfa
|
10.26434/chemrxiv.7068509.v1
|
A Series of Metal-Organic Frameworks for Selective CO2 Capture and Catalytic Oxidative Carboxylation of Olefins
|
<p>Three novel lanthanide metal˗organic frameworks (Ln-MOFs),
namely MOF-590, -591, and -592 were constructed from a naphthalene
diimide tetracarboxylic acid. Gas adsorption measurements of MOF-591 and
-592 revealed good adsorption of CO<sub>2</sub> (low pressure, at room
temperature) and moderate CO<sub>2</sub> selectivity over N<sub>2</sub> and
CH<sub>4</sub>. Accordingly, breakthrough measurements were performed on a
representative MOF-592, in which the separation of CO<sub>2</sub> from
binary mixture containing N<sub>2</sub> and CO<sub>2</sub> was
demonstrated without any loss in performance over three consecutive cycles.
Moreover, MOF-590, MOF-591, and MOF-592 exhibited catalytic activity in the
one-pot synthesis of styrene carbonate from styrene and CO<sub>2</sub> under
mild conditions (1 atm CO<sub>2</sub>, 80 °C, and solvent-free). Among the new
materials, MOF-590 revealed a remarkable efficiency with exceptional conversion
(96%), selectivity (95%), and yield (91%). </p><br />
|
Huong T. D. Nguyen; Y B. N. Tran; Hung N. Nguyen; Tranh C. Nguyen; Felipe Gándara; Phuong Nguyen
|
Hybrid Organic-Inorganic Materials; Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-09-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e9b702a9b2921189dfa/original/a-series-of-metal-organic-frameworks-for-selective-co2-capture-and-catalytic-oxidative-carboxylation-of-olefins.pdf
|
60c74e33337d6cb4d6e27f44
|
10.26434/chemrxiv.12722498.v1
|
Optical Control of Cannabinoid Receptor 2–Mediated Ca2+ Release Enabled By Synthesis of Photoswitchable Probes
|
Cannabinoid receptor 2 (CB2) is a promising target for the treatment of neuroinflammation and other diseases. Howev-er, lack of understanding of its complex signaling in cells and tissues complicates its therapeutic targeting. For the first time we show that HU308 increases cytosolic Ca<sup>2+</sup> levels in mammalian cells via CB2 and phospholipase C. We report the synthesis of pho-toswitchable derivatives of CB2 agonist HU308, azo-HU308s, from central building block 3-OTf-HU308. Azo-HU308s enable optical control over CB2 activity with spatiotemporal precision, as demonstrated in real-time Ca<sup>2+</sup> fluorescence imaging. Our findings reveal a novel messenger pathway by which HU308 and its derivatives can affect cellular excitability, and demonstrate the utility of chemical photoswitches to control CB2 signaling in real time.
|
Roman Sarott; Alexander E.G. Viray; Patrick Pfaff; Anastasiia Sadybekov; Gabriela Rajic; Vsevolod Katritch; Erick Carreira; James Frank
|
Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.); Cell and Molecular Biology; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e33337d6cb4d6e27f44/original/optical-control-of-cannabinoid-receptor-2-mediated-ca2-release-enabled-by-synthesis-of-photoswitchable-probes.pdf
|
671e71601fb27ce124c2aef3
|
10.26434/chemrxiv-2024-7s7p7
|
Cholesteryl-Tagged Fluorescent NAD+: A Membrane-Permeable Esterase-Sensitive Probe for ADP-ribosylation Studies
|
ADP-ribosylation is a key protein modification involved in cell signaling pathways, where ADP-ribose units are incorporated into the macromolecules by PARP enzymes, using NAD+ as a substrate. Over years many NAD+ tools have been developed for studies on the complex role of the ADP-ribosylation, although its inability to penetrate the cell membrane poses limitations. In this work, we present a straightforward synthesis of a cell-permeable, fluorescent NAD+ analog with an esterase-sensitive linker. The NAD+ double-conjugate contained a Texas Red fluorophore and a cholesterol ligand, incorporated via a [4-(acetyloxy)phenyl]methyl N-carbamate bond. This bond improved the probe’s stability in buffer compared to our previous design and allowed for efficient cleavage by human carboxylesterase. The probe was successfully accepted as an ADP-ribosylation substrate by PARP1 and PARP10, both before and after cleavage. We demonstrated the probe’s ability to penetrate the cell membrane and used it to visualize ADP-ribosylated proteins and monitor fluorescence changes in HeLa cells under oxidative stress.
|
Lea-Sophie Frings; Emma Lintfert; Robin Noel Kohler; Andreas Marx; Renata Kasprzyk
|
Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Chemical Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671e71601fb27ce124c2aef3/original/cholesteryl-tagged-fluorescent-nad-a-membrane-permeable-esterase-sensitive-probe-for-adp-ribosylation-studies.pdf
|
60c749a2337d6cf235e2775d
|
10.26434/chemrxiv.11320064.v2
|
Silicon incorporation in polymethine dyes
|
<p>Methods
to red-shift fluorophores have garnered considerable interest due to the broad
utility of low energy light. The incorporation of silicon into xanthene and
coumarin scaffolds has resulted in an array of visible and near-infrared
fluorophores. Here, we extend this approach to polymethine dyes, another popular
fluorophore class, performing experimental and computational analyses. We found
that when oxygen was replaced with SiMe<sub>2,</sub> bathochromic shifts of up
to 121 nm and fluorophores with emission above 900 nm were achieved. </p>
|
Monica Pengshung; Patrick Neal; Timothy Atallah; Junho Kwon; Justin Caram; Steven Lopez; Ellen Sletten
|
Dyes and Chromophores; Optical Materials; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749a2337d6cf235e2775d/original/silicon-incorporation-in-polymethine-dyes.pdf
|
652e53f88bab5d2055854fa1
|
10.26434/chemrxiv-2023-b7jfg
|
Electrical Anisotropy and its Mitigation in Conductive Polymers Printed by Digital Light Processing
|
In most 3D printing technologies, objects are realized layer by layer. This layer-by-layer construction leads to inherent anisotropic physical properties. Controlling, understanding and sometimes mitigating such anisotropy is a critical issue in the development of 3D printing. We demonstrate and quantify in this work electrical anisotropy in conductive materials processed by the so-called Digital Light Processing (DLP) method. In this method, which enjoys high resolution and high speed, layers of polymers, are successively cross-linked by UV irradiation of 2D patterns. Here, we use acrylate based resins and carbon nanotube as conductive fillers for their low percolation threshold that allows realizing conductive and still sufficiently transparent materials for UV irradiation. Conductivity parallel to the layers of 3D printed objects is found to be much greater than conductivity perpendicular to the layers. This electrical anisotropy is explained by the high contact resistance between printed layers. High contact resistance results from the slow diffusion of carbon nanotubes from the uncured material towards the interface of the cured object. We found that implementing a delay time before curing successive layers, or decreasing the matrix viscosity with temperature, to promote diffusion of the conductive particles allow substantial reduction of the contact resistance between layers. As a result, conductivity anisotropy can be reduced by almost two orders of magnitude. This control and mitigation of conductivity anisotropy allows reconciliation of the high resolution of the DLP technology with the possibility to realize uniform 3D materials.
|
David Tilve-Martinez; Wilfrid Neri; Nicolas Vukadinovic; Benoit Berton; Alain Penicaud; Jinkai Yuan; Philippe Poulin
|
Materials Science; Polymer Science; Nanoscience; Carbon-based Materials; Materials Processing; Nanostructured Materials - Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652e53f88bab5d2055854fa1/original/electrical-anisotropy-and-its-mitigation-in-conductive-polymers-printed-by-digital-light-processing.pdf
|
627d391044bdd57a46610c01
|
10.26434/chemrxiv-2022-1hf23
|
Magnetic order in a metal thiocyanate perovskite analogue
|
Metal thiocyanate perovskite analogues are a growing class of materials, but although they contain paramagnetic cations there have been no reports of their magnetic properties. Due to the large separations between the paramagnetic cations, with a shortest through-bond distance of 15.1Å, we would expect these materials to be good examples of paramagnets. In this communication we investigate the magnetic properties of a metal thiocyanate framework Cr[Bi(SCN)6]·xH2O. We find that Cr[Bi(SCN)6]·xH2O under- goes long-range magnetic order at TN = 4.0(2) K. We use neutron powder diffraction to determine that Cr[Bi(SCN)6]·xH2O has a MnO type {111}cubic-ordering as its ground state, consistent with frustrated nearest- and next-nearest-neighbour antiferromagnetic interactions. This suggests that appropriate design of metal thiocyanate perovskite analogue structures may reveal a rich vein of frustrated magnetism.
|
Matthew Cliffe; Oscar Fabelo; Laura Cañadillas Delgado
|
Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Magnetism; Solid State Chemistry; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2022-05-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627d391044bdd57a46610c01/original/magnetic-order-in-a-metal-thiocyanate-perovskite-analogue.pdf
|
640e7b92e53eff1af309157d
|
10.26434/chemrxiv-2023-ncmvj
|
Adsorption of PFAS onto secondary microplastics: A mechanistic study
|
Microplastics (MPs) are abundant in aquatic systems. The ecological risks of MPs may arise from their physical features, chemical properties, and/or their ability to concentrate and transport other contaminants, such as per- and polyfluoroalkyl substances (PFAS). PFAS have been extracted from MPs found in natural waters, but there is no mechanistic investigation of the effect of PFAS chemistry and water chemistry on how PFAS partition onto secondary MPs. Here, we studied the influence of pH, natural organic matter (NOM), ionic strength, and temperature on the adsorption of PFAS on MPs generated from PET water bottles. The adsorption of the PFAS to the MPs was spontaneous at 25C, based on Gibbs free energy (G -16 kJ/mol), primarily due to increased entropy. Adsorption reached equilibrium within 7-16 h. Hence, the PFAS will partition to the surface of PET MPs within a few hours to days in fresh and saline waters. Natural organic matter decreased the capacity of PET MPs for PFAS through electrosteric repulsion while higher ionic strength favored PFAS adsorption by decreasing electrostatic repulsion. Increased pH increased electrostatic repulsion, and negated PFAS adsorption. The study provides fundamental information for developing models to predict interactions between MPs and PFAS.
|
Omobayo Salawu; Adeyemi S. Adeleye
|
Earth, Space, and Environmental Chemistry; Hydrology and Water Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-03-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640e7b92e53eff1af309157d/original/adsorption-of-pfas-onto-secondary-microplastics-a-mechanistic-study.pdf
|
63ebfa86fcfb27a31fcad9e7
|
10.26434/chemrxiv-2023-wkfrk-v2
|
Influence of Mg2+ Distribution on the Stability of Folded States of the Twister Ribozyme Revealed using Grand Canonical Monte Carlo and Generative Deep Learning Enhanced Sampling
|
Metal ions, particularly magnesium ions (Mg2+), play a role in stabilizing the tertiary structures of RNA molecules. Theoretical models and experimental techniques show that metal ions can change RNA dynamics and how it transitions through different stages of folding. However, the specific ways in which metal ions contribute to the formation and stabilization of RNA's tertiary structure are not fully understood at the atomic level. Here, we combined oscillating excess chemical potential Grand Canonical Monte Carlo (GCMC) and metadynamics to bias towards the sampling of unfolded states using reaction coordinates generated by machine learning allowing for examination of Mg2+-RNA interactions that contribute to stabilizing folded states of the pseudoknot found in the Twister ribozyme. GCMC is used to sample diverse ion distributions around the RNA with deep learning applied to iteratively generate system-specific reaction coordinates to maximize conformational sampling during metadynamics simulations. Results from 6 s simulations performed on 9 individual systems indicate that Mg2+ ions play a crucial role in stabilizing the 3D structure of the RNA by stabilizing specific interactions of phosphate groups or phosphate groups and bases of neighboring nucleotides. While many phosphates are accessible to interactions with Mg2+ it is observed that multiple, specific interactions are required to sample conformations close to the folded state; coordination of Mg2+ at individual specific sites facilitates sampling of folded conformations though unfolding ultimately occurs. It is only when multiple specific interactions occur, including the presence of specific inner shell cation interactions linking two nucleotides, that conformations close to the folded state are stable. While many of the identified Mg2+ interactions are observed in the X-ray crystal structure of Twister, the present study suggests two new Mg2+ ion sites in the Twister ribozyme that contribute to stabilization. In addition, specific interactions with Mg2+ are observed that destabilize the local RNA structure, a process that may facilitate the folding of RNA into its correct structure.
|
Mert Sengul; Alexander MacKerell
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-02-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ebfa86fcfb27a31fcad9e7/original/influence-of-mg2-distribution-on-the-stability-of-folded-states-of-the-twister-ribozyme-revealed-using-grand-canonical-monte-carlo-and-generative-deep-learning-enhanced-sampling.pdf
|
648741004f8b1884b731451d
|
10.26434/chemrxiv-2023-5h4s7
|
Machine Learning-Guided Discovery of Polymer Membranes for CO2 Separation
|
Designing polymer membranes with high gas permeability and selectivity remains a grand challenge for energy, the environment, and economic sustainability. Increasing both the selectivity and permeability is a difficult multi-task constrained design problem for polymer membranes due to the trade-off between these two properties. The complexity of chemical composition and morphology of polymers makes this problem especially hard to attack with trial-and-error or intuition-based strategies. In this work, we instead present a machine learning (ML)-driven genetic algorithm to tackle the design problem of polymer membranes for CO2 separation from N2 and O2. Using literature data of permeability for three gases, CO2, N2, and O2, we constructed multiple ML models using different fingerprinting featurization schemes to predict all three gas permeabilities as well as the CO2/N2 and CO2/O2 selectivity values. Then, we employed a genetic algorithm to design new polymers and evaluated their performance with respect to the Robeson upper bounds using our machine learning models. We were able to identify new polymer membranes that are promising for both CO2/N2 and CO2/O2 separations. The top discovered polymers are predicted to have high glass transition temperatures, Tg. Similarly, the pyridine functionality was found in ~ 20% of the predicted polymers. Both of these facts are well in line with currently accepted experimental wisdom for CO2 based separations. The framework developed here can be used to design polymers for any application involving constrained optimization. Finally, we outlined the strengths and limitations of this approach, as well as the imminent challenges and opportunities with using machine learning guided data-driven inverse design of polymers.
|
Yasemin Basdogan; Dylan R. Pollard; Tejus Shastry; Matthew R. Carbone; Sanat K. Kumar; Zhen-Gang Wang
|
Theoretical and Computational Chemistry; Materials Science; Polymer Science; Organic Polymers; Computational Chemistry and Modeling; Machine Learning
|
CC BY 4.0
|
CHEMRXIV
|
2023-06-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648741004f8b1884b731451d/original/machine-learning-guided-discovery-of-polymer-membranes-for-co2-separation.pdf
|
60c74651842e653072db27c2
|
10.26434/chemrxiv.11302865.v1
|
Fingerprinting Redox Heterogeneity in Electrodes during Extreme Fast Charging
|
Conventionally, battery electrodes are rationalized as homogeneous reactors. It proves to be an erroneous interpretation for fast transients, where mass transport limitations amplify underlying heterogeneities. Given the lack of observability of associated fast spatiotemporal dynamics, redox activity in inhomogeneous electrodes is superficially explored. We resort to a physics-based description to examine extreme fast charging of lithium-ion battery electrodes. Representative inhomogeneity information is extracted from electrode tomograms. We discover such electrodes to undergo preferential intercalation, localized lithium plating and nonuniform heat generation as a result of distributed long- and short-range interactions. The spatial correlations of these events with the underlying inhomogeneity are found to be nonidentical. Investigation of multiple inhomogeneity fields reveals an exponential scaling of plating severity and early onset in contrast to the homogeneous limit. Anode and cathode inhomogeneities couple nonlinearly to grow peculiar electrodeposition patterns. These mechanistic insights annotate the complex functioning of spatially nonuniform electrodes.
|
Aashutosh Mistry; Francois L. E. Usseglio-Viretta; Andrew Colclasure; Kandler Smith; Partha P. Mukherjee
|
Composites; Theory - Computational; Energy Storage; Chemical Kinetics; Electrochemistry - Mechanisms, Theory & Study; Interfaces; Physical and Chemical Processes; Structure; Surface; Thermodynamics (Physical Chem.); Transport phenomena (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-12-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74651842e653072db27c2/original/fingerprinting-redox-heterogeneity-in-electrodes-during-extreme-fast-charging.pdf
|
60c747fa337d6c0019e27447
|
10.26434/chemrxiv.11826840.v1
|
Information Entropy as a Reliable Measure of Nanoparticle Dispersity
|
Nanoparticle size impacts properties vital to applications ranging from drug delivery to diagnostics and catalysis. As such, evaluating nanoparticle size dispersity is of fundamental importance. Conventional approaches, such as standard deviation, usually require the nanoparticle population to follow a known distribution and are illequipped to deal with highly poly- or heterodisperse populations. Herein, we propose the use of information entropy as an alternative and assumption-free method for describing nanoparticle size distributions. This approach works equally well for mono-, poly- and heterodisperse populations and provides an unbiased route to evaluation and optimisation of nanoparticle synthesis. We provide an intuitive tool for analysis with a user-friendly macro and provide guidelines for interpretation with respect to known standards.
|
Niamh Mac Fhionnlaoich; Stefan Guldin
|
Nanostructured Materials - Materials; Nanofabrication; Nanostructured Materials - Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-02-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747fa337d6c0019e27447/original/information-entropy-as-a-reliable-measure-of-nanoparticle-dispersity.pdf
|
60c759739abda25230f8eae7
|
10.26434/chemrxiv.14700045.v1
|
Catalysis with a Skip: Dynamically Coupled Addition, Proton Transfer, and Elimination During Au- and Pd-Catalyzed Diol Cyclization
|
Au and Pd complexes have emerged as highly effective π-bond cyclization catalysts to construct heterocycles. These cyclization reactions are generally proposed to proceed through multi-step addition-elimination mechanisms involving Au- or Pd-alkyl intermediates. For Au- and Pd-catalyzed allylic diol cyclization, while the DFT potential energy surface landscapes show a stepwise sequence of alkoxylation π-addition, proton transfer, and water elimination, quasiclassical direct dynamics simulations reveal new dynamical mechanisms that depend on the metal center. For Au, trajectories reveal that after π-addition the Au-alkyl intermediate is always skipped because addition is dynamically coupled with proton transfer and water elimination. In contrast, for Pd catalysis, due to differences in the potential-energy landscape shape, only about half of trajectories show Pd-alkyl intermediate skipping. The other half of the trajectories show the traditional two-step mechanism with the intervening Pd-alkyl intermediate. Overall, this work reveals that interpretation of a DFT potential-energy landscape can be insufficient to understand catalytic intermediates and mechanisms and that atomic momenta through dynamics simulations is needed to determine if an intermediate is genuinely part of a catalytic cycle.<br />
|
Matthew Teynor; Windsor Scott; Daniel Ess
|
Theory - Computational; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759739abda25230f8eae7/original/catalysis-with-a-skip-dynamically-coupled-addition-proton-transfer-and-elimination-during-au-and-pd-catalyzed-diol-cyclization.pdf
|
60c74e000f50db601d397131
|
10.26434/chemrxiv.12685928.v1
|
Modulating β Arrestin-2 Recruitment at the δ- and μ-Opioid Receptors
|
Opioid receptors can trigger two distinct pathways (G protein coupling and arrestin recruitment) that differentially regulate a host of desired and undesired pharmacological effects. Increasingly, “biased” opioids that selectively activate one pathway over the other are being developed to treat disorders in which µ- and κ-opioids receptors are involved, though the development of biased δ-opioid receptor agonists has remained rather quiescent. Herein, we identify the C-terminus of Tyr-ψ[(<i>Z</i>)CF=CH]-Gly-Leu-enkephalin as a key site to regulate bias of both δ- and µ-opioid receptor agonists. Using <i>in vitro</i> assays, substitution of the Leu<sup>5</sup> carboxylate reduced β-arrestin recruitment through both the δ- and µ-opioid receptors in a predictable structure-dependent fashion, while retaining affinity and cAMP potency comparable to the C-terminal carboxylate. These substitutions should enable discovery of a range of tool compounds for exploring δ-opioid receptor pharmacology and toxicology, which will enable reevaluation of this target within the context of biased signaling.
|
Krishna Sharma; Robert Cassell; HongYu Su; Arryn Blaine; Benjamin Cummins; Kendall Mores; David Johnson; Richard van Rijn; Ryan Altman
|
Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e000f50db601d397131/original/modulating-arrestin-2-recruitment-at-the-and-opioid-receptors.pdf
|
60c74b9ff96a000bc6287659
|
10.26434/chemrxiv.9897710.v3
|
Comparison of Umbrella Sampling and Steered Molecular Dynamics Methods for Computing Free Energy Profiles of Aromatic Substrates through Phospholipid Bilayers
|
Understanding the permeation of molecules through lipid membranes is fundamental for predicting the cellular uptake of solutes and drug delivery mechanisms. In molecular simulations the usual approach is to
compute the free energy (FE) profile of a molecule across a model lipid bilayer, which can then be used to
estimate the permeability of the molecule. Umbrella sampling (US), which involves carrying out a series of
biased simulations along a defined reaction coordinate (usually the bilayer normal direction), is a popular
method for the computation of such FE profiles. However, US can be challenging to implement because
the results are dependent on the strength of the biasing potential and the spacing of windows along the
reaction coordinate, which, in practice, are usually optimized by an inefficient trial and error approach. The
Steered Molecular Dynamics implementation of the Jarzynski Equality (JE-SMD) has been identified as an
alternative to equilibrium sampling methods for measuring the FE change across a reaction coordinate. In
the JE-SMD approach, equilibrium FE values are evaluated from the average of rapid non-equilibrium trajectories, thus avoiding the practical issues that come with US. Here, we use three different corrections of the
JE-SMD method to calculate the FE change for the translocation of two aromatic substrates, phenylalanine
and toluene, across a lipid bilayer, and compare the accuracy and computational efficiency of these approaches
to the results obtained using US. We show evidence that when computing the free energy profile, the JE-SMD
approach suffers from insufficient sampling convergence of the bilayer environment, and is dependent on the
characteristic of the aromatic substrate itself. We deduce that, despite its drawbacks, US remains the more
viable approach of the two for computing the FE profile.
|
Sang Noh; Rebecca Notman
|
Computational Chemistry and Modeling; Theory - Computational; Biophysical Chemistry; Statistical Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b9ff96a000bc6287659/original/comparison-of-umbrella-sampling-and-steered-molecular-dynamics-methods-for-computing-free-energy-profiles-of-aromatic-substrates-through-phospholipid-bilayers.pdf
|
62a2290d99b7834e58fab914
|
10.26434/chemrxiv-2022-qstvl
|
Stable D-xylose ditriflate in divergent syntheses of dihydroxy prolines, pyrrolidines, tetrahydrofuran-2-carboxylic acids, and cyclic sugar -amino acids
|
Double nucleophilic displacement of a sugar D-xylose ditriflate derived from diacetone-D-glucose by amines, water and alkyl cyanoacetates gave a series of bicyclic divergent intermediates for the synthesis of a wide range of highly functionalized targets, including hydroxylated prolines, pyrrolidines, THF carboxylic acids, and cyclopentanes
|
Estevez Cabanas Juan Carlos; Rosalino Balo; Alberto G. Fernandez; Adam Chopdat; Soufian El Ayadi; Alejandro Jiménez; Atsushi Kato; Ramon J. Estevez; George W. J. Fleet
|
Organic Chemistry; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-06-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a2290d99b7834e58fab914/original/stable-d-xylose-ditriflate-in-divergent-syntheses-of-dihydroxy-prolines-pyrrolidines-tetrahydrofuran-2-carboxylic-acids-and-cyclic-sugar-amino-acids.pdf
|
645e537cfb40f6b3ee7821f7
|
10.26434/chemrxiv-2022-1jpvc-v2
|
Data Quality, Data Sampling and Data Fitting: A Tutorial Guide for Constructing Full-dimensional Accurate Potential Energy Surfaces (PESs) of Small Molecular Systems
|
We provide discussions and considerations on data quality, data sampling and data fitting for developing full-dimensional accurate potential energy surfaces with ample interpretative examples, centering on accuracy, efficiency, and generality.
|
Jun Li; Yang Liu
|
Theoretical and Computational Chemistry; Theory - Computational; Machine Learning
|
CC BY 4.0
|
CHEMRXIV
|
2023-05-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645e537cfb40f6b3ee7821f7/original/data-quality-data-sampling-and-data-fitting-a-tutorial-guide-for-constructing-full-dimensional-accurate-potential-energy-surfaces-pe-ss-of-small-molecular-systems.pdf
|
661cd447418a5379b0df725d
|
10.26434/chemrxiv-2024-k4fbw
|
Tracking Li atoms in real-time with ultra-fast NMR simulations
|
We present for the first time a multiscale machine learning approach to jointly simulate atomic structure and dynamics with the corresponding solid state Nuclear Magnetic Resonance (ssNMR) observables. We study the use-case of spin-alignment echo (SAE) NMR for exploring Li-ion diffusion within the solid state electrolyte material Li3PS4 (LPS) by calculating quadrupolar frequencies of 7Li. SAE NMR probes long-range dynamics down to microsecond-timescale hopping processes. Therefore only a few machine learning force field schemes are able to capture the time and length scales required for accurate comparison with experimental results. By using a new class of machine learning interatomic potentials, known as ultra-fast potentials (UFPs), we are able to efficiently access timescales beyond the microsecond regime. In tandem, we have developed a machine learning model for predicting the full 7Li electric field gradient (EFG) tensors in LPS. By combining the long timescale trajectories from the UFP with our model for 7Li EFG tensors, we are able to extract the autocorrelation function (ACF) for 7Li quadrupolar frequencies during Li diffusion. We extract the decay constants from the ACF for both crystalline β-LPS and amorphous LPS, and find that the predicted Li hopping rates are on the same order of magnitude as those predicted from the Li dynamics. This demonstrates the potential for machine learning to finally make predictions on experimentally relevant timescales and temperatures, and opens a new avenue of NMR crystallography: using machine learning dynamical NMR simulations for accessing polycrystalline and glass ceramic materials.
|
Angela F Harper; Tabea Huss; Simone S Köcher; Christoph Scheurer
|
Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Computational Chemistry and Modeling; Machine Learning; Spectroscopy (Physical Chem.)
|
CC BY 4.0
|
CHEMRXIV
|
2024-04-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661cd447418a5379b0df725d/original/tracking-li-atoms-in-real-time-with-ultra-fast-nmr-simulations.pdf
|
63e5b7d6fcfb27a31f815e66
|
10.26434/chemrxiv-2023-1ddk8
|
Quantitative composition and mesoscale ion distribution in p-type organic mixed ionic-electronic conductors
|
Understanding the ionic composition and distribution in organic mixed ionic-electronic conductors (OMIECs) is crucial for understanding their structure-property relationships. However, direct measurement of OMIEC ionic composition and distribution is not common. In this work, we investigate the ionic composition and mesoscopic structure of three typical p-type OMIEC materials: an ethylene glycol treated crosslinked OMIEC with large excess fixed anionic charge (EG/GOPS-PEDOT:PSS), an acid treated OMIEC with tunable fixed anionic charge (crys-PEDOT:PSS), and a single component OMIEC absent any fixed anionic charge (pg2T-TT). A combination of X-ray fluorescence (XRF) and photoelectron spectroscopies (XPS), gravimetry, coulometry, and grazing incidence small angle X-ray scattering (GISAXS) techniques were employed to characterize these OMIECs following electrolyte exposure and electrochemical cycling. In particular, XRF provided quantitative ion-to-monomer compositions for these OMIECs from passive ion uptake following aqueous electrolyte exposure, and potential driven ion uptake/expulsion following electrochemical doping and dedoping. Single ion (cation) transport in EG/GOPS-PEDOT:PSS due to Donnan exclusion was directly confirmed, while despite significant fixed anion concentration in crys-PEDOT:PSS doping and dedoping was shown to occur through mixed anion and cation transport. Controlling the fixed anionic (PSS-) charge density in crys-PEDOT:PSS mapped the strength of Donnan exclusion in OMIEC systems following a Donnan-Gibbs model. Anion transport dominated pg2T-TT doping and dedoping, but a surprising degree of anionic charge trapping (~1020 cm-3) was observed. GISAXS revealed minimal ion segregation both between PEDOT- and PSS-rich domains in EG/GOPS-PEDOT:PSS, and between amorphous and semicrystalline domains in pg2T-TT, but showed significant ion segregation in crys-PEDOT:PSS at length scales of tens of nm, ascribed to inter-nanofibril void space. These results bring new clarity to the ionic composition and distribution of OMIECs that are crucial for accurately connecting structure and properties in these materials.
|
Ruiheng Wu; Bryan Paulsen; Qing Ma; Jonathan Rivnay
|
Physical Chemistry; Materials Science; Polymer Science; Conducting polymers
|
CC BY 4.0
|
CHEMRXIV
|
2023-02-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e5b7d6fcfb27a31f815e66/original/quantitative-composition-and-mesoscale-ion-distribution-in-p-type-organic-mixed-ionic-electronic-conductors.pdf
|
65bcfeff66c1381729d06807
|
10.26434/chemrxiv-2024-fg0t5
|
Overview of nanotherapeutics for bacterial infections
|
The rapid emergence of antibiotic-resistant bacteria poses one of the greatest threats to public health as conventional therapies and commercial antibiotics are dropping their effectiveness. In the race for the discovery of new strategies to prevent a scenario in which commonplace infections prove fatal, nanomaterials stand in the limelight due to their unique physicochemical properties that can be seized to overcome common resistance mechanisms.
Nanoparticle-driven drug delivery emerges as a beacon of hope, shielding antibiotics from enzymatic degradation, enhancing their targeted delivery to afflicted sites in therapeutically potent concentrations, and minimising undesired side effects. Drugs can either be entrapped or chemically conjugated to nanoparticles, with the latter offering a myriad of possibilities in orchestrating spatiotemporal controlled release of the therapeutic payload. Meanwhile, nanomaterials can also display intrinsic antimicrobial properties, either by direct disruption of bacterial cell membranes (e.g., nanoparticles functionalised with cationic groups) or by instigating the generation of ROS (e.g., metallic nanoparticles).
The clinical implementation of nanotherapeutics still faces considerable challenges, mainly related with their complex chemistry and polydispersity, which poses difficulties related to cost-effectiveness, scale-up, and Chemistry, Manufacturing, and Controls (CMC) management. Still, the development of computational approaches allowing a better understanding of nano-bio interactions and predictive biodistribution, pharmacokinetics, and toxicology, along with a harmonised international regulatory framework, is expected to facilitate clinical translation in the near future.
|
José Muñoz-López; Cátia D. F. Lopes; Iris L. Batalha
|
Biological and Medicinal Chemistry; Materials Science; Nanoscience; Controlled-Release Systems; Nanostructured Materials - Nanoscience; Microbiology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-02-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bcfeff66c1381729d06807/original/overview-of-nanotherapeutics-for-bacterial-infections.pdf
|
64acbbe19ea64cc167cd7ebe
|
10.26434/chemrxiv-2023-xd7tz
|
Protecting Group-Free Synthesis of the Antimalaria Drug MMV693183
|
MMV693183 is a promising antimalarial drug candidate that works for uncomplicated malaria treatment and resistance management. Herein, we report an efficient and highly regioselective synthesis of MMV693183. This efficient approach to MMV693183 is only three steps from readily available starting materials and provides the API in 46 % overall yield without requiring protecting groups.
|
Pankaj Khairnar; Sarah Aleshire; Ravikumar Ongolu; limei jin; Michael Laidlaw; Ryan Nelson; Kai Donsbach; Frank Gupton; Charles Shanahan
|
Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Stereochemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-07-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64acbbe19ea64cc167cd7ebe/original/protecting-group-free-synthesis-of-the-antimalaria-drug-mmv693183.pdf
|
60c73ea1337d6c5f27e263ba
|
10.26434/chemrxiv.7077458.v1
|
One-Step Femtosecond Laser Ablation Synthesis of Sub-5 Nm Gold Nanoparticles Embedded in Silica
|
<div>
<div>
<div>
<p>We report the synthesis of silica-gold nanoparticles (silica-Au NPs) using a
one-step femtosecond-reactive laser ablation in liquid (fs-RLAL) technique by
focusing femtosecond laser pulses onto a silicon wafer immersed in an aqueous
KAuCl4 solution. Characterization of the silica-Au NPs revealed two populations of Au NPs: (i) larger, isolated Au NPs with diameter 7.3±2.1 nm, and (ii)
smaller Au NPs (3.4±0.8 nm) embedded in an amorphous silica matrix, along
with new species of silicon observed from XPS analysis. The catalytic activity
of the silica-Au NPs towards the reduction of para-nitrophenol by NaBH4 is
significantly higher compared to the control Au NPs synthesized in the absence
of a silicon wafer and other Au NPs recently reported in literature. The formation of the two populations of silica-Au NPs is ascribed to reaction dynamics
occurring on two distinct timescales. First, the dense electron plasma formed
within tens of femtoseconds of the laser pulse initiates reduction of the [AuCl4]–
complex, leading to the formation of larger isolated Au NPs. Second, silicon
species ejected from the wafer surface hundreds of picoseconds or later after the
initial laser pulse reduce the remaining [AuCl4 ]– and encapsulate the growing
clusters, forming ultrasmall Au NPs embedded in the silica matrix. The morphologies of the silica-Au NPs generated from fs-RLAL are distinct from those
reported in recent RLAL experiments with nanosecond lasers, reflecting distinct
mechanisms occurring on the different pulse duration timescales.
</p>
</div>
</div>
</div>
|
Mallory John; Katharine Tibbetts
|
Nanocatalysis - Catalysts & Materials; Nanofabrication; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-09-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ea1337d6c5f27e263ba/original/one-step-femtosecond-laser-ablation-synthesis-of-sub-5-nm-gold-nanoparticles-embedded-in-silica.pdf
|
66fdb31dcec5d6c142f6e3f1
|
10.26434/chemrxiv-2024-hwh2g
|
The effect of pyridinecarboxaldehyde functionalisation on reactivity and N-terminal protein modification
|
The site-selective modification of protein N-termini represents a powerful strategy for producing homogeneous bioconjugates. 2-Pyridinecarboxaldehydes have emerged as a leading reagent class in this area, but conjugation suffers from relatively slow rates and a degree of reversibility. In this work, we therefore studied the effects of pyridinecarboxaldehyde functionalisation on N-terminal modification, providing insight into the factors governing relative contributions from competing reaction pathways and design criteria for second generation reagents for protein labelling. Importantly, this insight allowed us to identify several candidate reagents which provide both accelerated and more stable protein labelling, enabling further applications of this powerful technology.
|
Lydia Barber; Christopher Spicer
|
Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions; Chemical Biology
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-10-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fdb31dcec5d6c142f6e3f1/original/the-effect-of-pyridinecarboxaldehyde-functionalisation-on-reactivity-and-n-terminal-protein-modification.pdf
|
60c75345842e6501e8db3f24
|
10.26434/chemrxiv.13140980.v2
|
Precise and Efficient Phototheranostics: Molecular Engineering of Photosensitizers with Near-Infrared Aggregation-Induced Emission for Acid-Triggered Nucleus-Targeted Photodynamic Cancer Therapy
|
Phototheranostics involving both fluorescence imaging (FLI) and photodynamic
therapy (PDT) has been recognized to be potentially powerful for cancer
treatment by virtue of various intrinsic advantages. However, the state-of-the-art materials in this area are
still far from ideal towards practical applications, owing to their respective and collective
drawbacks, such as inefficient imaging quality, inferior reactive oxygen
species (ROS) production, the lack of subcellular-targeting capability, and dissatisfactory
theranostics delivery. In this contribution, these shortcomings are successfully addressed through the integration of finely engineered
photosensitizers having aggregation-induced emission (AIE) features and well
tailored nanocarrier system. The yielded AIE NPs simultaneously exhibit broad
absorption in visible light region, bright near-infrared fluorescence emission,
extremely high ROS generation, as well as tumor lysosomal acidity-activated and
nucleus-targeted delivery functions, making them dramatically promising for
precise and efficient phototheranostics. Both in vitro and in vivo evaluations
show that the presented nanotheranostic system bearing excellent photostability
and appreciable biosecurity well performed in FLI-guided photodynamic cancer
therapy. This study thus not only extends the applications scope of AIE
nanomaterials, but also offers useful insights into constructing a new
generation of cancer theranostics.
|
Zhijun Zhang; Wenhan XU; Peihong Xiao; Miaomiao Kang; Dingyuan Yan; Haifei Wen; Nan Song; Dong Wang; Ben Zhong Tang
|
Aggregates and Assemblies
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-12-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75345842e6501e8db3f24/original/precise-and-efficient-phototheranostics-molecular-engineering-of-photosensitizers-with-near-infrared-aggregation-induced-emission-for-acid-triggered-nucleus-targeted-photodynamic-cancer-therapy.pdf
|
65571f7a2c3c11ed719226be
|
10.26434/chemrxiv-2023-ksfb4-v2
|
Geometry and Electronic Structure of Yb(III)[CH(SiMe3)2]3 from EPR and solid-state NMR augmented by Computations
|
Characterization of paramagnetic compounds, in particular regarding the detailed conformation and electronic structure, remains a challenge, and - still today it often relies solely on the use of X-ray crystallography, thus limiting the access to electronic structure information. This is particularly true for lanthanide elements that are often associated with peculiar structural and electronic features in relation to their partially filled f-shell. Here, we develop a methodology based on the combined use of state-of-the-art magnetic resonance spectroscopies (EPR and solid-state NMR) and computational approaches as well as magnetic susceptibility measurements to determine the electronic structure and geometry of a paramagnetic Yb(III) alkyl complex, Yb(III)[CH(SiMe3)2]3, a prototypical example, which contains notable structural features according to X-ray crystallography. Each of these techniques revealed specific information about the geometry and electronic structure of the complex. Taken together, both EPR and NMR, augmented by quantum chemical calculations, provide a detailed and complementary understanding of such paramagnetic compounds. In particular, the EPR and NMR signatures point to the presence of three-centre-two-electron Yb-γ-Me-β–Si secondary metal-ligand interactions in this otherwise tri-coordinate metal complex, similarly to its diamagnetic Lu analogues. The electronic structure of Yb(III) can be described as a single 4f13 configuration, while an unusually large crystal-field splitting results in a thermally isolated ground Kramers doublet. Furthermore, the computational data indicate that the Yb-carbon bond contains some π-character, reminiscent of the so-called α-H agostic interaction.
|
Anton Ashuiev; Florian Allouche; Md. Ashraful Islam; José P. Carvalho; Kevin J. Sanders; Matthew P. Conley; Daniel Klose; Giuseppe Lapadula; Michael Wörle; Dirk Baabe; Marc D. Walter; Andrew J. Pell; Christophe Copéret; Gunnar Jeschke; Guido Pintacuda; Richard A. Andersen
|
Physical Chemistry; Inorganic Chemistry; Organometallic Chemistry; Lanthanides and Actinides; Organometallic Compounds; Spectroscopy (Organomet.)
|
CC BY 4.0
|
CHEMRXIV
|
2023-11-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65571f7a2c3c11ed719226be/original/geometry-and-electronic-structure-of-yb-iii-ch-si-me3-2-3-from-epr-and-solid-state-nmr-augmented-by-computations.pdf
|
6450f5f207c3f02937167e86
|
10.26434/chemrxiv-2023-dp5kt-v2
|
Predicted role of Acetyl-CoA synthetase and HAT p300 in extracellular lactate mediated lactylation in the tumor: In vitro and in silico models
|
Background
As per the Warburg effect, cancer cells are known to convert pyruvate into lactate. The accumulation of lactate is associated with metabolic and epigenetic reprogramming, which has newly been suggested to involve lactylation. However, the role of secreted lactate in modulating the tumor microenvironment through lactylation remains unclear. Specifically, there are gaps in our understanding of the enzyme responsible for converting lactate to lactyl-CoA and the nature of the enzyme that performs lactylation by utilizing lactyl-CoA as a substrate. It is worth noting that there are limited papers focused on metabolite profiling that detect lactate and lactyl-CoA levels intracellularly and extracellularly in the context of cancer cells.
Methods
Here, we have employed an in-house developed vertical tube gel electrophoresis (VTGE) and LC-HRMS assisted profiling of extracellular metabolites of breast cancer cells treated by anticancer compositions of cow urine DMSO fraction (CUDF) that was reported previously. Furthermore, we used molecular docking and molecular dynamics (MD) simulations to determine the potential enzyme that can convert lactate to lactyl-CoA. Next, the histone acetyltransferase p300 (HAT p300) enzyme (PDB ID: 6GYR) was evaluated as a potential enzyme that can bind to lactyl-CoA during the lactylation process.
Results
We collected evidence on the secretion of lactate in the extracellular conditioned medium of breast cancer cells treated by anticancer compositions. MD simulations data projected that acetyl-CoA synthetase could be a potential enzyme that may convert lactate into lactyl-CoA similar to a known substrate acetate. Furthermore, a specific and efficient binding (docking energy -9.6 kcal/mol) of lactyl-CoA with p300 HAT suggested that lactyl-CoA may serve as a substrate for lactylation similar to acetylation that uses acetyl-CoA as a substrate.
Conclusion
In conclusion, our data provide a hint on the missing link for the lactylation process due to lactate in terms of a potential enzyme that can convert lactate into lactyl-CoA. This study helped us to project the HAT p300 enzyme that may use lactyl-CoA as a substrate in the lactylation process of the tumor microenvironment.
|
Rushikesh Patel; Ajay Kumar; Kiran Bharat Lokhande; Mrudula Joshi; Kratika Khunteta; Jayanta K. pal; Prof. Nilesh Kumar Sharma
|
Biological and Medicinal Chemistry; Cell and Molecular Biology
|
CC BY 4.0
|
CHEMRXIV
|
2023-05-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6450f5f207c3f02937167e86/original/predicted-role-of-acetyl-co-a-synthetase-and-hat-p300-in-extracellular-lactate-mediated-lactylation-in-the-tumor-in-vitro-and-in-silico-models.pdf
|
62f6bf3de650df5f8c23f2ad
|
10.26434/chemrxiv-2022-314m3
|
Combining photochemical transformation of pyridinium salt with kinetic enzymatic resolution towards the total synthesis of (-)-agelastatin A
|
Agelastatin alkaloids were synthesized through early-stage construction of the synthetically challenging C ring via photochemical transformation of pyridinium salts. Kinetic enzymatic resolution of bicyclic vinyl aziridines allowed the synthesis of (-)-agelastatin A in 4% yield over 12 steps. The cytotoxicity of (±)-agelastatin A and two N3-derivates were tested against a series of cancer cell lines to evaluate the impact of N3-substituition of the biological activity of agelastatin derivatives and corroborated the importance of unsubstituted N3 in the cytotoxicity of (-)-agelastatin A.
|
Carlos Alberto Mateus Afonso; João Rafael Vale; Milene Fortunato; Késsia Andrade; Filipa Siopa
|
Organic Chemistry; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-08-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f6bf3de650df5f8c23f2ad/original/combining-photochemical-transformation-of-pyridinium-salt-with-kinetic-enzymatic-resolution-towards-the-total-synthesis-of-agelastatin-a.pdf
|
63401f0ee61502582635bad9
|
10.26434/chemrxiv-2022-2j3xp-v2
|
Ligand-directed Photocatalysts and Far-red Light Enable Catalytic Bioorthogonal Uncaging inside Live Cells
|
Described are ligand-directed catalysts for live-cell, photocatalytic activation of bioorthogonal chemistry. Catalytic groups are localized via a tethered ligand either to DNA or to tubulin, and red-light (660 nm) photocatalysis is used to initiate a cascade of DHTz-oxidation, intramolecular Diels-Alder reaction, and elimination to release phenolic compounds. Silarhodamine (SiR) dyes, more conventionally used as biological fluorophores, serve as photocatalysts that have high cytocompatibility and produce minimal singlet oxygen. Commercially-available conjugates of Hoechst dye (SiR-H) and Taxol (SiR-T) are used to localize SiR to the nucleus and tubulin, respectively. Computation was used to assist the design of a new class of redox-activated photocage to release either phenol or n-CA4, a microtubule-destabilizing agent. In model studies, uncaging is complete within 5 min using only 2 µM of SiR and 40 µM of the photocage. In situ spectroscopic studies support a mechanism involving rapid intramolecular Diels-Alder reaction and a rate determining elimination step. In cellular studies, this uncaging process is successful at low concentration of both the photocage (25 nM) and the SiR-H dye (500 nM). Uncaging n-CA4 causes microtubule depolymerization and an accompanying reduction in cell area. Control studies demonstrate that SiR-H catalyzes uncaging inside the cell, and not in the extracellular environment. With SiR-T, the same dye serves as photocatalyst and the fluorescent reporter for tubulin depolymerization, and with confocal microscopy it was possible to visualize tubulin depolymerization in real time as the result of photocatalytic uncaging in live cells.
|
Julia Rosenberger; Yixin Xie; Yinzhi Fang; Xinyi Lyu; William Trout; Olga Dmitrenko; Joseph Fox
|
Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Chemical Biology; Drug Discovery and Drug Delivery Systems; Photocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63401f0ee61502582635bad9/original/ligand-directed-photocatalysts-and-far-red-light-enable-catalytic-bioorthogonal-uncaging-inside-live-cells.pdf
|
646e0002e64f843f41b1f495
|
10.26434/chemrxiv-2023-sc6tf
|
One-pot Synthesis of Helical Azaheptalene and Chiroptical Switch with Isolable Radical Cation
|
A nitrogen-centered heptalene, azaheptalene, was designed as a representative of a new class of redox-responsive molecules with a large steric strain that originates from the adjacent seven-membered rings. The pentabenzo derivative of azaheptalene was efficiently synthesized by a palladium-catalyzed one-pot reaction of commercially available reagents. Bromination led to mono- and dibrominated derivatives, the latter of which is interconvertible with isolable radical cation species exhibiting near-infrared absorption. Since the azaheptalene skeleton shows configurationally stable helicity with a large torsion angle, enantiomers could be successfully separated. Thus, optically pure azaheptalenes with P- or M-helicity showed strong chiroptical properties (|gabs| ≥ 0.01), which could be changed by an electric potential.
|
Yuta Nishimura; Takashi Harimoto; Takanori Suzuki; Yusuke Ishigaki
|
Organic Chemistry; Physical Organic Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-05-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646e0002e64f843f41b1f495/original/one-pot-synthesis-of-helical-azaheptalene-and-chiroptical-switch-with-isolable-radical-cation.pdf
|
60c747da0f50db25763966af
|
10.26434/chemrxiv.11812053.v1
|
Automated Assessment of Binding Affinity via Alchemical Free Energy Calculations
|
Free energy calculations have seen increased usage in structure-based drug design. Despite the rising interest, automation of the complex calculations and subsequent analysis of their results are still hampered by the restricted choice of available tools. In this work, an application for automated setup and processing of free energy calculations is presented. Several sanity checks for assessing the reliability of the calculations were implemented, constituting a distinct advantage over existing open-source tools. The underlying workflow is built on top of the software Sire, SOMD, BioSimSpace and OpenMM and uses the AMBER14SB and GAFF2.1 force fields. It was validated on two datasets originally composed by Schrödinger, consisting of 14 protein structures and 220 ligands. Predicted binding affinities were in good agreement with experimental values. For the larger dataset the average correlation coefficient Rp was 0.70 ± 0.05 and average Kendall’s τ was 0.53 ± 0.05 which is broadly comparable to or better than previously reported results using other methods.
<br />
|
Maximilian Kuhn; Stuart Firth-Clark; Paolo Tosco; Antonia S. J. S. Mey; Mark Mackey; Julien Michel
|
Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-02-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747da0f50db25763966af/original/automated-assessment-of-binding-affinity-via-alchemical-free-energy-calculations.pdf
|
6723fce07be152b1d09cbc2c
|
10.26434/chemrxiv-2024-8t38n
|
Uncovering chemical principles governing nanophase formation in ternary solvents
|
Nanoscopic phases, such as oil-enriched pockets dispersed in water, have been observed in ternary mixtures of oil, water, and cosolvent in the absence of surfactants. Such nanophases are found across a portion of compositions within the single-phase region of the ternary phase diagram. However, the principles governing the formation of nanophases under certain conditions but not others, regarding both volumetric and chemical makeup, are unclear. Here, the nanophase behavior of ternary mixtures of water with a suite of cosolvents and oils containing strategically chosen functional groups is systematically analyzed to probe the role of intermolecular interactions. Dynamic light scattering is used to quantify the nanophase structure. It was found that stronger classes of intermolecular interactions such as H-bonding or n-Π* interactions between oil and cosolvent notably contribute to forming thermodynamically stable nanophases. Ternary mixtures in which the oil has only van der Waals interactions with the water and cosolvent do not stabilize nanophases detectable by dynamic light scattering. Aromatic groups favor nanophase formation. The most prominent structuring (highest number and largest sizes of nanophases) is found in water-rich compositions near the miscibility gap. This experimental study provides chemical insight into the chemical formulation of ternary solvent mixtures favoring nanophase formation.
|
Binish Ashfaq; Ayusman Sen; Lauren Zarzar
|
Physical Chemistry; Organic Chemistry; Analytical Chemistry; Interfaces; Solution Chemistry; Structure
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6723fce07be152b1d09cbc2c/original/uncovering-chemical-principles-governing-nanophase-formation-in-ternary-solvents.pdf
|
62be93bcf5193940817aead6
|
10.26434/chemrxiv-2022-1nvnj
|
Understanding the Aggregation and Flow Response of Donor-Acceptor Conjugated Polymers
|
Fluid flow is an inherent aspect of solution processing of conjugated polymers. Much of the existing work investigating the effect of flow has been phenomenological, lacking a direct and quantitative connection between the flow gradients and measurable quantities of the conformation or alignment of the conjugated polymers in solution. Furthermore, while aggregation of conjugated polymers in solution has been demonstrated to result in highly aligned thin-films, there are few studies that probe the interplay between the structures that form during aggregation and flow-induced alignment during processing. Here, we explore in detail the influence of flow type, solution aggregation, and concentration on the flow-induced alignment of conjugated polymers. We apply a microfluidic platform to systematically subject the conjugated polymer solution to large and controllable shear and extensional strain rates and use flow-induced retardance (birefringence) measurements to characterize the degree of alignment. By using flow-induced retardance in combination with small angle X-ray scattering (SAXS) and electron microscopy of freeze-dried solutions we are able to determine the solution state structure and clearly demonstrate the interplay between solution aggregation and fluid flow. We determine the overall relaxation time of the material and the strengths of shear and extensional flows required to align conjugated polymer aggregates. Furthermore, we find that although enhanced aggregation can facilitate flow-induced alignment, the type of aggregation and the presence of interparticle interactions at higher concentrations can diminish the effectiveness of flow. The results here demonstrate that there is a complex interplay between the conjugated polymer solution state and fluid flow and that simply increasing the conjugated polymer’s aggregation, concentration, or the strength of flow does not necessarily lead to better or more effective alignment in solution. A careful understanding of the synergy between these two aspects can help to establish design rules in solution processing for improving conjugated polymer film morphology.
|
Justin Kwok; Giridar Vishwanathan; Kyung Sun Park; Bijal Patel; Dongqi Zhao; Gabriel Juarez; Ying Diao
|
Materials Science; Polymer Science; Aggregates and Assemblies; Materials Processing; Conducting polymers
|
CC BY 4.0
|
CHEMRXIV
|
2022-07-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62be93bcf5193940817aead6/original/understanding-the-aggregation-and-flow-response-of-donor-acceptor-conjugated-polymers.pdf
|
62998df780f81c2f4d9a7fe1
|
10.26434/chemrxiv-2022-vtz66
|
Evaluation of binding preference of different microtubes for
nanoproteomics sample preparation
|
Non-specific binding of protein and plastics is a main cause of sample loss in proteomics sample preparation. In the nanoproteomics, researchers often adopt low binding plasticware to minimize the sample loss. However, there has been little discussion in the scientific literature on the differences of microtube performance in reducing protein/peptide binding. Therefore, the exact impact of sample loss during the sample preparation is not well studied. Here, we applied qualitative and quantitative approaches to investigate the protein/peptide loss during the nanoproteomics experiment process. Our results clearly showed that there are significant differences in non-specific binding among all the tested microtubes, with a protein recovery rate ranging from less than 10% to over 90% for different microtubes. We found that storage temperature is also one of the key factors that contribute to protein recovery from the plastic. In addition, we further investigated the binding preferences of different microtubes by the physical characteristics of protein and peptides, such as isoelectric point, hydrophobicity, length, and charge. Our findings contribute to a better understand-ing of protein/peptide loss in proteomics sample preparation and provide further guidance for researchers in choosing proper containers for their precious sample.
|
Ziwei Zhang; Yu Gao
|
Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-06-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62998df780f81c2f4d9a7fe1/original/evaluation-of-binding-preference-of-different-microtubes-for-nanoproteomics-sample-preparation.pdf
|
665641ad91aefa6ce1375c58
|
10.26434/chemrxiv-2024-5vcqd
|
Impact of a poly(ethylene glycol) corona block on drug encapsulation during polymerization induced self-assembly
|
Polymerization induced self-assembly (PISA) provides a facile platform for encapsulating therapeutics within block copolymer nanoparticles. Performing PISA in the presence of a hydrophobic drug alters both the nanoparticle shape and encapsulation efficiency. While previous studies primarily examined the interactions between the drug and hydrophobic core block, this work explores the impact of the hydrophilic corona block on encapsulation. Poly(ethylene glycol) (PEG) and poly(2-hydroxypropyl methacrylate) (PHPMA) are used as the model corona and core blocks, respectively, and phenylacetic acid (PA) is employed as the model drug. Attachment of a dithiobenzoate end group to the PEG homopolymer – transforming it into a macroscopic reversible addition–fragmentation chain transfer agent – causes the polymer to form a small number of nanoscopic aggregates in solution. Adding PA to the PEG solution encourages further aggregation and macroscopic phase separation. During the PISA of PEG-PHPMA block copolymers, inclusion of PA in the reaction mixture promotes faster nucleation of spherical micelles. Although increasing the targeted PA loading from 0 to 20 mg/mL does not affect the micelle size or shape, it alters the drug spatial distribution within the PISA microenvironment. PA partitions into either PEG-PHPMA micelles, deuterium oxide, or other polymeric species – including PEG aggregates and unimer chains. Increasing the targeted PA loading changes the fraction of drug within each encapsulation site. This work indicates that the corona block plays a critical role in dictating drug encapsulation during PISA.
|
Ralm Ricarte; Guanrui Li; Cassie Duclos
|
Polymer Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665641ad91aefa6ce1375c58/original/impact-of-a-poly-ethylene-glycol-corona-block-on-drug-encapsulation-during-polymerization-induced-self-assembly.pdf
|
6582df88e9ebbb4db9587770
|
10.26434/chemrxiv-2023-h5fdl
|
Biomimicry of Limpet Teeth with Hybrid Colloidal Liquid Crystals: Mechanical Enhancement by Structural Orderliness from Self-Assembly
|
The teeth of limpets, consisting of orderly aligned hard goethite (iron oxyhydroxides) nanocrystals and flexible chitin microfibers, are one of the hardest and stiffest biomaterials found in nature. However, the replication of their composition and ordered microstructures to artificial biomimetic materials remains a challenge. Here, we fabricated large-sized limpet tooth analogues with hierarchically ordered structures by applying long-range orientational control to the short-scale self-assembly of hybrid colloidal liquid crystals formed by chitin nanocrystals and goethite nanorods. The obtained lightweight composite laminates exhibited excellent bending resistance compared with biomaterials, cements, and ceramics. These results suggest that the mass production of structurally ordered materials with high strength and toughness may be achieved using lyotropic liquid crystals.
|
hongbo zhao; Renjun Pei; Pei-Xi Wang
|
Materials Science; Inorganic Chemistry; Nanoscience; Hybrid Organic-Inorganic Materials; Liquid Crystals
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6582df88e9ebbb4db9587770/original/biomimicry-of-limpet-teeth-with-hybrid-colloidal-liquid-crystals-mechanical-enhancement-by-structural-orderliness-from-self-assembly.pdf
|
65ead36a66c13817298a9643
|
10.26434/chemrxiv-2024-v4hfn
|
Accessing active fragments for drug discovery utilising nitroreductase biocatalysis
|
Biocatalysis has played a limited role in the early stages of drug discovery. This is often attributed to the limited substrate scope of enzymes not affording access to vast areas of novel chemical space. Here, we have shown a promiscuous nitroreductase enzyme (NR-55) can be used to produce a panel of functionalised anilines from a diverse panel of aryl nitro starting materials. After screening on analytical scale, we show that sixteen substrates could be scaled to 1 mmol scale, with several poly-functional anilines afforded with ease under the standard conditions. The aniline products were also screened for activity against several cell line of interest, with modest activity observed for one compound. This study demonstrates the potential for nitroreductase biocatalysis to provide access to functional fragments under benign conditions.
|
Lauren Holder; Eda Yuce; Gabriel Oriomah; Aimee Jenkins; Jóhannes Reynisson; Anja Winter; Sebastian Cosgrove
|
Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems; Biocatalysis
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-03-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ead36a66c13817298a9643/original/accessing-active-fragments-for-drug-discovery-utilising-nitroreductase-biocatalysis.pdf
|
675c3eae7be152b1d0dc99bd
|
10.26434/chemrxiv-2024-fmnw8-v2
|
Modeling swelling of pH-responsive microgels: Theory and simulations
|
Combining a mean-field swelling model—which incorporates the Poisson-Boltzmann cell model for describing the electrostatics of microgels and a Flory-Rehner-based model for describing the polymer network—with the law of mass action to account for chemical reactions, we present a comprehensive swelling model for weakly charged microgels. This model provides an expression for the microgel osmotic pressure, used to determine the equilibrium swelling and, consequently, the net charge of the microgel as a function of reservoir pH, salt concentration, degree of polymerization, and other suspension and microscopic network properties. The model allows us to relate microscopic microgel features with the equilibrium swelling properties. The weak-field limiting case of the Poisson-Boltzmann theory is analyzed, yielding closed formulas. We validate the model against state-of-the-art coarse-grained simulations of a microgel, utilizing molecular dynamics to explore configurational degrees of freedom and the Monte Carlo grand-reaction method to simulate chemical reactions in equilibrium with a pH and salt reservoir. We test the model predictions for equilibrium ionization, size, and net charge against particle-based simulations and experiment. Our findings show that the model accurately describes microgel swelling and net charge over a wide range of pH levels. Although the accuracy decreases for larger salt concentrations, its overall qualitative accuracy makes it a reliable tool for parameter exploration and data interpretation, aiding in the rational design of microgel suspensions.
|
Mariano E. Brito; Ellen Höpner; David Beyer; Christian Holm
|
Theoretical and Computational Chemistry; Materials Science; Polymer Science; Hydrogels; Polyelectrolytes - Polymers
|
CC BY 4.0
|
CHEMRXIV
|
2024-12-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675c3eae7be152b1d0dc99bd/original/modeling-swelling-of-p-h-responsive-microgels-theory-and-simulations.pdf
|
6613a2ff91aefa6ce1179bef
|
10.26434/chemrxiv-2024-g33f9
|
PCTpro: A Machine learning model for rapid prediction of Pressure-Composition-Temperature (PCT) isotherms
|
We present a machine-learning powered Pressure-Composition-Temperature isotherm Predictor (PCTpro) for metal compositions. To train the PCTpro, an experimental database of PCT isotherms (MH-PCT) is built from published literature. The database comprises over 14,000 data points extracted from 237 PCT isotherms, representing 138 distinct compositions. The dataset encom- passes more than 25 elements and spans a broad spectrum of absorption tem- peratures (263-653 K) and hydrogen pressures (0.001 to 40 MPa). The feature set includes weighted average of elemental properties, hydriding properties, and experimental parameters like absorption temperature and hydrogen pressure. The comprehensive feature set equips PCTpro to predict the PCT isotherms for a given composition. The model is validated on a wide range of alloy fam- ilies and its predictions are consistent with experimental results. The model also captures temperature-dependent variations in plateau pressure, enabling determination of enthalpy and entropy of hydride formation through Van’t Hoff plots. We also demonstrate that training PCTpro on a subset of relevant data provides improved PCT isotherm prediction. Hence, PCTpro can be used as an ML tool for guiding PCT experiments, offering PCT isotherm predictions and valuable thermodynamic insights into materials suitable for solid-state hydrogen storage.
|
Ashwini Verma; Kavita Joshi
|
Materials Science; Energy; Hydrogen Storage Materials; Energy Storage; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-04-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6613a2ff91aefa6ce1179bef/original/pc-tpro-a-machine-learning-model-for-rapid-prediction-of-pressure-composition-temperature-pct-isotherms.pdf
|
67c16f606dde43c908d5fc1a
|
10.26434/chemrxiv-2024-587vq-v3
|
Nanoflow Size Exclusion Chromatography – Native Mass Spectrometry of Intact Proteoforms and Protein Complexes
|
Native size-exclusion chromatography (SEC) coupled with native mass spectrometry (nMS) enables the characterization of proteins and protein complexes by combining liquid-phase separation (SEC) and mass measurement of the complexes (nMS). This approach allows for an increase in the throughput of native MS experiments, reduces the bias that may be present due to the co-ionization of oligomers, and facilitates online sample buffer exchange. SEC-nMS uses volatile buffers and relatively wide-diameter columns (e.g., ≥ 1 mm), with flow rates in the tens of µL/minute. To ionize sample components under this flow regime, relatively harsh electrospray ionization (ESI) desolvation conditions are needed, potentially resulting in protein dissociation/denaturation. Also, relatively large amounts of samples are required (several micrograms). Herein, we describe the development of a nanoflow SEC-nMS method using 200 µm I.D. columns, operated at 500 nL min-1. This approach allows buffer exchange, oligomer separation, and mild ionization conditions (e.g., without the assistance of heated gas flow or temperature). Compared to microflow (1 mm I.D. column), the nanoflow method achieved a 4-fold increase in MS peak intensity, despite using a sample 20 times less concentrated (0.05 mg mL-1 for nanoflow vs. 1 mg mL-1 for microflow). Furthermore, we evaluated the impact of three injection approaches on sensitivity and separation efficiency: large-volume (1 μL), nano-volume (50 nL), and online mix-bed ion-exchange capillary trap injection. To demonstrate its performance and applicability for sample-limited analysis, the final method using nano-volume injection was applied to several model proteins, protein complexes, and a urine sample from a pregnant donor.
|
Ziran Zhai; Thomas Holmark; Annika A. M. van der Zon; Andrea F.G. Gargano
|
Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-02-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c16f606dde43c908d5fc1a/original/nanoflow-size-exclusion-chromatography-native-mass-spectrometry-of-intact-proteoforms-and-protein-complexes.pdf
|
60c747819abda210a6f8c8fa
|
10.26434/chemrxiv.11695674.v1
|
Dynamic Structural Effects on the Second-Harmonic Generation of Tryptophane-Rich Peptides and Gramicidin A
|
<div>Chains of amino acids can model endogenous biotags for applications in second harmonic imaging microscopy. Such structures are inherently flexible which may strongly affect their structure-property relationship. Here, we explore quantum-mechanically the conformational space of a set of relatively large tryptophan-rich model peptides studied experimentally by Duboisset et al. [JPC B 2014 118]. This has become feasible because of the recently proposed meta-dynamics method based on efficient tight-binding (TB) quantum chemical calculations. The TB version of the simplified time-dependent density functional theory (sTD-DFT-xTB) method is used to evaluate the first hyperpolarizability. These new tools enable us to calculate nonlinear optical properties for systems with several thousand atoms and/or to screen large structure ensembles. First, we show that the first hyperpolarizability of these systems is dominated by the indole chromophore in the tryptophan residues. Their relative orientation mostly determines the global β tensor and affects the static first hyperpolarizability response drastically. The results underline the importance of finding low-energy conformers for modeling the first hyperpolarizabilities of flexible molecules. Additionally, we compare calculated and extrapolated experimental static first hyperpolarizabilities. <br /></div><div>We conclude that the sTD-DFT-xTB method is capable of providing reliable second-harmonic generation values for tryptophan-rich systems at a fraction of the computational cost of the commonly used TD-DFT/TD-HF levels of theory.</div>
|
Jakob Seibert; Benoît CHAMPAGNE; Stefan Grimme; Marc de Wergifosse
|
Physical and Chemical Properties
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-01-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747819abda210a6f8c8fa/original/dynamic-structural-effects-on-the-second-harmonic-generation-of-tryptophane-rich-peptides-and-gramicidin-a.pdf
|
67af316c6dde43c908d774b6
|
10.26434/chemrxiv-2025-6nqpf
|
Synthesis of aniline from dinitrogen and benzene mediated by supported sodium on magnesium oxide
|
The activation and transformation of small molecules such as dinitrogen (N2) and benzene has been a long-sought-after objective in synthetic chemistry. However, it remains a formidable challenge due to the chemical inertness of the highly robust N≡N and aryl C-H bonds. On the other hand, one of the significant challenges in C-N bond formation is the competitive adsorption and activation of N2 and benzene. Here we report the sodium supported on magnesium oxide (Na/MgO) nanoparticles possess reactive sites for the activation of both N2 and benzene, leading to C-N bond formation and providing the anilines with high selectivity on further protonation. The interplay of sodium, magnesium, and hydride species at the interface of Na and MgO plays a key role in N2 reduction and hydrogenation to NHx species, which then deprotonate the aryl C-H bond resulting in the formation of sodium anilide on MgO. The subsequent protonation of sodium anilide produces aniline with a high selectivity (>90%). This work demonstrates a strategy for the transformation of N2 and simple arenes into organic nitrogen-containing compounds via a solid surface-mediated process.
|
Shixiong Zhang; Yongli Cai; Hong Wen; Liang Liu; Lei Yu; Junnian Wei; Jianping Guo; Zhenfeng Xi; Ping Chen
|
Physical Chemistry; Inorganic Chemistry; Catalysis; Main Group Chemistry (Inorg.); Small Molecule Activation (Inorg.); Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-02-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67af316c6dde43c908d774b6/original/synthesis-of-aniline-from-dinitrogen-and-benzene-mediated-by-supported-sodium-on-magnesium-oxide.pdf
|
67c2c92b6dde43c908fd6f65
|
10.26434/chemrxiv-2025-kbr2q
|
Concise Enantioselective Total Syntheses of Rearranged ent-trachylobane diterpenoids: (-)-Wallichanol A, (-)-Wallichanol B and (-)-Sanguinolane
|
Herein, we report the first, 13-step enantioselective total syntheses of the rearranged ent-trachylobane diterpenoids wallichanol A, sanguinolane, and wallichanol B, achieved via a novel intramolecular [2+2] cycloaddition to construct the unique pentacyclic framework containing an unprecedented tricyclo[3.3.1.02,7]nonane motif. Other key steps in the synthetic route include a highly challenging, selective alkene reduction via hydrogen atom transfer (HAT), leveraging the thermodynamic preference for a tertiary carbon-centered radical; a Robinson-type annulation to construct the tricyclic terpenoid building block; and applying aerobic oxidation at two distinct points to form α-hydroxy ketones, facilitating the enantioselective syntheses of these diterpenoids.
|
DATTATRAYA DETHE; Nitin Sharma; Sakshi Juyal
|
Organic Chemistry; Natural Products
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c2c92b6dde43c908fd6f65/original/concise-enantioselective-total-syntheses-of-rearranged-ent-trachylobane-diterpenoids-wallichanol-a-wallichanol-b-and-sanguinolane.pdf
|
62348c802c501004ff7f857b
|
10.26434/chemrxiv-2022-w73zr
|
Radical Deoxyfunctionalisation Strategies
|
Due to their abundance and readily available synthesis, alcohols provide ideal handles for the selective derivatisation of organic molecules. Radical chemistry offers versatile strategies for the conversion of Csp3–O bonds into a wide range of Csp3–C or Csp3–heteroatom bonds. In these reactions, alcohols are readily derivatised with an activator group which can undergo facile mesolysis to generate a primary, secondary, or tertiary open-shell species that can engage in further transformations. These strategies are particularly effective at overcoming steric limitations associated with nucleophilic substitution pathways. Despite their potential, the use of radical deoxyfunctionalisation reactions as a general strategy for the synthesis of useful and complex molecules remains underutilised. Herein, we highlight recent advancements in this exciting field using photocatalysis, transition metal catalysis or electrochemistry to initiate the radical processes.
|
Khadijah Anwar; Kay Merkens; Francisco José Aguilar Troyano; Adrián Gómez-Suárez
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62348c802c501004ff7f857b/original/radical-deoxyfunctionalisation-strategies.pdf
|
656667d0cf8b3c3cd759729d
|
10.26434/chemrxiv-2023-vsf2q
|
Red-Shifted Circularly Polarized Luminescence in Chiral Planar Benzothiadiazole Carbon Nanohoop
|
We present synthesis and investigation of two chiral macrocycles that integrate in their structure a pseudo-meta [2.2]paracyclophane with planar chirality and a highly fluorescent benzothiadiazole. Both compounds display remarkably red-shifted fluorescence with high quantum yields and large Stokes shifts. The two compounds differ in the extent of π-electron conjugation that allowed, for the first time, to systematically examine the role of exciton delocalization in the transmission of chiral information from the chiral [2.2]paracyclophane inducing circularly polarized luminescence. By a combination of steady-state spectroscopy and quantum chemical calculations, we constructed a unique structure–property relationship offering critical insights that will aid and abet the development of robust design guidelines for materials with circularly polarized luminescence of exceptional brightness.
|
Kovida Kovida; Juraj Malinčík; Carlos M. Cruz; Araceli G. Campaña; Tomáš Šolomek
|
Physical Chemistry; Organic Chemistry; Photochemistry (Org.); Physical Organic Chemistry; Photochemistry (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-11-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656667d0cf8b3c3cd759729d/original/red-shifted-circularly-polarized-luminescence-in-chiral-planar-benzothiadiazole-carbon-nanohoop.pdf
|
65e95d1c66c13817296aba21
|
10.26434/chemrxiv-2024-qzfqq-v2
|
How do spin-scaled double hybrids designed for excitation energies perform for noncovalent excited-state interactions? An investigation on aromatic excimer models
|
Time-dependent double hybrids with spin-component or spin-opposite scaling to their second-order perturbative correlation correction have demonstrated competitive robustness in the computation of electronic excitation energies. Some of the most robust are those recently published by our group [M. Casanova-Páez, L. Goerigk, J. Chem. Theory Comput. 2021, 20, 5165]. So far, the implementation of these functionals has not allowed correctly calculating their ground-state total energies. Herein, we define their correct spin-scaled ground-state energy expressions which enables us to test our methods on the noncovalent excited-state interaction energies of four aromatic excimers. A range of 22 double hybrids with and without spin scaling are compared to the reasonably accurate wavefunction reference from our previous work [A. C. Hancock, L. Goerigk, RSC Adv. 2023, 13, 35964]. The impact of spin scaling is highly dependent on the underlying functional expression, however, the smallest overall errors belong to spin-scaled functionals with range separation: SCS- and SOS-ωPBEPP86, and SCS-RSX-QIDH. We additionally determine parameters for DFT-D3(BJ)/D4 ground-state dispersion corrections of these functionals, which reduce errors in most cases. We highlight the necessity of dispersion corrections for even the most robust TD-DFT methods but also point out that ground-state based corrections are insufficient to completely capture dispersion effects for excited-state interaction energies.
|
Amy C. Hancock; Erica Giudici; Lars Goerigk
|
Theoretical and Computational Chemistry; Theory - Computational
|
CC BY 4.0
|
CHEMRXIV
|
2024-03-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e95d1c66c13817296aba21/original/how-do-spin-scaled-double-hybrids-designed-for-excitation-energies-perform-for-noncovalent-excited-state-interactions-an-investigation-on-aromatic-excimer-models.pdf
|
635f9e96cf6de920cb296691
|
10.26434/chemrxiv-2022-2s9v6
|
High sensitivity near-infrared imaging of fluorescent nanosensors
|
Biochemical processes are fast and occur on small length scales, which makes them difficult to
measure. Optical nanosensors based on single-wall carbon nanotubes (SWCNTs) are able to
capture such dynamics. They fluoresce in the near-infrared (NIR, 850 3 1700 nm) tissue
transparency window and the emission wavelength depends on their chirality. However, NIR
imaging requires specialized and cooled InGaAs cameras with low resolution because the
quantum yield of normal Si-based cameras rapidly decreases in the NIR. Here, we developed
an efficient one-step phase separation approach to isolate monochiral (6,4)-SWCNTs (880 nm
emission) from mixed SWCNT samples. It enabled us to image them in the NIR with highresolution
standard Si-based cameras (>50 x more pixels). (6,4)-SWCNTs modified with
(GT)10-ssDNA become highly sensitive for the important neurotransmitter dopamine. These
sensors are 1.7-fold brighter and 7.5 x more sensitive and allow fast imaging (< 50 ms). They
enable high-resolution imaging of dopamine release from cells. Thus, the assembly of
biosensors from (6,4)-SWCNTs combines the advantages of nanosensors working in the NIR
with the sensitivity of (Si-based) cameras and enables broad usage of these nanomaterials.
|
Julia Ackermann; Jan Stegemann; Tim Smola; Eline Reger; Sebastian Jung; Anne Schmitz; Svenja Herbertz; Luise Erpenbeck; Karsten Seidl; Sebastian Kruss
|
Analytical Chemistry; Biochemical Analysis; Imaging; Separation Science
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-11-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635f9e96cf6de920cb296691/original/high-sensitivity-near-infrared-imaging-of-fluorescent-nanosensors.pdf
|
6171a7b8ff3ba97f699b48b8
|
10.26434/chemrxiv-2021-rff1d
|
Construction of vicinal 4°/3°-carbons via reductive Cope rearrangement
|
Herein reported is a strategy for constructing vicinal 4°/3° carbons via reductive Cope rearrangement. Substrates have been designed which exhibit Cope rearrangement kinetic barriers in the range of ~23 kcal/mol with isothermic favorability (G ~0). These fluxional/shape-shifting molecules can be driven forward by chemoselective reduction to useful polyfunctionalized building blocks.
|
Kristin Sobie; Matthew Albritton; Yinuo Yang; Mariana Alves; Adrian Roitberg; Alexander Grenning
|
Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-10-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6171a7b8ff3ba97f699b48b8/original/construction-of-vicinal-4-3-carbons-via-reductive-cope-rearrangement.pdf
|
650f09f5ed7d0eccc313c0bf
|
10.26434/chemrxiv-2023-q29fs
|
Structure-Activity Relationship in NOD2 Agonistic Muramyl Dipeptides
|
Nucleotide-binding oligomerization domain 2 (NOD2) is a receptor of the innate immune system that is capable of perceiving bacterial and viral infections. Muramyl dipeptide (MDP, N-acetyl muramyl ¬L-alanyl-D-isoglutamine), identified as the minimal immunologically active component of bacterial cell wall peptidoglycan (PGN), is recognized by NOD2. In terms of biological activities, MDP demonstrated vaccine adjuvant activity and stimulated non-specific protection against bacterial, viral, and parasitic infections and tumors. However, MDP has certain drawbacks including pyrogenicity, rapid elimination, andlack of oral bioavailability. Several detailed structure-activity relationship (SAR) studies around MDP scaffolds are being carried out to identify better NOD2 ligands. The present review elaborates a comprehensive SAR summarizing structural aspects of MDP derivatives in relation to NOD2 agonistic activity.
|
Aarzoo Kamboj; Madhuri Patil; Nikolai Petrovsky; Deepak Salunke
|
Biological and Medicinal Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-09-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650f09f5ed7d0eccc313c0bf/original/structure-activity-relationship-in-nod2-agonistic-muramyl-dipeptides.pdf
|
62f308f2a01447ccf3b1e7a2
|
10.26434/chemrxiv-2022-b39bb
|
Terminal Repeats in Collagen Triple-Helices
|
Nearly 30% of human proteins have tandem repeating sequences. Structural understanding of the terminal repeats is well-established for many repeat proteins with the common α-helix and β-sheet foldings. By contrast, the sequence-structure interplay of the terminal repeats of the collagen triple-helix remains unexplored to date. As the most abundant human repeat protein and the most prevalent structural component of the extracellular matrix, collagen features a hallmark triple-helix formed by three supercoiled polypeptide chains of long repeating sequences of the Gly-X-Y triplets. Here, with CD characterization of 28 collagen-mimetic peptides (CMPs) featuring various terminal motifs, as well as DSC measurements, crystal structure analysis, and computational simulations, we show that CMPs only differing in terminal repeat may have distinct end structures and stabilities. We reveal that the cross-chain hydrogen bonding mediated by the terminal repeat is key to maintaining the triple-helix’s end structure, and that disruption of it with a single amide to carboxylate substitution can lead to destabilization as drastic as 19 °C. We further demonstrate that the terminal repeat also impacts how strong the CMP strands form hybrid triple-helices with unfolded natural collagen chains in tissue. Our findings provide a fresh spatial profile of hydrogen bonding within the CMP triple-helix, marking a critical guideline for future crystallographic or NMR studies of collagen, and algorithms for predicting triple-helix stability, as well as peptide-based collagen assemblies and materials. This study will also inspire new understandings of the sequence-structure relationship of many other complex structural proteins with repeating sequences.
|
Yingying Qi; Daoning Zhou; Julian Kessler; Rongmao Qiu; S. Michael Yu; Gang Li; Zhao Qin; Yang Li
|
Biological and Medicinal Chemistry; Polymer Science; Biopolymers; Chemical Biology; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-08-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f308f2a01447ccf3b1e7a2/original/terminal-repeats-in-collagen-triple-helices.pdf
|
667d85e15101a2ffa8b8ca77
|
10.26434/chemrxiv-2024-3n866
|
A Bulk Phase Transformation Drives Ammonia Synthesis on Barium Hydride
|
It is believed by some that the key to a successful industrial heterogeneous catalyst is a complex dynamical behavior, in which the catalyst is more than just a provider of catalytic sites. With the help of machine learning-driven molecular dynamics simulations, we show that this is indeed the case for the thermally activated synthesis of ammonia catalysed by BaH2. This system has recently been experimentally investigated and shown to act as a highly efficient catalyst for ammonia synthesis, if and only if it is alternately exposed first to N2 and then to H2 in a chemical looping process. Our simulations reveal that when first exposed to N2, BaH2 undergoes a profound change and it is transformed into a superionic mixed compound, BaH(2-2x)(NH)x, characterized by a high mobility of both hydrides and imides. This transformation is not limited to the surface but involves the entire catalyst. When this compound is exposed to H2 in the second step of the looping process, the ammonia is readily formed and released, a process greatly facilitated by the high ionic mobility. Once all the nitrogen hydrides are hydrogenated, the system reverts to its initial state and it is ready for the next looping process.
|
Axel Tosello Gardini; Umberto Raucci; Michele Parrinello
|
Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Machine Learning; Heterogeneous Catalysis; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667d85e15101a2ffa8b8ca77/original/a-bulk-phase-transformation-drives-ammonia-synthesis-on-barium-hydride.pdf
|
661f832291aefa6ce1bbc389
|
10.26434/chemrxiv-2024-qw671
|
Spin-polarized white organic light-emitting diodes based on chirality-induced spin selectivity effect
|
Chirality-induced spin selectivity (CISS) effect refers to charge carriers become spin-polarized when traversing through chiral materials, but this unique phenomenon has never been reported for organic light-emitting diodes (OLEDs). Herein, robust chiral near-ultraviolet and deep-blue materials with wide energy gaps are explored and demonstrated to possess CISS effect. By aligning a chiral deep-blue layer next to an achiral green layer in OLEDs, spin-polarized charge carriers are generated from the chiral layer and get recombined to form spin-polarized excitons in the adjacent achiral green layer, furnishing green circularly polarized electroluminescence (CP-EL). Furthermore, by incorporating multiple achiral sky-blue, green and red layers with chiral near-ultraviolet or deep-blue layers, complex three-emitting-layer or four-emitting-layer spin-polarized white OLEDs are realized, providing distinct CP-EL signals from different achiral emitting layers simultaneously and outstanding EL performance with excellent external quantum efficiencies reaching 26.6% and high color rendering indexes of 94, much superior to the performances of the reported white OLEDs with circularly polarized light so far. This work introduces CISS effect into OLEDs for achieving CP-EL for the first time, and virtually presents a novel and feasible approach towards high-performance circularly polarized white OLEDs with a single organic chiral layer.
|
Letian Xu; Nuoling Qiu; Xiaoluo Peng; Kun Zhou; Jiajie Zeng; Hao Liu; Ben Zhong Tang; Zujin Zhao
|
Physical Chemistry; Materials Science; Multilayers; Optical Materials; Optics
|
CC BY 4.0
|
CHEMRXIV
|
2024-04-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661f832291aefa6ce1bbc389/original/spin-polarized-white-organic-light-emitting-diodes-based-on-chirality-induced-spin-selectivity-effect.pdf
|
60c753e1702a9b2a2d18c42f
|
10.26434/chemrxiv.13567481.v1
|
Towards Large-Scale Steady-State Enhanced Nuclear Magnetization with In Situ Detection
|
<div>Signal Amplification By Reversible Exchange (SABRE) boosts NMR signals of various nuclei enabling new applications spanning from magnetic resonance imaging to analytical chemistry and fundamental physics. SABRE is especially well positioned for continuous generation of enhanced magnetization on a large scale, however, several challenges need to be addressed for accomplishing this goal. Specifically, SABRE requires (i) a specialized catalyst capable of reversible H<sub>2</sub> activation and (ii) physical transfer of the sample from the point of magnetization generation to the point of detection (e.g., a high-field or a benchtop NMR spectrometer). Moreover, (iii) continuous parahydrogen bubbling accelerates solvent (e.g., methanol) evaporation, thereby limiting the experimental window to tens of minutes per sample.</div><div>In this work, we demonstrate a strategy to rapidly generate the best-to-date precatalyst (a compound that is chemically modified in the course of the reaction to yield the catalyst) for SABRE, [Ir(IMes)(COD)Cl] (IMes = 1,3-bis-(2,4,6-trimethylphenyl)-imidazol-2-ylidene, COD = cyclooctadiene) via a highly accessible synthesis. Second, we measure hyperpolarized samples using a home-built zero-field NMR spectrometer and study the field dependence of hyperpolarization directly in the detection apparatus, eliminating the need to physically move the sample during the experiment. Finally, we prolong the measurement time and reduce evaporation by presaturating parahydrogen with the solvent vapor before bubbling into the sample. These advancements extend opportunities for exploring SABRE hyperpolarization by researchers from various fields and pave the way to producing large quantities of hyperpolarized material for long-lasting detection of SABRE-derived nuclear magnetization.</div>
|
John Blanchard; Barbara Ripka; Benjamin A. Suslick; Dario Gelevski; Teng Wu; Kerstin Münnemann; Danila Barskiy; Dmitry Budker
|
Physical Organic Chemistry; Spectroscopy (Anal. Chem.); Magnetism; Organometallic Compounds; Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.); Process Control; Homogeneous Catalysis; Catalysis; Coordination Chemistry (Organomet.); Spectroscopy (Organomet.); Transition Metal Complexes (Organomet.); Chemical Kinetics; Optics; Physical and Chemical Processes; Quantum Mechanics; Solution Chemistry; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-01-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753e1702a9b2a2d18c42f/original/towards-large-scale-steady-state-enhanced-nuclear-magnetization-with-in-situ-detection.pdf
|
65309c8787198ede07969cbb
|
10.26434/chemrxiv-2023-mqzn0
|
A Scalable Solution to Constant Potential Flow Electrochemistry
|
The burgeoning interest in new electrochemical methods holds promise to provide a plethora of strategic disconnections for pharmaceutical compounds, which are safer, less wasteful, and more streamlined than traditional chemical strategies. The use of organic electrochemistry in the commercial production of pharmaceuticals is exceedingly rare due to the lack of a modular infrastructure. Herein, we describe the use of cascading continuous-stirred tank reactors (CSTRs) with individual cell potential control applied over reaction ‘stages’ which demonstrate a balance between high selectivity and throughput necessary for electrochemistry to be a viable strategy in the pharmaceutical space. Using the high degree of control of cell potential afforded by this reactor design, a 1 kg demonstration was achieved in 9 hours with high selectivity and yield (2.6 kg/day throughput).
|
Jeremy Griffin; Kaid Harper; Simon Velasquez; Westin Morrill; William Thornton; David Sutherland; Bradley Greiner
|
Organic Chemistry; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Process Chemistry; Pharmaceutical Industry
|
CC BY 4.0
|
CHEMRXIV
|
2023-10-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65309c8787198ede07969cbb/original/a-scalable-solution-to-constant-potential-flow-electrochemistry.pdf
|
66f432cecec5d6c1422c999e
|
10.26434/chemrxiv-2024-jncx1
|
A Dual Catalytic Approach for the Halogen-Bonding-Mediated Reductive Cleavage of α-Bromodifluoroesters and Amides
|
While charge-transfer complexes involving halogen-bonding interactions have emerged as an alternative strategy for the photogeneration of carbon radicals, examples using (fluoro)alkyl bromides are limited. This report describes a dual catalytic approach for radical generation from α-bromodifluoroesters and amides under visible light irradiation. Mechanistic studies suggest that the reaction proceeds through in-situ bromide displacement using a catalytic iodide salt, generating a C–I bond that can be engaged by our halogen-bonding photocatalysis platform.
|
Tarannum Tasnim; Negin Shafiei; Katelyn Laminack; Bailey Robertson; Nash Nevels; Christopher Fennell; Spencer Pitre
|
Organic Chemistry; Catalysis; Photochemistry (Org.); Homogeneous Catalysis; Photocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-09-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f432cecec5d6c1422c999e/original/a-dual-catalytic-approach-for-the-halogen-bonding-mediated-reductive-cleavage-of-bromodifluoroesters-and-amides.pdf
|
638650400146efdac70a7c92
|
10.26434/chemrxiv-2022-3x6jf
|
Mapping nanocrystalline disorder within an amorphous metal–organic framework
|
Intentionally disordered metal–organic frameworks (MOFs) display rich functional behaviour. However, the characterisation of their atomic structures remains incredibly challenging. X-ray pair distribution function techniques have been pivotal in determining their average local structure but are largely insensitive to spatial variations in the structure. Fe-BTC is a nanocomposite MOF, known for its catalytic properties, comprising crystalline nanoparticles and an amorphous matrix. Here, we use scanning electron diffraction to first map the crystalline and amorphous components to evaluate domain size and then to carry out electron pair distribution function analysis to probe the spatially separated atomic structure of the amorphous matrix. Further Bragg scattering analysis reveals systematic orientational disorder within Fe-BTC’s nanocrystallites, showing over 10° of continuous lattice rotation across single particles. Finally, we identify candidate unit cells for the crystalline component. These independent structural analyses quantify disorder in Fe-BTC at the critical length scale for engineering composite MOF materials.
|
Adam Sapnik; Chao Sun; Joonatan Laulainen; Duncan Johnstone; Rik Brydson; Timothy Johnson; Paul Midgley; Thomas Bennett; Sean Collins
|
Materials Science; Nanoscience; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-11-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638650400146efdac70a7c92/original/mapping-nanocrystalline-disorder-within-an-amorphous-metal-organic-framework.pdf
|
656f04b129a13c4d47b1a4b2
|
10.26434/chemrxiv-2023-rv9hs
|
Identification of Heavily Glycated Proteoforms by Hydrophilic-Interaction Liquid Chromatography and Native Size-Exclusion Chromatography – High-Resolution Mass Spectrometry
|
The non-enzymatic glycation of proteins and their advanced glycation end products (AGEs) are associated with protein transformations such as in the development of diseases and biopharmaceutical storage. The high heterogeneity that glycated proteins carry makes their detection and identification challenging. In this study, we investigated two novel LC-HRMS methods to study glycated reference proteins at the intact protein level: low-flow hydrophilic-interaction liquid chromatography (HILIC) and native size-exclusion chromatography (SEC). Three model proteins (RNase-A, hemoglobin, and NISTmab) were exposed to conditions that favored extensive glycation and the formation of AGEs. After glycation, complicated MS spectra were observed, along with a sharply reduced signal response, possibly due to protein denaturation and the formation of aggregates. When using HILIC-MS,
the glycated forms of the proteins could be resolved based on the number of reducing monosaccharides. Moreover, some positional glycated isomers were separated. The SEC-MS method under non-denaturing conditions provided insights into glycated aggregates but offered only a limited separation of glycated species based on molar mass. Overall, more than 25 different types of species were observed in both methods, differing in molar mass by 14 to 162 Da. 19 of these species have not been previously reported. By tracing the progress of glycation, the dynamic changes of the specific AGEs could be monitored over time.
|
Ziran Zhai; Peter J. Schoenmakers; Andrea F.G. Gargano
|
Analytical Chemistry; Biochemical Analysis; Mass Spectrometry; Separation Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656f04b129a13c4d47b1a4b2/original/identification-of-heavily-glycated-proteoforms-by-hydrophilic-interaction-liquid-chromatography-and-native-size-exclusion-chromatography-high-resolution-mass-spectrometry.pdf
|
646e133ae64f843f41b2ac35
|
10.26434/chemrxiv-2022-rn77b-v3
|
Imaging and quantifying the chemical communication between single particles in metal alloy
|
The communication within particle agglomerates in industrial alloys can have significant impact on the macroscopic reactivity, putting a high demand on the adaptation of wide-field methodologies to clarify this phenomenon. In this work, we report the application of correlated optical microscopies probing operando both local pH and local surface chemical transformation correlated with identical location scanning electron microscopy to quantify in-situ the structure-reactivity of particle agglomerates of foreign elements in Al alloy. The optical operando analyses allow (i) to reveal and quantify the local production of OH- from proton and oxygen reduction at individual Si- or Fe-rich microparticles and (ii) to quantify (and model) the chemical communication between these active sites, within a few µm range, on the local chemical transformation of the material. Wide-field image analysis highlights the statistical importance of the chemical communication that may introduce a new conceptual framework for the understanding the mechanisms in related fields of charge transfer, electrocatalysis and corrosion.
|
Louis Godeffroy; Aleksei Makogon; Sarra Derouich; Frédéric Kanoufi; Viacheslav SHKIRSKIY
|
Physical Chemistry; Analytical Chemistry; Nanoscience; Imaging; Electrochemistry - Mechanisms, Theory & Study; Interfaces
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646e133ae64f843f41b2ac35/original/imaging-and-quantifying-the-chemical-communication-between-single-particles-in-metal-alloy.pdf
|
60c742f0bdbb896b5ea385a3
|
10.26434/chemrxiv.8859422.v1
|
Efficient Copper Catalyzed Multi-component Synthesis of N-acyl amidines via Acyl Nitrenes
|
Direct synthetic routes to amidines are desired, as they are widely present in many biologically active compounds and organometallic complexes. N-Acyl amidines in particular can be used as a starting material for the synthesis of heterocycles and have several other applications. Here, we describe a fast and practical copper catalyzed 3-component reaction of aryl acetylenes, amines and easily accessible 1,4,2-dioxazol-5-ones to N-acyl amidines, generating CO<sub>2</sub> as the only by-product. Transformation of the dioxazolones on the Cu-catalyst generates acyl nitrenes that rapidly insert into the copper acetylide Cu-C bond rather than undergoing an undesired Curtius rearrangement. For non-aromatic dioxazolones, [Cu(OAc)(Xantphos)] is a superior catalyst for this transformation, leading to full substrate conversion within 10 minutes. For the direct synthesis of N-benzoyl amidine derivatives from aromatic dioxazolones, [Cu(OAc)(Xantphos)] proved to be inactive, but moderate to good yields were obtained when using simple CuI as the catalyst. Mechanistic studies revealed the aerobic instability of one of the intermediates at low catalyst loadings, but the reaction could still be performed in air for most substrates when using catalyst loadings of 5 mol%. The herein reported procedure does not only provide a new, practical and direct route to N-acyl amidines, but also represents a new type of<br />C-N bond formation.
|
K.M. van Vliet; Lara H. Polak; Maxime A. Siegler; J.I. van der Vlugt; Célia Fonseca Guerra; Bas de Bruin
|
Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-07-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742f0bdbb896b5ea385a3/original/efficient-copper-catalyzed-multi-component-synthesis-of-n-acyl-amidines-via-acyl-nitrenes.pdf
|
678312c1fa469535b99f4438
|
10.26434/chemrxiv-2025-zcj87
|
Nat-UV DB: A Natural Products Database Underlying of Veracruz-México
|
Natural products databases are well-structured data sources that offer new molecular development opportunities in drug discovery, agrochemistry, food, cosmetics, and several other research disciplines or chemical industries. The crescent world's interest in the development of these databases is related to the exploration of chemical diversity in geographical regions with rich biodiversity. In this work, we introduce and discuss Nat-UV DB, the first natural products database from a coastal zone of Mexico. We discuss its construction, curation, and chemoinformatic characterization of their content, and chemical space coverage compared with other compound databases, like approved drugs, and other Mexican (BIOFACQUIM and UNIIQUIM databases) and the Latin American natural products database (LaNAPDB). Nat-UV DB comprises 227 compounds that contain 112 scaffolds, of which 52 are not present in previous natural product databases. The compounds present in Nat-UV DB have a similar size, flexibility, and polarity to previously reported natural products and approved drug datasets. Finally, the results contained in this work showed that Nat-UV DB compounds have a higher structural and scaffold diversity than the approved drugs, but they have low structural and scaffold diversity in contrast with other natural products in the reference datasets.
|
Edgar López López; Ana Margarita Hernández-Segura; Carlos Lara-Cuellar; Carolina Barrientos-Salcedo; Carlos M. Cerda-García-Rojas; José L. Medina-Franco
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Organic Compounds and Functional Groups; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2025-01-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678312c1fa469535b99f4438/original/nat-uv-db-a-natural-products-database-underlying-of-veracruz-mexico.pdf
|
60c74da7bb8c1a2da83db621
|
10.26434/chemrxiv.12645356.v1
|
A Natural Orbital Branching Scheme for Time Dependent Density Functional Theory Nonadiabatic Simulations
|
Real time time dependent density functional theory (rt-TDDFT) has now been used to study a wide range of problems, from optical excitation, to charge transfer, to ion collision, to ultrafast phase transition. However, conventional rt-TDDFT Ehrenfest dynamics for nuclear movement lacks a few critical features to describe many problems: the detail balance between state transition, decoherence for the wave function evolution, and stochastic branching of the nuclear trajectory. There are many-body formalisms to describe such nonadiabatic molecular dynamics, especially the ones based on mixed quantum/classical simulations, like the surface hopping and wave function collapsing schemes. However, there are still challenges to implement such many-body formalisms to the rt-TDDFT simulations, especially for large systems where the excited state electronic structure configuration space is large. Here we introduce two new algorithm for nonadiabatic rt-TDDFT simulations: the first is a Boltzmann factor algorithm which introduces decoherence and detailed balance in the carrier dynamics, but uses mean field theory for nuclear trajectory. The second is a natural orbital branching (NOB) formalism, which use time dependent density matrix for electron evolution, and natural orbital to collapse the wave function upon. It provides decoherence, detailed balance and trajectory branching properties. We have tested these methods for a molecule radiolysis decay problem. We found these methods can be used to study such radiolysis problem in which the molecule is broken into many fragments following complex electronic structure transition paths. The computational time of NOB is similar to the original plain rt-TDDFT simulations
|
Lin-Wang Wang
|
Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74da7bb8c1a2da83db621/original/a-natural-orbital-branching-scheme-for-time-dependent-density-functional-theory-nonadiabatic-simulations.pdf
|
60c758149abda24f8bf8e83c
|
10.26434/chemrxiv.14498208.v1
|
Remodelling a Shp: Transmetallation in a Rare-Earth Cluster-Based Metal–Organic Framework
|
<div>
<p>Post-synthetic
modification (PSM) of metal–organic frameworks (MOFs) is an important strategy
for accessing MOF analogues that cannot be easily synthesized <i>de novo</i>.
In this work, the rare-earth (RE) cluster-based MOF, Y-CU-10, with <b>shp</b>
topology was modified through transmetallation using a series of RE ions,
including: La(III), Nd(III), Eu(III), Tb(III), Er(III), Tm(III), and Yb(III).
In all cases, metal-exchange higher than 70 % was observed, with reproducible
results. All transmetallated materials were fully characterized and compared to
the parent MOF, Y-CU-10, in regards to crystallinity, surface area, and
morphology. Additionally, single-crystal X-ray diffraction (SCXRD) measurements
were performed to provide further evidence of transmetallation occurring in the
nonanuclear cluster nodes of the MOF. </p>
</div>
|
Hudson de Aguiar Bicalho; P. Rafael Donnarumma; Victor Quezada-Novoa; Hatem M. Titi; Ashlee J Howarth
|
Coordination Chemistry (Inorg.); Lanthanides and Actinides; Solid State Chemistry; Supramolecular Chemistry (Inorg.); Crystallography – Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758149abda24f8bf8e83c/original/remodelling-a-shp-transmetallation-in-a-rare-earth-cluster-based-metal-organic-framework.pdf
|
66a26aef01103d79c5aaa7ea
|
10.26434/chemrxiv-2024-c1xqv
|
Multi-objective reaction optimization under uncertainties using expected quantile improvement
|
Multi-objective Bayesian optimization (MOBO) has shown to be a promising tool for reaction development. However, noise is usually unavoidable during experiments and makes it challenging to find reliable solutions. In this study, we focus on finding a set of optimal reaction conditions using multi-objective Euclidian expected quantile improvement (MO-E-EQI) under noisy settings. First, the performance of MO-E-EQI is evaluated by comparing with some recent MOBO algorithms \textit{in silico} with linear and log-linear heteroscedastic noise structures and different magnitudes. It is noticed that high noise can degrade the performance of MOBO algorithms. MO-E-EQI shows robust performance in terms of hypervolume-based metric, coverage metric and number of solutions on the Pareto front. Finally, MO-E-EQI is implemented in a real case to optimize an esterification reaction to achieve maximum space-time-yield and minimal E-factor. The algorithm identifies a clear trade-off between the two objectives.
|
Jiyizhe Zhang; Daria Semochkina; Naoto Sugisawa; David Woods; Alexei Lapkin
|
Chemical Engineering and Industrial Chemistry; Reaction Engineering
|
CC BY 4.0
|
CHEMRXIV
|
2024-07-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a26aef01103d79c5aaa7ea/original/multi-objective-reaction-optimization-under-uncertainties-using-expected-quantile-improvement.pdf
|
60c750bc337d6c2706e283cb
|
10.26434/chemrxiv.13077395.v1
|
Virtual Screening of Leishmanial Pyridoxal Kinase Enzyme Inhibitors by Repurposed Anti-Trypanosomal Libraries Reveals Two Core Scaffolds
|
Leishmania is an intracellular protozoal infection, and it is classified as a neglected
disease by the World Health Organization (WHO). Annually more than 2 million newly
diagnosed cases were treated with highly toxic drugs. Leishmanial pyridoxal kinase
enzyme (LPDxK) is an essential and druggable target. DNDI1103666 is the most
promising lead as a potential inhibitor for LPDxK
|
Sanad Alfadhel
|
Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-06-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750bc337d6c2706e283cb/original/virtual-screening-of-leishmanial-pyridoxal-kinase-enzyme-inhibitors-by-repurposed-anti-trypanosomal-libraries-reveals-two-core-scaffolds.pdf
|
6424647b91074bccd07d1aa5
|
10.26434/chemrxiv-2023-fg64s
|
Prediction of Toluene/Water Partition Coefficient in the SAMPL9 Blind Challenge: Assessment of Machine Learning and IEF-PCM/MST Continuum Solvation Models
|
In recent years the use of partition systems other than the widely used biphasic n-octanol/water has received increased attention to gain insight into the molecular features that dictate the lipophilicity of compounds. Thus, the difference between n-octanol/water and toluene/water partition coefficients has proven to be a valuable descriptor to study the propensity of molecules to form intramolecular hydrogen bonds and exhibit chameleon-like properties that modulate solubility and permeability. In this context, this study reports the experimental toluene/water partition coefficients (logPtol/w) for a series of 16 drugs that were selected as an external test set in the framework of the Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL) blind challenge. This external set has been used by the computational community to calibrate their methods in the current edition (SAMPL9) of this contest. Furthermore, the study also investigates the performance of two computational strategies for the prediction of logPtol/w. The first relies on the development of two machine learning (ML) models, which are built up by combining the selection of 11 molecular descriptors in conjunction with either multiple linear regression (MLR) and random forest regression (RFR) models to target a dataset of 252 experimental logPtol/w values. The second consists of the parametrization of the IEF-PCM/MST continuum solvation model from B3LYP/6-31G(d) calculations to predict the solvation free energies of 163 compounds in toluene and benzene. The performance of the ML and IEF-PCM/MST models has been calibrated against external test sets, including the compounds that define the SAMPL9 logPtol/w challenge. The results are used to discuss the merits and weaknesses of the two computational approaches.
|
William J. Zamora Ramírez; Antonio Viayna; Silvana Pinheiro; Carles Curutchet; Laia Bisbal; Rebeca Ruiz; Clara Ràfols; F. Javier Luque
|
Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6424647b91074bccd07d1aa5/original/prediction-of-toluene-water-partition-coefficient-in-the-sampl9-blind-challenge-assessment-of-machine-learning-and-ief-pcm-mst-continuum-solvation-models.pdf
|
66b49d96c9c6a5c07a73b9cc
|
10.26434/chemrxiv-2024-qlv3n
|
Heterologous Expression of a Cryptic BGC from Bilophila sp. Provides Access to a Novel Family of Antibacterial Thiazoles
|
Human health is greatly influenced by the gut microbiota and microbiota imbalance can lead to the development of diseases. It is widely acknowledged that the interaction of bacteria within competitive ecosystems is influenced by their specialized metabolites, which act, e.g., as antibacterials or siderophores. However, our understanding of the occurrence and impact of such natural products in the human gut microbiome remains very limited. As arylthiazole siderophores are an emerging family of growth-promoting molecules in pathogenic bacteria, we analyzed a metagenomic dataset from the human microbiome and thereby identified the bil-BGC, which originates from an uncultured Bilophila strain. Through gene synthesis and BGC assembly, heterologous expression and mutasynthetic experiments, we discovered bilothiazoles A-F, new arylthiazole natural products. While established activities of related molecules indicate their involvement in metal-binding and -uptake, which could promote the growth of pathogenic strains, we also found antibiotic activity for some bilothiazoles. This is supported by biosensor-experiments, where bilothiazoles C and E show PrecA-suppressing activity, while bilothiazole F induces PblaZ, a biosensor characteristic for -lactam antibiotics. These findings serve as a starting point for investigating the role of bilothiazoles in the pathogenicity of Bilophila species in the gut.
|
Maximilian Hohmann; Denis Iliasov; Martin Larralde; Widya Johannes; Klaus-Peter Janßen; Georg Zeller; Thorsten Mascher; Tobias Gulder
|
Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Natural Products; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b49d96c9c6a5c07a73b9cc/original/heterologous-expression-of-a-cryptic-bgc-from-bilophila-sp-provides-access-to-a-novel-family-of-antibacterial-thiazoles.pdf
|
65bd6c26e9ebbb4db98b47bf
|
10.26434/chemrxiv-2024-7hrtg
|
Diastereoselective β-Hydroxy Vinylsulfone Isomerizations
|
Vinylic phenylsulfones containing a β-hydroxyl stereocenter undergo a diastereoselective isomerization to the corresponding allylic isomer upon treatment with 1,8-diazabicyclo(5.4.0)undec-7-ene (DBU). Diastereoselectivity of this reaction increases with increasing size of the group attached to the carbinol carbon (up to >20:1 d.r. with a tert-butyl). Isolated yields of the isomerized allylic 1,2-hydroxy phenylsulfone products were comparable among the different vinylsulfones tested (59-66%). The major competing pathway was a C-C bond cleavage process, proposed to occur after the initial isomerization event. The sense of diastereoselection was consistent among all substrates investigated, in favor of the erythro-isomer based on NMR analysis.
|
Gregory O'Neil; Trevor Clark; D. Michael Carnahan; Henry Crockett; Calvin Wallace; Adam Jones
|
Organic Chemistry; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-02-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bd6c26e9ebbb4db98b47bf/original/diastereoselective-hydroxy-vinylsulfone-isomerizations.pdf
|
64adba939ea64cc167d8b481
|
10.26434/chemrxiv-2023-cjjs6
|
Cooperativity and Frustration Effects (or Lack Thereof) in Polarizable and Non-Polarizable Force Fields
|
Understanding cooperativity and frustration is crucial for studying biological processes, such as molecular recognition and protein aggregation. Force fields have been extensively utilized to explore cooperativity in the formation of protein secondary structures and self-assembled systems. Multiple studies have demonstrated that polarizable force fields provide more accurate descriptions of this phenomenon compared to fixed-charge pairwise non-polarizable force fields, thanks to the incorporation of polarization effects. In this study, we assess the performance of the AMOEBA polarizable force field and the AMBER and OPLS non-polarizable pairwise force fields in capturing positive and negative cooperativity recently explored in neutral and charged molecular clusters using Density Functional Theory. Our findings show that polarizable and non-polarizable force fields qualitatively reproduce the relative cooperativity observed in electron structure calculations. However, AMBER and OPLS fail in describing absolute cooperativity. In contrast, AMOEBA accounts for absolute cooperativity by considering interactions beyond pairwise interactions. According to the energy decomposition analysis, it is observed that the electrostatic interactions calculated with the AMBER and OPLS force fields seems to play an important and counter-intuitive role in reproducing the adiabatic interaction energies calculated with Density Functional Theory. However, it is important to note that these force fields, due to their nature, do not explicitely incorporate many-body effects, which limits their ability to accurately describe cooperativity. On the other hand, frustration in polarizable and non-polarizable force fields is caused by changes in bond stretching and angle bending terms of the building blocks when they are forming a complex.
|
Jorge Nochebuena; Jean-Philip Piquemal; Shubin Liu; G. Andrés Cisneros
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-07-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64adba939ea64cc167d8b481/original/cooperativity-and-frustration-effects-or-lack-thereof-in-polarizable-and-non-polarizable-force-fields.pdf
|
60c757cfbb8c1a2fdb3dc8f6
|
10.26434/chemrxiv.14465379.v1
|
Pressure-Induced Jahn-Teller Switch in the Homoleptic Hybrid Perovskite [(CH3)2NH2]Cu(HCOO)3: Orbital Reordering by Unconventional Degrees of Freedom
|
<p><b>Through in-situ, high-pressure x-ray diffraction experiments
we have shown that the homoleptic perovskite-like coordination polymer [(CH<sub>3</sub>)<sub>2</sub>NH<sub>2</sub>]Cu(HCOO)<sub>3</sub>
undergoes a pressure-induced orbital reordering phase transition above 5.20
GPa. This transition is distinct from previously reported Jahn-Teller switching
in coordination polymers, which required at least two different ligands that
crystallize in a reverse spectrochemical series. We show that the orbital
reordering phase transition in [(CH<sub>3</sub>)<sub>2</sub>NH<sub>2</sub>]Cu(HCOO)<sub>3</sub>
is instead primarily driven by unconventional octahedral tilts and shifts in
the framework, and/or a reconfiguration of A-site cation ordering. These
structural instabilities are unique to the coordination polymer perovskites,
and may form the basis for undiscovered orbital reorientation phenomena</b><b> in this
broad family of materials.</b></p>
|
Rebecca Scatena; Michał Andrzejewski; Roger Johnson; Piero Macchi
|
Hybrid Organic-Inorganic Materials; Magnetic Materials; Bonding; Coordination Chemistry (Inorg.); Magnetism; Transition Metal Complexes (Inorg.); Structure; Crystallography; Crystallography – Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757cfbb8c1a2fdb3dc8f6/original/pressure-induced-jahn-teller-switch-in-the-homoleptic-hybrid-perovskite-ch3-2nh2-cu-hcoo-3-orbital-reordering-by-unconventional-degrees-of-freedom.pdf
|
60c73f659abda24b66f8bad0
|
10.26434/chemrxiv.7378445.v1
|
Theoretical Study of the Microhydration of 1-Chloro and 2-Chloro Ethanol as a Clue for Their Relative Propensity Toward Dehalogenation
|
<p>This work reports a computational
analysis of hydrogen bonded clusters of mono-, di-, tri- and tetra hydrates of
the chlorohydrins CH<sub>3</sub>CHClOH (1ClEtOH) and CH<sub>2</sub>ClCH<sub>2</sub>OH
(2ClEtOH). The goal of the study is to assess the role of the water solvent into
the facilitation of the initial step for dehalogenation of these compounds, a
process of interest in several contexts. Molecular orbital methods (MP2),
density functional methods (B3LYP, M06 and wB97X-D)
and composite model chemistries (CBS-QB3, G4) were employed to investigate the
structure, electronic distribution and hydrogen-bonded structure of 7 monohydrates,
6 dihydrates, 5 trihydrates and 5 tetrahydrates of both species. Standard
reaction enthalpy and standard Gibbs free reaction energy were computed for all aggregates with
respect to <b><i>n</i></b> independent water molecules and with respect to the dimer,
trimer and tetramer of water, respectively, in order to evaluate stability and
hydrogen bonding network. The influence of the water chains on the length and
vibrational frequencies, especially of the C-Cl and O-H bonds, was evaluated.</p>
|
George Petsis; Zoi Salta; Agnie M. Kosmas; Oscar Ventura
|
Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-11-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f659abda24b66f8bad0/original/theoretical-study-of-the-microhydration-of-1-chloro-and-2-chloro-ethanol-as-a-clue-for-their-relative-propensity-toward-dehalogenation.pdf
|
62c451e8e60d986820f860d5
|
10.26434/chemrxiv-2022-4w95p
|
Exploring the effects of processing methods on telmisartan-phospholipid complex: A comparative study
|
Drug-phospholipid complexes have emerged as potential drug delivery systems for poorly soluble drugs. The purpose of this study was to investigate the effect of processing methods on the physicochemical and biopharmaceutical performance of the telmisartan-phospholipid complex. In this study, telmisartan-phospholipid complexes were prepared using solvent evaporation (TELPLC-SE), freeze-drying (TELPLC-FD), and spray drying (TELPLC-SD) methods and subjected to a comparative investigation of solid-state characteristics (FTIR, DSC, and PXRD analysis), solubility, dissolution profiles, particle size, zeta potential, particle morphology (SEM analysis) and pharmacokinetic studies. The solvent evaporation method was found to be associated with the most significant FTIR peak shift/shape change, highest solubility advantage (TELPLC-SE 8.98 ± 1.08 µg/mL, TELPLC-SD 6.98 ± 1.38 µg/mL, TELPLC-FD 7.95 ± 1.02 µg/mL), maximum in-vitro drug release (TELPLC-SE 87.81 ± 4.64%, TELPLC-FD 84.71 ± 4.84 %, TELPLC-SD 79.93 ± 3.54 %) and highest peak plasma concentration (Cmax) of telmisartan (TELPLC-SE Cmax: 2.40 ± 1.34 µg/mL, TELPLC-SD Cmax: 2.20 ± 1.1 µg/mL, TELPLC-FD Cmax: 1.4 ± 1.3 µg/mL) whereas freeze-drying method was linked to the highest depression in melting point endotherm and spray drying method was associated to the maximum reduction in XRD peak intensity, the largest particle size and the lowest zeta potential. This study definitively answers the questions regarding the effect of processing methods on the telmisartan-phospholipid complex. Further studies are needed to explore the effect of process and formulation parameters.
|
Mahendra Singh; Charan Singh; Sarasija Suresh; Sabyasachi Roy; Uttam Chand Banerjee
|
Materials Science; Nanoscience; Biodegradable Materials; Nanofabrication; Nanostructured Materials - Nanoscience; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-07-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c451e8e60d986820f860d5/original/exploring-the-effects-of-processing-methods-on-telmisartan-phospholipid-complex-a-comparative-study.pdf
|
60c73f14bdbb89da3da37ef0
|
10.26434/chemrxiv.7205693.v1
|
Introducing DDEC6 Atomic Population Analysis: Part 5. New Method to Compute Polarizabilities and Dispersion Coefficients
|
Polarizabilities and London dispersion forces
are important to many chemical processes. Leading terms in these forces are
often modeled using polarizabilities and C<sub>n</sub> (n=6, 8, 9, 10 …)
dispersion coefficients. Force fields for classical atomistic simulations can
be constructed using atom-in-material dispersion coefficients and
polarizabilities. This article addresses the key question of how to efficiently
assign these parameters to constituent atoms in a material so that properties
of the whole material are better reproduced. We develop a new set of scaling
laws and computational algorithms (called MCLF) to do this in an accurate and
computationally efficient manner across diverse material types. We introduce a
conduction limit upper bound and m-scaling to describe the different behaviors
of surface and buried atoms. We validate MCLF by comparing results to
high-level benchmarks for isolated neutral and charged atoms, diverse diatomic
molecules, various polyatomic molecules (e.g., polyacenes, fullerenes, and
small organic and inorganic molecules), and dense solids (including metallic,
covalent, and ionic). MCLF provides the non-directionally screened
polarizabilities required to construct force fields, the directionally-screened
static polarizability tensor components and eigenvalues, and environmentally
screened C<sub>6</sub> coefficients. Overall, MCLF has improved accuracy and
lower computational cost than the TS-SCS method. For TS-SCS, we compared charge
partitioning methods and show DDEC6 partitioning yields more accurate results
than Hirshfeld partitioning. MCLF also gives approximations for C<sub>8</sub>,
C<sub>9</sub>, and C<sub>10</sub> dispersion coefficients and Quantum Drude
Oscillator parameters. For sufficiently large systems, our method’s required
computational time and memory scale linearly with increasing system size. This
is a huge improvement over the cubic computational time of direct matrix
inversion. As demonstrations, we study an ice crystal containing >250,000
atoms in the unit cell and the HIV reverse transcriptase enzyme complexed with
an inhibiter molecule. This method should find widespread applications to
parameterize classical force fields and DFT+dispersion methods.
|
Thomas Manz; Taoyi Chen; Daniel J. Cole; Nidia Gabaldon Limas; Benjamin Fiszbein
|
Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Properties; Quantum Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-10-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f14bdbb89da3da37ef0/original/introducing-ddec6-atomic-population-analysis-part-5-new-method-to-compute-polarizabilities-and-dispersion-coefficients.pdf
|
67795521fa469535b9bf360a
|
10.26434/chemrxiv-2025-xqvks
|
Molecular orientation in amorphous calcium phosphate-pyrophosphate
|
Solids in nature typically exist in amorphous or crystalline states depending on the order of their constituent atoms. Generally, the multi-atom molecules (including ions) are highly ordered and oriented in crystals, but their orientation in amorphous solids is disordered except in certain organic materials formed by external regulations. This study finds that the amorphous calcium phosphate-pyrophosphate nanowire (ACPPN), which is prepared without external regulations, displays a molecular orientation of pyrophosphate ions. This discovery broadens our knowledge of the unique structural characteristics of amorphous materials, which would pave a way for further development of advanced solid materials.
|
Chaobo Feng; Feng Chen; Bing-Qiang Lu
|
Inorganic Chemistry; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67795521fa469535b9bf360a/original/molecular-orientation-in-amorphous-calcium-phosphate-pyrophosphate.pdf
|
672557815a82cea2fac28a81
|
10.26434/chemrxiv-2024-f8gtc
|
Revised 4-point Water Model for the Classical Drude Oscillator Polarizable Force Field: SWM4-HLJ
|
In this work the 4-point polarizable SWM4 Drude water model is reparametrized. Multiple models were developed using different strategies towards reproduction of specific target data. Results indicate that no individual model can reproduce all the selected target data in the context of the present form of the potential energy function. The changes considered in the new models include, 1) variations in the gas phase dipole moment, 2) variations in the molecular polarizability, 3) variations of the distance between the oxygen and the M site, 4) variation of the oxygen Lennard-Jones (LJ) parameters, 5) introduction of a LJ potential to the hydrogen atoms, and 6) variations of the H-O-H angle. Detailed analysis is presented for 3 new water models from which a final model, SWM4-HLJ, is selected as the future default model for the Drude polarizable force field. The model maintains the gas phase dipole moment as the experimental value while the remaining listed terms were adjusted including a larger H-O-H angle (108.12°). Compared to its predecessor, SWM4-NDP, the self-diffusion coefficient, water dimer properties, and water cluster energies are greatly improved. The temperature dependence of the density of the new model also performs better. Overall, the new SWM4-HLJ water model is a general improvement and a good balance between microscopic and bulk properties is achieved.
|
Xiaojing Teng; Wenbo Yu; Alex MacKerell
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672557815a82cea2fac28a81/original/revised-4-point-water-model-for-the-classical-drude-oscillator-polarizable-force-field-swm4-hlj.pdf
|
6601924b66c1381729c8ba9c
|
10.26434/chemrxiv-2024-q4tws
|
Control of Heparin Surface Density in Multilayers of Partially Hydrolyzed Poly(2-ethyl-2-oxazoline) by Degree of Hydrolysis
|
Controlling the surface density of heparin in active anticoagulant coatings is important in applications where an optimum is required. An approach based on tuning the degree of hydrolysis of poly(2-ethyl-2-oxazoline) (PEOX) is presented to control the surface density of heparin in layer-by-layer (LbL) assembled films. Multilayers are prepared at pH5 in 0.5M aqueous NaCl solutions by electrostatic interactions between negatively charged heparin and the positively charged amine groups in hydrolyzed PEOX. Characterization of the multilayers by QCM-D, TBO assay and XPS all show that the amount of heparin deposited increases with the degree of hydrolysis. While non-hydrolyzed PEOX/Heparin multilayers do not grow, the average deposited mass per area per bilayer, as determined by QCM-D measurements, increases with the degree of hydrolysis. At 50% hydrolysis, ITC measurements exhibit an exothermic enthalpy below -500 kJ/mol, TBO assay gives a heparin surface density of 1.03 ug/cm2 and atomic % of sulfur as determined by XPS leveled off at ~14%. These results show the potential of acidic hydrolysis of PEOX combined with LbL assembly of heparin as a reproducible method for controlling the surface density of heparin in anticoagulant coatings.
|
Ghazaleh Azizi Saadatlou; Pinar Tatar Guner; A. Levent Demirel
|
Materials Science; Polymer Science; Coating Materials; Multilayers; Thin Films; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6601924b66c1381729c8ba9c/original/control-of-heparin-surface-density-in-multilayers-of-partially-hydrolyzed-poly-2-ethyl-2-oxazoline-by-degree-of-hydrolysis.pdf
|
6522e87745aaa5fdbb8e8070
|
10.26434/chemrxiv-2023-4711l
|
Ligand control of hydrocarbon C-H bond functionalization by uranyl photocatalysts
|
The aqueous uranyl dication has long been known to facilitate the UV light-induced decomposition of aqueous VOCs (volatile organic compounds), via the long-lived highly efficient, uranyl excited state. However, the lower-energy visible light excited uranyl ion is also able to cleave unactivated hydrocarbon C-H bonds, yet the development of this reactivity into controlled and catalytic C-H bond functionalization is still in its infancy, with almost all studies still focused on uranyl nitrate as the precatalyst. Here, hydrocarbon-soluble, uranyl nitrate and chloride complexes supported by substituted phenanthroline (Ph2phen) ligands are compared to each other, and to the parent salts, as photocatalysts for the functionalization of cyclooctane by H atom abstraction. Analysis of the absorption and emission spectra, and emission lifetimes of Ph2phen-coordinated uranyl complexes demonstrate the utility of the ligand in light absorption in the photocatalysis, which is related to the energy and kinetic decay profile of the uranyl photoexcited state. Density Functional Theory computational analysis of the C-H activation steps in the reaction show how a set of dispersion forces between the hydrocarbon substrate and the Ph2phen ligand provide control over the H atom abstraction, and provide predictions of selectivity of H atom abstraction by the uranyl oxo of the ring CH over the ethyl C-H in an ethylcyclohexane substrate.
|
Ryte Rutkauskaite; Xiaobin Zhang; Adam Woodward; James Purkis; Sean Woodall; Mark Sarsfield; Georg Schreckenbach; Louise Natrajan; Polly Arnold
|
Inorganic Chemistry; Catalysis; Organometallic Chemistry; Bonding; Lanthanides and Actinides; Kinetics and Mechanism - Organometallic Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6522e87745aaa5fdbb8e8070/original/ligand-control-of-hydrocarbon-c-h-bond-functionalization-by-uranyl-photocatalysts.pdf
|
60c7503e9abda20b67f8d9d5
|
10.26434/chemrxiv.13007870.v1
|
A Multiuse Nanopore Platform with Disposable Paper Analytical Device for the Detection of Heavy Meatal Ions
|
The pollution of heavy metal ions
within the environmental is a global problem. The rapid and precise removal of
these contaminants can be aided by identifying and quantifying the composition
of the sample. It is therefore crucial to develop effective portable analytical
techniques to determine the levels of heavy metal contamination. Paper-based
analytical devices (PADs) offer a low cost method making them an excellent
platform for onsite environmental sensors. Here we demonstrate how a PAD can be
integrated into a multi-use Nanopore platform. The PAD was functionalised with
different recognition ligands, who’s surface charge densities varied in the
presence of an analyte. The surface of the PAD was placed in contact with a
Nanopore which exhibited Ion Current Rectification (ICR). The extent of ICR,
was dependent upon the PAD’s surface charge, and the presence of the analyte of
interest i.e. the ICR phenomena was exaggerated or diminished indicating the
presence of the metal ion in solution.
We demonstrate the
potential of PAD-ICR using a PAD functionalised with a peptide aptamer specific
for nickel ions. Allowing the detection of nickel(II) as low as 0.25 μM even in
the presence of other metal ions. After any measurement, the Nanopore surface can
be wiped clean, and reused.
|
Imogen Heaton; Mark Platt
|
Analytical Chemistry - General
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-09-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7503e9abda20b67f8d9d5/original/a-multiuse-nanopore-platform-with-disposable-paper-analytical-device-for-the-detection-of-heavy-meatal-ions.pdf
|
60c74533567dfe237bec43ff
|
10.26434/chemrxiv.9616991.v2
|
Dyson Orbitals within the fc-CVS-EOM-CCSD Framework: Theory and Application to X-ray Photoelectron Spectroscopy of Ground and Excited States
|
We report on the implementation of Dyson orbitals within the recently introduced frozen-core (fc) core-valence separated (CVS) equation-of-motion (EOM) coupled-cluster singles and doubles (CCSD) method, which enables efficient and reliable characterization of core-level states. The ionization potential (IP) variant of fc-CVS-EOM-CCSD, in which the EOM target states have one electron less than the reference, gives access to core-ionized states thus enabling modeling of<br /><div>X-ray photoelectron spectra (XPS) and its time-resolved variant (TR-XPS). Dyson orbitals are reduced quantities that can be interpreted as correlated states of the ejected/attached electron; they enter the expressions of various experimentally relevant quantities. In the context of photoelectron spectroscopy, Dyson orbitals can be used to estimate the strengths of photoionization transitions. We illustrate the utility of Dyson orbitals and fc-CVS-EOM-IP-CCSD by calculating XPS of the ground state of adenine and TR-XPS of the excited states of uracil.</div>
|
Marta L. Vidal; Anna Krylov; Sonia Coriani
|
Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-10-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74533567dfe237bec43ff/original/dyson-orbitals-within-the-fc-cvs-eom-ccsd-framework-theory-and-application-to-x-ray-photoelectron-spectroscopy-of-ground-and-excited-states.pdf
|
631f583749042a8631d4a2e0
|
10.26434/chemrxiv-2022-q72lk
|
A unified approach to the synthesis of amines through a highly selective and broadly applicable imine reduction using modified Pd-nanoparticles
|
A remarkably broad range of substrates is facilitated in a highly selective imine reduction using PVP stabilised Pd nanoparticles, molecular hydrogen at 1 atm, at just above RT in aqueous ethanol. Very good yields are achieved across previously-problematic substrate classes, and the protocol circumvents issues associated with more popular synthetic approaches. The utility of this system was further demonstrated in the context of late-stage functionalisation of APIs, deuterium incorporation and one-pot multi-step reaction sequences. Through a combination of synthetic mechanistic studies, surface analysis and computational approximations, insights into the features governing the selectivity of this system, and the key binding interactions between the PVP and Pd surface have been gleaned.
|
Gerard McGlacken; David Jones; Justin Holmes; Gillian Collins; Eadaoin Casey; Roberta Kehoe; Andreas Larsson; Mikael Rasander; Scott May; Alison Campbell ; Humphrey Moynihan
|
Catalysis; Nanocatalysis - Reactions & Mechanisms
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631f583749042a8631d4a2e0/original/a-unified-approach-to-the-synthesis-of-amines-through-a-highly-selective-and-broadly-applicable-imine-reduction-using-modified-pd-nanoparticles.pdf
|
60c75581f96a00294a2888b0
|
10.26434/chemrxiv.14113109.v1
|
Operando Monitoring the Insulator-Metal Transition of LiCoO2
|
LiCoO<sub>2</sub> (LCO) is one of the most-widely used cathode active materials for Li-ion batteries. Even though the material undergoes an electronic two-phase transition upon Li-ion cell charging, LCO exhibits competitive performance in terms of rate capability. Herein the insulator-metal transition of LCO is investigated by <i>operando</i> Raman spectroscopy complemented with DFT calculations and a newly-developed sampling volume model. We confirm the presence of a Mott insulator α-phase at dilute Li-vacancy concentrations (x > 0.87) that transforms into a metallic β-phase at x < 0.75. In addition, we find that the charge-discharge intensity trends of LCO Raman-active bands exhibit a characteristic hysteresis, which, unexpectedly, narrows at higher cycling rates. When comparing these trends to a newly-developed numerical model of laser penetration into a spatially-heterogeneous particle we provide compelling evidence that the insulator-metal transition of LCO follows a two-phase route at very low cycling rates, which is suppressed in favor of a solid-solution route at rates above 10 mA/g<sub>LCO</sub> (~C/10). The observations explain why LCO exhibits competitive rate capabilities despite being observed to undergo an intuitively slow two-phase transition route: a kinetically faster solid-solution transition route becomes available when the active material is cycled at rates >C/10. <i>Operando</i> Raman spectroscopy combined with sample volume modelling and DFT calculations is shown to provide unique insights into fundamental processes governing the performance of state-of-the-art cathode materials for Li-ion batteries.
|
Eibar Flores; Nataliia Mozhzhukhina; Ulrich Aschauer; Erik Berg
|
Computational Chemistry and Modeling; Energy Storage; Physical and Chemical Processes; Spectroscopy (Physical Chem.); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75581f96a00294a2888b0/original/operando-monitoring-the-insulator-metal-transition-of-li-co-o2.pdf
|
64ff1ea1b338ec988a49fb1a
|
10.26434/chemrxiv-2023-6h2c9-v3
|
DockOpt: A Tool for Automatic Optimization of Docking Models
|
Molecular docking is a widely used technique for leveraging protein structure in ligand discovery, but as a method, it remains difficult to utilize due to limitations that have not been adequately addressed. Despite some progress towards automation, docking still requires expert guidance, hindering its adoption by a broader range of investigators. To make docking more accessible, we have developed a new utility called DockOpt, which automates the creation, evaluation, and optimization of docking models prior to their deployment in large-scale prospective screens. DockOpt outperforms our previous automated pipeline across all 43 targets in the DUDE-Z benchmark dataset, and the generated models for ~84% of targets demonstrate sufficient enrichment to warrant their use in prospective screens, with normalized LogAUC values of at least 15%. DockOpt is available as part of the Python package Pydock3 included in the UCSF DOCK 3.8 distribution, which is available for free to academic researchers at https://dock.compbio.ucsf.edu and free for everyone upon registration at https://tldr.docking.org.
|
Ian Knight; Khanh Tang; Olivier Mailhot; John Irwin
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling
|
CC BY 4.0
|
CHEMRXIV
|
2023-09-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ff1ea1b338ec988a49fb1a/original/dock-opt-a-tool-for-automatic-optimization-of-docking-models.pdf
|
60c7478fee301c7bdac79713
|
10.26434/chemrxiv.10316681.v2
|
Tuning the Redox Activity of Metal−Organic Frameworks for Enhanced, Selective O<sub>2</sub> Binding: Design Rules and Ambient Temperature O<sub>2</sub> Chemisorption in a Cobalt−Triazolate Framework
|
<p>Metal−organic frameworks (MOFs) with coordinatively
unsaturated metal sites are appealing as adsorbent materials due to their
tunable functionality and ability to selectively bind small molecules. Through
the use of computational screening methods based on periodic density functional
theory, we investigate O<sub>2</sub> and N<sub>2</sub> adsorption at the
coordinatively unsaturated metal sites of several MOF families. A variety of
design handles are identified that can be used to modify the redox activity of
the metal centers, including changing the functionalization of the linkers
(replacing oxido donors with sulfido donors), anion exchange of bridging
ligands (considering μ-Br<sup>-</sup>, μ-Cl<sup>-</sup>, μ-F<sup>-</sup>, μ-SH<sup>-</sup>,
or μ-OH<sup>-</sup> groups), and altering the formal oxidation state of the
metal. As a result, we show that it is possible to tune the O<sub>2</sub>
affinity at the open metal sites of MOFs for applications involving the strong
and/or selective binding of O<sub>2</sub>. In contrast with O<sub>2</sub>
adsorption, N<sub>2</sub> adsorption at open metal sites is predicted to be
relatively weak across the MOF dataset, with the exception of MOFs containing
synthetically elusive V<sup>2+</sup> open metal sites. As one example from the
screening study, we predicted that exchanging the μ-Cl<sup>-</sup> ligands of M<sub>2</sub>Cl<sub>2</sub>(BBTA)
(H<sub>2</sub>BBTA = 1<i>H</i>,5<i>H</i>-benzo(1,2-d:4,5-d′)bistriazole) with
μ-OH<sup>-</sup> groups would significantly enhance the strength of O<sub>2</sub>
adsorption at the open metal sites without a corresponding increase in the N<sub>2</sub>
affinity. Experimental investigation of Co<sub>2</sub>Cl<sub>2</sub>(BBTA) and
Co<sub>2</sub>(OH)<sub>2</sub>(BBTA) confirms that the former exhibits weak
physisorption of both N<sub>2</sub> and O<sub>2</sub>, whereas the latter is
capable of chemisorbing O<sub>2</sub> at room temperature in a highly selective
manner. The O<sub>2</sub> chemisorption behavior is attributed to the greater
electron-donating character of the μ-OH<sup>-</sup><sub> </sub>ligands and the
presence of H-bonding interactions between the μ-OH<sup>-</sup> bridging
ligands and the reduced O<sub>2</sub> adsorbate.<br /></p>
|
Andrew Rosen; M. Rasel Mian; Timur Islamoglu; Haoyuan Chen; Omar Farha; Justin Notestein; Randall Q. Snurr
|
Hybrid Organic-Inorganic Materials; Separation Science; Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-01-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7478fee301c7bdac79713/original/tuning-the-redox-activity-of-metal-organic-frameworks-for-enhanced-selective-o-sub-2-sub-binding-design-rules-and-ambient-temperature-o-sub-2-sub-chemisorption-in-a-cobalt-triazolate-framework.pdf
|
6170a6bad7e1ee09922b8ebe
|
10.26434/chemrxiv-2021-5lhjx-v2
|
Revealing the contest between triplet-triplet exchange and triplet-triplet energy transfer coupling in correlated triplet pair states in singlet fission
|
Understanding the separation of the correlated triplet pair state 1(TT) intermediate is critical for leveraging singlet fission to improve solar cell efficiency. This separation mechanism is dominated by two key interactions: (i) the exchange interaction (K) between the triplets which leads to the spin splitting of the biexciton state into 1(TT),3(TT) and 5(TT) states, and (ii) the triplet-triplet energy transfer integral (t) which enables the formation of the spatially separated (but still spin entangled) state 1(T...T). We develop a simple ab initio technique to compute both the biexciton exchange (K) and biexciton transfer coupling. Our key findings reveal new conditions for successful correlated triplet pair state dissociation. The biexciton exchange interaction needs to be ferromagnetic or negligible to the triplet energy transfer for favourable dissociation. We also explore the effect of chromophore packing to reveal geometries where these conditions are achieved for tetracene.
|
Vibin Abraham; Nicholas Mayhall
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-10-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6170a6bad7e1ee09922b8ebe/original/revealing-the-contest-between-triplet-triplet-exchange-and-triplet-triplet-energy-transfer-coupling-in-correlated-triplet-pair-states-in-singlet-fission.pdf
|
62da093f13e3659590e0d5eb
|
10.26434/chemrxiv-2022-bt3f6
|
A FAIR approach for detecting and sharing PFAS hot-spot areas and water systems
|
Per- and polyfluoroalkyl substances (PFAS) contamination in water sources near potential PFAS users is well known. Therefore, it is useful for PFAS stakeholders to visualize hot-spot areas and bring attention to the water systems that are near to those areas. Towards this end, we extracted information about PFAS sources, drinking water information, sewer water information, and Source Water Assessment Protection Program (SWAPP) information from publicly available sources to create five different maps in ArcGIS Online that highlight PFAS contamination in relation to potential PFAS users. Following the FAIR (Findable, Accessible, Interoperable and Reusable) principles, we created a Figshare repository that includes all data and associated metadata with these five ArcGIS maps. Moreover, the Figshare repository includes a metadata description of the maps in JSON format that adheres to a draft Minimum Information about Geospatial Information System (MIAGIS) standard we have developed. We hope this MIAGIS draft will assist in establishing a GIS standards group that will develop the draft into a full standard for the wider GIS community. We have also developed a miagis Python package that facilitates the generation of a MIAGIS-compliant JSON metadata file.
|
Sweta Ojha; P. Travis Thompson; Christian D. Powell; Hunter N.B. Moseley; Kelly G. Pennell
|
Earth, Space, and Environmental Chemistry; Wastes
|
CC BY 4.0
|
CHEMRXIV
|
2022-07-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62da093f13e3659590e0d5eb/original/a-fair-approach-for-detecting-and-sharing-pfas-hot-spot-areas-and-water-systems.pdf
|
6647458f418a5379b088d15e
|
10.26434/chemrxiv-2024-xpzhc-v2
|
High-resolution Raman imaging of >300 patient-derived cells from nine different leukemia subtypes: a global clustering approach
|
Leukemia comprises a diverse group of bone marrow tumors marked by immature cell proliferation. Current diagnosis involves identifying leukemia subtypes through visual assessment of blood and bone marrow smears, a subjective and time-consuming method. Our study introduces the characterization of different leukemia subtypes using a global clustering approach of Raman hyperspectral maps of cells. We analyzed bone marrow samples from 19 patients, each presenting one of nine distinct leukemia subtypes, conducting high spatial resolution Raman imaging on 319 cells, generating over 1.3 million spectra in total. An automated pre-processing pipeline followed by a single-step global clustering approach performed over the entire dataset identified relevant cellular components (cytoplasm, nucleus, carotenoids, myeloperoxidase (MPO) and hemoglobin (HB)) enabling the unsupervised creation of high-quality pseudo-stained images at the single-cell level. Furthermore, this approach provided a semi-quantitative analysis of cellular component distribution, and multivariate analysis of clustering results revealed the potential of Raman imaging in leukemia research, highlighting both advantages and challenges associated with global clustering.
|
Renzo Vanna; Andrea Masella; Manuela Bazzarelli; Paola Ronchi; Aufried T. M. Lenferink; Cristina Tresoldi; Carlo Morasso; Marzia Bedoni; Giulio Cerullo; Dario Polli; Fabio Ciceri; Giulia De Poli; Matteo Bregonzio; Cees Otto
|
Biological and Medicinal Chemistry; Analytical Chemistry; Imaging; Microscopy; Spectroscopy (Anal. Chem.)
|
CC BY 4.0
|
CHEMRXIV
|
2024-05-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6647458f418a5379b088d15e/original/high-resolution-raman-imaging-of-300-patient-derived-cells-from-nine-different-leukemia-subtypes-a-global-clustering-approach.pdf
|
60c74a47337d6cf7a2e2783e
|
10.26434/chemrxiv.12089730.v1
|
Scope of phytotherapeutics in targeting ACE2 mediated Host-Viral Interface of SARS‐CoV2 that causes COVID-19
|
<p>Severe acute respiratory
syndrome coronavirus (SARS-CoV-2) that cause COVID-19 becomes a global threat
and spread its pandemicity across the boundaries. Recent demography issued by
WHO forecasting the severity of disease prevalence in more than 200 countries resulted
in 16,96,588 laboratory confirmed cases excluding 1,05,952 deaths as on 12 April
2020. Countries like USA (4,92,881), Italy (1,52,271), Spain (1,61,852),
Germany (1,20,479) are struggling hard to flatten their epidemic curve of
COVID-19. Dynamic strategies are of utmost important in order to manage the
crucial spread of SARS-CoV-2. Drug of herbal origin may offer reliable
therapeutic opportunity in controlling widespread transmission. It was evident
from the scientific outcomes that SARS‐CoV-2 gains access in to the host cell through
angiotensin-converting enzyme 2 (ACE2) receptors. Hence drugs that reveals
potential binding affinity with core amino acid of ACE-2 may expected to
interfere the host-viral interaction. In our present investigation 28 lead
molecules from well documented medicinal herbs were subjected to molecular
docking analysis targeting ACE2 receptor and their potential of impeding
host-viral interface were evaluated. Results of computational analysis
signifies that out of 28 ligands nearly 11 bioactive lead molecules exhibit
potential binding affinity of about 100% with the target amino acid residue (31
Lys and 353 Lys)<br /></p>
|
Sivaraman Dhanasekaran; Pradeep P.S
|
Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Plant Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a47337d6cf7a2e2783e/original/scope-of-phytotherapeutics-in-targeting-ace2-mediated-host-viral-interface-of-sars-co-v2-that-causes-covid-19.pdf
|
67c5ad126dde43c9084bacf8
|
10.26434/chemrxiv-2025-3x72f
|
Investigating fine particulate matter transport in a multi-story house using low-cost sensor measurements and different modeling approaches
|
This work investigates the transport of fine particulate matter (PM2.5) in a multi-story test house using cooking emissions as a point source. The test house was instrumented with 13 PM2.5 monitors, and the particle sources included pan cooking and air frying, as well as ambient PM2.5 penetration during periods of no indoor activity. In the absence of indoor sources, we observed about 10 % of ambient PM2.5 concentrations penetrating indoors with a time lag of 1 h. Similar peak PM2.5 concentrations were observed for pan frying and air frying of the same food ingredients. A cross-correlation analysis showed that it took 2 to 4 min for kitchen peak concentrations to reach other sensors on the first floor and about 8 min to reach the second floor. PM2.5 concentrations were heterogeneous on the first floor, with non-kitchen areas peaking at 45 % ± 9 % of kitchen levels. Second-floor concentrations were more homogeneous, peaking at 18 % ± 2 % of kitchen levels. Using a typical occupancy scenario, the highest estimated personal PM2.5 exposure (44 %) was experienced in the kitchen/dining area, which accounted for 9 % of the time spent at home. We used three modeling approaches to analyze particle transport throughout the house, with increasing input requirements: a multi-box model, an empirical model, and the NIST CONTAM model. All models predicted time integrated PM2.5 concentrations on the 1st and 2nd floors, with R2 between 0.57 and 0.82 and RMSE from 6 µg m-3 to 11 µg m-3.
|
Andrew B. Martin; Stephen M. Zimmerman; Liora Mael; Dustin Poppendieck; Delphine K. Farmer; Marina E. Vance
|
Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c5ad126dde43c9084bacf8/original/investigating-fine-particulate-matter-transport-in-a-multi-story-house-using-low-cost-sensor-measurements-and-different-modeling-approaches.pdf
|
633a9d0d114b7ee37d265d6d
|
10.26434/chemrxiv-2022-xwq9n-v2
|
A microfluidic platform for the controlled synthesis of higher-order liquid crystalline nanoparticles
|
Soft-matter nanoparticles are of great interest in biotechnology, particularly for fields such as therapeutic delivery and in vivo imaging. Underpinning this is their biocompatibility, potential for selective targeting, attractive pharmacokinetic properties, and amenability to downstream functionalisation. Morphological diversity inherent to soft-matter particles can give rise to enhanced functionality. However, this diversity remains underexplored, and only the simplest of particle architectures (spherical lipid vesicles and lipid/polymer nanoparticles (LNPs)) have been exploited at a clinical level. This is largely due to limitations associated with existing particle synthesis methods that rely on poorly controlled bulk mixing conditions and high-energy input. To address this, we have designed a scalable microfluidic hydrodynamic focusing (MHF) technology for the controllable, rapid, and continuous production of lyotropic liquid crystalline (LLC) nanoparticles (both cubosomes and hexosomes); colloidal dispersions of higher-order lipid assemblies with intricate internal structures of 3-D and 2-D symmetry. These particles have been proposed as the next generation of soft-matter nano-carriers, with unique fusogenic and physical properties. Using our platform, we produce stable nanoparticles with varied architectural features. Crucially, our microfluidic method gives unprecedented control over LLC size, a feature we go on to exploit in fusogenic studies with model cell membranes, in which a dependency on particle diameter is evident. We believe our platform has the potential to serve as a tool for future studies around non-lamellar soft nanoparticles, and anticipate it to allow for the rapid prototyping of LLC particles of diverse functionality, paving the way toward their eventual uptake at an industrial level.
|
Colin P Pilkington; Claudia Contini; Joseph D Barritt; Paul A Simpson; John M Seddon; Yuval Elani
|
Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2022-10-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633a9d0d114b7ee37d265d6d/original/a-microfluidic-platform-for-the-controlled-synthesis-of-higher-order-liquid-crystalline-nanoparticles.pdf
|
60d61c6f2616116df18c441d
|
10.26434/chemrxiv-2021-w0nx3
|
Americium preferred: Lanmodulin, a natural lanthanide-binding protein favors an actinide over lanthanides
|
The separation and recycling of lanthanides is an active area of research with a growing demand that calls for more environmentally friendly lanthanide sources. Likewise, the efficient and industrial separation of lanthanides from the minor actinides (Np, Am - Fm) is one of the key questions for closing the nuclear fuel cycle; reducing costs and increasing safety. With the advent of the field of lanthanide dependent bacterial metabolism, bio-inspired applications are in reach. Here, we utilize the natural lanthanide chelator Lanmodulin and the luminescent probes Eu3+ and Cm3+ to investigate the inter-metal competition behavior of all lanthanides (except Pm) and four actinides (Np, Pu, Am, Cm) to Lanmodulin. Using time resolved laser induced fluorescence spectroscopy we show that Lanmodulin has the highest relative binding affinity to Nd3+ and Eu3+ among the lanthanide series. When equimolar mixtures of Cm3+ and Am3+ are added to Lanmodulin, Lanmodulin preferentially binds to Am3+ over Cm3+ whilst Nd3+ and Cm3+ bind with similar relative affinity. The results presented show that a natural lanthanide binding protein can bind various actinides with high relative affinity, paving the way to bio inspired separation applications. In addition, an easy and versatile method was developed, using the fluorescence properties of only two elements, Eu and Cm, for inter-metal competition studies regarding lanthanides and selected actinides and their binding to biological molecules.
|
Helena Singer; Björn Drobot; Cathleen Zeymer; Robin Steudner; Lena Daumann
|
Biological and Medicinal Chemistry; Inorganic Chemistry; Analytical Chemistry; Bioinorganic Chemistry; Lanthanides and Actinides; Biochemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-06-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d61c6f2616116df18c441d/original/americium-preferred-lanmodulin-a-natural-lanthanide-binding-protein-favors-an-actinide-over-lanthanides.pdf
|
63905efd44ccbc0422114226
|
10.26434/chemrxiv-2022-n3kvl
|
Deep Reactive Ion Etching of Cylindrical Nanopores in Silicon for Photonic Crystals
|
Periodic arrays of deep nanopores etched in silicon by deep reactive ion etching are desirable structures for photonic crystals and other nanostructure for silicon nanophotonics. Previous studies focused on realizing as deep as possible nanopores with as high as possible aspect ratios. The resulting nanopores suffered from structural imperfections of the nanopores, such as mask undercut, uneven and large scallops, depth dependent pore radii and tapering. Therefore, our present focus is to realize nanopores that have as cylindrical as possible shapes, in order to obtain a better comparison of nanophotonic observations with theory and simulations. To this end in our 2-step Bosch process we have improved the mask undercut, the uneven scallops, pore widening and positive tapering by optimizing a plethora of parameters such as the etch step time, capacitively coupled plasma (ion energy) and pressure. To add further degrees of control, we implemented a 3-step DREM (deposit, remove, etch, multistep) process. Optimization of the etching process results in cylindrical nanopores with a diameter in the range between 280 and 500 nm and a depth around 7 µm, corresponding to high depth-to-diameter aspect ratios between 14 and 25, that are very well suited for the realization of silicon nanophotonic structures.
|
Melissa J Goodwin; Cornelis A M Harteveld; Meint J de Boer; Willem L Vos
|
Nanoscience; Nanofabrication
|
CC BY 4.0
|
CHEMRXIV
|
2022-12-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63905efd44ccbc0422114226/original/deep-reactive-ion-etching-of-cylindrical-nanopores-in-silicon-for-photonic-crystals.pdf
|
669a627d5101a2ffa8f1b757
|
10.26434/chemrxiv-2024-906jf-v2
|
Characterization of Monoclonal Antibody Charge Variants under Near-Native Separation Conditions using Nanoflow Sheath Liquid Capillary Electrophoresis-Mass Spectrometry
|
Monoclonal antibodies (mAbs) undergo multiple post-translational modifications (PTMs), e.g., charge variants, oxidation, etc., during production and storage, necessitating evaluation of the resulting PTMs as critical quality attributes (CQA) for protein quality and safety. Charge variants PTMs can be separated using capillary zone electrophoresis (CZE). The CZE EACA method developed by He et al. (2011) with UV detection is applied routinely in the pharmaceutical industry for analyzing charge variants. However, the method cannot be directly hyphenated with mass spectrometry (MS), preventing direct identification of separated charge variants due to the non-volatile background electrolyte (BGE), which hinders reliable charge variant identification. This study presents a CZE-UV/MS method using a neutral static capillary coating of hydroxypropyl methylcellulose combined with a volatile BGE at pH 5.0 to allow MS-compatible mAb charge variant separations. The effect of several parameters, including pH and concentration of BGE, voltage, and injected mAb concentrations in terms of separation performance on a panel of mAbs was investigated. The final method was tested with mAbs of IgG subclasses (IgG1 and IgG4) with different pI (7.4-9.2), and degrees of heterogeneity. Basic and acidic variants were separated from the parent mAb using a BGE of 50 mM acetic acid adjusted at pH 5.0. A linear correlation in relative charge variant abundance was obtained between our method and the EACA method. CZE-MS coupling was accomplished using the nanoCEasy, a low-flow sheath liquid interface, which enabled the identification and quantitation of basic, acidic, and incomplete pyroglutamate variants, and glycoforms of the tested mAbs.This method can be a useful tool for in-depth charge variants characterization of mAbs.
|
Annika A.M. van der Zon; Alisa Höchsmann; Tijmen S. Bos; Christian Neusüß; Govert W. Somsen; Kevin Jooß; Rob Haselberg; Andrea F.G. Gargano
|
Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry; Separation Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669a627d5101a2ffa8f1b757/original/characterization-of-monoclonal-antibody-charge-variants-under-near-native-separation-conditions-using-nanoflow-sheath-liquid-capillary-electrophoresis-mass-spectrometry.pdf
|
6336cf2a0e3c6ac4782e5236
|
10.26434/chemrxiv-2022-5fdnf-v2
|
Synthesis, Properties, and Intermolecular Interactions in the Solid States of π-Congested X-Shaped 1,2,4,5-Tetra(9-anthryl)benzenes
|
A Negishi coupling based synthesis of 1,2,4,5-tetra(9-anthryl)benzene derivatives, possessing X-shaped molecular structures, is described. The results of X-ray crystallographic analysis show that two-dimensional highly ordered packing structure of the crystalline state of the unsubstituted derivative is a consequence of intermolecular π-π and CH-π interactions between anthracene units. Photoirradiation of the unsubstituted derivative as a precipitated solution promotes intramolecular [4+4] photocycloaddition reactions between both adjacent pairs of anthracene units to produce a crystalline polycyclic product having a unique 1.700 Å long carbon-carbon single bond. Furthermore, charge-transfer complexes, displaying near-infrared absorption and emission, are generated by co-crystallization of the X-shaped unsubstituted member of the group with electron-acceptor molecules.
|
Tomohiko Nishiuchi; Shino Takeuchi; Yuta Makihara; Ryo Kimura; Shohei Saito; Hiroyasu Sato; Takashi Kubo
|
Organic Chemistry; Physical Organic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6336cf2a0e3c6ac4782e5236/original/synthesis-properties-and-intermolecular-interactions-in-the-solid-states-of-congested-x-shaped-1-2-4-5-tetra-9-anthryl-benzenes.pdf
|
60c7512c469df4608cf4499c
|
10.26434/chemrxiv.13130228.v1
|
Multiphoton Excitation of Organic Molecules in a Cavity – Superradiance as a Measure of Coherence
|
<div>Coherent excitation of a molecular ensemble coupled to a common radiation mode can lead to the collective emission of radiation known as superradiance. This collective emission only occurs if there is an entanglement between the molecules in their ground and excited state and can therefore serve as a macroscopic measure of coherence in the ensemble. Reported here are wave packet propagations for various pyrazine models of increasing complexity and molecular ensembles thereof. We show that ensemble coherence upon photoexcitation can prevail up to relatively long time scales, although the effect can diminish quickly with increasing ensemble size. Coherence can also build up over time and even reemerge after the molecules have passed through a conical intersection. The effect of the pump-pulse characteristics on the collective response of the molecular ensemble is also studied. A broad-band pulse imprints a large amount of initial coherence to the system, as compared to a longer pulse with a smaller spread in the frequency domain. However, the differential effects arising from a different pulse duration and coherent bandwidth become less prominent if the emission of light from the ensemble takes place after a non-adiabatic decay process.</div>
|
Inga Ulusoy; Johana A. Gomez; Oriol Vendrell
|
Theory - Computational; Photochemistry (Physical Chem.); Physical and Chemical Processes; Quantum Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-10-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7512c469df4608cf4499c/original/multiphoton-excitation-of-organic-molecules-in-a-cavity-superradiance-as-a-measure-of-coherence.pdf
|
66ec1f68cec5d6c1428e44ee
|
10.26434/chemrxiv-2024-031n4
|
Deciphering Isotopic Fine Structures of Silylated Compounds in Gas Chromatography - Vacuum Photoionization Orbitrap Mass Spectrometry of Bio-Oils
|
We introduce vacuum resonance-enhanced multiphoton ionization (REMPI) with high-resolution Orbitrap Fourier transform mass spectrometry (FTMS) for analyzing silylated polar compounds. UV laser radiation at 248 nm sensitively and selectively targets aromatic constituents, while high-resolution mass spectrometry (HRMS) enables high-performance mass spectrometric detection. This workflow enhances the detection confidence of polar constituents by identifying unique isotopologue patterns, including at the isotopic fine structure (IFS) level, in analytical standards and complex bio-oils. A direct and derivatized gas chromatography (GC) procedure on a polar standard component mixture allowed us to explore the general ionization and detection characteristics of REMPI FTMS. HRMS enabled the examination of the complex isotopologue profiles, revealing distinct patterns for the CHOxSiy-class compounds. Particularly in complex mixtures, this isobaric complexity exceeded the classical mass resolution capabilities of the employed Orbitrap D30 series and prompted the usage of prolonged transients via an external data acquisition system. This procedure substantially improved mass spectrometric results by recording the unprocessed time-domain transient data for up to 2 seconds. Notably, the ability to distinguish diagnostic isotopic pairs, such as 12C/29Si vs. 13C/28Si with a mass split of ∼3.79 mDa and 13C12C/28Si29Si vs. 13C2/28Si2, with an approximate mass difference of ∼3.32 mDa, demonstrates a significant and expected performance improvement. Finally, we benchmark the GC HRMS methodology to identify silylated oxygenated and nitrogen-containing constituents in ultra-complex bio-oil samples.
|
Silvia Juliana Vesga Martínez; Christopher Paul Rüger; Paul Kösling; Julian Schade; Sven Ehlert; Yury O. Tsybin; Ralf Zimmermann
|
Analytical Chemistry; Energy; Analytical Apparatus; Mass Spectrometry; Fuels - Energy Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-09-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ec1f68cec5d6c1428e44ee/original/deciphering-isotopic-fine-structures-of-silylated-compounds-in-gas-chromatography-vacuum-photoionization-orbitrap-mass-spectrometry-of-bio-oils.pdf
|
65e0481b66c1381729d553e4
|
10.26434/chemrxiv-2024-tx5t7
|
Proton transport in water is doubly gated by sequential hydrogen-bond exchanges
|
The transport of excess protons in water is central to acid-base chemistry, biochemistry, and energy production. However, elucidating its mechanism has been challenging. Recent nonlinear vibrational spectroscopy experiments could not be explained by existing models. Here, we combine neural network-based molecular dynamics simulations considering nuclear quantum effects for all atoms and vibrational spectroscopy calculations to determine the proton transport mechanism. Our simulations reveal the equilibrium between two stable proton-localized structures with distinct Eigen-like and Zundel-like hydrogen-bond motifs. Proton transport follows a three-step mechanism gated by two successive hydrogen-bond exchanges: the first reduces the proton-acceptor water coordination, leading to proton transfer, and the second, the rate-limiting step, prevents rapid back-transfer by increasing the proton-donor coordination. This sequential mechanism is consistent with experimental characterizations of proton diffusion, explaining the low activation energy and the prolonged intermediate lifetimes in vibrational spectroscopy. These results are crucial for understanding proton dynamics in biochemical and technological systems.
|
Axel Gomez; Ward Thompson; Damien Laage
|
Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Machine Learning; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e0481b66c1381729d553e4/original/proton-transport-in-water-is-doubly-gated-by-sequential-hydrogen-bond-exchanges.pdf
|
66fa7276cec5d6c142a99cfc
|
10.26434/chemrxiv-2024-lj757
|
Advancements in loop cyclisation approaches for enhanced pep1de therapeutics for targeting protein-protein
interactions
|
Protein-protein interactions (PPIs) are pivotal in regulating cellular functions and life processes, making them promising therapeutic targets in modern medicine. Despite their potential, developing PPI inhibitors poses significant challenges due to their large and shallow interfaces that complicate ligand binding. This study focuses on mimicking peptide loops as a strategy for PPI inhibition, utilising synthetic peptide loops for replicating critical binding regions. This current work explores turn-inducing elements and highlights the importance of proline in promoting favourable conformations for lactamisation, yielding high-purity cyclic peptides. Notably, our one-pot method offers enhanced versatility and represents a robust strategy for efficient and selective macrolactamisation, expanding the scope of peptide synthesis methodologies. This approach, validated through the synthesis of AAV capsid-derived loops, offers a robust platform for developing peptide-based therapeutics and highlights the potential of peptide macrocycles in overcoming PPI drug discovery challenges and advancing new therapeutics development.
|
Lucia Lombardi; Luke A. Granger; Robin J. Shattock; Daryl R. Williams
|
Biological and Medicinal Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fa7276cec5d6c142a99cfc/original/advancements-in-loop-cyclisation-approaches-for-enhanced-pep1de-therapeutics-for-targeting-protein-protein-interactions.pdf
|
634ac5264b0af33a81c66ba5
|
10.26434/chemrxiv-2022-pn7rj
|
Enantioselective Single and Dual a-C–H Bond Functionalization of Cyclic Amines via Enzymatic Carbene Transfer
|
Cyclic amines are ubiquitous structural motifs found in pharmaceuticals and biologically active natural products, making methods for their elaboration via direct C–H functionalization of considerable synthetic value. Herein, we report the development of an iron-based biocatalytic strategy for enantioselective a-C–H functionalization of pyrrolidines via a carbene transfer reaction with diazoacetone. Currently unreported for organometallic catalysts, this transformation can be accomplished in high yields, high catalytic activity and high stereoselectivity (up to 99:1 e.r. and 20,350 TON) using engineered variants of cytochrome P450 CYP119 from Sulfolobus solfataricus. This methodology was further extended to enable enantioselective a-C–H functionalization in the presence of ethyl diazoacetate as carbene donor (up to 89:11 e.r. and 8,920 TON), and the two strategies were combined to achieve a one-pot as well as a tandem dual C–H functionalization of the cyclic amine substrate with enzyme-controlled diastereo- and enantiodivergent selectivity. This biocatalytic approach is amenable to gram-scale synthesis and can be applied to drug scaffolds for late-stage C–H functionalization. This work provides an efficient and tunable method for direct asymmetric a-C–H functionalization of saturated N-heterocycles which should offer new opportunities for the synthesis, discovery, and optimization of bioactive molecules.
|
Xinkun Ren; Bo M. Couture; Ningyu Liu; Manjinder S. Lall; Jeffrey T. Kohrt; Rudi Fasan
|
Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Bioengineering and Biotechnology; Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634ac5264b0af33a81c66ba5/original/enantioselective-single-and-dual-a-c-h-bond-functionalization-of-cyclic-amines-via-enzymatic-carbene-transfer.pdf
|
60c746060f50db4dff39639b
|
10.26434/chemrxiv.10413779.v1
|
The Influence of Ozone: Superstoichiometric Oxygen in Atomic Layer Deposition of Fe2O3 Using tert-Butylferrocene and O3
|
This work demonstrates a mechanistic study of iron oxide deposited by ALD, revealing a growth mechanism involving uptake of superstoichiometric oxygen. Material characterization shows ozone exposure can be used to convert the crystallographic phase and domain orientation of the materials. This mechanism has implications for wider classes of ozone-based ALD processes and can generalize to other systems.<br />
|
Joel Schneider; Jon Baker; Stacey Bent
|
Materials Processing; Thin Films; Organometallic Compounds; Spectroscopy (Inorg.); Crystallography – Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-11-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746060f50db4dff39639b/original/the-influence-of-ozone-superstoichiometric-oxygen-in-atomic-layer-deposition-of-fe2o3-using-tert-butylferrocene-and-o3.pdf
|
66686aace7ccf7753a833598
|
10.26434/chemrxiv-2024-th0d9-v2
|
Towards Efficient and Unified Treatment of Static and Dynamic Correlations in Generalized Kohn-Sham Density Functional Theory
|
Accurate description of the static correlation poses a persistent challenge for electronic structure theory, particularly when it has to be concurrently considered with the dynamic correlation. We develop here a ground breaking method in the generalized Kohn-Sham density functional theory (DFT) framework, named R-xDH7-SCC15, which achieves an unprecedented accuracy in capturing the static correlation, while maintaining a good description of the dynamic correlation on par with the state-of-the-art DFT and wave function theory methods, all grounded in the same single-reference black-box methodology. Central to R-xDH7-SCC15 is a novel, general-purpose static correlation correction (SCC) model applied to the renormalized XYG3-type doubly hybrid method (R-xDH7). The SCC model development pioneers a hybrid machine learning strategy that ingeniously harmonizing symbolic regression with nonlinear parameter optimization, to strike a balance between enhanced generalization capability, rigorous numerical accuracy, and retained interpretability of the SCC model. Extensive benchmark studies confirm the robustness and broad applicability of R-xDH7-SCC15 across a diverse array of chemical scenarios. Notably, it displays exceptional aptitude in accurately characterizing intricate reaction kinetics and dynamic processes in regions distant from equilibrium, where the influence of static correlation is most profound. Its capability to consistently and efficiently predict energy profiles, activation barriers, and reaction pathways within a user-friendly “black-box” framework, signifies a paradigm shift in our ability to model and comprehend complex chemical transformations, thereby marking a significant stride in the field of electronic-structure theory.
|
Yizhen Wang; Zihan Lin; Runhai Ouyang; Bin Jiang; Igor Ying Zhang; Xin Xu
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66686aace7ccf7753a833598/original/towards-efficient-and-unified-treatment-of-static-and-dynamic-correlations-in-generalized-kohn-sham-density-functional-theory.pdf
|
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.