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62529e63bdc9c24e22d07fea | 10.26434/chemrxiv-2022-3z76v | Structure-Activity Relationships of Antibody-Drug Conjugates: A Systematic Review of Chemistry on the Trastuzumab Scaffold | Antibody-drug conjugates (ADCs) are a rapidly growing class of cancer therapeutics. The goal of ADCs is to overcome the low therapeutic index of conventional cytotoxic agents. However, realizing this goal has been a significant challenge. Consisting of an antibody linked to a therapeutic payload, ADCs comprise many components which can be modified, including the target, payload, linker, and bioconjugation method. Many approaches have been developed to improve the physical properties, potency, and selectivity of ADCs. The anti-HER-2 antibody trastuzumab, first approved in 1998, has emerged as an exceptional targeting agent for ADCs, as well as a broadly used platform for testing new technologies, The extensive work in this area enables the comparison of various linker strategies, payloads, drug-to-antibody ratios (DAR), and mode of attachment. In this review, these conjugates, ranging from the first clinically approved trastuzumab ADC, Kadcyla (T-DM1) to the latest variants, are described with the goal of providing a broad overview and comparison of existing and emerging conjugate technologies. | Siddharth Matikonda; Ryan Mclaughlin; Pradeep Shrestha; Carol Lipshultz; Martin Schnermann | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62529e63bdc9c24e22d07fea/original/structure-activity-relationships-of-antibody-drug-conjugates-a-systematic-review-of-chemistry-on-the-trastuzumab-scaffold.pdf |
60c74681ee301cf695c79538 | 10.26434/chemrxiv.11340170.v1 | Full Energy Range Resonant Inelastic X-Ray Scattering of O2 and CO2: Direct Comparison with Oxygen Redox State in Batteries | The varying oxygen state plays key roles in the performance and stability of various electrochemical systems. However, the nature of the non-divalent state remains elusive with speculations under active debates. A direct comparison between these unconventional states on their full oxygen spectroscopic profile is critical but remains missing. Here, high-efficiency full energy range O-K mapping of resonant inelastic x-ray scattering (mRIXS) was collected from O<sub>2</sub> (O<sup>0</sup>) and CO<sub>2</sub> (O<sup>2-</sup>) gas molecules. The results are compared directly with Li<sub>2</sub>O<sub>2</sub> (O<sup>1-</sup>) and more importantly, the oxidized oxygen (O<sup>n-</sup>, 0-n-2) state in representative Na-ion and Li-ion battery electrodes. All the mRIXS features of O<sub>2</sub> and CO<sub>2</sub> are interpreted, and we focus on the contrasts of two characteristic features among all oxidized oxygen species, especially on the striking 523.7 eV emission feature. The full mRIXS profile reveals that oxygen redox states in batteries have distinct distributions along the excitation energy compared with Li<sub>2</sub>O<sub>2</sub> and O<sub>2</sub>. This work provides not only the first full range mRIXS results of O<sub>2</sub> and CO<sub>2</sub>, but also the direct comparison of four different oxygen states, i.e., O<sup>2-</sup>, O<sup>1-</sup>, O<sup>n-</sup>(0-n-2), and O<sup>0</sup>. Our results indicate that the nature of the oxidized oxygen state in oxide electrodes is beyond a simple molecular configuration of either peroxide or O<sub>2</sub>. | Zengqing Zhuo; Yi-Sheng Liu; Jinghua Guo; Yi-de Chuang; Feng Pan; Wanli Yang | Energy Storage; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74681ee301cf695c79538/original/full-energy-range-resonant-inelastic-x-ray-scattering-of-o2-and-co2-direct-comparison-with-oxygen-redox-state-in-batteries.pdf |
66d349d020ac769e5f79ac5f | 10.26434/chemrxiv-2024-13wd7 | Water-in-Bisalt Electrolytes with Enhanced Transport Properties and Electrochemical Stability | This study introduces a binary salt approach for achieving high K+ concentration with tunable solvation sphere composed of acetate (Ac⁻) and trifluoromethane sulfonate (OTf⁻) anions, and water, suited for potassium-ion batteries. By the elimination of the free water molecules from the electrolyte through the judicious selection of the hydrophobic and hydrophilic anions and the solvation disproportion resulting from the bi-salt approach, very high K+ concentration was achieved while simultaneously maintaining good transport properties and widened electrochemical stability window. | Burcu Gurkan; Mukhilan Dhasarathaboopathy; Palani Sabhapathy | Physical Chemistry; Energy | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d349d020ac769e5f79ac5f/original/water-in-bisalt-electrolytes-with-enhanced-transport-properties-and-electrochemical-stability.pdf |
66a99655c9c6a5c07a8d95a5 | 10.26434/chemrxiv-2024-lmbjp | Broad Range Material-to-System Screening of Metal-Organic Frameworks for Hydrogen Storage Using Machine Learning | Hydrogen is pivotal in the transition to sustainable energy systems, serving essential roles in both power generation and industrial applications. Metal-organic frameworks have emerged as promising candidates for efficient hydrogen storage. However, identifying promising candidates for deployment is challenging due to the vast number of synthesized MOFs. This study integrates molecular simulations, machine learning, and techno-economic analysis to evaluate the performance of MOFs across broad operation conditions for different scales and durations of hydrogen storage applications. While previous screenings of the MOF database have predominantly emphasized high hydrogen capacities under cryogenic conditions, we identify that optimal temperatures and pressures for cost minimization depend on the raw price of the MOF. Specifically, when MOFs are priced at $15/kg, 99.72% exhibit optimal cost-efficiency within a temperature range of 180 K to 250 K and 98.9% achieve this at pressure of 150 bar. Furthermore, we characterize correlations between system cost and material properties, identifying key promising features of MOFs for low-cost systems including low densities (<1 g/cm³), high surface areas (>1500 m²/L), large void fractions (>0.6), and high pore volumes (>0.8 cm³/g). | Xinyi Wang; Hanna Breunig; Peng Peng | Materials Science; Energy | CC BY NC 4.0 | CHEMRXIV | 2024-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a99655c9c6a5c07a8d95a5/original/broad-range-material-to-system-screening-of-metal-organic-frameworks-for-hydrogen-storage-using-machine-learning.pdf |
60c74bd1337d6cf2a8e27b3a | 10.26434/chemrxiv.12380660.v1 | Pressure-Dependent Kinetics of Peroxy Radicals Formed in Isobutanol Combustion | Bio-derived isobutanol has been approved as a gasoline additive in the
U.S., but our understanding of its combustion chemistry still has
significant uncertainties. Detailed quantum calculations could improve
model accuracy leading to better estimation of isobutanol’s combustion
properties and its environmental impacts. This work examines 47
molecules and 38 reactions involved in the first oxygen addition to
isobutanol’s three alkyl radicals located α, β, and γ to the hydroxide.
Quantum calculations were mostly done at
CCSD(T)-F12/cc-pVTZ-F12//B3LYP/CBSB7, with 1-D hindered rotor
corrections obtained at B3LYP/6-31G(d). The resulting potential energy
surfaces are the most comprehensive isobutanol peroxy networks published
to date. Canonical transition state theory and a 1-D microcanonical
master equation are used to derive high-pressure-limit and
pressure-dependent rate coefficients, respectively. At all conditions
studied, the recombination of α- isobutanol radical with O2 forms HO2
and isobutanal. The recombination of γ-isobutanol radical with O2 forms
a stabilized hydroperoxy alkyl radical below 400 K, water and an alkoxy
radical at higher temperatures, and HO2 and an alkene above 1200 K. The
recombination of β-isobutanol radical with O2 results in a mixture of
products between 700-1100 K, forming acetone, formaldehyde and OH at
lower temperatures and forming HO2 and alkenes at higher temperatures.
The barrier heights, high-pressure-limit rates, and pressure-dependent
kinetics generally agree with the results from previous quantum
chemistry calculations. Six reaction rates in this work deviate by over
three orders of magnitude from kinetics in detailed models of isobutanol
combustion, suggesting the rates calculated here can help improve
modeling of isobutanol combustion and its environmental fate. | Mark Goldman; Jesse Kroll; William H. Green | Physical Organic Chemistry; Chemical Kinetics; Quantum Mechanics; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2020-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bd1337d6cf2a8e27b3a/original/pressure-dependent-kinetics-of-peroxy-radicals-formed-in-isobutanol-combustion.pdf |
65ae13fd66c1381729fde3dd | 10.26434/chemrxiv-2024-9f3jx | Synthesis and Characterization of a Dioxomolybdenum Complex [cis-MoO2(OV)2] Using Ortho-Vanilline (OV) as a Ligand | This work presents a comprehensive exploration of the synthesis and experimental characterization of cis-MoO2(OV)2. The study includes a thorough analysis of the single crystal structure of the complex and also validates the experimental findings and establishes the high purity of the synthesized Mo-complex using Density Functional Theory (DFT). The combined experimental and computational approach enhances the reliability of the results, contributing to a more robust understanding of the synthesized cis-MoO2(OV)2 compound. | Priyangana Deb | Inorganic Chemistry; Coordination Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ae13fd66c1381729fde3dd/original/synthesis-and-characterization-of-a-dioxomolybdenum-complex-cis-mo-o2-ov-2-using-ortho-vanilline-ov-as-a-ligand.pdf |
60c744df567dfe5a6eec4359 | 10.26434/chemrxiv.9918470.v1 | Simultaneous Generation of a [2×2] Grid-like Complex and a Linear Double Helicate: A Three-Level Self-Sorting Process | <div>Two constitutional dynamic libraries (CDLs)—each
containing two amines, two dialdehydes and two metal salts—have been
found to self-sort, generating two pairs of imine-based
metallosupramolecular architectures sharing no component, a [2×2]
grid-like complex and a linear double helicate. These CDLs provided
unique examples of a three-level self-sorting process, as only two
imine-based ligand constituents, two metal complexes and two
architectures were selected during their assembling out of all the
possible combinations of their initial components. The
metallosupramolecular architectures assembled were characterized by NMR,
mass spectroscopy, and X-ray crystallography.</div> | Jean-François Ayme; Jean-Marie Lehn; Corinne Bailly; Lydia Karmazin | Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744df567dfe5a6eec4359/original/simultaneous-generation-of-a-2-2-grid-like-complex-and-a-linear-double-helicate-a-three-level-self-sorting-process.pdf |
63fe1546937392db3d34fa4a | 10.26434/chemrxiv-2021-r621x-v3 | Constant inner potential DFT for modelling electrochemical systems under constant potential and bias | Electrochemical interfaces and reactions play a decisive role in \textit{e.g.} clean energy conversion but understanding their complex chemistry remains an outstanding challenge. Constant potential or grand canonical ensemble (GCE) simulations are indispensable for unraveling the properties of electrochemical processes as a function of the electrode potential. Currently, GCE calculations at the density functional theory (DFT) level are carried out by fixing the Fermi level of the simulation cell. Here we show that this method is inadequate for modelling semiconductor electrodes, outer sphere reactions, and a biased two-electrode cell; for these systems the Fermi level obtained from DFT calculations does not reflect the experimentally controlled electrode potential or describe the thermodynamic independent variable in GCE-DFT. To remedy this deficiency, we developed and implemented a constant inner potential (CIP) method as a more robust and general approach to carry out GCE-DFT simulations of electrochemical systems under constant potential or bias conditions. In CIP-DFT the electrode inner potential and hence the thermodynamically relevant electron bath electrochemical are directly controlled which makes the method widely applicable in simulating electrochemical interfaces. We demonstrate that the CIP and Fermi level GCE-DFT approaches are equivalent for metallic electrodes and inner-sphere reactions but CIP is also applicable to systems for which the constant Fermi level approach fails. A key advantage of CIP is that, unlike the Fermi level method, it does not require any electronic structure information. This is because only the inner potential of the systems is needed, CIP is also more compatible with classical force field or machine learning potentials. Altogether, the CIP approach emerges as a general and efficient GCE-DFT method to simulate (photo)electrochemical interfaces from first principles. | Marko Melander; Tongwei Wu; Karoliina Honkala | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Theory - Computational; Electrocatalysis; Electrochemistry - Mechanisms, Theory & Study | CC BY 4.0 | CHEMRXIV | 2023-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63fe1546937392db3d34fa4a/original/constant-inner-potential-dft-for-modelling-electrochemical-systems-under-constant-potential-and-bias.pdf |
649aa081ba3e99daef1cdd86 | 10.26434/chemrxiv-2023-lwj87 | CASNet: Learning Complete Active Space Orbitals using Message Passing Neural Networks | Machine learning has demonstrated success in predicting molecular orbitals obtained from common single-configurational quantum chemistry methods, such as Hartree-Fock or Kohn-Sham Density Functional Theory. In this work, we present an extension of this supervised learning framework to multi-configurational quantum chemistry methods and compare different approaches for learning excited-state molecular wavefunctions. More specifically, by utilizing recent advances in message passing neural networks designed for learning molecular properties, we investigate the learning of molecular orbitals from State-Averaged Complete Active Space Self Consistent Field as a means of speeding up the corresponding calculations. We demonstrate the advantage of this general approach, referred to as \textit{CASNet}, over traditional orbital initialization techniques on different datasets of pentafulvene and evaluate its practical utility. | Ruard van Workum; Joao Malhado; Philipp Marquetand | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649aa081ba3e99daef1cdd86/original/cas-net-learning-complete-active-space-orbitals-using-message-passing-neural-networks.pdf |
67da2e7f81d2151a02f23f80 | 10.26434/chemrxiv-2025-w4vvr | Carboranes without Cage Carbons: closo-Dodecaborate Mimics of Neutral closo-Carboranes | Substituted two-dimensional aromatic systems, such as arenes, exhibit well-established reactivity patterns at specific sites, largely due to the pronounced electronic directing effects of attached substituents. In contrast, the regioselectivity of three-dimensional aromatic molecules as a function of substituents remains less understood and documented. In this work, we demonstrate that a series of closo-dodecaborate ([B12H12]2-) cluster isomers containing two -NMe₃⁺ moieties exhibit unprecedented regioselective reactivity at boron vertices farthest from the charged substituents. Through a combination of theoretical and experimental studies, we reveal that these boron clusters display near-perfect regioselectivity with multiple electrophiles, ultimately enabling vertex differentiation chemistry within these systems. This observed phenomenon closely parallels the reactivity patterns typically associated with icosahedral closo-carboranes, where a carbon-based vertex induces a strong electronic dipole, leading to pronounced vertex-specific reactivity differences at boron sites. Our findings suggest that these modified closo-dodecaborates serve as electronic analogs of closo-carboranes, achieving similar electronic directing effects without the need for cage-based carbon atoms. Instead, exopolyhedral substituents alone govern the regioselective behavior, expanding the potential for tailored functionalization in boron cluster chemistry. | Austin Ready; Varun Tej Raviprolu; Tyler Kerr; Joseph W. Treacy; Mei Matsumoto; Prairie Hammer; Ellen Sletten; K. N. Houk; Alexander Spokoyny | Theoretical and Computational Chemistry; Inorganic Chemistry; Bonding; Main Group Chemistry (Inorg.); Reaction (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67da2e7f81d2151a02f23f80/original/carboranes-without-cage-carbons-closo-dodecaborate-mimics-of-neutral-closo-carboranes.pdf |
64e8c60279853bbd786af71a | 10.26434/chemrxiv-2023-b9mr1 | Identification of RNA-containing virus particles using a triple correlative morphological and microscopic approach | Viral characterization based on different characteristics such as size or morphology is an important step towards a quick identification of virus infection. In this contribution, the identification and size determination of an isolated RNA virus with an atomic force microscope (AFM) in combination with conventional fluorescence microscopy is presented. Despite all the advantages of AFM for imaging individual viruses, discrimination by chemical composition and reliable differentiation of morphologically similar structures at the single particle level is hardly possible with the current state of the art. An effective method for identifying single virus particles based on their chemical structure is specific labeling and subsequent conventional fluorescence microscopic investigation. However, this method lacks morphologic information, and the resolution is generally above the virus size, impeding size determination. As a result, labeled hollow particles or viral fragments cannot be distinguished from intact particles of a similar size.
In our experiments, the goal was to characterize and investigate the morphology, particularly the height of a model virus, here SARS-CoV-2 as an example, and unambiguously differentiate it from other sample components such as debris. The first step was topography mapping of inactivated virus samples using AFM. In the second step, the RNA-containing core and the spike proteins on the virus surface were labeled, and conventional fluorescence images were correlated with the topographic height images of the same particles, providing an accurate information about the actual stages of the viruses. As a main achievement, the experiments allow identification of individual intact SARS-CoV-2 particles and a distinction between viral fragments and potential false staining. The height range of virus particles under our specific inactivation conditions with paraformaldehyde treatment could be determined to be 60-110 nm. Following our results, pre-selection and distinction of viral particles from other sample components will be feasible by morphological characteristics alone, with a precision comparable to staining methods, prior to further specific identification. In general, our correlative approach combining information from scanning probe and conventional fluorescence microscopy can be applied to other virus strains as well, taken that virus-specific antibodies are known.
| Tanja Deckert-Gaudig; Xiaobin Yao; Erwan Darussalam; Franziska Hornung; Pablo Carravilla; Ziliang Zhao; Kourosh Rezaei; Christian Eggeling; Stefanie Deinhardt-Emmer; Volker Deckert | Biological and Medicinal Chemistry; Analytical Chemistry; Nanoscience; Imaging; Microscopy; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e8c60279853bbd786af71a/original/identification-of-rna-containing-virus-particles-using-a-triple-correlative-morphological-and-microscopic-approach.pdf |
61ae695702d90d24a656f23d | 10.26434/chemrxiv-2021-bwwfv | Organic Photoredox Catalyzed Direct Hydroamination of
Ynamides with Azoles | Disclosed herein is a novel photoinduced
selective hydroamination of ynamides with nitrogen
heteroaromatic nucleophiles. By using an
organocatalytic photoredox system, a direct method to
construct a diverse of (Z)-α-azole enamides from
ynamides and pyrazoles, as well as triazoles,
benzotriazoles, indazoles, and tetrazoles, is developed,
thus providing a concise route to heterocyclic motifs
common in medicinal agents. Based on the mechanistic
studies, the hydroamination is postulated to operate via a
mechanism in which the single-electron oxidation of
ynamide and the intermediacy of an alkyne radical
cation, is responsible for the observed reactivity. | Yongming Deng; Ban Wang; Gavin Mccabe ; Mitchell Parrish ; Jujhar Singh; Matthias Zeller | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2021-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ae695702d90d24a656f23d/original/organic-photoredox-catalyzed-direct-hydroamination-of-ynamides-with-azoles.pdf |
66f5783acec5d6c1424b65a5 | 10.26434/chemrxiv-2024-llv6q | Discovery of a broad-spectrum, fluorinated macrobicyclic antibiotic through chemical synthesis | We report the discovery through chemical synthesis of BT-33, a fluorinated macrobicyclic oxepanoprolinamide antibiotic. BT-33 potently inhibits the growth of multidrug-resistant clinical isolates of Gram-positive and Gram-negative bacteria and has an extended half-life in vivo relative to its predecessors cresomycin and iboxamycin. We report structure-activity relationships within the macrobicyclic substructure, which reveal structural features that are essential to the enhanced potency of BT-33 as well as its increased metabolic stability. We determine the structure of BT-33 in complex with the bacterial ribosome by X-ray crystallography, analysis of which suggests that the newly introduced fluorine atom makes an additional Van der Waals contact with nucleobase G2505. Finally, we show that the C7-methyl group of BT-33 rigidifies the macrocyclic ring in a conformation that is highly preorganized for ribosomal binding by using variable-temperature 1H-NMR experiments, density-functional theory calculations, and vibrational circular dichroism spectroscopy to compare macrobicyclic homologs of BT-33 and a C7-desmethyl analog. | Ben Tresco; Kelvin Wu; Antonio Ramkissoon; Elena Aleksandrova; Michael Purdy; Dominic See; Richard Liu; Yury Polikanov; Andrew Myers | Biological and Medicinal Chemistry; Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f5783acec5d6c1424b65a5/original/discovery-of-a-broad-spectrum-fluorinated-macrobicyclic-antibiotic-through-chemical-synthesis.pdf |
674ff2a15a82cea2faea06f3 | 10.26434/chemrxiv-2024-k2k3l | Neural Mulliken Analysis: Molecular Graphs from Density Matrices for QSPR on Raw Quantum-Chemical Data | Since the introduction of Graph Neural Networks (GNNs), molecular graphs have become useful tools in chemical informatics. However, in property prediction tasks, graph embeddings often still resemble traditional fingerprints. Here, we propose a straightforward approach to provide modern GNNs with raw quantum-chemical data, enabling efficient solutions to a range of chemical machine-learning problems. The central role is played by the 1-electron density matrix derived from quantum chemical calculations (e.g. Hartree-Fock, DFT). The diagonal blocks of the density matrix are used as embeddings for the atomic nodes (“atoms”) in the molecular graph. Unlike conventional molecular graph representations, the chemical bond concept is not used. Instead, an additional set of nodes (“links”) between pairs of atoms is introduced. Their embeddings are the off-diagonal blocks of the density matrix, related to particular atom pairs. Directed graph edges connect either “atoms” with “links” or vice versa. The embeddings of the edges are derived from the basis set overlap matrix. The overlaps serve two purposes: first, they encode structural information such as distances and angles. Second, they act as weights in pooling operations. The use of element-wise multiplication of densities and overlaps is inspired by the Mulliken population analysis scheme. The proposed concept was further tested using the Solubility Challenge (2008) by Llinàs et al. (DOI: 10.1021/ci800058v). A GNN was trained on a small dataset comprising 94 aqueous solubilities of drug-like molecules and subsequently used to predict the aqueous solubilities of 28 test molecules. The model achieved an RM SE of 0.68 and an R 2 of 0.76, outperforming all methods proposed at that time. In our view, this represents a promising approach, particularly considering that even in a preliminary test the proposed architecture seems to be able to achieve state-of-the-art accuracy. | Oleg Gromov | Theoretical and Computational Chemistry; Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674ff2a15a82cea2faea06f3/original/neural-mulliken-analysis-molecular-graphs-from-density-matrices-for-qspr-on-raw-quantum-chemical-data.pdf |
60c74f890f50db631e397414 | 10.26434/chemrxiv.12919235.v1 | Doubly Protonated Species Collision Induced Dissociation for Identification of Isocyclosporins | Nonribosomal cyclopeptide cyclosporin A (CsA), produced by fungus <i>Tolypocladium inflatum</i>, is an extremely
important immunosuppressive drug used in organ transplantations and for therapy
of autoimmune diseases. Here we report for the first time production of CsA,
along with related cyclosporins B and C, by <i>Tolypocladium
inflatum </i>strains of marine origin (White Sea). Cyclosporins A–C contain an
unusual amino acid, (4<i>R</i>)-4-((<i>E</i>)-2-butenyl)-4,<i>N</i>-dimethyl-l-threonine
(MeBmt), and are prone to isomerization to non-active isocyclosporine by N→O
acyl shift of valine connected to MeBmt in acidic conditions. CsA and isoCsA
are not distinguishable in MS analysis of [M+H]<sup>+</sup> ions due to the rapid
[CsA+H]<sup>+</sup>→[isoCsA+H]<sup>+</sup> conversion. We found that the N→O
acyl shift is completely suppressed in cyclosporine [M+2H]<sup>2+</sup> ions,
and their MS/MS fragmentation can be used for rapid and unambiguous analysis of
cyclosporins and isocylosporins. The fragmentation patterns of [CyA+2H]<sup>2+</sup>
and [isoCyA+2H]<sup>2+</sup> ions were analyzed and explained. The developed
approach could be useful for MS analysis of other peptides containing β-hydroxy-α-amino
acids. | Anna Baranova; Alexey Chistov; Maxim Shuvalov; Anton Tyurin; Mikhail Biryukov; Igor Ivanov; Vera Sadykova; Aleksander Kurakov; Albina Sregeeva; Vladimir Korshun; Vera Alferova | Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f890f50db631e397414/original/doubly-protonated-species-collision-induced-dissociation-for-identification-of-isocyclosporins.pdf |
60c740624c891984e1ad210f | 10.26434/chemrxiv.7722359.v1 | From Inhibition to Degradation: Targeting the Anti-apoptotic Protein Myeloid Cell Leukemia 1(MCL1) | <div>
<div>
<div>
<p>Here we show the
development of heterobifunctional small molecules capable of selectively targeting MCL1 using
a Proteolysis Targeting Chimera (PROTAC) methodology leading to successful degradation. We
have confirmed the involvement of the E3 ligase CUL4A-DDB1 cereblon (CRBN) ubiquitination
pathway, making these PROTACs a first step toward a new class of anti-apoptotic BCL-2 family
protein degraders.
</p>
</div>
</div>
</div> | James Papatzimas; Evgueni Gorobets; Ranjan Maity; Mir Ishruna Muniyat; Justin L. MacCallum; Paola Neri; Nizar J. Bahlis; Darren Derksen | Bioorganic Chemistry; Organic Synthesis and Reactions; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740624c891984e1ad210f/original/from-inhibition-to-degradation-targeting-the-anti-apoptotic-protein-myeloid-cell-leukemia-1-mcl1.pdf |
6737a0027be152b1d0323125 | 10.26434/chemrxiv-2024-9xw6v | Possible Applications of the Polli Dissolution Mechanism: A Case Study Using Molecular Dynamics Simulation of Bupivacaine | The recently proposed Polli equation [Polli JE. A simple one-parameter percent dissolved versus time dissolution equation that accommodates sink and non-sink conditions via drug solubility and dissolution volume. AAPS J 2023;25:1] has been discussed in the context of its ability to fit experimental dissolution transients obtained under either sink or non-sink conditions. In this work, we reveal that the Polli equation describes a complex dissolution mechanism that combines classical first-order (Noyes-Whitney) kinetics with a second-order mechanism. Possible origins of the second-order process are discussed within the framework of small-molecule drug dissolution, after first probing the general utility of the higher-order rate term in more precisely fitting typical dissolution transients (for ibuprofen and ketoconazole) taken from the referenced work. Lastly, molecular dynamics (MD) simulations are performed using the prototypical drug, bupivacaine, that is shown to dimerize in aqueous solution under acidic conditions. Our findings point us to conclude that the Polli mechanism best describes cases where the drug forms dimers in solution at a rate comparable to that with which it dissolves (per the N-W mechanism), given non-sink conditions. Under sink conditions, the Polli mechanism is second-order in drug concentration. | Peter Skrdla; Andrea Browning; Shiva Sekharan; Jacob Gavartin | Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry; Theory - Computational; Chemical Kinetics; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6737a0027be152b1d0323125/original/possible-applications-of-the-polli-dissolution-mechanism-a-case-study-using-molecular-dynamics-simulation-of-bupivacaine.pdf |
6441ba4cdf78ec50151d1e5c | 10.26434/chemrxiv-2022-1vmjt-v2 | Pharmacology and Therapeutic Potential of Benzothiazole Analogues for Cocaine Use Disorder | The dopamine D4 receptor (D4R), a G protein-coupled receptor, is predominantly expressed in brain regions that control cognition, attention, and decision making. Previous studies have indicated that D4R-targeted ligands could be promising therapeutic targets for the treatment of several neuropsychiatric conditions, including substance use disorders (SUDs). There are currently no FDA-approved medications that selectively target D4Rs. New ligands may facilitate better understanding of the role of D4R-mediated signaling in drug-taking and drug-seeking behaviors. The present study focuses on the synthesis and evaluation of a novel series of benzothiazole analogues designed to target D4R. We identified several compounds with high D4R binding affinity (Ki ≤ 6.87 nM) and >91-fold selectivity over other D2-like receptors (D2R, D3R) with diverse partial agonist and antagonist profiles. Based on receptor affinity and functional analyses, 5f was identified as a potent low-efficacy partial agonist of the D4R and selected for further investigation. 5f was metabolically stable in rat and human liver microsome assays and displayed excellent brain penetration in rats. Using a within-session multidosing procedure, 5f (5, 15 and 30 mg/kg, i.p.) dose-dependently decreased i.v. infusions of three-unit doses of cocaine under a fixed-ratio (FR) FR3 schedule of reinforcement. These results are consistent with previous results produced by D4R-selective antagonists in SUD models, however off-target antagonism of 5-HT2A or 5-HT2B receptors may also contribute to these effects. Results with compound 5f support further efforts to target D4R in the treatment of SUDs. Further development of the benzothiazole scaffold may engineer out any serotonergic activity. | Comfort A. Boateng; Ashley N. Nilson; Rebekah Placide; Mimi L. Pham; Franziska M. Jakobs; Noelia Boldizsar; Scot McIntosh; Leia S. Stallings; Ivana V. Korankyi; Shreya Kelshikar; Nisha Shah; Diandra Panasis; Abigail Muccilli; Maria Ladik; Brianna Maslonka; Connor McBride; Moises Ximello Sanchez; Ebrar Akca; Mohammad Alkhatib; Julianna Saez; Catherine Nguyen; Emily Kurtyan; Jacquelyn DePierro; Raymond Crowthers; Dylan Brunt; Alessandro Bonifazi; Amy H. Newman; Rana Rais; Barbara S. Slusher ; R. Benjamin Free; David R. Sibley; Kent D. Stewart ; Chun Wu; Scott E. Hemby; Thomas M. Keck | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6441ba4cdf78ec50151d1e5c/original/pharmacology-and-therapeutic-potential-of-benzothiazole-analogues-for-cocaine-use-disorder.pdf |
60c73fe3842e65ab92db1bc4 | 10.26434/chemrxiv.7553444.v1 | A Revised Modular Approach to D8-THC and Derivatives Through Late-Stage Suzuki-Miyaura Cross-Coupling Reactions | <p>In this manuscript we describe a modular pathway
to synthesize biologically relevant (–)-<i>trans</i>-Δ<sup>8</sup>-THC
derivatives, which can be used to modulate the pharmacologically important CB<sub>1</sub>
and CB<sub>2</sub> receptors. This pathway involves a one-pot Friedel-Crafts
alkylation/cyclization protocol, followed by Suzuki-Miyaura cross-coupling
reactions and gives rise to a series of new Δ<sup>8</sup>-THC derivatives. In addition, we
demonstrate using extensive NMR evidence that similar halide-substituted
Friedel-Crafts alkylation/cyclization products in previous articles were
wrongly assigned as the para-isomers, which also has consequence for the
assignment of the subsequent cross-coupled products and interpretation of their
biological activity. </p>
<p>Considering the importance of the availability
of THC derivatives in medicinal chemistry research and the fact that previously
synthesized compounds were wrongly assigned, we feel this research is describing a
straightforward pathway into new cannabinoids.</p> | Victor Bloemendal; Floris P. J. T. Rutjes; Thomas
J. Boltje; Daan Sondag; Hidde Elferink; Jan C.M. van Hest | Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fe3842e65ab92db1bc4/original/a-revised-modular-approach-to-d8-thc-and-derivatives-through-late-stage-suzuki-miyaura-cross-coupling-reactions.pdf |
6785a3e781d2151a02fe8b5f | 10.26434/chemrxiv-2024-nmnr8-v4 | Degradation pathways in lithium-ion batteries with ethylene carbonate-free electrolytes | The development of stable electrolyte solutions is critical for improving the lifetime and performance of lithium-ion batteries (LIBs). Electrolyte instability is a prominent issue with many next-generation electrode materials, such as Ni-rich cathodes, with recent reports identifying ethylene carbonate (EC) as a bad actor at the cathode surface. Herein, electrochemical methods, operando pressure measurements, and post-mortem X-ray and solution NMR studies are combined to investigate electrolyte and interfacial degradation phenomena in Ni-rich LiNi0.8Mn0.1Co0.1O2 (NMC811)/graphite full cells with EC-containing and EC-free electrolytes. One key finding is that the mechanism for improved performance in EC-free electrolyte – 1.5 M LiPF6 in ethyl methyl carbonate (EMC) with 10 wt.% fluoroethylene carbonate (FEC) – arises from improved stability at both electrode-electrolyte interfaces. The EC-free electrolyte is found to suppress lattice oxygen release and reduced surface layer formation at NMC, leading to improved ion transport into the cathode particles, suppressed electrolyte solvent oxidation reactions, less formation and crossover of species that disrupt the graphite solid electrolyte interphase (SEI), and ultimately improved capacity retention. These insights are helpful to understand and mitigate degradation in LIBs with Ni-rich cathodes. | Jason S. Terreblanche; Tongjun Luo; Louis F. J. Piper; Wesley M. Dose | Energy; Energy Storage | CC BY NC 4.0 | CHEMRXIV | 2025-01-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6785a3e781d2151a02fe8b5f/original/degradation-pathways-in-lithium-ion-batteries-with-ethylene-carbonate-free-electrolytes.pdf |
6703d47c51558a15ef5b3b15 | 10.26434/chemrxiv-2024-l6wnt-v2 | Deep learning methods for de novo peptide sequencing | Protein tandem mass spectrometry data is most often interpreted by matching observed mass spectra to a protein database derived from the reference genome of the sample being analyzed. In many application domains, however, a relevant protein database is unavailable or incomplete, and in such settings de novo sequencing is required. Since the introduction of the DeepNovo algorithm in 2017, the field of de novo sequencing has been dominated by deep learning methods, which use large amounts of labeled mass spectrometry data to train multi-layer neural networks to translate from observed mass spectra to corresponding peptide sequences. Here, we describe these deep learning methods, outline procedures for evaluating their performance, and discuss the challenges in the field, both in terms of methods development and evaluation protocols. | Wout Bittremieux; Varun Ananth; William E. Fondrie; Carlo Melendez; Marina Pominova; Justin Sanders; Bo Wen; Melih Yilmaz; William Stafford Noble | Theoretical and Computational Chemistry; Analytical Chemistry; Mass Spectrometry; Machine Learning; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2024-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6703d47c51558a15ef5b3b15/original/deep-learning-methods-for-de-novo-peptide-sequencing.pdf |
646e2ad7e64f843f41b3a0e6 | 10.26434/chemrxiv-2023-t6s5l | A monometallic approach for the C(sp2)-C(sp2) cross-electrophile coupling: Bypassing the demand of transmetalation | Transition metal catalyzed cross-coupling is a versatile tool for the construction of (hetero)biaryl scaffolds. However, the cross-electrophile coupling using abundant (hetero)aryl halides and pseudohalides is still in its infancy. In particular, a robust and general method for the cross-electrophile coupling would allow unparalleled entry into the vast collection of commercially available, structurally-diverse (hetero)aryl halides and pseudohalides as coupling partners. We demonstrate herein a ligand controlled visible light driven monometallic cross-electrophile coupling platform in which the synergistic operation of dual palladium catalytic cycle differentiates the electrophiles based on the bond dissociation enthalpy. This method is mild, robust, selective, and displays unique efficacy towards a wide range of functional groups and challenging heteroaryls, providing access to structurally diverse (hetero)biaryl scaffolds. The power of the transformation has been revealed through the synthesis of (hetero)biaryl core of various pharmaceuticals, and diversification of peptides. The synthesis of more than 54% new (hetero)biaryl core has been demonstrated, allowing access to an expanded chemical space for further exploration in functional materials, drug discovery, and bioconjugation-based therapeutics development. Bypassing the traditional transmetalation step, this technology enables a general strategy for the cross-electrophile coupling of (hetero)aryl halides and pseudohalides. | Debabrata Maiti; Sudip Maiti; Pintu Ghosh; Dineshkumar Raja; Sudev Ghosh; Sagnik Chatterjee; Velayudham Sankar; Sayan Roy; Goutam Kumar Lahiri | Catalysis; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2023-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646e2ad7e64f843f41b3a0e6/original/a-monometallic-approach-for-the-c-sp2-c-sp2-cross-electrophile-coupling-bypassing-the-demand-of-transmetalation.pdf |
60c74fca702a9b653918bc51 | 10.26434/chemrxiv.12942305.v1 | Hadoop Spark Based Hydrogen Bond Analysis Tool (H-BAT) for Molecular Dynamics Simulation Trajectory Data | Molecular dynamics (MD) is a computational technique that works on the Newton's equations of motion to study the dynamics of various biomolecules and, is commonly used by structural biologists. With the development of advanced simulation techniques and increasing computing power, large amounts of data are being generated from these simulations. Various enhanced sampling techniques are currently being used, that are able to capture rare events and generate simulation data in the form of multiple trajectories. Analyzing the simulation trajectory data and extracting meaningful information using the traditional sequential post-simulation data analysis methods are becoming increasingly untenable. Currently, molecular dynamics simulation algorithms that are scalable on high-performance computing clusters are available which generate a huge amount of MD data in short span of time. The need of the hour lies in developing a advanced and high-performance analytics platform based tool that can analyze this huge simulation data in a faster and more efficient way. The Hadoop Spark framework, provides an excellent platform that meets these requirements of handling large amounts of data parallely and perform analytics with high scalability. In this study, a tool name H-BAT has been developed using the Hadoop Spark platform to calculate hydrogen bonding within all solute-solute, solute-solvent and solvent-solvent molecules in large MD simulation trajectories. Vector geometry has been used for calculation of angle and distance between the atoms which are present in the form of triplets of filtered atoms taking part in hydrogen bond formation. The benchmarking was performed up to a data size of 48 GB which showed linear scalability. Additionally, the tool is capable of handling multiple similar trajectories simultaneously. Future enhancement of the tool would include various other analysis like normal mode analysis, RMSD, 2DRMSD and Water Density Analysis using the Hadoop Spark framework.<br /> | Sandeep Surendra Malviya; Ramakrishnan Edyapatti Periyasamy; Vinod Jani; Mallikarjunachari Uppuladinne V N; Ankita Sonawane; Shruti Koulgi; Uddhavesh Sonavane; Rajendra Joshi | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fca702a9b653918bc51/original/hadoop-spark-based-hydrogen-bond-analysis-tool-h-bat-for-molecular-dynamics-simulation-trajectory-data.pdf |
60c756480f50dbbb1739806b | 10.26434/chemrxiv.14226554.v1 | Solvent Vapor Annealing, Defect Analysis, and Optimization of Self-assembly of Block Copolymers Using Machine Learning Approaches | Self-assembly of block copolymers (BCP) is an alternative patterning technique that promises sublithographic resolution and density multiplication. Defectivity of the resulting nanopatterns remains too high for many applications in microelectronics, and is exacerbated by small variations of processing parameters, such as film thickness, and fluctuations of solvent vapour pressure and temperature, among others. In this work, a solvent vapor annealing (SVA) flow-controlled system is combined with Design of Experiments (DOE) and machine learning (ML) approaches.<br /> | Gayashani Ginige; Youngdong Song; Brian Olsen; Erik Luber; Cafer Yavuz; Jillian Buriak | Nanostructured Materials - Materials; Nanofabrication | CC BY 4.0 | CHEMRXIV | 2021-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756480f50dbbb1739806b/original/solvent-vapor-annealing-defect-analysis-and-optimization-of-self-assembly-of-block-copolymers-using-machine-learning-approaches.pdf |
6741d4b95a82cea2fa856ca0 | 10.26434/chemrxiv-2024-sbzfx | Redox Tuning of Metals with High Coordination Numbers: Quantifying Systematic Charge Density Effects of Co-encapsulated Cations | Heavy element cations with large ionic radii naturally tend to adopt high coordination numbers (C.N. ≥ 8), endowing them with unique chemical and physical properties. Rational control of the redox chemistry or electronic properties of such systems with high C.N. values must overcome these ions’ high degree of structural freedom. Here, a tailored tripodal ligand has been used to establish stereochemical control over co-encapsulated cerium centers with C.N. = 7–9 and secondary monovalent (Li, Na, K) or divalent cations (Ca, Sr, Ba) with C.N. = 6–9. Spectroscopic and electrochemical studies reveal that Ce(III) and Ce(IV) forms of the complexes are accessible, enabling correlation of the characteristics manifested by the cerium cores with the properties of the incorporated secondary cations. The Ce(IV/III) reduction potential can be shifted systematically across a span of > 600 mV, representing a higher sensitivity to cation identity than in any tunable heterobimetallic nd- and 5f-element complexes studied to date. A structural model for understanding these effects was formulated on the basis of comprehensive X-ray diffraction analysis, revealing well-defined roles for both the ionic radius (position) and Lewis acidity (charge density) of the co-encapsulated secondary metal ions in influencing the cerium core. Formation of shared triangular faces between coordination polyhedra drives enables the high tuning sensitivity by generating an internuclear axis upon which the secondary cations adopt unique positions that are dictated by their size and coordination preferences rather than their charge states alone. | Julie Leseberg; Thaige Gompa; Emily Mikeska; Allen Oliver; Victor Day; Henry La Pierre; James Blakemore | Inorganic Chemistry; Lanthanides and Actinides | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6741d4b95a82cea2fa856ca0/original/redox-tuning-of-metals-with-high-coordination-numbers-quantifying-systematic-charge-density-effects-of-co-encapsulated-cations.pdf |
650413c1b6ab98a41c7aa4eb | 10.26434/chemrxiv-2023-6kq29-v2 | A machine learning framework for remaining useful lifetime prediction of li-ion batteries using diverse neural networks | Accurate prediction of the remaining useful life (RUL) of li-ion batteries (LIBs) is essential for enhancing the operational efficiency and safety of LIB-powered applications. It also facilitates improvements in the cell design process and the evolution of fast charging methodologies, thereby minimizing cycle testing time. While artificial neural networks (ANNs) have emerged as
promising tools for this task, identifying the optimal architecture across diverse datasets and optimization strategies is non-trivial. To address this challenge, a machine learning framework is developed for a systematic evaluation of diverse ANN architectures. Utilizing just 30% of the training dataset from 124 li-ion batteries cycled under various charging policies, hyperparameter optimization is conducted within this framework. This ensures that each model is evaluated at its optimal configuration, facilitating a balanced comparison for RUL prediction tasks. Furthermore, the study examines the influence of varied cycle windows on model efficacy. Employing a stratified partitioning method highlights the importance of uniform dataset representation across different subsets. Notably, the top-performing model, using cycle-by-cycle features from just 40 cycles, achieves a mean absolute percentage error of 10.7%. | Junghwan Lee; Huanli Sun; Yongshan Liu; Xue Li | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650413c1b6ab98a41c7aa4eb/original/a-machine-learning-framework-for-remaining-useful-lifetime-prediction-of-li-ion-batteries-using-diverse-neural-networks.pdf |
67099e0712ff75c3a12a09a2 | 10.26434/chemrxiv-2024-vwpww | Running and analyzing massively parallel molecular simulations | Protein conformational landscapes contain the functionally relevant information useful for understanding biological processes. Mapping out conformational landscapes provides valuable insights into protein behaviors and biological phenomena, and has relevance to therapeutic design. While experimental structural biology (X-ray, Cryo-EM, NMR) can provide high resolution structures, they struggle to provide information about the full conformational landscapes of biomolecules. Molecular dynamics (MD) simulations are a powerful tool for exploring these landscapes at atomic-scale resolution. However, inferring functionally relevant information, such as the full conformational pathway of long-timescale processes, the impact of mutations on binding, or allosteric coupling between residues across long distances, requires too extensive sampling that a single MD simulation may not achieve. This sampling limitation can be circumvented by generating datasets of parallel molecular simulations, a powerful approach to sample long-timescale events and study complex biological phenomena. Here, we discuss recent advances and present a practical guide to generating massively parallel molecular dynamics datasets. We start by detailing the practical considerations prior to generating a dataset, spanning from storage needs to the timescales addressed by the dataset, as well as modern simulation engines. Subsequently, we discuss how to analyze thee datasets to build unified models of conformational space, including future insights to be made possible by distributed simulation architectures. | Sukrit Singh; Sonya Hanson | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Biophysics; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67099e0712ff75c3a12a09a2/original/running-and-analyzing-massively-parallel-molecular-simulations.pdf |
64ca05b8dfabaf06ff91d465 | 10.26434/chemrxiv-2023-20hqn | (R/S-ClMBA)3GeI5: A Novel Low-Dimensional Ge-Containing Chiral Perovskite | We report here the first chiral perovskite containing germanium, namely (R/S-ClMBA)3GeI5. Single crystal x-ray diffraction shows the for-mation of a crystal structure composed of GeI6 octahedra arranged in linear zig-zag chains running along the b-axis, providing a one-dimensional (1D) system with a novel structural motif. The presence of Ge leads to the highest values of octahedral distortion parameters among chiral perovskites. Chiroptical properties determination by circular dichroism confirms the effective chirality transfer from the ligands to the in-organic framework with asymmetry factors of the order 10–3, with maximum absorbance around 420 nm. The demonstration of the successful preparation of Ge-based chiral perovskites with clear chiroptical properties may open the way for the future design of novel and optimized materials. | Lorenzo Malavasi; Massimo Boiocchi; Marco Moroni; Alessandro Stroppa; Yali Yang; Clarissa Coccia | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ca05b8dfabaf06ff91d465/original/r-s-cl-mba-3ge-i5-a-novel-low-dimensional-ge-containing-chiral-perovskite.pdf |
66bd4ba420ac769e5fa04a4e | 10.26434/chemrxiv-2024-5zmzn | ortho-Aromatic Polyamides by Ring-opening Polymerization of N-carboxyanhydrides | We report the ring-opening polymerization of N-alkylated aromatic six-membered ring N-carboxyanhydrides (6-NCA-R) catalyzed by transition metal Schiff base complexes in the presence of a base. This system allows the facile synthesis of ortho-aromatic polyamides with high molecular weights via chain-growth polymerization. A mechanism is proposed based on the results of polymerizations performed under various reaction conditions. Copolymerization of 6-NCA-R with heterocyclic monomers is performed to prepare heteroatom (N, O, and S) containing copolymers. The thermal properties of the polymers with different N-alkyl side chains were investigated by thermogravimetric analysis, differential scanning calorimetry, and powder X-ray diffraction. | Shijie Deng; Hyuk-Joon Jung; Yi Shen; Hootan Roshandel; Varit Chantranuwathana; Hieu Nguyen; Thi Tran; Kimberly Vasquez; Joseph Chang; Takeo Iwase; Parisa Mehrkhodavandi; Jeffery Byers; Loi Do; Paula Diaconescu | Catalysis; Organometallic Chemistry; Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66bd4ba420ac769e5fa04a4e/original/ortho-aromatic-polyamides-by-ring-opening-polymerization-of-n-carboxyanhydrides.pdf |
651e8b07bda59ceb9ae96d1f | 10.26434/chemrxiv-2023-cqrb6-v2 | A conjugated heat and mass transfer model to implement reaction in particle-resolved CFD simulations of catalytic fixed bed reactors | Modeling catalytic fixed bed reactors with a small tube-to-particle diameter ratio requires a detailed description of the interactions between fluid flow, intra-particle transport, and the chemical reaction(s) within the catalyst. Particle-resolved computational fluid dynamics (PRCFD) simulations are the most promising approach to accurately predict the behavior of these reactors, since they take explicitly into account the local packed bed structure. In this work, a conjugated heat and mass transfer model for use in PRCFD simulations is presented to couple the fluid flow through the fixed bed with transport and reaction in the porous catalyst, while guaranteeing the no-slip boundary condition at the fluid-solid interface. For this purpose, the solutions of the solid and fluid domain are computed separately and are coupled by calculation and updating the boundary condition at the particle surface. Due to the consideration of secondary gradients, the developed transfer model is also valid for unstructured calculation meshes containing non-orthogonal cells at the fluid-solid interface. Such meshes are often used to resolve complex geometries, such as a packed bed, in a computationally efficient manner. The coupling approach is validated using cases for which an analytical solution or literature correlations derived from experimental data are available. The simulation results of a short catalytic packed bed with rings catalyzing the partial oxidation of n-butane to maleic anhydride exemplify the potential of PRCFD involving reactions to analyze the catalyst performance in great detail. | Martin Kutscherauer; Scott Anderson ; Sebastian Böcklein; Gerhard Mestl; Thomas Turek; Gregor D. Wehinger | Catalysis; Chemical Engineering and Industrial Chemistry; Fluid Mechanics; Transport Phenomena (Chem. Eng.); Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2023-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651e8b07bda59ceb9ae96d1f/original/a-conjugated-heat-and-mass-transfer-model-to-implement-reaction-in-particle-resolved-cfd-simulations-of-catalytic-fixed-bed-reactors.pdf |
66cfabde20ac769e5f26911a | 10.26434/chemrxiv-2024-9d08f | Aqueous Zr/Hf(IV)-Oxo Cluster Speciation and Separation | Many industrial separations of chemically-similar elements are achieved by solvent extraction, exploiting differences in speciation and solubility across aqueous-organic interfaces. We recently identified [OM4(OH)6(SCN)12]4- (OM4, M=Zr/HfIV) tetrahedral oxoclusters as the main species in industrial processes that produce nuclear-grade Zr and Hf from crude ore. However, the isostructural/isoelectronic OM4-oxoclusters did not explain the selective extraction of Hf into the organic phase. Here we have characterized heterometal Hf-Zr clusters in solution and the solid-state yielding key information about their fundamentally different chemistry that engenders separation. Clusters prepared with both ammonium (industrial process) and tetramethylammonium counter cations revealed that 1) mixed-metal clusters (instead of self-sorted) assemble, and 2) Hf-rich OM4 selectively precipitates over Zr-rich OM4, providing a separation process that does not require an organic extractant. Mass spectrometry, small-angle X-ray scattering, solution-state 1H nuclear magnetic resonance (NMR) spectroscopy, and solid-state 17O NMR evidence both mixed-metal speciation and selective Hf-precipitation. Raman spectroscopy suggests greater Zr-ligand lability than Hf-ligand lability, consistent with higher aqueous solubility of Zr-rich clusters, enabling both extraction and precipitation-based separation. Fundamentally, these studies also identify a key difference between these chemically similar elements that has enabled diversification of Zr-polyoxocation chemistry over the last decade, while Hf-polyoxocation chemistry lags. | Alexander Roseborough; Ryan Loughran; Christopher Colla; May Nyman | Inorganic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cfabde20ac769e5f26911a/original/aqueous-zr-hf-iv-oxo-cluster-speciation-and-separation.pdf |
60c74f85842e650257db3858 | 10.26434/chemrxiv.12917930.v1 | An Algorithm to Correct for the CASSCF Active Space in Multiscale QM/MM Calculations Based on Geometry Ensembles | The convolution of the excitation energies, computed by the complete active space self-consistent field (CASSCF) or other CAS-based methods, of an ensemble of geometries generated by molecular dynamic simulations is a usual recipe to obtain the absorption spectrum or the density of states of a chromophore. This approach requires that all the considered geometries have the same molecular orbitals within the active space. However, the different geometrical features and/or the different influence of the solvent or biological environments along the sample geometries makes the preservation of the active space a challenging task, which is usually ignored. In this work, we present an algorithm to correct for the active space of geometry ensembles in CASSCF calculations. The algorithm is based on the calculation of the molecular orbital overlap matrix between a previously selected reference geometry, with the desired active space, and each of the sampled geometries. Depending on the value of the overlap matrix elements, the algorithm determines whether one or more pairs of molecular orbitals of the sampled geometry have to be swapped for a subsequent CASSCF calculation. We have applied the developed algorithm to quantum mechanics/molecular mechanics CASSCF/MM and CASPT2/MM calculations for sets of geometries of the five canonical nucleobases in aqueous solution obtained from classical molecular dynamics simulations. The algorithm shows a very good efficacy since it recovered the correct active space for 76\% of the geometries which presented undesired molecular orbitals in the active space after the first CASSCF wavefunction optimization. In addition, the importance of having the same orbitals within the active space for all the geometries is discussed based on the computed density of states for the solvated nucleobases. | Gustavo Cárdenas; Juan Jose Nogueira | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f85842e650257db3858/original/an-algorithm-to-correct-for-the-casscf-active-space-in-multiscale-qm-mm-calculations-based-on-geometry-ensembles.pdf |
60c74df8f96a002ee0287a35 | 10.26434/chemrxiv.12611861.v2 | Drug Repurposing Commonly Against Dengue Virus Capsid and SARS-CoV-2 Nucleocapsid: An in Silico Approach | <p></p><p>In
the middle of SARS-CoV-2 pandemic, dengue virus (DENV) is giving a silent
warning as the season approaches nearer. There is no specific antiviral against
DENV for use in the clinics. Thus, considering these facts we can potentially
face both these viruses together increasing the clinical burden. The search for
anti-viral drugs against SARS-CoV-2 is in full swing and repurposing of already
‘in-use’ drugs against other diseases or COVID-19 has drawn significant
attention. Earlier we had reported few FDA approved anti-viral and
anti-microbial drugs that could be tested for binding with SARS-CoV-2
nucleocapsid N terminal domain. We explored the possibility of interactions of
the drugs screened for SARS-CoV2 with Dengue virus capsid protein. We report five
FDA approved drugs that were seen to be docking onto the SARS-CoV-2
nucleocapsid RNA binding domain, also docking well with DENV capsid protein on
the RNA binding site and/or the capsid’s membrane fusion domain. Thus, the present
study proposes these five drugs as common antiviral candidates against both
SARS-CoV-2 and DENV although the <i>in silico</i> study is subject to further
validations.</p><br /><p></p> | Debica Mukherjee; Rupesh Roy; UPASANA RAY | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74df8f96a002ee0287a35/original/drug-repurposing-commonly-against-dengue-virus-capsid-and-sars-co-v-2-nucleocapsid-an-in-silico-approach.pdf |
6398c00e0fd9924a1944ebb8 | 10.26434/chemrxiv-2022-1v6rk | Atherosclerotic-derived endothelial cell response conducted by titanium oxide nanotubes | Atherosclerosis lesions are described by the formation of an occlusive wall-vessel plaque that can exacerbate infarctions, strokes, and even death. Furthermore, atherosclerosis damages the endothelium integrity, avoiding proper regeneration after stent implantation. Therefore, we investigate the beneficial effects of TiO2 nanotubes (NTs) in promoting the initial response of detrimental human atherosclerotic-derived endothelial cells (AThEC). We synthesized and characterized NTs on Ti6Al4V by anodization. We isolated AThEC and tested the adhesion and long-lasting proliferation activity promoted by the surfaces. Furthermore, the cytoskeleton arrangement and the modulation of focal adhesions were studied on the materials. Moreover, ultrastructural cell-surface contact at the nanoscale and membrane roughness were evaluated to explain the results. Our findings depicted improved filopodia and focal adhesions stimulated by the NTs. Similarly, the NTs harbored long-lasting proliferative metabolism after 5 days, explained by the overcoming cell-contact interactions at the nanoscale. Furthermore, the senescent activity detected in the AThEC could be mitigated by the modified membrane roughness and cellular stretch orchestrated by the NTs. Despite the dysfunctional status of the AThEC, our study brings new evidence for the potential application of nano-configured biomaterials for innovation in stent technologies. | Ernesto Beltran-Partida; Benjamin Valdez-Salas; Martha García-López Portillo; Claudia Gutierrez-Perez; Sandra Castillo-Uribe; Jorge Salvador-Carlos; José Alcocer-Cañez; Nelson Cheng | Biological and Medicinal Chemistry; Materials Science; Nanoscience; Biocompatible Materials; Nanostructured Materials - Materials; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6398c00e0fd9924a1944ebb8/original/atherosclerotic-derived-endothelial-cell-response-conducted-by-titanium-oxide-nanotubes.pdf |
612e623390051e96a1e5addc | 10.26434/chemrxiv-2021-mtt8j | Effects of pH and vanadium concentration during the impregnation of Na-SiO2 supported catalysts for the oxidation of propane | SiO2 supported NaVOx catalysts have raised interest due to reports showing an increase in the selectivity to propene in propane oxidation; a process that may become an alternative to conventional petrochemical routes for producing this valuable olefin. In this work, the effects of pH, the concentration of vanadium in solution, [V]Sol, and of their interaction; i.e., non-additive effect, over the properties of Na-SiO2 used for the oxidation of propane under oxygen rich conditions were studied. In general, the studied experimental factors had no net effects over the difference between the nominal and final loadings of vanadium in the catalysts, the surface area, and porosity. However, all catalysts presented a ~50% decrease in surface area due to partial mesopore blocking reflected by a ~30% increase in the average pore diameter. On the other hand, NaVO3 microcrystals and particles constituted -NaVO3 and -NaVO3 were formed at acidic pH, whereas Na metavanadate nanoparticles were formed at pH=9.0. These nanoparticles transformed into an -NaVO3 type phase upon dehydration. The reducibility of the catalysts was a function of the impregnation pH, where the catalysts synthesized at pH=3.8 and 9.0 displayed similar reduction patterns but lower reducibility than those synthesized at pH=1.5. The produced patterns were correlated to the existence of a mixture of V5+ and V4+ species among which V4+ was prevalent for the catalysts synthesized at pH=3.8 and 9.0. Consequently, the basicity of the catalysts decreased with the increase in pH. The surface concentration of vanadium increased with the increase in the concentration of vanadium in solution, while the pH had a weak negative effect over the former. On the other hand, it was established that chemical surface state of oxygen in the synthesized catalysts was influenced weakly by the synthesis pH and, more importantly, by non-additive effects between the pH and the concentration of vanadium in solution. The latter was coherent with the detection of surface oxygen species related to the partial dissolution of the Na-SiO2 support; a phenomenon that seemed to be favored at acidic pH. The latter properties were correlated to changes in basicity. Concerning the catalytic performance, the catalysts synthesized at pH=9.0 displayed the best steady state performance in terms of the selectivity to propene and oxygen consumption. The collected evidence allowed corroborating that both the oxidative dehydrogenation of propane to propene and its combustion to CO and CO2 are kinetically controlled by the initial activation of one of the C-H bonds of propane. But, the production of CO2 depended on the level of consumption of O2; where, a surplus of the latter compared to the conversion of propane combusted the hydrocarbon into CO2. Such a finding agreed with what has already been established for supported vanadium oxides for hydrocarbon oxidation. An analysis of the Raman spectra of the spent catalysts suggested that under the applied reaction conditions, all catalysts were provided of an active phase mostly constituted by -NaVO3 type structures. Therefore, the observed differences in catalytic behavior were rather associated to changes in particle size, reducibility, and acidity. | Mery S. Hernández-Maya; Carol B. Espinosa-Lobo; Rafael Cabanzo Hernández; Enrique Mejía-Ospino; Víctor Gabriel Baldovino Medrano | Catalysis; Chemical Engineering and Industrial Chemistry; Petrochemicals; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612e623390051e96a1e5addc/original/effects-of-p-h-and-vanadium-concentration-during-the-impregnation-of-na-si-o2-supported-catalysts-for-the-oxidation-of-propane.pdf |
62555a6ced4d8801a207f3e3 | 10.26434/chemrxiv-2022-lvptc | On the mechanism of theta capillary nanoelectrospray ionization for the formation of highly charged protein ions directly from native solutions | Theta capillary nanoelectrospray ionization (θ-nanoESI) can be used to ‘supercharge’ protein ions directly from solution for detection by mass spectrometry (MS). In native top-down MS, the extent of protein charging is low. Given that ions with more charge fragment more readily, increasing charge can enhance the extent of sequence information obtained by top-down MS. For θ-nanoESI, dual-channelled nanoESI emitters are used to mix two solutions in low to sub-μs prior to MS. The mechanism for θ-nanoESI mixing has been reported to occur in the Taylor cone prior to ESI-droplet formation, or by the fusion of droplets formed from separate Taylor cones. Using θ-nanoESI-ion mobility-MS, native protein solutions were rapidly mixed with denaturing supercharging solutions to form protein ions in significantly higher charge states and with more elongated structures than those formed by pre-mixing the solutions prior to nanoESI-MS. If θ-nanoESI mixing occurred in the Taylor cone, then the extent of protein charging and unfolding should be comparable or less than that obtained by pre-mixing solutions. Thus, these data are consistent with mixing occurring via droplet fusion rather than in the Taylor cone prior to ESI droplet formation. The presence of supercharging additives in pre-mixed solutions can suppress volatile electrolyte evaporation, limiting the extent of protein charging compared to when the additive is delivered via one channel of a θ-nanoESI emitter. In θ-nanoESI, the formation of two Taylor cones can presumably result in substantial electrolyte evaporation from the ESI droplets containing native-like proteins prior to droplet fusion, thereby enhancing ion charging. | Susannah Brown; Muhammad Zenaidee; Joseph Loo; Rachel Ogorzalek Loo; William Donald | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62555a6ced4d8801a207f3e3/original/on-the-mechanism-of-theta-capillary-nanoelectrospray-ionization-for-the-formation-of-highly-charged-protein-ions-directly-from-native-solutions.pdf |
63e702279da0bc6b33b6e6ac | 10.26434/chemrxiv-2023-ghv4t | Revealing the Impacts of Chemical Complexity on Submicron Sea Spray Aerosol Morphology | Sea spray aerosol (SSA) ejected through bursting bubbles at the ocean surface are complex mixtures of salts and organic species. Composition affects their ability to form marine clouds which cover nearly three-quarters of the Earth and play a critical role in the climate system. Submicron SSA particles have long lifetimes in the atmosphere and impact the Earths climate, yet their cloud-forming potential is difficult to study at the single-particle level using conventional experimental techniques due to their small size. Here, we use large-scale molecular dynamics (MD) simulations as a computational microscope to provide never-before-seen, dynamical views of 40-nm model aerosol particles and their detailed molecular morphologies. We investigate how increasing chemical complexity impacts the distribution and partitioning of organic material throughout individual particles for a range of organic constituents with varying chemical properties. Our simulations show that organic surfactants commonly found in SSA readily partition between both the surface and interior of the aerosol, indicating that nascent SSA may be more heterogeneous than traditional morphological models suggest. We support our computational observations of heterogeneity at the SSA surface with Brewster angle microscopy on model interfaces. Ultimately, our work establishes large-scale MD simulations as a novel technique for interrogating aerosols at the single-particle level, and shows the morphological mechanisms underlying why submicron SSA readily absorb waterand thus have a higher cloud forming potentialthan would otherwise be predicted for organic-rich aerosols. | Abigail Dommer; Nicholas Wauer; Kyle Angle; Aakash Davasam; Patiemma Rubio; Man Luo; Clare Morris; Kimberly Prather; Vicki Grassian; Rommie Amaro | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science | CC BY 4.0 | CHEMRXIV | 2023-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e702279da0bc6b33b6e6ac/original/revealing-the-impacts-of-chemical-complexity-on-submicron-sea-spray-aerosol-morphology.pdf |
643565c7a41dec1a56e0dd51 | 10.26434/chemrxiv-2022-0jghq-v2 | Design Principles for Grain Boundaries in Solid-State Lithium-Ion Conductors | Although polycrystalline solid electrolytes are central to the utilization of solid- state batteries with lithium metal anodes, lithium dendrite formation and reduced Li-ion conductivity at their grain boundaries remain primary concerns. Given that experimental studies on polycrystalline materials are notoriously difficult to perform and interpret, computational techniques are invaluable for providing insight at the atomic scale. Here, we carry out first-principles calculations on representative grain boundaries in three important Li-based solid electrolyte families, namely, an anti-perovskite oxide, Li3OCl, a thiophosphate, Li3PS4, and a halide, Li3InCl6, to demonstrate the significantly different impacts that grain boundaries have on their electronic structure, ion conductivity and correlated ion transport. Our results show that even when grain boundaries do not significantly impact ionic conductivity, they can still strongly perturb the electronic structure and contribute to undesirable electrical conductivity and potential lithium dendrite propagation. We also illustrate, for the first time, how cor- related motion, including the so-called paddle-wheel mechanism, which has so far only been considered for the bulk, can vary substantially at grain boundaries. Our findings reveal the dramatically different behaviour of solid electrolytes at the grain boundary compared to the bulk and its potential consequences and benefits for the design of solid-state batteries. | James Dawson; James Quirk | Materials Science; Nanoscience; Energy; Ceramics; Energy Storage | CC BY 4.0 | CHEMRXIV | 2023-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643565c7a41dec1a56e0dd51/original/design-principles-for-grain-boundaries-in-solid-state-lithium-ion-conductors.pdf |
63f27c3cfcfb27a31f11c6ae | 10.26434/chemrxiv-2024-g10ch | MinKLIFSAI: a simple machine learning approach toward selective kinase inhibitor | The aim of achieving selectivity in kinase inhibition is a big challenge within the realm of drug discovery, particularly due to the structural similarities between various kinases. Can machine learning be leveraged to overcome this hurdle? Utilizing different fingerprints may indeed lead to improved results. However, is there a single machine-learning approach that can effectively address selectivity across all kinases. In this study, the author collect kinase activity data from PubChem database (January 2023) using Uniprot IDs for each kinase. Each Uniprot ID is associated with its unique dataset, and duplicate points were removed to ensure accuracy. The data was then appended together, and any datasets containing fewer than 120 points were discarded. Each data point was categorized as either Active (1) or Inactive (0) based on the activity data. Two fingerprinting approaches were employed for predictions: MACCS fingerprints and Morgan2 (ECFP2) with a 2048-bit representation. The combined dataset was then divided into two subsets, one featuring imbalance data and another with balanced data. Random Forest and Artificial Neural Network models were applied to both datasets. To evaluate the performance of these models, various metrics were employed, including accuracy, sensitivity, specificity, and area under the curve (AUC). The results showed that Morgan fingerprinting performed slightly better than MACCS fingerprinting. A total of 480 target IDs was produced, with 452 unique IDs identified. On each dataset(balance and imbalance), two models were developed for both fingerprints, resulting in a combined total of 1920 predictions. Interestingly, the imbalance data yielded higher specificity compared to the balanced data. Each model has been deployed and made publicly available at (github.com/phalem/minKLIFSAI). However, the current data on all kinases is not yet sufficient to enable machine learning to reliably discover selective inhibitors | Mohamed Abdelalim | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Cell and Molecular Biology; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f27c3cfcfb27a31f11c6ae/original/min-klifsai-a-simple-machine-learning-approach-toward-selective-kinase-inhibitor.pdf |
60c73e15567dfe063aec3755 | 10.26434/chemrxiv.6377372.v1 | First Principles Mechanistic Study of Self-Limiting Oxidative Adsorption of Remote Oxygen Plasma During the Atomic Layer Deposition of Alumina | Plasma-enhanced atomic layer deposition (ALD) of metal oxides is a
rapidly gaining interest especially in the electronics industry because of its
numerous advantages over the thermal process. However, the underlying reaction
mechanism is not sufficiently understood, particularly regarding saturation of
the reaction and densification of the film. In this work, we employ first
principles density functional theory (DFT) to determine the predominant reaction pathways, surface intermediates
and by-products formed when constituents of O<sub>2</sub>-plasma or O<sub>3</sub>
adsorb onto a methylated surface typical of TMA-based alumina ALD. The main outcomes are that a wide variety of barrierless and highly
exothermic reactions can take place. This leads to the spontaneous production
of various by-products with low desorption energies and also of surface
intermediates from the incomplete combustion of –CH<sub>3</sub> ligands.
Surface hydroxyl groups are the most frequently observed intermediate and are formed
as a consequence of the conservation of atoms and charge when methyl ligands
are initially oxidized (rather than from subsequent re-adsorption of molecular
water). Anionic intermediates such as formates are also commonly observed at the
surface in the simulations. Formaldehyde, CH<sub>2</sub>O, is the most
frequently observed gaseous by-product. Desorption of this by-product leads to
saturation of the redox reaction at the level of two singlet oxygen atoms per
CH<sub>3</sub> group, where the oxidation state of C is zero, rather than
further reaction with oxygen to higher oxidation states. We conclude that the
self-limiting chemistry that defines ALD comes about in this case through the
desorption by-products with partially-oxidised carbon. The simulations also show that densification occurs when ligands are
removed or oxidised to intermediates, indicating that there may be an inverse relationship
between Al/O coordination numbers in the final film and the concentration of
chemically-bound ligands or intermediate fragments covering the surface during
each ALD pulse. Therefore reactions that generate a bare surface
Al will produce denser films in metal oxide ALD. | Glen N. Fomengia; Michael Nolan; Simon D. Elliott | Thin Films; Theory - Computational; Physical and Chemical Processes; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2018-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e15567dfe063aec3755/original/first-principles-mechanistic-study-of-self-limiting-oxidative-adsorption-of-remote-oxygen-plasma-during-the-atomic-layer-deposition-of-alumina.pdf |
60c7461fee301c4c7ec79466 | 10.26434/chemrxiv.10693025.v1 | Two-Dimensional Noble-Metal Dichalcogenides and Phosphochalcogenides | Noble-metal chalcogenides, dichalcogenides and phosphochalcogenides are an emerging class of two-dimensional materials. Their properties can be broadly tuned via quantum confinement (number of layers) and defect engineering, including metal-to-semiconductor transitions, magnetic ordering, and topological surface states. They possess various polytypes, often of similar formation energy, which can be assessed by selective synthesis approaches. They excel in mechanical, optical and chemical sensing applications, and feature long-term air- and moisture stability. In this review, we summarize the recent progress in the field of noble metal chalcogenides and phosphochalcogenides and highlight the structural complexity and its impact on applications. | Roman Kempt; Agnieszka Kuc; Thomas Heine | Nanostructured Materials - Materials; Solid State Chemistry; Theory - Inorganic; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7461fee301c4c7ec79466/original/two-dimensional-noble-metal-dichalcogenides-and-phosphochalcogenides.pdf |
635bd8baca86b85a3fc75ed0 | 10.26434/chemrxiv-2022-6rhq8 | Molybdenum disulfide field-effect transistor biosensor for ultrasensitive detection of matrix metallopeptidase 9 (MMP9) gene | Background Biosensors are an emerging field in biomedical diagnostics. In the field of biosensors, field-effect transistor (FET)-based biosensors are widely used in clinical, environmental, and food analysis fields because of their high sensitivity, specificity, and real-time detection. Matrix metallopeptidase 9 (MMP9) is a gene closely related to various diseases, which is considered to have a predictive role in disease diagnosis and qualitative treatment.
Methods In this study, an all-solid-state, ultrasensitive FET biosensor based on monolayer molybdenum disulfide (MoS2) was designed and constructed. We synthesized a series of MMP9-targeted probes and obtained the optimal hybridization conditions (including optimal hybridization temperature, hybridization concentration, and hybridization time) for the MoS2 FET biosensors.
Results The data show that this MoS2 FET biosensor detects the MMP9 gene at a minimum of 3.86 pM with promising selectivity, specificity, and reproducibility.
Conclusion The MoS2 FET biosensor detects the MMP9 gene at a minimum of 3.86 pM with promising selectivity, specificity, and reproducibility. Our work not only provides a potential strategy for the diagnosis and treatment of MMP9-related diseases, but also is helpful for the design of nanodevices, the development of portable diagnostic devices, and the implementation of personalized medicine.
| huijuan li; shibin Liu; qingliang Feng; jie Tan; jiezhang Luo; yinghao Chen | Biological and Medicinal Chemistry; Materials Science; Nanoscience; Biological Materials; Nanodevices | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635bd8baca86b85a3fc75ed0/original/molybdenum-disulfide-field-effect-transistor-biosensor-for-ultrasensitive-detection-of-matrix-metallopeptidase-9-mmp9-gene.pdf |
60c7453e469df4c4cef43497 | 10.26434/chemrxiv.9922211.v2 | Synthesis, Characterization of Immobilized Thiosalicylic-Mercaptoethanol Bi-Ligand System and its Application in Detoxification of Chromium III and Iron III ions from Tannery Wastewater | <div>Background: Effective wastewater treatments are paramount to modern-day Scientists. The available methods are ineffective in detoxifying tannery wastewater. </div><div>Aim: This study synthesize and characterized polysiloxane-Immobilized thiosalicylic-mercaptoethanol ligand system (PITSMCBLS) and used in detoxification of Cr3+ and Fe3+ from tannery wastewater.</div><div>Method: Porous solid PITSMCBLS was prepared by hydrolytic polycondensation of tetraethylorthosilicate with mixture of 3-chloropropyltrimethoxysilane, methanol and sodium hydroxide as catalyst. The gelation formed (3-CPP) after 40 min, was functionalized (F-3CPP) with excess ethylchloroacetate, triethylamine and grafted with thiosalicylic-mercaptoethanol bi-ligand. The PITSMCBLS was characterized using FTIR and SEM-EDX. The competitive sorption characteristics of metal ions (Cr3+ and Fe3+) were studied using Microwave Plasma Atomic-Emission Spectrophotometer.</div><div>Result: The FTIR spectrum of PITSMCBLS showed vibrational frequencies (cm-1) at: 3339, (O-H); 2928, (C-H); 2685, (SH); 2497, (Si-H); 1587–1707, (C=O) and 1028, (Si-O). The SEM-EDX showed irregular particle sizes (4.4294 ± 1.7187 nm) and elemental composition (wt %): 3-CPP, Si (50.45); O (25.02) and Cl (24.57). The F-3CPP showed, O (58.68) and Si (41.32), while PITSMCBLS showed 11.94 of S. Gibbs free energy yielded negative range values for ΔGo (Cr3+ -14.187 to -14.832 and Fe3+ - 14.369 to -14.843 kJmol-1), positive values for: ΔHo (Cr3+ 5.345 and Fe3+ 0.000 kJmol-1) and ΔSo (Cr3+ 64.459 and Fe3+ 47.421 Jmol1K1) respectively.</div><div>Conclusion: PITSMCBLS exhibits high potential for extraction of Cr3+ and Fe3+ in tannery wastewater. The Thermodynamic values indicate spontaneous, endothermic reactions and high degree of disorderliness with respect to metal ion binding capacity to the ligand system. This development would improve tannery wastewater treatment.</div> | Bulus Habila; Pius Onyeoziri Ukoha; Stanley I.R. Okoduwa; Ahmed Salim; Muazu B. Babangida; Adamu Simon | Analytical Chemistry - General; Biochemical Analysis; Environmental Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7453e469df4c4cef43497/original/synthesis-characterization-of-immobilized-thiosalicylic-mercaptoethanol-bi-ligand-system-and-its-application-in-detoxification-of-chromium-iii-and-iron-iii-ions-from-tannery-wastewater.pdf |
62a99671eb1f0cfb1d8986d6 | 10.26434/chemrxiv-2022-fk36d-v3 | Modelling of Electrocatalytic Double Layers with Refined Treatment of Metal-Water Interactions and Chemisorption | The double layer on transition metals features chemical metal-water interactions and chemisorption of partially charged adsorbates, which have not been adequately described in previous double layer models developed for mercury-like metals. A new model with an improved description of both is developed herein. The first water layer is treated statistically, considering chemical interactions with the metal and a continuous spectrum of water orientational states. Chemisorption processes are described using Langmuir adsorption isotherms with distributed equilibrium potentials. In addition, the surface dipole moment induced by partially charged chemisorbates, markedly changing double layer behaviors, is considered. The model is then used to study how the potential of zero charge and the double-layer capacitance are influenced by the first-layer water molecules and partially charged chemisorbates. The model provides an alternative interpretation for recent capacitance data of Pt(111)-aqueous solution interfaces calculated from cyclic voltammetry (CV). The present interpretation is appealing for it does not introduce any unknown metal-ion interactions as previously, and for it resolves the discrepancy that the CV-based capacitance is several fold higher than that obtained using electrochemical impedance spectroscopy. The implications and limitations of the model are discussed. | Jun Huang | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study | CC BY 4.0 | CHEMRXIV | 2022-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a99671eb1f0cfb1d8986d6/original/modelling-of-electrocatalytic-double-layers-with-refined-treatment-of-metal-water-interactions-and-chemisorption.pdf |
644125f971383d0921033632 | 10.26434/chemrxiv-2023-62vzx | Band Gap Tuning Through Cation and Halide Alloying in Mechanochemical Synthesized Cs3(Sb1-xBix)2Br9 and Cs3Sb2(I1-xBrx)9 Solid Solutions | Modulation of optical properties of lead-free defective perovskites can contribute to design optimized materials for several applications ranging from photodetection to photocatalysis. Here, we explored two novel alloying strategies on Cs3Sb2Br9, by preparing by mechanochemical synthesis Sb/Bi and Br/I mixed systems. An unexpected band gap bowing has been observed in alloyed Sb/Bi compositions, showing lower absorption edges with respect to pure compounds. Such behavior has been computationally modelled suggesting the presence of local aggregates as the source of such reduction of the band gap. Further modulation of the optical properties has been achieved by halide alloying showing a progressive red-shift by increasing the iodide content. In both cases a full solubility at the solid state has been determined by means of diffraction and Raman spectroscopy. Overall, this study proposes and rationalizes doping strategies in the Cs3Sb2Br9 defective perovskite achieved through the use of a sustainable synthetic procedure such as mechanochemistry. | Lorenzo Malavasi; Pietro Galinetto; Benedetta Albini; Giulia Giovilli; Marco Moroni; Edoardo Mosconi; Filippo De Angelis; Waldemar Kaiser; Virginia Grisci | Inorganic Chemistry; Energy; Solid State Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644125f971383d0921033632/original/band-gap-tuning-through-cation-and-halide-alloying-in-mechanochemical-synthesized-cs3-sb1-x-bix-2br9-and-cs3sb2-i1-x-brx-9-solid-solutions.pdf |
62bd7c24d66f683b75b7a07a | 10.26434/chemrxiv-2022-tln0p-v2 | Water-soluble Bioisosteres of the ortho-substituted Phenyl Ring | Water-soluble analogues of the ortho-substituted phenyl ring were developed. Replacement of the phenyl ring in bioactive compounds with 2 oxabicyclo[2.1.1]hexanes in many cases improved solubility, reduced lipophilicity, enhanced metabolic stability, and most importantly – retained bioactivity. | Aleksandr Denisenko; Pavel Garbuz; Nataliya Voloshchuk; Yuliia Holota; Pavel Mykhailiuk | Organic Chemistry; Bioorganic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bd7c24d66f683b75b7a07a/original/water-soluble-bioisosteres-of-the-ortho-substituted-phenyl-ring.pdf |
60c7557e9abda20d84f8e363 | 10.26434/chemrxiv.11571225.v3 | Liquid-Phase Exfoliation of Biochars in Green Solvents and Correlation with Solvent Parameters | <div>
<div>
<div>
<div>
<p>Liquid-phase exfoliation (LPE) is a process frequently used to overcome the interactions between layers in layered materials
to produce small sheets of material, with remarkable properties and high value applications. Materials are prepared via
direct or indirect sonication in a solvent that must be able to effectively disperse and stabilize the sheets produced.
Unfortunately, the preferred solvents for exfoliation processes are often toxic and possess several health risks. In this work,
we show that LPE in greener solvents can be used to access nanostructures of biochar and further improve the applications
of this renewable and bio-based material. Herein, pristine and oxidized biochars prepared from hardwood and softwood
biomass waste (e.g. sludge, bark, and sawdust) are exfoliated in a range of solvents to allow the identification of benign
alternatives that could afford highly concentrated dispersions. The majority of biochar nanostructures produced after
exfoliation are stacked nanosheets containing between 2-8 layers (average 15 nm thickness). Correlations between
effective LPE of biochar in solvents and different solvent parameters, including Kamlet-Taft, were established and allowed
greener solvents to be used. Surface modification of biochars (e.g. via oxidation) has potential to increase their dispersibility
in more benign solvents. LPE of oxidized biochars is more efficient in hydrogen-bond accepting solvents due to the
increased concentration of carboxylic acid and alcohol functional groups on the surface of particles, when compared to non-
functionalized biochars. Dispersions containing 0.20-0.75 mg/mL exfoliated oxidized biochar were obtained in solvents such
as polyethylene glycols, glycerol formal and e-caprolactone. Moreover, LPE of pristine biochars in dimethyl carbonate, ethyl
acetate, and solketal gave similar yields to more commonly used solvent for this process, N-methyl-2-pyrrolidone (NMP) a
known reprotoxic molecule.
</p>
</div>
</div>
</div><br /></div> | Juliana Vidal; Stephanie Gallant; Evan Connors; Douglas Richards; Stephanie MacQuarrie; Francesca Kerton | Carbon-based Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7557e9abda20d84f8e363/original/liquid-phase-exfoliation-of-biochars-in-green-solvents-and-correlation-with-solvent-parameters.pdf |
60c756d6bdbb892ab6a3aafc | 10.26434/chemrxiv.14331737.v1 | Singlet and Triplet Exciton Dynamics of Violanthrone | <div>The exciton dynamics of violanthrone-79 are investigated in solution and in the solid</div><div>state. In solution, the photo-prepared singlet is found to exhibit a strong ground-state bleach</div><div>and stimulated emission feature, but when sensitized in its triplet state, exhibits only a narrow</div><div>and weak ground-state bleach. As supported by density functional theory calculations,</div><div>this is explained by the triplet state having absorptions in the same region, with a similar</div><div>oscillator strength, as the ground state molecule. In solid films, the excited singlet is</div><div>found to survive only 100 ps, giving way to a long-lived transient absorption spectrum with</div><div>characteristics reminiscent of the triplet in solution. This is interpreted in terms of singlet</div><div>fission in the solid film.</div> | Elham Gholizadeh; Shyamal Prasad; Lara Gillan; Dane R. McCamey; Murad
J. Y. Tayebjee; Timothy Schmidt | Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756d6bdbb892ab6a3aafc/original/singlet-and-triplet-exciton-dynamics-of-violanthrone.pdf |
6304e1b2d147b217aeb5c56c | 10.26434/chemrxiv-2022-j8hn7 | Spatiotemporal Design of the Metal-Organic Framework DUT-8(M) | Switchable metal-organic frameworks change their structure in time and selectively open their pores adsorbing guest molecules, leading to highly selective separation, pressure amplification, sensing and actuation applications. The three-dimensional engineering of metal-organic frameworks has reached a high level of maturity, but spatiotemporal evolution opens a new perspective towards engineering materials in the 4th dimension (time) by t-axis design, in essence exploiting the deliberate tuning of activation barriers. This work demonstrates the first example in which an explicit temporal engineering of a switchable metal-organic framework (DUT-8, M1M2(ndc)2dabco, ndc = 2,6,-naphthalenedicarboxylate, dabco = 1,4 diazabicyclo[2.2.2]octane, M1 = Ni, M2 = Co) is presented. The temporal response is deliberately tuned by variation of cobalt content. We present a spectrum of advanced analytical methods for analyzing the switching kinetics stimulated by vapor adsorption using in situ time resolved techniques ranging from ensemble adsorption and advanced synchrotron X-ray diffraction experiments to individual crystal analysis. A novel analysis technique based on microscopic observation of individual crystals in a microfluidic channel reveals the lowest limit for adsorption switching reported so far. The time constants for the bulk ensembles range from 2 - 300 s. Differences in spatiotemporal response of crystal ensembles originate from a delay (induction) time that varies statistically and widens characteristically with increasing cobalt content reflecting increasing activation barriers. | Hiroki Miura; Volodymyr Bon; Irena Senkovska; Sebastian Ehrling; Nadine Bönisch; Gerrit Mäder; Stefan Grünzner; Azat Khadiev; Dmitri Novikov; Kartik Maity; Andreas Richter; Stefan Kaskel | Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Solid State Chemistry; Physical and Chemical Properties; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6304e1b2d147b217aeb5c56c/original/spatiotemporal-design-of-the-metal-organic-framework-dut-8-m.pdf |
67c6d8d981d2151a02031317 | 10.26434/chemrxiv-2025-5t6t2 | Structural and dynamical impact of water dilution on egg yolk properties | Since antiquity, artists have been using egg yolk as an additive in the preparation of \textit{tempera} paints. Mixture of egg yolk and water is the dispersing medium for pigments to start with, but once on the canvas, it acts as a binder and plasticiser, procuring adhesive properties to the applied paint. A series of water/egg yolk mixtures is investigated here using a combination of rheology, Fourier Transform Infrared (FTIR) spectroscopy, Nuclear Magnetic Resonance spectroscopy (NMR) and small angle X-ray scattering (SAXS). The effects of water dilution on the organisation of the main egg yolk components, plasma and granules, is explored. The results show that added water affects the tertiary/quaternary protein structure leading to a destabilization of the lipoprotein dispersion. | Floriane Gerony; Agathe Fanost; Zlanseu Ruth Tan; Natalie Malikova; Laurent Michot; Marie Poirier-Quinot; Laurence de Viguerie; Maguy Jaber; Guillaume Mériguet; Anne-Laure Rollet | Physical Chemistry; Materials Science; Biological Materials; Physical and Chemical Properties; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c6d8d981d2151a02031317/original/structural-and-dynamical-impact-of-water-dilution-on-egg-yolk-properties.pdf |
63c43474a5c3547ab2948578 | 10.26434/chemrxiv-2023-h1q45 | The Role of Water in Carbon Dioxide Adsorption in Porphyrinic Metal-Organic Frameworks | Capturing and converting CO2 in photoactive, porous materials to mimic photosynthesis is not only an appealing but also an important approach to combat increasing CO2 concentrations. Porphyrinic Zr-based metal-organic frameworks (MOFs) incorporate a photoactive dye in a porous material and are therefore promising candidates for artificial photosynthesis. The photochemical conversion of CO2 relies on the interactions between CO2, the proton source H2O, and the photoactive sites in the MOF pores. However, our understanding of these interactions and the photoreaction mechanism is still rather limited. Here, we studied the initial step of the artificial photosynthesis: CO2 sorption and activation in the presence of water. We have developed a combined vibrational and visible spectroscopic setup to simultaneously monitor the adsorption of CO2 into porphyrinic Zr-MOFs, namely PCN-222 and PCN-223, and the photophysical changes in the porphyrin linker as function of water concentration. Computational simulations further corroborate the experimentally obtained adsorption enthalpies. We found a shift of CO2 sorption site from the Zr-cluster to the center of the porphyrin macrocycle when PCN-MOFs were brought in contact with humidity greater than the water pore condensation concentration. The shift in sorption site was accompanied by a bending of the porphyrin macrocycle, which induced a change in color and, thus, a change in spectral overlap with light. Furthermore, CO2/H2O competition experiments revealed that the exchange of CO2 by H2O is pore-size-dependent. Therefore, both humidity and pore-size allow to tune the CO2 sorption site, CO2 capacity, and light harvesting in porphyrinic MOFs, which are key factors for CO2 photoreduction. | Bettina Baumgartner; P. Tim Prins; Jaap N. Louwen; Matteo Monai; Bert M. Weckhuysen | Physical Chemistry; Catalysis; Photocatalysis; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c43474a5c3547ab2948578/original/the-role-of-water-in-carbon-dioxide-adsorption-in-porphyrinic-metal-organic-frameworks.pdf |
60c744b0469df44531f4338d | 10.26434/chemrxiv.7938137.v2 | uMBD: A Materials-Ready Dispersion Correction that Uniformly Treats Metallic, Ionic, Covalent, and van der Waals Bonding | <p>Materials design increasingly relies on
first-principles calculations for screening important candidates and for
understanding quantum mechanisms. Density functional theory (DFT) is by far the
most popular first-principles approach due to its efficiency and accuracy.
However, to accurately predict structures and thermodynamics, DFT must be
paired with a van der Waals (vdW) dispersion correction. Therefore, such
corrections have been the subject of intense scrutiny in recent years. Despite
significant successes in organic molecules, no existing model can adequately
cover the full range of common materials, from metals to ionic solids,
hampering the applications of DFT for modern problems such as battery design.
Here, we introduce a universally optimized vdW-corrected DFT method that
demonstrates an unbiased reliability for predicting molecular, layered, ionic,
metallic, and hybrid materials without incurring a large computational
overhead. We use our method to accurately predict the intercalation potentials
of layered electrode materials of a Li-ion battery system – a problem for which
the existing state-of-the-art methods fail. Thus, we envisage broad use of our
method in the design of chemo-physical processes of new materials.</p> | Minho Kim; won june kim; Tim Gould; Eok Kyun Lee; Sébastien Lebègue; Hyungjun Kim | Theory - Computational; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744b0469df44531f4338d/original/u-mbd-a-materials-ready-dispersion-correction-that-uniformly-treats-metallic-ionic-covalent-and-van-der-waals-bonding.pdf |
6285cd1d87d01f2dd7ea4f87 | 10.26434/chemrxiv-2022-31wqt | Isolation, characterization and UPLC-DAD based quantification of antiplasmodial isoquinoline alkaloids from Cissampelos pareira L. | C. pareira L. is a centuries-old traditional medicinal plant utilized to treat various diseases like asthma, diarrhea, fever, heart disorders, snakebite, vomiting, malaria, pneumonia, dog bite, inflammation and abdominal pain. Globally, based on traditional knowledge, different parts of this plant are being used individually or in combination in various forms to manage malaria. However, the scientific investigation for validating the most effective part of this plant against malaria parasite has not been done. Therefore, current study aimed to evaluate in vitro antiplasmodial activity of extracts/fractions (whole plant) and decoctions from different parts (roots, stem, leaves and whole plant) of C. pareira against different strains of Plasmodium falciparum followed by antiplasmodial activity guided isolation and quantification of isoquinoline alkaloids in extracts/fractions and decoctions. All extracts/fractions/decoctions and molecules isolated from active fractions were investigated for antiplasmodial activity. Results showed that the chloroform fraction of whole plant was the most promising with IC50 (µg/mL) of 0.79 (Pf3D7) and 2.26 (PfINDO) followed by root decoction having IC50 (µg/mL) 10.22 (Pf3D7) and 7.7 (PfINDO). Among three isolated molecules, two bisbenzylisoquinoline alkaloids namely curine (2) [IC50 (µM) 1.46 (Pf3D7) and 0.51 (PfINDO)], and O,O-dimethylcurine (1) [IC50 (µM) 0.92 (Pf3D7) and 2.6 (PfINDO)], were found to be the most potent against P. falciparum strains. The antiplasmodial activity of chloroform fraction was further validated by the developed UPLC-DAD method, which showed the highest quantities of curine (2) (~107 mg/g) and O,O-dimethylcurine (1) (~15 mg/g) in this fraction. This study showed that the root decoction was more effective than decoctions of each of the other parts of the plant and whole plant hydroalcoholic extract. Further, for the first time, this study validates the traditional use of C. pareira whole plant to manage malaria, providing further opportunity to explore the tremendous structural and chemical diversity of isoquinoline alkaloids for antimalarial drug development. | Upendra Sharma; Surekha Kumari; Anmol -; Shivani -; Prakhar Agrawal; Dinkar Sahal | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Analytical Chemistry - General; Biochemical Analysis; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6285cd1d87d01f2dd7ea4f87/original/isolation-characterization-and-uplc-dad-based-quantification-of-antiplasmodial-isoquinoline-alkaloids-from-cissampelos-pareira-l.pdf |
67aed238fa469535b94028ba | 10.26434/chemrxiv-2025-9gg7z-v2 | Study of evolution of three-dimensional
porous structure in zeolite-templated carbons
| The clogging of zeolites with carbon-containing precursors is an industrial challenge in some applications but when the deposition of carbon is deliberate and ‘works well’, a source of carbon material with intriguing properties in others. Zeolite-templated carbons (ZTCs) are often compared to activated carbons due to their shared characteristics, such as high surface area, chemical composition, and thermal and chemical stability under various conditions. However, the key distinction lies in their controllable pore size, which makes ZTCs exceptionally interesting materials.
Since the late 1990s, extensive research has been conducted on ZTCs, exploring different zeolite templates, carbon precursors, and synthesis parameters. Yet, despite significant progress, the field still faces unresolved questions, controversies, and aspects that have been overlooked.
We report synthesis and characterization of three-dimensional porous carbon structures by using ion-exchanged faujasite zeolite as template. The progression of carbon networks from the initial to the final stages of growth inside zeolite channels was studied by transmission and scanning electron microscopy, gas adsorption, thermogravimetric analysis, X-ray diffraction, Raman spectroscopy, and solid state nuclear magnetic resonance. Atomic-resolution images obtained with integrated differential phase contrast scanning transmission electron microscopy (iDPC-STEM) were used to study both the zeolite and carbon structure inside the zeolite pores.
Argon and CO2 adsorption isotherms show that the inner and the outer pore volumes (that we label V1 and V2) and surface areas (that we label S1 and S2) of the hollow carbon networks can be distinguished in the pore size distribution curves; to the best of our knowledge, this is the first time that these pore volumes and BET surface areas have been separately determined. For this porous carbon product, V1=0.14 cm3/g and S1=500 m2/g, and V2=0.99 cm3/g and S2=1640 m2/g. The iDPC-STEM and gas adsorption studies, as a function of time of exposure to acetylene during synthesis, provide new insights into the growth of zeolite-templated carbons and thus of carbons having both “inner” (enclosing V1 and generating S1) and “outer” (enclosing V2 and generating S2) volumes and surfaces after removal of the zeolite. | Madi Arsakay; Boyuan Shen; Xiao Chen; Hao Xiong; Korlan Duisenova; Alisher Fatkhulloev; Carola Vorndran; Guangwu Yang; Bayrammuhammet Annageldyyev; Sun Hwa Lee; Won Kyung Seong; Matthias Thommes; Fei Wei; Rodney Ruoff | Materials Science; Inorganic Chemistry; Carbon-based Materials; Composites; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67aed238fa469535b94028ba/original/study-of-evolution-of-three-dimensional-porous-structure-in-zeolite-templated-carbons.pdf |
67652eb3fa469535b93873f8 | 10.26434/chemrxiv-2024-bq9ct-v2 | An in vitro one-pot synthetic biology approach to simulating diverging Golgi O-glycosylation of tumor-associated MUC1 from normal tissue MUC1 | Peptide O-glycosylation is a non-template-driven process that relies on the coordinated action of glycosyltransferases (GTs) within the endoplasmic reticulum (ER) and Golgi apparatus. An in vitro one-pot synthetic biology approach was developed to investigate the specificity and kinetics of GT O-GalNAc glycosylation that leads to tumor antigen glycoforms of mucin 1 (MUC1). The focus is to experimentally simulate the divergent glycosylation pathways that lead to the synthesis of cancer-associated antigens (Tn, T) and their sialylated derivatives. First, the biosynthetic details of the defining first step of GALNT re-localization from the ER to the Golgi was modeled using the one-pot method. Our findings reveal that an ER enriched with GALNTs results in complete Galnac (Tn) MUC1 site occupancy. This comes about as a function of two pro-cesses that are i) extended GALNT reaction time and ii) prevention of inhibition by subsequent glycosylation enzymes like C1GALT1. The modeling confirms that B3GNT6 has negligible specificity for MUC1 Tn, explaining the absence of core 3 and core 4 structures in MUC1 in both normal and cancerous breast cell lines. Moreover, ST6GALNAC1, and not ST6GALNAC2, is primarily responsible for α-2-6 sialylation of Tn and T antigens. Computer reaction dynamic simulations combined with kinetic experimental analysis show that ST6GALNAC1 prefers fully glycosylated MUC1 but moreover that its preference is the sialyation the S9 and T13 sites in the SAPDTR motif. This is especially the case when MUC1 concentra-tion is great (i.e., highly expressed), suggesting that sTn upregulation on MUC1 in cancer is linked to the occupancy status of S9 and T13 glycosylated sites, that were previously found to be cancer-associated. The results from the one-pot synthesis approach presented here demonstrate its ability to simulate cellular glycosylation within the Golgi-ER. This systems model-ling unpacks the molecular details of enzyme localization and substrate glycan occupancy that is fundamental to the regulatory mechanisms that gives rise to tumor-associated MUC1 antigens. | Abdullateef Nashed; Kyllen Dilsook; Tharindu Senapathi; Kevin Naidoo | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67652eb3fa469535b93873f8/original/an-in-vitro-one-pot-synthetic-biology-approach-to-simulating-diverging-golgi-o-glycosylation-of-tumor-associated-muc1-from-normal-tissue-muc1.pdf |
652da7bd45aaa5fdbb25d734 | 10.26434/chemrxiv-2023-v2j2l | Driving t-Butyl Axial: The Effect of Small Spirocyclic Rings on A-Values | The presence of a small spirocyclic ring at an adjacent position alters the conformational preference for equatorial substitution in cyclohexane and piperidine rings. DFT and low-temperature 1H NMR experiments demonstrate that alkyl groups larger than methyl possess negative A-values when geminal to a spirocyclohexane. Similar observations are made for halogen and other electron withdrawing substituents. For small groups such as methyl and hydroxy, the A-value is near zero, while for groups such as amino, acetamido and aryl, the A-values are positive, but significantly smaller than for simple cyclohexanes. Similar effects are observed for other strained rings (epoxide, cyclobutane, ox-etane) and the concepts extend to acyclic models. The origin of the effect is traced to an increase in torsional strain in combination with hyperconjugative effects in the case of electron poor groups. | Anthony Izzotti; James Gleason | Organic Chemistry; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652da7bd45aaa5fdbb25d734/original/driving-t-butyl-axial-the-effect-of-small-spirocyclic-rings-on-a-values.pdf |
64777b23e64f843f4118cf9b | 10.26434/chemrxiv-2023-njh44-v2 | Paired Site Characterization in Aluminosilicate Zeolites through Limited Alkylammonium Stability | The spatial distribution of tetrahedrally coordinated aluminum incorporated into a mordenite framework inverse framework zeolite was investigated through the proton site-selective probe chemistry of alkylamine Hofmann elimination. Protons associated with paired Al sites were exclusively exchanged with divalent cobalt, while isolated protons remained intact and readily quantified through Hofmann elimination of adsorbed alkylammonium species. Through a combination of temperature-programmed methods and spectroscopic characterization, the stability of the adsorbed alkylammonium was found to be crucial to the accurate estimation of isolated protons. Only alkylammonium species undergoing Hofmann elimination through a primary carbocation were found to exclusively probe isolated protons on the surface of cobalt-exchanged ZSM-5. More stable secondary and tertiary carbocations typically used in the characterization of acid sites, resulted in significant overestimates of protonic site densities. The result is contrary to purely protonic zeolites, where alkylammonium stability is inconsequential to the quantification of the acid sites they are coordinated with. Consequently, n-propylamine was found to be a suitable reactive probe molecule for the quantification of isolated protonic sites on divalent metal-cation zeolite surfaces, forming n-propylammonium upon adsorption. Ensuring accurate probing of isolated protons on the surface of metal cation exchanged zeolites was also demonstrated to require control of ion-exchange conditions and sufficient extent of zeolite exposure to the adsorbing n-propylamine. The fraction of paired Al sites in ZSM-5 was measured to systematically increase with Al content, ranging between 6 and 63 % across a Si/Al of 140 and 11.5, respectively. Experimentally measured Al pairing was in excellent quantitative agreement with a binomial distribution, suggesting a random incorporation of Al into the tetrahedral sites of ZSM-5 at next-nearest-neighboring positions. | Omar Abdelrahman; Ajibola Lawal | Materials Science; Catalysis; Nanostructured Materials - Materials; Acid Catalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64777b23e64f843f4118cf9b/original/paired-site-characterization-in-aluminosilicate-zeolites-through-limited-alkylammonium-stability.pdf |
66c5fef4a4e53c48761f9a07 | 10.26434/chemrxiv-2024-62sv6 | Assessing Darkness of the Human Kinome from a Medicinal Chemistry Perspective | In drug discovery, human protein kinases (PKs) represent one of the major target classes, due to their central role in cellular signaling, implication in various diseases as a consequence of deregulated signaling, and their notable druggability. Individual PKs and their disease biology have been explored to different degrees, giving rise to heterogeneous functional knowledge and disease associations across the human kinome. The U.S. National Institutes of Health previously designated 162 understudied (“dark”) human PKs and lipid kinases, due to the lack of functional annotations and high-quality molecular probes for functional investigations. Given large volumes of available PK inhibitors (PKIs) and activity data, we have systematically analyzed the distribution of PKIs and associated data at different confidence levels across the human kinome and distinguished between chemically explored, underexplored, and unexplored PKs. The analysis provides a medicinal chemistry-centric view of PK exploration and further extends prior assessment of the dark kinome. | Selina Voßen; Elena Xerxa; Jürgen Bajorath | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c5fef4a4e53c48761f9a07/original/assessing-darkness-of-the-human-kinome-from-a-medicinal-chemistry-perspective.pdf |
60c7476d337d6c497be27345 | 10.26434/chemrxiv.11648598.v1 | Active Coacervate Droplets as a Model for Membraneless Organelles and a Platform Towards Synthetic Life | Membraneless organelles like stress granules are active liquid-liquid phase-separated droplets that are involved in many intracellular processes. Their active and dynamic behavior is often regulated by ATP-dependent reactions. However, how exactly membraneless organelles control their dynamic composition remains poorly understood. Herein, we present a model for membraneless organelles based on RNA-containing active coacervate droplets regulated by a fuel-driven reaction cycle. These droplets emerge when fuel is present, but decay without. Moreover, we find these droplets can transiently up-concentrate functional RNA, and that this up-take is accelerated by the chemical reaction cycle. Finally, we show that in their pathway towards decay, these droplets self-divide asymmetrically. Self-division combined with emergence, decay, rapid exchange of building blocks, and functionality are all hallmarks of life, and we believe that our work could be a stepping stone towards its synthesis. | Carsten Donau; Fabian Späth; Marilyne Sosson; Brigitte Kriebisch; Fabian Schnitter; Marta Tena-Solsona; Hyun-Seo Kang; Elia Salibi; Michael Sattler; Hannes Mutschler; Job Boekhoven | Supramolecular Chemistry (Org.); Biochemistry; Biophysics; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7476d337d6c497be27345/original/active-coacervate-droplets-as-a-model-for-membraneless-organelles-and-a-platform-towards-synthetic-life.pdf |
60c73fe8bb8c1a817c3d9c6b | 10.26434/chemrxiv.7568696.v1 | An Insight on the Effect of Azobenzene Functionalities Studied in UiO-66 Framework for Low Energy CO2 Capture and CO2/N2 Membrane Separation | <div><b>Abstract</b><br /></div><div>In this paper, we report a simple approach to study the fundamental aspect of light-responsive metal organic framework (MOF) in UiO-66 topology through a mixed-ligand approach. Apart from change in the structural property, the loading of azobenzene linker inside the framework also affects the CO<sub>2</sub> light-responsive property and CO<sub>2</sub>/N<sub>2</sub> selectivity which could help to design future low-energy CO<sub>2</sub> adsorbents. Further study to incorporate the MOFs into mixed matrix membranes also indicates the benefit of higher azobenzene loading in the MOF to enhance the CO2/N2 separation performance since it can improve the separation performance which could not be obtained in non-functionalized fillers.</div><div><br /></div><div><b>Data Repository</b></div><div>Research data and additional high-resolution images are available from the open repository: https://doi.org/10.5281/zenodo.2533852</div> | Bradley P. Ladewig; Nicholaus Prasetya | Nanostructured Materials - Materials; Separation Science; Coordination Chemistry (Organomet.); Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fe8bb8c1a817c3d9c6b/original/an-insight-on-the-effect-of-azobenzene-functionalities-studied-in-ui-o-66-framework-for-low-energy-co2-capture-and-co2-n2-membrane-separation.pdf |
60c7544abdbb89ae6da3a603 | 10.26434/chemrxiv.13643654.v1 | Sulfur Versus Nitrogen Chelation in C-H Activation: Cobalt(III)-Catalyzed Unsymmetrical Double Annulation of Thioamides | An unconventional cobalt(III)-catalyzed one-pot domino double annulation of aryl thioamides with unactivated alkynes is presented. Sulfur (S), nitrogen (N), and o,o'-C-H bonds of aryl thioamides are involved in this reaction, enabling access to rare 6,6-fused thiopyrano-isoquinoline derivatives. A reverse ‘S’ coordination over more conventional ‘N’ coordination of thioamides to Co-catalyst specifically regulates the formation of four [C-C and C-S at first and then C-N and C-C] bonds in a single operation, a concept which is uncovered for the first time. The power of the N-masked methyl phenyl sulfoximine (MPS) directing group in this annulation sequence is established. The transformation is successfully developed, building a novel chemical space of structural diversity (56 examples). In addition, late-stage annulation of biologically relevant motifs and drug candidates are disclosed (17 examples). Preliminary photophysical properties of thiopyrano-isoquinoline derivatives are discussed. Density functional theory (DFT) studies authenticate the participation of a unique 6p-electrocyclization of a 7-membered S-chelated cobaltacycle in the annulation process.<br /> | Majji Shankar; Arijit Saha; Somratan Sau; Arghadip Ghosh; Vincent Gandon; Akhila Sahoo | Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7544abdbb89ae6da3a603/original/sulfur-versus-nitrogen-chelation-in-c-h-activation-cobalt-iii-catalyzed-unsymmetrical-double-annulation-of-thioamides.pdf |
6268519cd048ed4c80525a27 | 10.26434/chemrxiv-2022-xglq9 | Umbrella Sampling Simulations Simultaneously Measure Switch Peptide Binding and Hydrophobic Patch Opening Free Energies in Cardiac Troponin | The cardiac troponin complex (cTn) is an important regulatory protein in heart contraction. Upon binding of Ca2+, cTn undergoes a conformational shift that allows the troponin I switch peptide (cTnISP) to be released from the actin filament and bind to the troponin C hydrophobic patch (cTnC). Mutations and modifications to this complex can change its sensitivity to Ca2+ and alter the energetics of the transition from the Ca2+-unbound, cTnISP-unbound form to the Ca2+-bound, cTnISP-bound form. We utilized targeted MD (TMD) to obtain a trajectory of this transition pathway, followed by umbrella sampling to estimate the free energy associated with the cTnISP-cTnCHP binding and the cTnCHP opening events for wild-type (WT) cTn. We were able to reproduce experimental values for the cTnISP-cTnCHP binding event and obtain cTnCHP opening free energies in agreement with previous computational measurements of smaller cTnC systems. This excellent agreement for WT cTn demonstrated the strength of computational methods in studying the dynamics and energetics of cTn complex. We then introduced mutations to the cTn complex that cause cardiomyopathy or alter its Ca2+-sensitivity and observed a general decrease in the free energy of opening the cTnCHP. For these same mutations, we observed no general trend in the effect on the cTnISP-cTnCHP binding event. Our method sets the stage for future computational studies on this system that predict the consequences of yet uncharacterized mutations on cTn dynamics and energetics. | Austin Cool; Steffen Lindert | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6268519cd048ed4c80525a27/original/umbrella-sampling-simulations-simultaneously-measure-switch-peptide-binding-and-hydrophobic-patch-opening-free-energies-in-cardiac-troponin.pdf |
60c74bc59abda206e7f8d15f | 10.26434/chemrxiv.12373973.v1 | Entering the Augmented Era: Immersive and Interactive Virtual Reality for Battery Education and Research | We present a series of innovative serious games we develop since four years using Virtual Reality (VR) technology to teach battery concepts at the University and also to the general public in the context of science festivals and other events. These serious games allow interacting with battery materials, electrodes and cells in a immersive way. <br /><br /> | Alejandro A. Franco; Jean-Nöel Chotard; Emilie Loup-Escande; Yinghui Yin; Ruijie Zhao; Alexis Rucci; Alain Ndganjong; Benjamin Beye; Simon Herbulot; Jan Ciger; Romain Lelong | Chemical Education - General; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bc59abda206e7f8d15f/original/entering-the-augmented-era-immersive-and-interactive-virtual-reality-for-battery-education-and-research.pdf |
667965d601103d79c502a0e5 | 10.26434/chemrxiv-2024-p2tcc | Efficient and expedited access to polyunsaturated fatty acids and biofunctional analogs by full solid-phase synthesis | Polyunsaturated fatty acids (PUFAs) represent a fundamental and essential lipid class, exhibiting versatile biofunctions. Lipidomic analysis has identified a growing number of lipid species, including PUFAs with diverse structural variations and biofunctions, yet the structure–function relationships are still largely unknown. In this context, there is a long-sought demand to synthesize various PUFAs efficiently. However, no practical methodology exists, unlike the case with peptides and nucleic acids, where diverse molecules are accessible through a well-established solid-phase synthesis. Herein, we report an efficient and expedited method to access a wide array of PUFAs by full solid-phase synthesis. This method allows the synthesis of various PUFAs and analogs in rapid and facile operations. Moreover, we have discovered an artificial fatty acid, Antiefin, with a high anti-inflammatory effect in vivo within our PUFA library. This report provides a practical synthetic pathway for PUFAs, a crucial lipid class, expected to contribute to lipid science. | Yutaro Saito; Mayuko Akita; Azusa Saika; Yusuke Sano; Masashi Hotta; Jumpei Morimoto; Akiharu Uwamizu; Junken Aoki; Takahiro Nagatake; Jun Kunisawa; Shinsuke Sando | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667965d601103d79c502a0e5/original/efficient-and-expedited-access-to-polyunsaturated-fatty-acids-and-biofunctional-analogs-by-full-solid-phase-synthesis.pdf |
62c613b4638326359b42d15d | 10.26434/chemrxiv-2022-k8ws1-v3 | Tuning Ionic Screening to Accelerate Electrochemical CO2 Reduction in Ionic Liquid Electrolytes | Electric double layer formation often governs the rate and selectivity of CO2 electrochemical reduction. Ionic correlations critically define double layer properties that are essential to electrocatalytic performance, including capacitance and localization of potential gradients. However, the influence of ionic correlations on CO2 electro-reduction remains unexplored. Here, we use electrochemical conversion of CO2 to CO in ionic liquid-based electrolytes to investigate how the emergence of ionic correlations with increasing ion concentration influences reaction rates and selectivity. Remarkably, we find substantial acceleration of potential-dependent CO2 reduction rates and notable enhancement of faradaic efficiency to CO at intermediate concentrations of 0.9 M ionic liquid in acetonitrile, a concentration regime that has not been studied previously. We find that onset potentials for CO2 reduction remain relatively unchanged at -2.01 V vs. Ag/Ag+ from 0.025 M up to 1.1 M and increase to -2.04 V vs. Ag/Ag+ in the limit of neat ionic liquids. Hence, the acceleration of CO2 reduction we observe originates from the amplification of potential-dependent driving forces, as opposed to changes in onset potential. Importantly, our findings are general across co-catalytic and non-catalytic ions. We propose that concentrations of maximum reactivity correspond to conditions where electric double layers exhibit the strongest screening, which would localize electric fields to stabilize polar intermediates. Our study demonstrates that tuning bulk electrostatic screening lengths via modulation of ionic clustering provides a general approach to accelerating both inner sphere and outer sphere electrochemical reactions. | Beichen Liu; Wenxiao Guo; Matthew Gebbie | Catalysis; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c613b4638326359b42d15d/original/tuning-ionic-screening-to-accelerate-electrochemical-co2-reduction-in-ionic-liquid-electrolytes.pdf |
66f7ad4d51558a15ef6440f2 | 10.26434/chemrxiv-2022-24qv4-v2 | Asymmetrical Calcium Ions Induced Stress and Remodeling in Lipid Bilayer Membranes | Ca2+ ions play crucial roles in regulating many chemical and biological processes, but their impact on lipid bilayer membranes remains elusive, especially when the impacts on the two leaflets are asymmetrical. Using a recently developed multisite Ca2+ model, we performed molecular dynamics simulations to study the impact of Ca2+ on the properties of membranes composed of POPC and POPS and observed that both the structure and fluidity of the membranes were significantly affected. In particular, we examined the influence of asymmetrically distributed Ca2+ on asymmetric lipid bilayers and found that imbalanced stress in the two leaflets was generated, with the negatively charged leaflet on the Ca2+-rich side becoming more condensed, which in turn induced membrane curvature that bent the membrane away from the Ca2+-rich side. We employed continuum mechanics to study the large-scale deformations of a spherical vesicle and found that the vesicle can go through vesiculation to form a multi-spherical shape in which a number of spheres are connected with infinitesimal necks, depending on the specific Ca2+ distributions. These results provide new insights into the underlying mechanisms of many biological phenomena involving Ca2+-membrane interactions and may lead to new methods for manipulating the membrane curvature of vesicles in chemical, biological, and nanosystems. | Chang Liu; Qi Zhong; Kai Kang; Rui Ma; Chen Song | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Theory - Computational; Biophysical Chemistry | CC BY 4.0 | CHEMRXIV | 2024-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f7ad4d51558a15ef6440f2/original/asymmetrical-calcium-ions-induced-stress-and-remodeling-in-lipid-bilayer-membranes.pdf |
60c7491a567dfed884ec4b30 | 10.26434/chemrxiv.12027009.v1 | Base-Catalyzed Aryl Halide Isomerization Enables the 4-Selective Substitution of 3-Bromopyridines | <div>The base-catalyzed isomerization of simple aryl halides is presented and utilized to achieve the 4-selective etherification, hydroxylation and amination of 3bromopyridines. Mechanistic studies support isomerization of 3-bromopyridines to 4-bromopyridines proceeds via pyridyne intermediates and that 4-substitution selectivity is driven by a facile SNAr reaction. Beneficial aspects of a tandem aryl halide isomerization/selective interception approach to aromatic functionalization are demonstrated.<br /></div> | Thomas
R. Puleo; Jeffrey Bandar | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7491a567dfed884ec4b30/original/base-catalyzed-aryl-halide-isomerization-enables-the-4-selective-substitution-of-3-bromopyridines.pdf |
658cbf8f66c13817292c3459 | 10.26434/chemrxiv-2023-4bddw | Naringenin-7-O-glucoside: Targeting SERPINE1, MMP7, and MMP1 for COVID-19 Lung Pathology and Immune Modulation | The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has been a defining global health crisis, marked by severe respiratory distress and high mortality rates. The search for effective treatments against this highly mutable virus has been a significant challenge. Here, we explored the therapeutic potential of Naringenin-7-O-glucoside (N7G), a bioactive flavone glycoside, in the context of COVID-19. Known for its wide-ranging pharmacological effects, including antiviral, antibacterial, antimalarial, and anticancer properties, Utilizing gene expression data from the EBI Expression Atlas, we analyzed lung samples from deceased COVID-19 patients and healthy individuals to understand N7G’s molecular mechanisms and potential therapeutic targets. Our enrichment analysis revealed a significant association of N7G targets with biological functions and pathways crucial in immune responses and cellular signaling. We highlighted the importance of pathways such as HIF-1, AGE-RAGE, and IL-17 in the pathogenesis of diseases like COVID-19. Suppressing the HIF-1 pathway could mitigate lung inflammation, while targeting the AGE-RAGE pathway, a key player in oxidative stress and inflammation, emerges as a promising strategy. Modulating the IL-17 pathway, implicated in cytokine storms during infection, could also be effective. Furthermore, the relaxin signaling pathway, known for its anti-inflammatory and anti-fibrotic properties, was identified as a potential target for post-COVID-19 syndrome or long-haul COVID. We prioritized SERPINE1, MMP7, and MMP1 as key therapeutic targets. Elevated SERPINE1 levels in COVID-19 patients have been linked to early mortality risk and are involved in processes like platelet degranulation and fibrinolysis impairment, contributing to thrombocytopenia. MMP1 and MMP7, part of the matrix metalloproteinases family, play crucial roles in tissue homeostasis and have been identified as biomarkers and potential therapeutic targets in COVID-19, linked to pulmonary edema and severe inflammatory responses. Our molecular docking and MD simulation studies, conducted over 200 ns in triplicates, demonstrated stable complex formation of N7G with MMP7 and SERPINE1. N7G consistently occupied the zinc binding catalytic site of MMP7, similar to other MMP7 inhibitors, and tightly bound to the inhibitor site of SERPINE1, indicating strong interactions. The MMGBSA analysis confirmed the stability of these complexes, suggesting the effective inhibitory potential of N7G against these targets. Although N7G showed transient complex formation with MMP1, its role in COVID-19 pathogenesis, particularly in inflammation, cannot be ignored. Elevated MMP1 levels have been associated with increased inflammatory responses in COVID-19 patients, underscoring its importance as a therapeutic target. In conclusion, our study identifies MMP7, MMP1, and SERPINE1 as critical immune-related targets of N7G in combating COVID-19. The results position N7G as a potential novel inhibitor for treating COVID-19-induced lung inflammation and long-haul COVID. However, these initial findings require further validation. This study contributes to the understanding of natural compounds in viral infection treatment, opening pathways for exploring flavonoids like N7G against SARS-CoV-2 and other viruses. It underscores the importance of diverse therapeutic strategies, including natural substances, in combating the global challenge of COVID-19. | Vibha Mishra; Shivangi Agrawal; Divya Malik; Ekta Pathak; Rajeev Mishra | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Agriculture and Food Chemistry; Food; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658cbf8f66c13817292c3459/original/naringenin-7-o-glucoside-targeting-serpine1-mmp7-and-mmp1-for-covid-19-lung-pathology-and-immune-modulation.pdf |
65dc627de9ebbb4db9489e14 | 10.26434/chemrxiv-2024-dlpcs | Functionalised Al(III) metal organic frameworks for fluorescence sensing of nitroaromatic vapours | The employment of fluorescence sensors provides a platform for rapid and efficient in-field detection of nitroaromatic compounds and is gaining increasing reserach ground. Herein, we report the synthesis and characterisation of three new fluorescent Al(ΙΙΙ) MOFs, structurally analogous to MIL–53, with the assigned formula {Al(OH)(bdc)1-n(L–1)n}·xsolv (bdc2- = terephthalate; L–1 = 2–((benzyl)amino)-terephthalate). L–1 is a strongly fluorescent dicarboxylic ligand with a pendant π–electron rich aromatic group suitable for electron transfer processes towards electron–deficient nitroaromatic guests. Our MOFs show strong fluorescence quenching upon exposure to vapours of nitrobenzene, 1,3-dinitrobenzene, 4-nitrotoluene, 2,4-dinitrotoluene. Additionally, we prepare and study MOF-polymer composites in the form of thin films that are strongly quenched in the presence of nitrobenzene vapours. | Amina Haj-Yahya; Dimitra Kouskouki; Antigoni G. Margellou; Evangelos K. Andreou; Gerasimos S. Armatas; Theodore Lazarides | Inorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65dc627de9ebbb4db9489e14/original/functionalised-al-iii-metal-organic-frameworks-for-fluorescence-sensing-of-nitroaromatic-vapours.pdf |
65836c6ae9ebbb4db9609135 | 10.26434/chemrxiv-2023-fz84h-v2 | Enhancing the Features of DNA Mimic Foldamers for Structural Investigations | DNA mimic foldamers based on aromatic oligoamide helices bearing anionic phosphonate side chains have been shown to bind to DNA-binding proteins sometimes orders of magnitude better than DNA itself. Here, we introduce new features in the DNA mimic foldamers to facilitate structural investigations of their interactions with proteins. Thirteen new foldamer sequences have been synthesized and characterized using NMR, circular dichroism, molecular modeling, and X-ray crystallography. The results show that foldamer helix handedness can be quantitatively biased by means of a single stereogenic center, that the foldamer structure can be made C2-symmetrical as in palindromic B-DNA sequences, and that associations between foldamer helices can be promoted utilizing dedicated C-terminal residues that act as sticky ends in B-DNA structures. | Valentina Corvaglia; Jiaojiao Wu; Deepak Deepak; Manuel Loos; Ivan Huc | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65836c6ae9ebbb4db9609135/original/enhancing-the-features-of-dna-mimic-foldamers-for-structural-investigations.pdf |
65e858909138d23161cb5ee6 | 10.26434/chemrxiv-2024-g8jgb | Water and q-Gaussians (Raman Spectroscopy) | A large literature exists about the Raman spectroscopy of water. Here we present some articles regarding the spectral region between 2800 and 3800 cm−1, that is the O-H stretching Raman band, and the proposed decomposition obtained by means of Gaussian profiles. We will also consider the decomposition of this region with three q-Gaussian functions, instead of the five Gaussians usually considered. Being the q-parameter of q-Gaussians related to the correlation time of stochastic Kubo approach to fluctuations, we propose its use to characterize the local environment of O-H bonds. | Amelia Carolina Sparavigna | Materials Science | CC BY 4.0 | CHEMRXIV | 2024-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e858909138d23161cb5ee6/original/water-and-q-gaussians-raman-spectroscopy.pdf |
60c740f20f50db7d53395a50 | 10.26434/chemrxiv.7892513.v1 | Copper-Catalyzed Insertion of Diazo Compounds into Vinyl Hypervalent Iodine Reagents to Generate Allylic Esters | An
unprecedented copper(I)-catalyzed vinylation of (donor)-acceptor
diazo compounds
with VinylBenziodoXolone reagents (VBX) as partners is reported. The
transformation tolerates variation of both donor- and acceptor substituents on
the diazo compounds, delivering the corresponding benzoylated allylic alcohol
products in good to excellent yields. Through the development of a protocol for
the synthesis of functionalized alkanes-, dienes- and enynes-substituted VBX
reagents, a broad scope of substituents on the alkene could be accessed. The
obtained products contain synthetically versatile functional groups, such as an
aryl iodide, an ester and an allylic leaving group, enabling selective further
modification. | Guillaume Pisella; Alec Gagnebin; Jerome Waser | Organic Synthesis and Reactions; Homogeneous Catalysis; Catalysis | CC BY NC 4.0 | CHEMRXIV | 2019-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740f20f50db7d53395a50/original/copper-catalyzed-insertion-of-diazo-compounds-into-vinyl-hypervalent-iodine-reagents-to-generate-allylic-esters.pdf |
63049a3611986c398142dbb9 | 10.26434/chemrxiv-2023-mx5dk | Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host-guest Binding: III. Force-Field Comparison, Three-Trajectory Realization and Further Dielectric Augmentation | Host-guest binding, despite the relatively simple structural and chemical features of individual components, still poses a challenge in computational modelling. The problems lie in both the accuracy of the employed Hamiltonian (often fixed-charge force fields) and the exhaustiveness of conformational sampling. End-point free energy calculations as fast alternatives to rigorous but costly methods are widely applied in virtual screening in protein-ligand and host-guest systems. However, the extreme underperformance of standard end-point methods makes them practically useless. Modifications of the end-point procedure could bring these methods back to the pool of usable tools, e.g., regression considered in our previous work. In the current work, we explore a potentially promising modification, the three-trajectory realization of the end-point simulation protocol. The alteration couples the binding-induced structural reorganization into free energy estimation and suffers from dramatic fluctuations of internal energies in protein-ligand situations. Fortunately, the relatively small size of host-guest systems minimizes the magnitude of internal fluctuations and makes the three-trajectory realization practically suitable. Due to the incorporation of intra-molecular interactions in free energy estimation, a strong dependence on the force field parameters could be incurred. Thus, a term-specific investigation of transferable GAFF derivatives is presented, and noticeable differences in many aspects are identified between commonly applied GAFF and GAFF2. These force-field differences lead to different dynamic behaviors of the macrocyclic host, which ultimately would influence the end-point sampling and binding thermodynamics. Therefore, the three-trajectory end-point free energy calculations are performed with both GAFF versions to investigate the force-field dependent behavior of computed binding affinities. Also, due to the noticeable differences between host dynamics under GAFF and GAFF2, we add additional benchmarks of the single-trajectory end-point calculations. Numerical results suggest that the single-trajectory realization, regardless of the GAFF version, is still not useful in host-guest binding, although the prediction quality of the GAFF2 parameter set is slightly better than GAFF. As for the three-trajectory realization, the absolute values of computed binding thermodynamics exhibit pronounced force-field-dependent behaviors, which are less significant for ranking information. When only the ranks of binding affinities are pursued, the three-trajectory realization performs very well, comparable to and even better than the regressed PBSA_E scoring function and the dielectric-constant-variable regime. With the GAFF parameter set, the TIP3P water in explicit-solvent sampling and either PB or GB implicit-solvent model in free energy estimation, the predictive power of the three-trajectory realization in ranking calculations surpasses all existing end-point methods on this dataset. We further combine the three-trajectory realization with another promising modified end-point regime of varying the interior dielectric constant. The predicted binding affinities exhibit monotonic responses to the variation of the internal dielectric constant, but the deviations from experiment exhibit non-monotonic variations, which are related to the systematic overestimation of the binding strength under the original three-trajectory realization. By contrast, the combined regime does not incur sizable improvements for ranks, although for most systems the dielectric constant 2 seems to be the best option. | Xiao Liu; Lei Zheng; Chu Qin; Yalong Cong; John Z. H. Zhang; Zhaoxi Sun | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63049a3611986c398142dbb9/original/comprehensive-evaluation-of-end-point-free-energy-techniques-in-carboxylated-pillar-6-arene-host-guest-binding-iii-force-field-comparison-three-trajectory-realization-and-further-dielectric-augmentation.pdf |
67af571b6dde43c908da6b2c | 10.26434/chemrxiv-2025-42hh2 | Origins of crystallisation-induced dual emission of
terephthalic and isophthalic acid crystals | Metal-free organic crystals with room-temperature phosphorescence (RTP) present an innovative alternative to conventional inorganic materials for optoelectronic applications and sensing. Recently, substantial attention has been directed towards the design of new phosphorescent crystals through crystal engineering and functionalisation. In this paper, we investigate the excited-state deactivation mechanisms of two simple organic molecules: terephthalic acid (TPA) and isophthalic acid (IPA) using embedding models based on multiconfigurational MS-CASPT2 calculations. These molecules exhibit prompt and delayed fluorescence and RTP in the solid state. We explore intramolecular internal conversion pathways using high-level quantum chemistry methods in both solution and crystalline phases. We analyse deactivation mechanisms involving singlet and triplet states, quantifying direct and reverse intersystem crossing rates from the lowest triplet states, as well as fluorescence and phosphorescence rates. Additionally, our study examines singlet exciton transport in single crystals of TPA and IPA. Our findings clarify the mechanisms underlying the prompt and delayed fluorescence and RTP of crystalline TPA and IPA, revealing distinct differences in their deactivation processes. Notably, we explain the enhanced fluorescence and phosphorescence in IPA compared to TPA, emphasising how the positioning of the carboxylic group influences electronic delocalisation in excited states, (de)stabilising delocalised ππ* states along the reaction coordinate, thereby significantly impacting deactivation mechanisms. | Ljiljana Stojanovic; Michael Dommett ; Rachel Crespo Otero | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67af571b6dde43c908da6b2c/original/origins-of-crystallisation-induced-dual-emission-of-terephthalic-and-isophthalic-acid-crystals.pdf |
617fd7009b583af2f5e76dd1 | 10.26434/chemrxiv-2021-jjwfv-v2 | Molecular Alignment of a Meta-Aramid on Carbon Nanotubes by In-Situ Interfacial Polymerization. | Molecularly organized nanocomposites of polymers and carbon nanotubes (CNTs) have great promise as high-performance materials; in particular, conformal deposition of polymers can control interfacial properties for mechanical load transfer, electrical or thermal transport, or electro/chemical transduction. However, controllability of polymer-CNT interaction remains a challenge with common processing methods that combine CNTs and polymers in melt or in solution, often leading to non-uniform polymer distribution and/or aggregation of CNTs. Here, we demonstrate CNTs within net-shape sheets can be controllably coated with a thin, conformal coating of meta-aramid by simultaneous capillary infiltration and interfacial polymerization. We determine that π interaction between the polymer and CNTs results in chain alignment parallel to the CNT outer wall. Subsequent nucleation and growth of the precipitated aramid forms a smooth continuous layered sheath around the CNTs. These findings motivate future investigation of mechanical and interfacial properties of the resulting CNT composites, and adaptation of the in-situ polymerization method to other substrates. | Cécile Chazot; Behzad Damirchi; Adri van Duin; John Hart | Materials Science; Polymer Science; Composites; Polymerization (Polymers); Polymer morphology; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617fd7009b583af2f5e76dd1/original/molecular-alignment-of-a-meta-aramid-on-carbon-nanotubes-by-in-situ-interfacial-polymerization.pdf |
65df54dfe9ebbb4db9798a42 | 10.26434/chemrxiv-2024-fmrnw-v2 | Dual optical cycling centers mounted on an organic scaffold: New insights from quantum chemistry calculations and symmetry analysis | Molecules cooled to the ultracold temperatures are desirable for applications in fundamental physics and quantum information science. However, cooling polyatomic molecules with more than six atoms has not yet been achieved. Building on the idea of an optical cycling center (OCC), a moiety supporting a set of localized and isolated electronic states within a polyatomic molecule, molecules with two OCCs (bi-OCCs) may afford a better cooling efficiency by doubling the photon scattering rate. By using quantum chemistry calculations, we assess the extent of the coupling of the two OCCs with each other and with the molecular scaffold. We show that promising coolable bi-OCC molecules can be proposed following chemical design principles. | Taras Khvorost; Pawel Wojcik; Cecilia Chang; Mia Calvillo; Claire Dickerson; Anna Krylov; Anastassia Alexandrova | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65df54dfe9ebbb4db9798a42/original/dual-optical-cycling-centers-mounted-on-an-organic-scaffold-new-insights-from-quantum-chemistry-calculations-and-symmetry-analysis.pdf |
60c74fc04c89197b6bad3c68 | 10.26434/chemrxiv.12925214.v1 | Rapid Profiling of Isomeric Unsaturated Lipids Through Online Photochemical Derivatization of C=C Bonds | Unraveling the complexity of the lipidome requires
the development of novel approaches for the structural characterization of
lipid species with isomeric resolution. Herein,
we introduce an online photochemical approach for lipid isomer identification
through selective derivatization of double bonds by reaction with singlet
oxygen. Lipid hydroperoxide products are
generated promptly after laser irradiation. Fragmentation of these species in a mass spectrometer produces diagnostic
fragments, which reveal the C=C locations in the unreacted lipids. This
approach uses an inexpensive light source and photosensitizer making it easy to
incorporate into any lipidomics workflow. We demonstrate the utility of this
approach for the shotgun profiling of C=C locations in different lipid classes present
in tissue extracts using electrospray
ionization (ESI) and for spatially-resolved analysis of lipids in tissue sections using nanospray desorption electrospray ionization (nano-DESI). These results provide a path for both
rapid profiling and ambient imaging of positional isomers in biological samples. | Daisy Unsihuay; Pei Su; Yingju Li; Xiaofei Sun; Sudhansu Dey; Julia Laskin; Shihuan Kuang; Jiamin Qiu | Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fc04c89197b6bad3c68/original/rapid-profiling-of-isomeric-unsaturated-lipids-through-online-photochemical-derivatization-of-c-c-bonds.pdf |
66ae9906c9c6a5c07af1bf12 | 10.26434/chemrxiv-2024-bm7rq | Analysis of the OH coverage on low-coordinated Pt sites at low potentials | In a previous study, we demonstrated the presence of OH species adsorbed on low-coordinated Pt sites (or steps) at low potentials using spectroscopy and electrochemical experiments. This investigation was specifically conducted on a Pt(311) surface in an electrolyte with pH=1. In this work, we extend our study to other surfaces featuring (111) terraces but varying in step geometry and step density. Additionally, we explored the influence of pH on these systems.
Our findings reveal that the OH coverage on Pt steps at low potentials is independent of pH but sensitive to surface structure. Specifically, we observed an OH coverage of approximately 0.5 on surfaces with (110) steps and 0.33 on surfaces with (100) steps. Furthermore, the potential of zero total charge aligns with the local potential of zero charge for the steps and is predominantly influenced by adsorbed species on these low-coordinated sites.
| Rubén Rizo; Lorena Chico-Mesa; Rosa M. Arán-Ais; Víctor Climent; Enrique Herrero; Juan M. Feliu | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ae9906c9c6a5c07af1bf12/original/analysis-of-the-oh-coverage-on-low-coordinated-pt-sites-at-low-potentials.pdf |
660866909138d23161c55fe1 | 10.26434/chemrxiv-2024-1bpwh | The Formation and Architecture of Surface-Initiated Polymer Brush Gene Delivery Complexes | Understanding the architecture and mechanism of assembly of polyelectrolyte-nucleic acid complexes is critical to the rational design of their performance for gene delivery. Surface-initiated polymer brushes were recently found to be particularly effective at delivering oligonucleotides and maintaining high knock down efficiencies for prolonged periods of time, in highly proliferative cells. However, what distinguishes their binding capacity for oligonucleotides from that of larger therapeutic macromolecules remains unknown. In this report, we characterise the binding capacity and adsorption kinetics of different types of nucleic acid materials for gene delivery (single and double stranded oligo RNA and DNA, mRNA and plasmid DNA) to PDMAEMA and PMETAC brushes, using surface plasmon resonance. The type and size of these nucleic acid macromolecules are found to have an important impact on their maximum surface density, and the association and adsorption constants of the resulting complexes. To gain further insight into the mechanisms that restrict the adsorption of higher molecular weight materials, and promote particularly effective RNA capture, the architecture of PDMAEMA brushes prior and after complexation is investigated by in situ ellipsometry and neutron reflectometry. Deep infiltration of oligonucleotides was found, irrespective of their binding capacity, suggesting that their infiltration is not a limiting factor in their dense capture on polymer brushes. In contrast, mRNA and pDNA were found to partially infiltrate within PDMAEMA brushes, although some of the nucleic acid materials could be found deep into the brush layer. This indicates that the size of these macromolecules and their partial infiltration may restrict further adsorption and high binding capacities, but also suggests that oligonucleotides will experience enhanced protection within polymer brushes, with fewer residues accessible for enzymatic degradation. | Carlos Neri-Cruz; Lan Chang; Franciane Teixeira; Shoghik Hakobyan; Philipp Gutfreund; Mario Campana; Ali Zarbakhsh; Julien Gautrot | Physical Chemistry; Polymer Science; Nanoscience; Drug delivery systems; Polymer brushes; Polymer morphology | CC BY 4.0 | CHEMRXIV | 2024-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660866909138d23161c55fe1/original/the-formation-and-architecture-of-surface-initiated-polymer-brush-gene-delivery-complexes.pdf |
654f784c2c3c11ed713289d0 | 10.26434/chemrxiv-2023-hr2bs | On Maintaining Standards in Chemistry | ARISING FROM C. Yang et al., Nature Chemistry https://doi.org/10.1038/s41557-023-01212- 2 (2023)
In this work Yang et al. [1] claim that an enantioselective Michael addition reaction with a barrier of 16 kcal/mol occurs at the single molecule level in frozen solvent by measuring fluctuations in current flowing across graphene based molecular devices. If true, such methods would provide a leap forward in understanding reaction mechanisms. However such strong conclusions need strong experimental evidence, which, as we detail in this Matters Arising, is lacking in the work of Yang et al. [1].
Typically, advances in synthetic chemistry have thrived based on a strong tradition of providing analytical evidence for compounds formed using methods such as nuclear magnetic resonance (NMR), high-performance liquid chromatography (HPLC), high resolution mass spectroscopy (HRMS) as well as structure identification using x-ray techniques. These methods often require macroscopic quantities of the products. This makes such characterizations difficult when molecules are synthesized one at a time. Although there are no techniques available for single molecule NMR analysis yet, there are many other experiments that could have been performed to show proof of synthesis at the single molecule level. Unfortunately, as we show here, in the work of Yang et al. [1] the evidence provided is insufficient, often inconsistent, and even misleading, leaving us to conclude that the results appear to be too good to be true. | Latha Venkataraman; Jan van Ruitenbeek | Nanoscience; Nanodevices | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654f784c2c3c11ed713289d0/original/on-maintaining-standards-in-chemistry.pdf |
63d8c54501ecc690f9175bc0 | 10.26434/chemrxiv-2023-f3bc5 | Synergizing ontologies and graph databases for highly flexible materials-to-device workflow representations | The escalating adoption of high-throughput methods in applied materials science dramatically increases the amount of generated data, demandingthe deployment and use of sophisticated data-driven methods. To exploit the full potential of these accelerated approaches, the generated data needs to be managed, preserved, and shared. Its heterogeneity calls for highly flexible data models to represent data from fabrication workflows, measurements, and simulations. We propose employing a native graph database to store the data instead of relying on rigid relational data models. To develop a flexible and extendable data model, we have created an EMMO-based ontology, where EMMO stands for European Materials Modelling Ontology. The Python framework Django is used to allow for the intuitive integration into the virtual materials intelligence platform, VIMI. The Django framework relies on the Object-Graph-Mapper (OGM) neomodel to create a mapping between database classes and python objects. The model can store the whole bandwidth of data, from fabrication to simulation data. Implementing the database into a platform will encourage researchers to share data while profiting from rich and highly curated data to accelerate their research. | Max Dreger; Kourosh Malek; Mohammed J. Eslamibidgoli; Michael H. Eikerling | Theoretical and Computational Chemistry; Materials Science; Energy; Theory - Computational; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d8c54501ecc690f9175bc0/original/synergizing-ontologies-and-graph-databases-for-highly-flexible-materials-to-device-workflow-representations.pdf |
6338ca4ae665bd367019e037 | 10.26434/chemrxiv-2022-79tzx | Automated Platform for the Synthesis of Heparan Sulfate Oligosaccharide Libraries for Decoding Glycosaminoglycan-Protein Interactions | Glycosaminoglycans (GAGs) are abundant, ubiquitous carbohydrates in biology, yet their structural complexity has limited an understanding of their biological roles and structure-function relationships. Synthetic access to large collections of well-defined, structurally diverse GAG oligosaccharides would provide critical insights into this important class of biomolecules and represent a major advance in glycoscience. Here, we report a new automated platform for synthesizing heparan sulfate (HS) oligosaccharide libraries displaying comprehensive arrays of sulfation patterns. Library synthesis is made possible by improving the overall synthetic efficiency through universal building blocks derived from natural heparin and a traceless fluorous tagging method for rapid purification and automated synthesis. We used this approach to generate the first comprehensive library of 64 HS tetrasaccharides displaying all possible 2-O-, 6-O-, and N-sulfation sequences. These diverse structures provide an unprecedented view into the sulfation code of GAGs and identify sequences for modulating the activities of important growth factors and chemokines. | Lei Wang; Bo-Shun Huang; Alexander Sorum; Mallory Kern; Guowei Su; Xuefei Huang; Jian Liu; Nicola Pohl; Linda Hsieh-Wilson | Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6338ca4ae665bd367019e037/original/automated-platform-for-the-synthesis-of-heparan-sulfate-oligosaccharide-libraries-for-decoding-glycosaminoglycan-protein-interactions.pdf |
60c7539ff96a006bf62884cc | 10.26434/chemrxiv.13516550.v1 | Quantifying Nanoparticle Assembly States in Polymer Matrix Through Deep Learning | <p>There is great interest in controlling the spatial dispersion of inorganic nanoparticles (NPs) in an organic polymer matrix, because this centrally underpins the property enhancements obtained from these hybrid materials. Currently, qualitative information on NP spatial distribution is obtained by visual inspection of transmission electron microscopy (TEM) images. Quantitative information is only indirectly obtained through the use of scattering probes such as small angle X-ray/neutron scattering. While the main challenge, that scattering probes operate in reciprocal space, can be remedied by Fourier inverting the data into real space, a much harder issue is deconvolving the contribution of the particle form factor (which is affected by the details of the NP size and shape) from the structure factor which contains information on the NP spatial distribution. These problems become acute when we deal with the popular topic of NPs grafted with polymer chains, because the polymeric corona, and hence the particle form factor, becomes context dependent and hard to quantify. To make progress, we develop and apply a deep-learning based image analysis method to quantify the distribution of spherical NPs in a polymer matrix directly from their real-space TEM images. A dataset of NP detection (DOPAD) is built by manually labeling particle positions on experimental TEM images of diverse polymer composite systems. A convolutional neural network (CNN) object detection model is then trained on DOPAD. Together with sliding-window and merging algorithms, an automated pipeline is established, which takes a large TEM image as input and extracts NP locations and sizes. We validate the structural information resulting from this method against SAXS derived structural information for NPs ordered by polymer crystallization, and then use it to distinguish between different states of the assembly of polymer grafted NPs in a polymer matrix achieved by using their surfactancy. We show that this data-rich protocol allows us to draw critical facets of experimental behavior which have previously not been accessible. The DOPAD dataset, Python source code and trained model are shared on GitHub.</p> | Eric Qu; Andrew Jimenez; Sanat Kumar; Kai Zhang | Composites | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7539ff96a006bf62884cc/original/quantifying-nanoparticle-assembly-states-in-polymer-matrix-through-deep-learning.pdf |
60c74fccbdbb89bcd0a39e1b | 10.26434/chemrxiv.12943106.v1 | On the Polymorph-Selective Role of Hydrogen Bonding and π - π Stacking in Para-Aminobenzoic Acid Solutions | <div><div><div><p>Understanding molecular self-association in solution is vital for uncovering polymorph- selective crystal nucleation pathways. In this paper, we combine solution NMR spectroscopy and molecular dynamics simulations to shed light on the structural and dynamical features of para-aminobenzoic acid (pABA) in solution, and on their role in pABA crystals nucleation. pABA is known to yield different crystal forms (α, and β) depending on solvent choice and su- persaturation conditions. NMR reveals that dominant interactions stabilising pABA oligomers are markedly solvent-dependent: in organic solvents, hydrogen bonds dominate, while water promotes π - π stacking. Despite this clear preference, both types of interactions contribute to the variety of self-associated species in all solvents considered. MD simulations support this observation and show that pABA oligomers are short-lived and display a fluxional character, therefore indicating that the growth unit involved in pABA crystallisation is likely to be a single molecule. Nevertheless, we note that the interactions dominating in pABA oligomers are indicative of the polymorph obtained from precipitation. In water, at low pABA concen- trations - conditions that are known to yield crystals of the β form - carboxylic-carboxylic hydrogen bonds are exclusively asymmetric. At higher pABA concentration conditions in which the crystallisation is known to yield the α form - a small but statistically significant fraction of symmetric carboxylic-carboxylic hydrogen-bonded dimers is present. We interpret the presence of these interactions in solvated pABA oligomers as indicative of the fact that a simultaneous and complete desolvation of two carboxylic groups, necessary to form the sym- metric hydrogen-bonded dimer typical of the α crystal form, is accessible, therefore directing the nucleation pathway towards the nucleation of α-pABA.</p></div></div></div> | Raitis Bobrovs; Laura Drunka; Andrievis Auseklis Auzins; Kristaps Jaudzems; Matteo Salvalaglio | Aggregates and Assemblies; Self-Assembly; Solution Chemistry; Thermodynamics (Physical Chem.); Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fccbdbb89bcd0a39e1b/original/on-the-polymorph-selective-role-of-hydrogen-bonding-and-stacking-in-para-aminobenzoic-acid-solutions.pdf |
652804138bab5d205534af3b | 10.26434/chemrxiv-2023-wxv2b-v2 | Does Storage Post Sampling Influence the Stability of Sebum when used for Mass Spectrometry Metabolomics Analysis? | Sebum is a biofluid excreted by sebaceous glands in the skin. In recent years sebum has been shown to contain endogenous metabolites diagnostic of disease, with remarkable results for Parkinson’s Disease. Given that sebum sampling is facile and non-invasive, its potential for use in clinical biochemistry diagnostic assays should be explored including the parameters for standard operating procedures around collection, transport, and storage. To this aim we have here investigated the reproducibility of mass spectrometry data from sebum in relation to both storage temperature and length of storage. Sebum samples were collected from volunteers and stored for up to four weeks at a range of temperatures: ambient (circa 17 ˚C), -20 ˚C and -80 ˚C. Established extraction protocols were employed and the samples were analysed by two chromatographic mass spectrometry techniques and data investigated using PCA, PLS-DA and ANOVA.
We cannot discriminate samples as a function of storage temperature or time stored in unsupervised analysis using data acquired via TD-GC-MS and LC-IM-MS, although the sampling of volatiles was susceptible to batch effects. This study indicates that the requirements for storage and transport of sebum samples that may be used in clinical assays are far less stringent than for liquid samples and indicate that sebum is suitable for remote and at home sampling prior to analysis.
| Caitlin Walton-Doyle; Eleanor Sinclair; Humayra Begum; Katherine Hollywood; Drupad Trivedi; Perdita Barran | Biological and Medicinal Chemistry; Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652804138bab5d205534af3b/original/does-storage-post-sampling-influence-the-stability-of-sebum-when-used-for-mass-spectrometry-metabolomics-analysis.pdf |
67042053cec5d6c1427928b0 | 10.26434/chemrxiv-2024-c8m0b-v2 | Oxygen Isotope Fractionation of O2 Consumption Through Abiotic Photochemical Singlet Oxygen Formation Pathways | Oxygen isotope ratios of O2 are important tracers for assessing biological activity in biogeochemical processes in aquatic environments. In fact, changes of 18O/16 O and 17O/16 O ratios of O2 have been successfully implemented as measures for quantifying photosynthetic O2 production and biological O2 respiration. Despite evidence for light-dependent O2 consumption in sunlit surface waters, however, photochemical O2 loss processes have so far been neglected in the stable isotope-based evaluation of oxygen cycling. Here, we established the magnitude of O isotope fractionation for abiotic photochemical O2 elimination through formation of singlet O2, 1O2, and the ensuing oxygenation and oxidation reactions with organic compounds through experiments with rose bengal as 1O2 sensitizer and three different amino acids and furfuryl alcohol as chemical quenchers. Based on the kinetic analysis of lightdependent O2 removal in the presence of different quenchers, we rationalize the observable O isotope fractionation of O2 and the corresponding, apparent 18O kinetic isotope effects (18O-AKIE) with a pre-equilibrium model for the reversible formation of 1O2 and its irreversible oxygenation reactions with organic compounds. While 18O-AKIEs of oxygenation reactions amount to 1.03, the O isotope fractionation of O2 vanishes systematically with increasing ratio of the rates of oxygenation reaction of 1O2 vs. 1O2 decay to ground state oxygen, 3O2 . Our findings imply that O isotope fractionation through photochemical O2 consumption can match contributions from biological respiration at typical dissolved organic matter concentrations of lakes, rivers, and oceans and should therefore be included in future evaluations of biogeochemical O2 cycling. | Sarah G. Pati; Lara M. Brunner; Martin Ley; Thomas B. Hofstetter | Earth, Space, and Environmental Chemistry; Hydrology and Water Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67042053cec5d6c1427928b0/original/oxygen-isotope-fractionation-of-o2-consumption-through-abiotic-photochemical-singlet-oxygen-formation-pathways.pdf |
67c928b581d2151a0244f287 | 10.26434/chemrxiv-2025-j4d6s | Oxygen reduction reaction on Mn-doped Cu Oxide Electrodes | The manuscript explores the oxygen reduction activity of Mn-doped Cu oxide electrodes. Mn is redox-active within the ORR potential range, exhibiting oxidation states from +2 to +7. The Cu[Mn]Ox/Au catalyst demonstrates superior ORR performance, surpassing both pure CuOx and MnOx electrodes. In situ Raman spectroscopy shows that the peak at 612cm-1 demonstrated stark tuning ~0.7V, indicating a redox-active structural framework containing Cu-O-Mn type linkages. In general, this study reinforces the idea that mixing a first-row transition metal into a CuO system can create mixed phases with coordinative unsaturation that can enhance O-O bond breaking. | Sekhar Biswal; chinmoy ranjan | Physical Chemistry; Catalysis; Electrocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c928b581d2151a0244f287/original/oxygen-reduction-reaction-on-mn-doped-cu-oxide-electrodes.pdf |
662a026291aefa6ce1603837 | 10.26434/chemrxiv-2024-wff0j | Elucidating Charge Transfer Processes and Enhancing Electrochemical Performance of Laser-Induced Graphene via Surface Engineering with Sustainable Hydrogel Membranes: An Electrochemist's Perspective | Laser-induced graphene (LIG) has emerged as a promising solvent-free strategy for producing highly porous, 3D graphene structures, particularly for electrochemical applications. However, the unique character of LIG and hydrogel membrane (HM) coated LIG requires accounting for the specific conditions of its charge transfer process. This study investigates electron transfer kinetics and the electroactive surface area of LIG electrodes, finding efficient kinetics for the [Fe(CN)6]3-/4- redox process, with a high rate constant of 4.12 x 10-3 cm/s and an electroactive area 28 times higher than the geometric area. The impact of polysaccharide HM coatings (cationic chitosan, neutral agarose and anionic sodium alginate) on LIG's charge transfer behavior is elucidated, considering factors like Ohmic drop across porous LIG and Coulombic interactions/permeability affecting diffusion coefficients, estimated from amperometry. Experimental findings are supported by ab-initio calculations showing a electrostatic potential map’s negative charge distribution upon chitosan chain protonation, having an effect in over a two-fold redox current increase upon switching the pH from 7.48 to 1.73. This feature is absent for other studied HMs. It was also revealed that the chitosan's band gap was reduced to 3.07 eV upon acetylation, due to the introduction of a new LUMO state. This study summarizes the operating conditions enhanced by HM presence, impacting redox process kinetics and presenting unique challenges for prospective LIG/HM systems’ electrochemical applications. | Mohsen Khodadadiyazdi; Aiswarya Manohar; Adrian Olejnik; Agata Smułka; Agnieszka Kramek; Mattia Pierpaoli; Mohammad Reza Saeb; Robert Bogdanowicz; Jacek Ryl | Analytical Chemistry; Electrochemical Analysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662a026291aefa6ce1603837/original/elucidating-charge-transfer-processes-and-enhancing-electrochemical-performance-of-laser-induced-graphene-via-surface-engineering-with-sustainable-hydrogel-membranes-an-electrochemist-s-perspective.pdf |
63eb95009da0bc6b33ebb6df | 10.26434/chemrxiv-2022-n0tnc-v2 | Modeling the Photo-Absorption Properties of Noble Metal Nanoclusters: a Challenge for Density-Functional Theory | Modeling the emergence of the plasmon resonance in noble metal nanoclusters is still a challenge to overcome for theoretical chemistry. The systems are indeed too small to neglect quantum-size effects but too large to be easily addressed with quantum mechanics. We test here a robust answer to this still open question: the simplified variant to time-dependent density-functional theory (TDDFT). Applied to extended systems, this electronic structure-based method succeeds to compute a sufficient number of excitations to cover the emergence of plasmon-like states. By employing it under a semilocal exchange-correlation approximation such as PBE, we show that the most intense absorption band, that could be wrongly assigned to the plasmon band, has a strong interband character. We suspect the too low energy gap between $(n-1)d$ and $ns$ valence orbitals as the origin of the $d$-contamination of the excitations. We demonstrate however that a global or range-separated hybrid exchange-correlation approximation such as PBE0 or RSX-PBE0 is a robust answer to the problem. We notice that both approximations are not able to solve at the same time the energy positioning and intensity of the plasmon band, PBE0 being more accurate for energy positioning and RSX-PBE0 for intensity. All in all, we warn the user that a random choice of the exchange-correlation approximation opens the door to getting the correct answer for the wrong reason. | Priscila SEVEUR; Leïla BOUBEKEUR-LECAQUE; François MAUREL; Éric BRÉMOND | Physical Chemistry; Clusters; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-02-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63eb95009da0bc6b33ebb6df/original/modeling-the-photo-absorption-properties-of-noble-metal-nanoclusters-a-challenge-for-density-functional-theory.pdf |
672e98c7f9980725cf9a7111 | 10.26434/chemrxiv-2024-l9fn9 | The transfection potency of lipid nanoparticles containing mRNA depends on relative loading levels | When formulating mRNA into lipid nanoparticles (LNP), various copy numbers of mRNA are encapsulated, leading to a distribution of mRNA loading levels within LNPs. It is unclear if the mRNA loading level affects the functional delivery of the message. Here we show that depending on the mRNA loading level, LNPs exhibit distinct mass densities and can be fractionated via ultracentrifugation. Upon fractionation, we investigated if mRNA loading levels influence LNP sizing, lipid composition and morphology. We further conducted in vitro and in vivo functional delivery of mRNA and found that the LNP fraction with highest mRNA loading levels were the least transfection competent. | Suiyang Liao; Shuangyu Wang; Abishek Wadhwa; Alex Birkenshaw; Kevin Fox; Miffy Hok Yan Cheng; Irafasha C. Credo; Armando Alcazar Magana ; Nuthan Vikas Bathula; Chiao Hao Ho; Melody Cheng; Leonard J. Foster; Kenneth W. Harder; Colin J.D. Ross; Pieter R. Cullis; Anna K. Blakney | Biological and Medicinal Chemistry; Biochemistry; Bioengineering and Biotechnology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672e98c7f9980725cf9a7111/original/the-transfection-potency-of-lipid-nanoparticles-containing-m-rna-depends-on-relative-loading-levels.pdf |
653256a287198ede07e00d40 | 10.26434/chemrxiv-2023-w98xc | Chloromethylation of Lignin as a Route to Functional Material with Catalytic Properties in Cross-Coupling and Click Reactions | We present a novel, greener chloromethylation procedure for organosolv aspen lignin under mild reaction conditions without Lewis acid as a catalyst and in acetic acid as a solvent. This synthetic protocol provides a reliable approach to chloromethylated lignin (CML) and means to obtain valuable lignin derivatives The resulted CML was subsequently transformed into 1-methylimidazolium lignin (ImL), which effectively serves as a stabilizing agent for Pd/CuO nanoparticles (Pd/CuO-NPs). To evaluate the versatility of developed lignin-based catalyst, we investigate its performance in a series of carbon-carbon bond formation reactions, including Suzuki-Miyaura, Sonogashira, Heck reactions, and azide-alkyne cycloaddition (click) reaction. Remarkably, this catalyst exhibited a high degree of catalytic efficiency, resulting in reactions with yields ranging from average to excellent. The heterogeneous catalyst demonstrated outstanding recyclability, enabling its reuse for at least 10 consecutive reaction cycles, with yields consistently falling within the range of 42% to 84%. A continuous flow reactor cartridge prototype employing Lignin@Pd/CuO-NPs was developed, yielding results comparable to those achieved in batch reactions. The utilization of Lignin@Pd/CuO-NPs as a catalyst showcases its potential to facilitate diverse carbon-carbon bond formation reactions and underscores its promising recyclability, aligning with the green chemistry metrics and principles of sustainability in chemical processes | Mahendra Kothottil Mohan; Oleg Silenko; Illia Krasnou; Olga Volobujeva; Maria Kulp; Maksim Ošeka; Tiit Lukk; Yevgen Karpichev | Catalysis; Polymer Science; Biopolymers; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653256a287198ede07e00d40/original/chloromethylation-of-lignin-as-a-route-to-functional-material-with-catalytic-properties-in-cross-coupling-and-click-reactions.pdf |
60c75693702a9b104818c91d | 10.26434/chemrxiv.14269004.v1 | “CinNapht” Dyes as New Cinnoline/Naphthalimide Fused Hybrids Fluorophores: Synthesis, Photo-Physical Study and Use for Bio-Imaging | Six-membered diaza ring of
Cinnoline have been fused on Naphthalimide dye to give donor–acceptor system called
CinNapht. These red shifted fluorophore, that can be synthetised in gram scale,
exhibits a large Stoke Shift and quantum yield up to 0.33. It is also
caracterized by strong solvatochromic effect for green to red emission as well
and can be used for bio-imaging | Minh-Duc Hoang; Jean-Baptiste Bodin; Farah Savina; Vincent Steinmetz; Jérôme Bignon; Philippe Durand; Gilles Clavier; Rachel Méallet-Renault; Arnaud Chevalier | Bioorganic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75693702a9b104818c91d/original/cin-napht-dyes-as-new-cinnoline-naphthalimide-fused-hybrids-fluorophores-synthesis-photo-physical-study-and-use-for-bio-imaging.pdf |
60c759740f50db6b89398694 | 10.26434/chemrxiv.14365592.v2 | Adiabatic versus Non-Adiabatic Electron Transfer at 2D Electrode Materials | <div><div><div><p>Outer-sphere electron transfer (OS-ET) is a cornerstone elementary electrochemical reaction, yet microscopic understanding is largely based on idealized theories, developed in isolation from experiments that themselves are often close to the kinetic (diffusion) limit. Focusing on graphene as-grown on a copper substrate as a model 2D material/metal-supported electrode system, this study resolves the key electronic interactions in OS-ET, and identifies the role of graphene in modulating the electronic properties of the electrode/electrolyte interface. An integrated experimental-theoretical approach combining co-located multi-microscopy, centered on scanning electrochemical cell microscopy (SECCM), with Raman microscopy and field emission-scanning electron microscopy, together with rate theory and density functional theory (DFT) calculations is used to address OS-ET kinetics of hexaamineruthenium (III/II) chloride, [Ru(NH3)6]3+/2+. The experimental methodology allows spatially-resolved electrochemical measurements to be targeted at distinct regions of monolayer, bilayer and multilayer graphene on copper, with high diffusion rates, to reveal ET kinetics in the order: monolayer > bilayer > multilayer. To rationalize these findings we extended the Schmickler-Newns-Anderson model Hamiltonian for electron transfer and parametrized it using constant potential DFT. Combining this model with rate theory reveals that the difference in kinetics at monolayer and bilayer graphene can be rationalized in the context of a dominantly adiabatic mechanism, where the addition of subsequent graphene layers increases the contact potential, producing an increase in the effective barrier to electron transfer. This study provides a roadmap for the integration of experiments, theory, and simulations in order to understand the nature of heterogeneous electron transfer at complex nanostructured electrode materials.</p></div></div></div> | Dan-Qing Liu; Minkyung Kang; David Perry; Chang-Hui Chen; Geoff West; Xue Xia; Zachary P.L. Laker; Neil R. Wilson; Marko Melander; Reinhard Maurer; Patrick R. Unwin | Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759740f50db6b89398694/original/adiabatic-versus-non-adiabatic-electron-transfer-at-2d-electrode-materials.pdf |
60c75036bdbb8906afa39ecc | 10.26434/chemrxiv.13011491.v1 | Modeling of Nucleation, Growth, Dissolution, and Disappearance of Paracetamol in Ethanol Solution for Unseeded Batch Cooling Crystallization with Temperature-Cycling Strategy | A population balance model (PBM) is developed for unseeded batch crystallization, with temperature-cycling strategies to control the crystal size distribution. The model is able to predict the evolution of crystal size distributions of crystallizing paracetamol from ethanol solutions considering the characteristics of primary nucleation, secondary nucleation, growth, dissolution, and disappearance of crystals. Process analytical technology (PAT) tools were employed to collect solute concentration data and crystal size distribution data. This model employs a boundary condition to describe the disappearance of crystals in temperature-cycling strategies where the temperature is increased and decreased repeatedly. As a result, the obtained model can describe the evolution of crystal size distribution when repetition of cooling and heating is carried out. Moreover, this model can be applied to investigate phenomena that are challenging to explain with experimental data alone, thereby we can gain insight and optimize the operation of the process. | Youngjo Kim; Yoshiaki Kawajiri; Ronald
W. Rousseau; Martha A. Grover | Pharmaceutical Industry | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75036bdbb8906afa39ecc/original/modeling-of-nucleation-growth-dissolution-and-disappearance-of-paracetamol-in-ethanol-solution-for-unseeded-batch-cooling-crystallization-with-temperature-cycling-strategy.pdf |
664bac91418a5379b0d35d4f | 10.26434/chemrxiv-2024-p5l5m | Cathodic Decomposition Electrodes (CDEs) As Standard Reference Electrodes for Molten Salts: Example of the Lithium Eutectic Electrode (LEE) for the LiCl-KCl Eutectic | Alternatives to the widely-used standard anodic decomposition reference electrodes in molten salts are necessary to enable more easily reproduced thermochemical and electrochemical data in molten salt electrolytes. The class of standard reference electrodes called cathodic decomposition electrodes (CDEs) are easily constructed and can be used to make thermochemical measurements in molten salts more directly compared to anodic decomposition electrodes. The lithium eutectic electrode (LEE) was chosen as a sample test case for validation and was applied to thermochemical measurements of electroactive species in molten LiCl-KCl eutectic. Transient measurements were made to measure the Li+ /Li reduction potential at zero current in pure LiCl-KCl eutectic relative to a Li-alloy reference electrode to validate the reference potential of the LEE. Literature-reported electromotive force (emf) measurements against Li-alloy reference electrodes were used to generate a relationship between the LEE and the standard chlorine electrode (SClE) and this relationship was used to evaluate measured and reported formal potential measurements for the LiCl-KCl-GdCl3 system. This work demonstrates the general framework for defining CDEs for any molten salt system and a method for calibrating external reference electrodes against a CDE standard reference electrode, improving the ease of obtaining thermochemical and electrochemical measurements in any molten salt system. | Timothy Lichtenstein; Mark Schvaneveldt; Jarrod Gesualdi; Krista Hawthorne | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664bac91418a5379b0d35d4f/original/cathodic-decomposition-electrodes-cd-es-as-standard-reference-electrodes-for-molten-salts-example-of-the-lithium-eutectic-electrode-lee-for-the-li-cl-k-cl-eutectic.pdf |
617a159a913a7460eb6d8b20 | 10.26434/chemrxiv-2021-cq50f | Crystal Phase Mediated Restructuring of Pt on TiO2 with Tunable Re-activity: Redispersion versus Reshaping | Restructuring of supported metal nanoparticles (NPs) e.g., reshaping and redispersion are of tremendous interest for the rational design of high-efficiency catalyst materials with precise particle sizes, shapes, and reactivities. Here we show a crystal phase mediated restructuring of Pt NPs on TiO2, as a simple approach for fabricating either atomically dispersed single atoms (SAs) or reshaped planar NPs of Pt catalysts with tunable reactivities. Utilizing a variety of state-of-the-art characterizations, we showed that rutile TiO2 favors the reshaping of 2D planar Pt NPs, whereas the anatase surface facilitates the redispersion of Pt NPs to SAs upon calcination in the air up to 400 ºC. Environmental transmission electron microscopy (ETEM) and density function theory (DFT) calculations were employed to directly visualize the dynamic transformation of Pt NPs and reveal the specific role that TiO2 supports play in promoting the stability and diffusion of Pt SAs. As a result, the reverse reactivity was achieved by tunning their distinct restructuring behaviors. Thus, the Pt SAs on anatase TiO2 preferentially activated selective hydrogenation of phenylacetylene (21.22 x 10-2 s-1 at 50 ºC), while planar Pt NPs on rutile significantly enhanced the combustion of methane (3.11 x 10-2 s-1 at 310 ºC). Our results therefore open up new routes for tuning the restructuring behavior of supported metal catalysts and designing catalysts with controlled catalytic structures and reactivities. | Xiaoben Zhang; Zhimin Li; Wei Pei; Gao Li; Wei Liu; Pengfei Du; Zhen Wang; Zhaoxian Qin; Si Zhou; Jijun Zhao; Bing Yang; Wenjie Shen | Physical Chemistry; Catalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617a159a913a7460eb6d8b20/original/crystal-phase-mediated-restructuring-of-pt-on-ti-o2-with-tunable-re-activity-redispersion-versus-reshaping.pdf |
60c743b0bdbb893a9ea3868c | 10.26434/chemrxiv.8145986.v2 | Machine Learning Optimization of P-Type Transparent Conducting Films | Strategic design of experiments combined with machine learning is used to optimize the synthesis of p-type transparent conductors. <br /> | Lingfei Wei; Xiaojie Xu; Gurudayal; James Bullock; Joel Ager | Materials Processing; Optical Materials; Thin Films; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743b0bdbb893a9ea3868c/original/machine-learning-optimization-of-p-type-transparent-conducting-films.pdf |
64d46f7fdfabaf06ff05f9d9 | 10.26434/chemrxiv-2023-vn492 | Observation of an emissive intermediate in a liquid singlet fission and triplet fusion system at room temperature | The photophysical processes of singlet fission and triplet fusion have numerous emerging applications. They respectively involve the separation of a photo-generated singlet exciton into two dark triplet excitons and the fusion of two dark triplet excitons into an emissive singlet exciton. The role of the excimer state, and the nature of the triplet-pair state in these processes have been a matter of contention. Here we carefully analyse the room temaperature time-resolved emission of a neat liquid singlet fission chromophore, 5,12-bis(n-octyldiisopropylsilylethynyl)tetracene. It is demonstrated to exhibit three spectral components: Two that correspond to the bright singlet and excimer states, and a third component that becomes more prominent during triplet fusion. A spectrum consistent with this third compoment is found to be enhanced with magnetic fields, confirming its origins in radiation from weakly-coupled triplet pairs. This magnetically enhanced emission is attributed to the emission from the strongly coupled triplet pair state. These observations serve to unite the view that there is an emissive intermediate in singlet fission and triplet fusion, and that this species is distinct from the broad, unstructured excimer emission. | Jiale Feng; Parisa Hosseinabadi; Damon de Clercq; Michael Nielsen; Matthew Brett; Shyamal Prasad; Abbas Farahani; Hsiu Li; Samuel Sanders; Jonathon Beves; Ned Ekins-Daukes; Jared Cole; Pall Thordarson; Murad Tayebjee; Timothy Schmidt | Physical Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d46f7fdfabaf06ff05f9d9/original/observation-of-an-emissive-intermediate-in-a-liquid-singlet-fission-and-triplet-fusion-system-at-room-temperature.pdf |
65fdcc8ee9ebbb4db949cf97 | 10.26434/chemrxiv-2024-vs39h | Electrochemical Techniques for Uranium Extraction from Water | Electrochemical removal of uranium from water is an emerging topic that addresses the treatment of drinking water, remediation of contaminated sites, and mining from seawater. Electrochemical strategies compare favorably to conventional processes, such as adsorption and coagulation/flocculation, with advantages in speed and efficiency, materials regeneration, uranium recovery, and recycling. This review assesses all published work on electrochemical techniques for uranium extraction from water, including capacitive deionization (electrosorption), electrodeposition, electrodialysis, and electrocoagulation. This work compares these approaches with conventional techniques and discusses their applicability in different use cases. Environmental and economic considerations are discussed, as well as the current outlook and opportunities for engagement in this emerging field. | Savan K. Raj; Andrew J. Carrier; Brian C. Youden; Mark R. Servos; Ken D. Oakes; Xu Zhang | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fdcc8ee9ebbb4db949cf97/original/electrochemical-techniques-for-uranium-extraction-from-water.pdf |
658562d29138d231614055f2 | 10.26434/chemrxiv-2023-h76dn | GH172 difructose dianhydride I synthase: A two-stepped journey via glycosylation and cyclization using QM/MM metadynamics | Difructose dianhydride I synthase/hydrolase (αFFase1) is a member of the family 172 of glycoside
hydrolases which catalyzes the reversible transformation of inulobiose into difructose dianhydride
I (DFA I). This transformation was hypothesized to go through a double-displacement mechanism
formed by a glycosylation step and a cyclization step. During the glycosylation step, E270 protonates
the O2 of the α-D-fructofuranosyl group in the subsite –1 (–1 sugar), and E291 attacks the anomeric
carbon forming a glycosyl-enzyme intermediate (GEI) and releasing a water molecule. During the
cyclization, activated by a complex torsional mechanism, the O1 of the β -D-fructofuranosyl group
in the subsite +1 attacks the anomeric carbon, cleaving the glycosyl-E291 bond and transferring a
proton to the E270. Using hybrid QM/MM metadynamics methods, we demonstrate the energetic
accessibility of the glycosylation + cyclization mechanism for the αFFase1-inulobiose complex. Our
simulations show a slightly exothermic global reaction (∆G 0 = –1.3 kcal·mol−1) in good agreement
with the experimental inulobiose/DFA I resulting ratios (1:8.9). The ∆G ‡ and ∆G 0 for the glyco-
sylation are 12.3 and –2.8 kcal·mol−1. The rate-limiting step is the cyclization with a ∆G ‡ = 15.3
kcal·mol−1. Our study shows that the –1 sugar follows the E5 → E5/4T5 → E3 and E3 → 4E →
4E conformational pathways. Further analysis of the cyclization simulation shows the role of E85,
K147, and N226 stabilizing the rotation of the +1 sugar and facilitating the attack of the O1’ to
the anomeric carbon. | Bruno Di Geronimo; Toma Kashima; Akihiro Ishiwata; Katsunori Tanaka; Pedro Alejandro Sánchez-Murcia; Kiyotaka Fujita; Shinya Fushinobu; Santiago Alonso-Gil | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Computational Chemistry and Modeling; Biocatalysis; Homogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2023-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658562d29138d231614055f2/original/gh172-difructose-dianhydride-i-synthase-a-two-stepped-journey-via-glycosylation-and-cyclization-using-qm-mm-metadynamics.pdf |
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