id
stringlengths 24
24
| doi
stringlengths 28
32
| title
stringlengths 8
495
| abstract
stringlengths 17
5.7k
| authors
stringlengths 5
2.65k
| categories
stringlengths 4
700
| license
stringclasses 3
values | origin
stringclasses 1
value | date
stringdate 1970-01-01 00:00:00
2025-03-24 00:00:00
| url
stringlengths 119
367
⌀ |
|---|---|---|---|---|---|---|---|---|---|
6398a48f7b7c913628f00380 | 10.26434/chemrxiv-2022-24j10 | Trapping hydrogen: Confined catalysis for improved hydrogen borrowing selectivity | Alcohol amination via hydrogen borrowing is an established method for the clean and simple alkylation of amines with alcohols, which are stable and available in bulk; it also does not require the addition of hydrogen to reduce the imines or the use of coupling agents. A common problem however in those systems is the need to employ additives to prevent stagnation of the product at the imine stage, which indicates inefficient usage of the borrowed hydrogen atoms. In this work, we designed a catalyst series to demonstrate that confined environments can assist with improved selectivity. To this end, we encapsulated Al2O3/Ru(OH)x nanocatalysts inside mesoporous silica in a yolk-shell architecture and were able to trap the hydrogens to increase the amine yield from 12% to 82%, with a 3-fold increase in selectivity without the need of any additive; we found the presence of mesopores in the silica shells to be essential to enable access to the cata-lytic sites and the yolk-shell gap size to be the key parameter influencing the reactivity of the catalytic system. To the best of our knowledge, this is the first report of a confined hydrogen borrowing reaction, an approach that can be extended to the other types of cascade reactions that produce labile intermediates. | Julio Terra; Jackson DeWolfe; Jesus Angel Valdez; Audrey Moores | Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6398a48f7b7c913628f00380/original/trapping-hydrogen-confined-catalysis-for-improved-hydrogen-borrowing-selectivity.pdf |
60c74b1aee301c005fc79d71 | 10.26434/chemrxiv.11908503.v2 | Tuning Activity and Selectivity During Alkyne Activation by Gold(I)/Platinum(0) Frustrated Lewis Pairs | Introducing transition metals into frustrated
Lewis pair systems has attracted considerable attention in recent years. Here
we report a selection of three metal-only frustrated systems based on Au(I)/Pt(0)
combinations and their reactivity towards alkynes. We have inspected the
activation of the simplest alkyne, namely acetylene, as well as of other
internal and terminal triply bonded hydrocarbons. The gold(I) fragments are
stabilized by three bulky phosphines bearing terphenyl groups. We have observed
that subtle modifications on the substituents of these ligands proved critical
to control the regioselectivity of acetylene activation and the product
distribution resulting from C(sp)—H cleavage of phenylacetylene. A mechanistic
picture based on experimental observations and computational analysis is
provided. As a result of the cooperative action of the two metals of the
frustrated pairs, several uncommon heterobimetallic structures have been fully
characterized. | Nereida Hidalgo; Juan Jose Moreno; Marina Pérez-Jiménez; Celia Maya; Joaquin López-Serrano; Jesus Campos | Frustrated Lewis Pairs; Organometallic Compounds; Small Molecule Activation (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b1aee301c005fc79d71/original/tuning-activity-and-selectivity-during-alkyne-activation-by-gold-i-platinum-0-frustrated-lewis-pairs.pdf |
60c74cc5bdbb896b6ba39875 | 10.26434/chemrxiv.11828256.v2 | Hole-Hole Tamm-Dancoff-Approximated Density Functional Theory: A Highly Efficient Electronic Structure Method Incorporating Dynamic and Static Correlation | <div>
<div>
<div>
<p>The study of photochemical reaction dynamics requires accurate as well
as computationally efficient electronic structure methods for the ground
and excited states. While time-dependent density functional theory
(TDDFT) is not able to capture static correlation, complete active space
self-consistent field (CASSCF) methods neglect much of the dynamic
correlation. Hence, inexpensive methods that encompass both static and
dynamic electron correlation effects are of high interest. Here, we
revisit hole-hole Tamm-Dancoff approximated (<i>hh</i>-TDA) density functional
theory for this purpose. The <i>hh</i>-TDA method is the hole-hole counterpart
to the more established particle-particle TDA (<i>pp</i>-TDA) method, both of
which are derived from the particle-particle random phase approximation
(<i>pp</i>-RPA). In <i>hh</i>-TDA, the <i>N</i>-electron electronic states are obtained
through double annihilations starting from a doubly anionic (<i>N</i>+2
electron) reference state. In this way, <i>hh</i>-TDA treats ground and excited
states on equal footing, thus allowing for conical intersections to be
correctly described. The treatment of dynamic correlation is introduced
through the use of commonly-employed density functional approximations
to the exchange-correlation potential. We show that hh-TDA is a
promising candidate to efficiently treat the photochemistry of organic
and biochemical systems that involve several low-lying excited states –
particularly those with both low-lying pipi* and npi* states where
inclusion of dynamic correlation is essential to describe the relative
energetics. In contrast to the existing literature on <i>pp</i>-TDA and <i>pp</i>-RPA,
we employ a functional-dependent choice for the response kernel in <i>pp</i>-
and <i>hh</i>-TDA, which closely resembles the response kernels occurring in linear response and collinear spin-flip TDDFT.</p>
</div>
</div>
</div> | Christoph Bannwarth; Jimmy K. Yu; Edward G. Hohenstein; Todd J. Martínez | Computational Chemistry and Modeling; Theory - Computational; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cc5bdbb896b6ba39875/original/hole-hole-tamm-dancoff-approximated-density-functional-theory-a-highly-efficient-electronic-structure-method-incorporating-dynamic-and-static-correlation.pdf |
6299a60e468a08811c49f7cb | 10.26434/chemrxiv-2022-hj910 | Control of vibration-metasurface coupling at mid-infrared spectral window for inorganic thermal emitters | Coupling between light and molecular vibrational modes is dependent on efficiency of molecular absorption. Here we demonstrate how to control coupling between molecular mid-infrared absorption/emission at chemical fingerprinting spectral window and metasurface using SiO2 as the absorber/emitetr and CaF2 as a spacer to optimise strength of coupling. Use of inorganic dielectric I-spacer in Metal-Insulator-Metal (MIM) metasurface opens applications in narrow-band emitters at IR spectral window at elevated temperatures (> 350C) where polymer/organic I-spacers degrade | Yoshiaki Nishijima; Saulius Juodkazis | Nanoscience; Plasmonic and Photonic Structures and Devices | CC BY 4.0 | CHEMRXIV | 2022-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6299a60e468a08811c49f7cb/original/control-of-vibration-metasurface-coupling-at-mid-infrared-spectral-window-for-inorganic-thermal-emitters.pdf |
6386adfd0146ef3ac50aec0c | 10.26434/chemrxiv-2022-2ws41 | Targeted photodynamic neutralization of SARS-CoV-2 mediated by singlet oxygen | The SARS-CoV-2 virus has been on a rampage for more than two years. Vaccines in combination with neutralizing antibodies (NAbs) against SARS-CoV-2 carry great hope in the treatment and final elimination of COVID-19. However, the relentless emergence of variants of concern (VOC), including the most recent Omicron variants, presses for novel measures to counter these variants that often show immune evasion. Hereby we developed a targeted photodynamic approach to neutralize SARS-CoV-2 by engineering a genetically encoded photosensitizer (SOPP3) to a diverse list of antibodies targeting the WT spike protein, including human antibodies isolated from a 2003 SARS patient, potent monomeric and multimeric nanobodies targeting RBD, and non-neutralizing antibodies (non-NAbs) targeting the more conserved NTD region. As confirmed by pseudovirus neutralization assay, this targeted photodynamic approach significantly increased the efficacy of these antibodies, especially that of non-NAbs, against not only the WT but also the Delta strain and the heavily immune escape Omicron strain (BA.1). Subsequent measurement of infrared phosphorescence at 1270 nm confirmed the generation of singlet oxygen (1O2) in the photodynamic process. Mass spectroscopy assay uncovered amino acids in the spike protein targeted by 1O2. Impressively, Y145 and H146 form an oxidization “hotspot”, which overlaps with the antigenic “supersite” in NTD. Taken together, our study established a targeted photodynamic approach against the SARS-CoV-2 virus and provided mechanistic insights into the photodynamic modification of protein molecules mediated by 1O2. | Ruhui Yao; Jian Hou; Xin Zhang; Yi Li; Junhui Lai; Qinqin Wu; Qinglian Liu; Lei Zhou | Biological and Medicinal Chemistry; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6386adfd0146ef3ac50aec0c/original/targeted-photodynamic-neutralization-of-sars-co-v-2-mediated-by-singlet-oxygen.pdf |
61b926e37284d051ebebb91a | 10.26434/chemrxiv-2021-ch3ts | Non-metal photochemical reduction of CO2 to formate with organohydride-recycle strategy | The increasing CO2 concentration in the atmosphere is an urgent social problem that has to be resolved. Reducing CO2 into compounds useful as energy sources and carbon materials is desirable. For the CO2 reduction reaction (CO2RR) to be operational on a global scale, the catalyst system must: (1) use only renewable energy, (2) be built from abundantly available elements, and (3) not require high-energy reactants. Although light is an alluring energy source, most existing methods utilize electricity. Furthermore, catalyst systems are based on rare heavy metals. Herein, we present a transition-metal-free catalyst system for CO2RR using visible light and containing a carbazole photocatalyst and an organohydride co-catalyst based on benzimidazoline. It produced formate with a turnover number exceeding 8000. No other reduced products such as H2 and CO were generated, confirming the high selectivity of the system. This finding is essential for operating artificial photosynthesis on a useful scale. | Weibin Xie; Jiasheng Xu; Ubaidah Md Idros; Jouji Katsuhira; Masaaki Fuki; Masahiko Hayashi; Yasuhiro Kobori; Ryosuke Matsubara | Organic Chemistry; Catalysis; Photochemistry (Org.); Organocatalysis; Photocatalysis | CC BY NC 4.0 | CHEMRXIV | 2021-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b926e37284d051ebebb91a/original/non-metal-photochemical-reduction-of-co2-to-formate-with-organohydride-recycle-strategy.pdf |
60c75304567dfe143eec5da2 | 10.26434/chemrxiv.13379975.v1 | Ionic Charge Manipulation Using Solution and Gas-Phase Chemistry to Facilitate Analysis of Highly Heterogeneous Protein Complexes in Native Mass Spectrometry | Ionic signal in native MS typically populates high <i>m/z</i> regions of mass spectra, which frequently extend beyond the
precursor ion isolation limits of most commercial mass spectrometers. An approach
explored in this work relies on adding supercharging reagents to protein
solutions as a means of increasing the extent of multiple charging of
non-covalent complexes in ESI MS without compromising their integrity. This
shifts the ionic signal down the <i>m/z</i>
scale to the region where ion selection and isolation can be readily
accomplished, followed by limited charge reduction of the isolated ionic
population. The feasibility of the new approach is demonstrated using
non-covalent complexes formed by hemoglobin with structurally heterogeneous haptoglobin. | Yang Yang; Chendi Niu; Cedric Bobst; Igor Kaltashov | Biochemical Analysis; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75304567dfe143eec5da2/original/ionic-charge-manipulation-using-solution-and-gas-phase-chemistry-to-facilitate-analysis-of-highly-heterogeneous-protein-complexes-in-native-mass-spectrometry.pdf |
67d7a45781d2151a02a67219 | 10.26434/chemrxiv-2025-9fdpb | Dynamic Glassy Molecular Solids | Ranging from the intricate stained-glass windows in medieval cathedrals to the sleek, transparent facades of modern architecture, glass constitutes an excellent blend of beauty and functionality. Its inherent brittleness, however, hinders its application in high-stake scenarios. While small molecule-based glassy materials have recently garnered attention, they often lack the ability to self-heal autonomously. Here we report a biocompatible glassy solid based on vitamin D3, which combines uniquely, the advantages of both glassy and rubbery states. The glassy solid demonstrates rapid, autonomous self-healing within seconds without requiring any external stimuli. This property is attributable to the dynamic intermolecular interactions, which have been characterized by spatially resolved Raman spectroscopy. Moreover, glassy fibers display remarkable flexibility, while the glassy solid displays optical properties similar to that of conventional glass. | Pramita Kundu; SUROJIT BHUNIA; James Fraser Stoddart | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d7a45781d2151a02a67219/original/dynamic-glassy-molecular-solids.pdf |
66fc23bccec5d6c142cddf8a | 10.26434/chemrxiv-2024-f9djd-v2 | Nickel (II) Complexes Bearing Electron Donating OR/OH Groups on a Tetradentate Ligand Scaffold for Photocatalytic Carbon Dioxide Reduction | Nickel (II) complexes bearing tetradentate NCCN ligands comprised of optionally protic pyridine and N-heterocyclic carbene (NHC) donors have been synthesized and used as catalysts for carbon dioxide reduction. These complexes were synthesized bearing OMe, OBn, or OH substituents on the pyridine rings and were characterized by 1H NMR, 13C NMR, UV-Vis, IR, HR-MS, and single crystal X-ray diffraction. The OH substituent was partially deprotonated as shown by the crystal structure. Electrochemical studies show that these nickel complexes undergo two electron reduction events prior to CO2 reduction. Catalytic current enhancement under CO2 relative to N2 is not observed under dry conditions, but the addition of proton sources leads to modest current enhancement (icat/ip < 2). Visible light driven photochemical CO2 reduction with a photosensitizer (Ir(ppy)3 where ppy = 2-phenylpyridine) and sacrificial electron and proton donors was studied, and formate is the major product with ~10:1 formate to CO production. Electron donor groups (OMe, OBn, OH) do not enhance formate production (relative to H analog), and CO production is only slightly enhanced. Overall with Ni(II), the tetradentate ligands are comparable to recently published pincer ligands for sensitized CO2 reduction, but pincer ligands offer a clear advantage in self-sensitized catalysis. | Sonya Manafe; Gbolagade Olajide; Chance Boudreaux; Fengrui Qu; Logan Whitt; Patrick Pridemore; James Fletcher Hall; Tibor Szilvasi; Elizabeth Papish | Inorganic Chemistry; Catalysis; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fc23bccec5d6c142cddf8a/original/nickel-ii-complexes-bearing-electron-donating-or-oh-groups-on-a-tetradentate-ligand-scaffold-for-photocatalytic-carbon-dioxide-reduction.pdf |
674f1b517be152b1d0cda7b9 | 10.26434/chemrxiv-2024-jxwnq | Arrangement and dynamics of individual cyclodextrins on the surface of core-shell micelles | Efficient site-specific drug delivery systems (DDS) would require sophisticated surface structure to overcome challenges arising from currently inevitable interactions with components of complex biological environment. One way to endow nanoparticles (NPs) with the designed surface properties is to use excipients that enable appropriate multivalent surface modifications. In this respect, cyclodextrins (CDs) is a versatile building block that can be used to provide NPs various surface modifications as well as drug loading capacity by means of host-guest interactions. On the other hand, structural properties of CD-decorated NPs including localization, orientation, and mobility of individual CDs should be assessed for rational design of DDS and control over its surface properties. In this paper, we used combination of transmission electron microscopy (TEM), small-angle X-ray scattering (SAXS) and molecular dynamics(MD) to assess these structural and dynamical properties of α- and β-CD-decorated core-shell micelles based on NPs topography maps. Micelles self-assemble from function-spacer-lipid (FSL) constructs that are conjugates of CDs, phospholipid DOPE and hydrophylic N-carboxymethyloligoglycine spacer. It was found that most of CD residues lose their functionality because of their clustering and unfavorable orientation, that results in CD cavity becomes inaccessible for binding. Dynamics of NPs surface structure reveals that CDs have low mobility, due to their interactions with oligoglycine spacer that prone to form static shell. Reducing the density of CD and spacer by 5 times prevents clusterization suggesting optimal density of CD residues, but does not affect CDs orientations and mobility. These findings indicate that the functionality of CD residues depends on the type of spacer and CD and their junction, and simple conjugation may not be enough to properly orient CDs on the surface. The combination of oligoglycine spacer with CD can be used as an excipient that turn hydrophobic core into stable multivalent scaffold to which various functional compounds can be attached through guest-host interactions. Obtained insights could be useful in development of CD-based NPs surface modifications towards rational design of smart next generation drug delivery systems. | Ivan Vaskan; Veronika Dimitreva; Alexey Piryazev; Elena Subcheva; Nicolai Bovin; Alexander Tuzikov; Vladimir Oleinikov; Anton Zalygin | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674f1b517be152b1d0cda7b9/original/arrangement-and-dynamics-of-individual-cyclodextrins-on-the-surface-of-core-shell-micelles.pdf |
610984191f990c68b3a67b07 | 10.26434/chemrxiv-2021-6zndd | Amphiphile Conformation Impacts Aggregate Morphology and Solution Structure Across Multiple Lengthscales | Although the self-assembly of amphiphiles is well-studied in aqueous solutions, much less is understood about the fundamental driving forces and structure property relationships in non-polar media. In recent work [Journal of Physical Chemistry B, 2020, 124, 10822.] the authors have studied a series of malonomide-based amphiphiles that are relevant to liquid-liquid extraction. That work demonstrated that aggregation is largely driven by local dipole-dipole interactions between molecules. Here, we build upon this observation to develop a more detailed understanding of how the balance of dipole-dipole interactions (controlled by conformation) and molecular architecture influences the morphology of the aggregates across lengthscale. Using constrained molecular dynamics about key degrees of freedom, we demonstrate that the conformation of N,N’-dimethyl,N,N’-dioctylhexylethoxy malonamide (DMDOHEMA) and N,N’-dimethyl,N,N’-dibutyltetradecyl malonamide (DMDBTDMA) has a significant impact upon self-association - where appropriate conformational sampling is essential. To quantify the aggregate morphology, several graph theoretic and persistent homology based properties are determined. The former examines the patterns of intermolecular interactions within clusters, while the latter examines the 3-dimensional spatial distribution across lengthscales. Based upon these analyses, we find that the morphology of aggregates, particularly at higher malonamide concentration, depends on a balance of dipole alignment and alkyl tail sterics. Dipole alignment encourages linear patterns of the intermolecular interactions within aggregates, while the the alkyl tail steric interactions between the malonamide result in noticeably less linear aggregates for DMDOHEMA than DMDBTDMA. This is reflected in the spatial distribution, where more holes or voids exist between extractants within the DMDOHEMA that distribute within the solution in more of a ``swiss cheese" arrangement as opposed to the more filamentous distribution of DMBDTDMA. This study links conformation and molecular structure to the morphology of amphiphile assemblies, and serves as a basis for ongoing study of multicomponent amphiphile solutions with polar and other solutes, and how these impact aggregation phenomena. | Michael Servis; Biswajit Sadhu; Lynda Soderholm; Aurora Clark | Theoretical and Computational Chemistry; Physical Chemistry; Self-Assembly; Solution Chemistry; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610984191f990c68b3a67b07/original/amphiphile-conformation-impacts-aggregate-morphology-and-solution-structure-across-multiple-lengthscales.pdf |
60c740a44c891971f9ad219b | 10.26434/chemrxiv.7415210.v2 | Polymer Nucleation under High-Driving Force, Long-Chain Conditions: Heat Release and the Separation of Timescales | This study reveals important features of polymer crystal formation at high-driving forces in entangled polymer melts based on simulations of polyethylene. First and in contrast to small-molecule crystallization, the heat released during polymer crystallization does not appreciably influence structural details of early-stage, crystalline clusters (crystal nuclei). Second, early-stage polymer crystallization (crystal nucleation) can occur without substantial chain-level relaxation and conformational changes. This study's results indicate that local structures and environments guide crystal nucleation in entangled polymer melts under high-driving force conditions. Given that such conditions are often used to process polyethylene, local structures and the separation of timescales associated with crystallization and chain-level processes are anticipated to be of substantial importance to processing strategies. This study highlights new research directions for understanding polymer crystallization. | Kyle Hall; Simona Percec; Michael Klein | Polymer chains; Computational Chemistry and Modeling; Physical and Chemical Processes; Self-Assembly | CC BY 4.0 | CHEMRXIV | 2019-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740a44c891971f9ad219b/original/polymer-nucleation-under-high-driving-force-long-chain-conditions-heat-release-and-the-separation-of-timescales.pdf |
651e2c2445aaa5fdbb52b7c1 | 10.26434/chemrxiv-2023-r84wd-v2 | Droplet tilings in precessive fields: Hysteresis, Elastic Defects, and Annealing | Two-component Marangoni contracted droplets can be arranged into arbitrary two-dimensional tiling patterns where they display rich dynamics due to vapor mediated long-range interactions. Recent work has characterized the centered hexagonal honeycomb lattice, showing it to be a highly frustrated system with many metastable states and relaxation occurring over multiple timescales [Molina et al., PNAS, 2021, 18, 34]. Here, we study this system under the influence of a rotating gravitational field. High amplitudes are able to completely disrupt droplet-droplet interactions, making it possible to identify a transition between field-dominated to interaction-dominated regimes. The system displays complex hysteresis behavior, the details of which are connected to the emergence of linear mesoscale structures. These mesoscale features display an elasticity that is governed by the balance between gravity and long-ranged vapor-mediated attractions. We find that disorder plays an important role in determining the dynamics of these features. Finally, we demonstrate the ability to anneal the system by progressively reducing the field amplitude, a process that reduces configurational energy compared to a rapid quench. The ability to manipulate vapor-mediated interactions in deliberately designed droplet tilings provides a novel platform for table-top explorations of multi-body interactions. | Anton Molina; Manu Prakash | Physical Chemistry; Self-Assembly; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651e2c2445aaa5fdbb52b7c1/original/droplet-tilings-in-precessive-fields-hysteresis-elastic-defects-and-annealing.pdf |
60c74474ee301c02d6c7916e | 10.26434/chemrxiv.8864204.v5 | Popular Integration Grids Can Result in Large Errors in DFT-Computed Free Energies | Density functional theory (DFT) has emerged as a powerful tool for analyzing (bio-)organic and organometallic systems and proved remarkably accurate in computing the small free energy differences that underpin many chemical phenomena (e.g. regio- and stereoselective reactions). We show that the lack of rotational invariance of popular DFT integration grids reveals large uncertainties in computed free energies for some isomerizations, torsional barriers, and regio- and stereoselective reactions. The result is that predictions based on DFT-computed free energies for systems with very low-frequency vibrational modes can change qualitatively depending on molecular orientation. For example, for a metal-free propargylation of benzaldehyde, predicted enantioselectivities based on B97-D/def2-TZVP free energies using a popular pruned (75,302) integration grid can vary from 62:38 to 99:1 by simply rotating the transition state structures. Relative free energies for the regiocontrolling transition state structures for an Ir-catalyzed C–H functionalization reaction computed using M06/6-31G(d,p)/LANL2DZ and the same grid can vary by more than 5 kcal/mol, resulting in predicted regioselectivities that range anywhere from 14:86 to >99:1. Errors of these magnitudes occur for different functionals and basis sets, are potentially widespread among modern applications of DFT, and can be reduced by using much denser integration grids than commonly employed.<br /> | Andrea
N. Bootsma; Steven Wheeler | Physical Organic Chemistry; Computational Chemistry and Modeling; Theory - Computational; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74474ee301c02d6c7916e/original/popular-integration-grids-can-result-in-large-errors-in-dft-computed-free-energies.pdf |
6182f1ab7a0021bcbd4565b9 | 10.26434/chemrxiv-2021-3qrlg | Assignment-free chirality detection in unknown samples via microwave three-wave mixing | Straightforward identification of chiral molecules in multi-component mixtures of unknown composition is extremely challenging. Current spectrometric and chromatographic methods cannot unambiguously identify components while the state of the art spectroscopic methods are limited by the difficult and time-consuming task of spectral assignment. Here, we introduce a highly sensitive generalized version of microwave three-wave mixing that uses broad-spectrum fields to detect chiral molecules in enantiomeric excess without any prior chemical knowledge of the sample. This method does not require spectral assignment as a necessary step to extract information out of a spectrum. We demonstrate our method by recording three-wave mixing spectra of multi-component samples that provide direct evidence of enantiomeric excess. Our method opens up new capabilities in ultrasensitive phase-coherent spectroscopic detection that can be applied for chiral detection in real-life mixtures, raw products of chemical reactions and difficult to assign novel exotic species. | Greta Koumarianou; Irene Wang; Lincoln Satterhwaite; David Patterson | Physical Chemistry; Analytical Chemistry; Analytical Apparatus; Spectroscopy (Anal. Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6182f1ab7a0021bcbd4565b9/original/assignment-free-chirality-detection-in-unknown-samples-via-microwave-three-wave-mixing.pdf |
650d38e6b927619fe79a7638 | 10.26434/chemrxiv-2023-l5crz-v2 | Contrast variation method applied to structural evaluation of catalysts by X-ray small-angle scattering | In the process of developing carbon-supported metal catalysts, determining the catalyst particle-size distribution is an essential step, because this parameter is directly related to the catalytic activities. The particle-size distribution is most effectively determined by small-angle X-ray scattering (SAXS). When metal catalysts are supported by high-performance mesoporous carbon materials, however, their mesopores may lead to erroneous particle-size estimation if the sizes of the catalysts and mesopores are comparable. Here we propose a novel approach to particle-size determination by introducing contrast variation-SAXS (CV-SAXS). In CV-SAXS, a multi-component sample is immersed in an inert solvent with a density equal to that of one of the components, thereby rendering that particular component invisible to X-rays. We used a mixture of tetrabromoethane and dimethyl sulfoxide as a contrast-matching solvent for carbon. As a test sample, we prepared a mixture of a small amount of platinum (Pt) catalyst and a bulk of mesoporous carbon, and subjected it to SAXS measurement in the absence and presence of the solvent. In the absence of the solvent, the estimated Pt particle size was affected by the mesopores, but in the presence of the solvent, the Pt particle size was correctly estimated in spite of the low Pt content. The results demonstrate that the CV-SAXS technique is useful for correctly determining the particle-size distribution for low-Pt-content catalysts, for which demands are increasing to reduce the use of expensive Pt. | Albert Mufundirwa; Yoshiharu Sakurai; Hideto Imai; Hiroyuki Iwamoto | Materials Science; Catalysis | CC BY NC 4.0 | CHEMRXIV | 2023-09-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650d38e6b927619fe79a7638/original/contrast-variation-method-applied-to-structural-evaluation-of-catalysts-by-x-ray-small-angle-scattering.pdf |
679954d36dde43c908c2ad62 | 10.26434/chemrxiv-2024-bxr73-v3 | Discovery of Clonixeril as a Sub-Femtomolar Modulator of the Human STING Receptor | Stimulator of interferon genes (STING) is a transmembrane endoplasmic reticulum (ER) resident protein involved in innate immunity. STING activation occurs by binding of cyclic guanosine-(2'→5')-monophosphate-adenosine-(3'→5')-monophosphate (2’,3’-cGAMP) to STING, which leads to downstream production of type 1 interferons (IFN-1). We generated molecular dynamics (MD) equilibrated agonist and antagonist models of human STING (hSTING) for computer based screening and now report the discovery of clonixeril (CXL) as the most potent non-nucleotide hSTING modulator discovered to date. We demonstrate in vitro and in cellulo that CXL has two modes of interaction with hSTING, one with an EC50 above 1 nM and the other with an EC50 in the 1 fM - 100 aM range (10-15–10-16 M). In cell based experiments, when CXL is titrated below 1 nM, it displays inverse dose dependent antagonistic behavior toward hSTING. We have substantiated that CXL displays this exceptionally strong inhibitory effect on hSTING mediated IFN 1 production using a THP 1 cell luciferase reporter for interferon regulatory factor 3 (IRF3). Further characterization of CXL was performed in HEK293 cells and by using biophysical and biochemical techniques. | Robert Sparks; William Lawless; Anna Kharitonova; Rainer Metcalf; Jamie Nunziata; Grace Binder; Sauradip Chaudhury; Christine Gambino; Michelle Wilde; Linette Harding; Jaret Crews; Mansi Gopu; Emilia Dalamangus; Sarah Lawless; Mark Eschenfelder; Robert Green; Elizabeth Nompleggi; Timothy Tran; Yan Yang; Donna Trask; Paul Thompson; Niketa Patel; Rekha Patel; Wesley Brooks; Guy Bradley; Mildred Acevedo-Duncan; Alan Mullen; James Leahy; Kenyon Daniel; Wayne Guida | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Biochemistry; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679954d36dde43c908c2ad62/original/discovery-of-clonixeril-as-a-sub-femtomolar-modulator-of-the-human-sting-receptor.pdf |
60c74626337d6ca613e270d2 | 10.26434/chemrxiv.10838249.v1 | Resolution of the Equilibrium Constant for the T State → RState Conformational Change of Human Hemoglobin into Endothermic and Exothermic Component Reactions | <p> The dimensionless
equilibrium constant for the allosteric conformation change, K<sub>ΔC</sub> =
0.02602 (Knowles & Magde, linked ms 2) following binding of O<sub>2</sub>
by α-chains in <sup>T</sup>state Hb<sub>4</sub>/BPG (whole blood under standard
conditions) is shown to be comprised of: (i) an endothermic change in
conformation, from <sup>T</sup>state to <sup>R</sup>state, of 24.3 kJ/mol; (ii)
exothermic conversion of <sup>T</sup>state <sup>T</sup>αO<sub>2</sub>-chains to
<sup>R</sup>state <sup>R</sup>αO<sub>2</sub>-chains of -13.8 kJ/mol;
(iii)exothermic binding of BPG by R-states.
Eq. (1) defines the component steps whereby the <sup>T</sup>state
conformation is converted to the <sup>R</sup>state conformation.</p>
<p>ΔG<sup>o</sup>(<sup>R</sup>(Hb<sub>4</sub>), BPG) describes
the endothermic decomposition of the binary complex, <sup>T</sup>Hb<sub>4</sub>/BPG
into <sup>R</sup>Hb<sub>4</sub> and BPG, equal to + 33.7 kJ/mol (DeBruin et al.
(1973). J. Biol. Chem. <u>248</u>, 2774-2777).
ΔG<sup>o</sup> for the
equilibrium constant for ΔG<sup>O</sup>(K<sub>ΔC</sub>)
and Σ ΔG<sup>o</sup> for binding of O<sub>2</sub> by the pair of equivalent <sup>T</sup>state
α-chains, ΔG<sup>O</sup>(<sup>T</sup>α<sup>*</sup>O<sub>2</sub>), + 9.41 kJ/mol
and – 49.6 kJ/mol, respectively, are determined by fitting of O<sub>2</sub> equilibrium
binding data to the Perutz-Adair equation.
ΔG<sup>o</sup> for reaction of a pair of equivalent <sup>R</sup>state
α-chains with O<sub>2</sub>, ΔG<sup>O</sup>(<sup>R</sup>αO<sub>2</sub>), was
estimated from the known affinity of myoglobin for O<sub>2</sub> at 37<sup>o</sup>C
(Theorell H. (1936). Biochem. Z., <u>268</u>,
73-81), -63.4 kJ/mol. The unknown
quantity, ∆G<sup>O</sup>(<sup>R</sup>(HbO<sub>2</sub>)<sub>4</sub>/BPG), was obtained
by solving Eq. (1), being -10.5 kJ/mol, K (<sup>R</sup>(HbO<sub>2</sub>)<sub>4</sub>/BPG)
= 58.4 L/mol. The value of the equilibrium
constant for binding BPG to R-state conformations represents 0.0073% of the value
of the binding constant of BPG to <sup>T</sup>state conformations: 800,000
L/mol. The value of K<sub>ΔC</sub>; (i) accounts
for the ability of O<sub>2</sub> to escape, virtually unhindered from rbcs and
(ii) provides a biophysical basis for manifestation of high resting rates of
metabolism in warm blooded species.</p> | Francis Knowles; Douglas Magde | Biochemistry; Biophysics; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74626337d6ca613e270d2/original/resolution-of-the-equilibrium-constant-for-the-t-state-r-state-conformational-change-of-human-hemoglobin-into-endothermic-and-exothermic-component-reactions.pdf |
60c75904ee301c236bc7b828 | 10.26434/chemrxiv.14632572.v1 | Neither Sphere nor Cube - Analyzing the Particle Shape Using Small-Angle Scattering and the Superball Model | <div>Accurate characterization of the nanocrystal shape with high statistical relevance is essential for exploiting the strongly shape-dependent properties of cuboidal nanoparticles towards applications. <br /></div><div>This work presents the development of a new small-angle scattering form factor based on the superball geometry. The superball quantifies the characteristic rounding of corners and edges of cuboidalnanoparticles with a single parameter. Applied to small-angle scattering data of sufficiently monodisperse nanoparticles, the superball form factor enables differentiation between the effects of extended<br /></div>particle size distribution and irregular particle shape. The quantitative application of the superball form factor is validated against microscopy data for a series of monodisperse nanoparticles and implemented into the user-friendly, open source software Sasview. | Dominique Dresen; Asmaa Qdemat; Dominika Zákutná; Erik Wetterskog; Emmanuel Kentzinger; Germán Salazar-Alvarez; Sabrina Disch | Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Structure; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75904ee301c236bc7b828/original/neither-sphere-nor-cube-analyzing-the-particle-shape-using-small-angle-scattering-and-the-superball-model.pdf |
60c73d51842e6576b6db1777 | 10.26434/chemrxiv.5743305.v1 | An NBO-TS predictive approach for torquoselectivity of ring opening in 3-substituted cyclobutenes | <p>The torquoselectivity, the inward or outward ring opening of 3-substituted cyclobutenes, is conventionally guided by the donor and/or acceptor ability of the substituent (S). It is typically predicted by estimating the respective ring opening transition state (TS) barriers. While there is no known dissent in regard to the outward rotation of electron-rich substituents from the approaches of TS calculations, the inward rotation was predicted for some electron-accepting substituents and outward for others. To address this divergence in predicting the torquoselectivity, we have used reliable orbital descriptors through natural bond orbital theoretical calculations and demonstrated that (a) interactions <i>n</i><i><sub>S</sub></i>→s*<sub>C3C4</sub> for a lone pair containing substituent, s<sub>S</sub>→s*<sub>C3C4</sub> for a s-donor substituent, s<sub>C3C4</sub>→p*<sub>S</sub> for a resonance-accepting substituent and s<sub>C3C4</sub>→s*<sub>S</sub> for a s-acceptor substituent constitute the true electronic controls of torquoselectivity, and (b) reversibility of the ring opening event is an additional important contributor to the observed product distribution.</p> | Arpita Yadav; Dasari L V K Prasad; Veejendra Yadav | Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2017-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d51842e6576b6db1777/original/an-nbo-ts-predictive-approach-for-torquoselectivity-of-ring-opening-in-3-substituted-cyclobutenes.pdf |
63e2348e1f23f0032d473f98 | 10.26434/chemrxiv-2023-g9gbd | Practical post-Kohn-Sham methods for time-reversal symmetry breaking references | Reduced scaling algorithms based on auxiliary subspace methods for correlation energies from the random phase approximation(RPA) as well as correlation self-energies from the GW method are derived for time-reversal symmetry breaking Kohn-Sham (KS) references. This allows for an efficient evaluation of RPA energies and GW quasiparticle energies for molecular systems with KS references that break time-reversal symmetry. The latter occur for example in magnetic fields. Furthermore, KS references for relativistic open-shell molecules also break time-reversal symmetry due to the single determinant ansatz used. Errors of the newly developed reduced-scaling algorithms are shown to be negligible compared to reference implementations, while the overall computational scaling is reduced by two orders of magnitude. Ionization energies obtained from the GW approximation are shown to be robust even for the electronically complicated group of trivalent lanthanoid ions. Starting from GW quasiparticle energies, it is subsequently shown that light-matter interactions of these systems can be calculated using the Bethe-Salpeter equation (BSE). Using the combined GW -BSE method, the absorption and emission spectra of a molecular europium(III) complex can be obtained including spin-orbit coupling. | Christof Holzer | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e2348e1f23f0032d473f98/original/practical-post-kohn-sham-methods-for-time-reversal-symmetry-breaking-references.pdf |
655ca3e2dbd7c8b54bb47d08 | 10.26434/chemrxiv-2023-m38mp | Luminescence of lanthanide complexes in mesoporous silica matrices: a textbook example of tris-dipicolinate europium complex adsorbed in SBA-15 | Incorporation of luminescent lanthanide complexes in inorganic matrices opens appealing possibilities in the rational upstream conception of new luminescent materials with easier recyclability. In this regard, the influence of SBA-15 mesoporous silica, as a host matrix, on the photophysical properties of Europium-trisdipicolinate cesium salt was investigated. The lanthanide complex can be completely and reversibly adsorbed on the silica, using incipient wetness impregnation (IWI) in water, without the need of anchoring groups or covalent bonding on the silica surface. This specific procedure allows the homogeneous dispersion of the lanthanide complex into the host silica matrix. Appropriately assessing the photophysical properties of the targeted luminescent material proved remarkably challenging, demanding utmost caution, particularly due to the strong scattering of the mesoporous matrices. Additionally, while our observations confirm an important increase of luminescence lifetimes of lanthanide complexes upon integration into these mediums, we attribute this variation to the differing refractive indexes and not to specific surface interactions or confinement effect. Indeed, it appeared that previous literature precedents depicted erroneous exhalations of the complexes intrinsic quantum yield due to the repeated use of erroneous refractive index values. In the meantime, the luminance of these materials under UV irradiation improves drastically in comparison to what is obtained with the physical dispersion of micro-crystals of the lanthanide complex onto silica. We demonstrate that this improvement is due to a reduced inner filter effect in the adsorbed samples. In this regards, IWI of lanthanide complexes in mesoporous matrices method could be of interest in the development of recyclable emitting layers, less demanding in terms of emitter quantity. | Cristina Balogh; Isis N’Dala-Louika; Iurii Suleimanov; Anais Pons; Matthias Jouffrieau; Clément Camp; Laurent Veyre; Chloé Thieuleux; François Riobé; Olivier Maury | Physical Chemistry; Materials Science; Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655ca3e2dbd7c8b54bb47d08/original/luminescence-of-lanthanide-complexes-in-mesoporous-silica-matrices-a-textbook-example-of-tris-dipicolinate-europium-complex-adsorbed-in-sba-15.pdf |
646c6fd4b3dd6a653097644e | 10.26434/chemrxiv-2023-2zwhl | Multimerizations, Aggregation, and Transfer Reactions of Small Numbers of Molecules | Chemical equilibria of multimerizations in systems with small numbers of particles exhibit behavior seemingly at odds with that observed macroscopically. In this paper we apply the recently proposed expression of equilibrium constant for binding, that include cross-correlations in reactants' concentrations, to write an equilibrium constant for the formation of clusters larger than two (e.g., trimer, tetramer, and pentamer) as series of two-body reactions. Results obtained by molecular dynamics simulations demonstrate the value of this expression is constant for all concentrations and system sizes, as well as, at an onset of a phase transition to an aggregated state where densities in the system change discontinuously. In contrast, the value of the commonly utilized expression of equilibrium constant, which ignores correlations, is not constant and its variations can reach few orders of magnitude. Considering different paths for the same multimer formation, with elementary reactions of any order, yields different expressions for the equilibrium constant, yet, with exactly the same value. This is true also for routes with essentially zero probability to occur. Existence of different expressions for the same equilibrium constant imposes equalities between averages of correlated, along with uncorrelated, concentrations of participating species. Moreover, a relation between average particle number and relative fluctuations derived for two-body reactions is found to be obeyed here as well, despite couplings to additional equilibrium reactions in the system. Analyzes of transfer reactions, where association and dissociation events take place on both sides of the chemical equation, further indicate the necessity to include cross-correlations in the expression of the equilibrium constant. However in this case the magnitudes of discrepancies of the uncorrelated expression are smaller, likely because of partial cancellation of correlations which exist on, both, the reactants and products sides. | Ronen Zangi | Theoretical and Computational Chemistry; Physical Chemistry; Biophysical Chemistry; Self-Assembly; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646c6fd4b3dd6a653097644e/original/multimerizations-aggregation-and-transfer-reactions-of-small-numbers-of-molecules.pdf |
60c752ab842e6501bbdb3dec | 10.26434/chemrxiv.13309454.v1 | TArget-Responsive Subcellular Catabolism Analysis for Early-stage Antibody-Drug Conjugates Screening and Assessment | <p></p><p>Key events including antibody-antigen affinity, ADC
internalization, trafficking and lysosomal proteolysis-mediated payload release
combinatorially determine the therapeutic efficacy and safety for ADCs. Nevertheless, a universal technology that efficiently and
conveniently evaluates the involvement of these above elements to ADC payload release and hence the final therapeutic
outcomes for mechanistic studies and quality assessment is lacking. Considering
the plethora of ADC candidates under development owing to the ever-evolving
linker and drug chemistry, we developed a TArget-Responsive Subcellular
Catabolism (TARSC) approach that measures catabolites kinetics for given ADCs
and elaborates how each individual step ranging from antigen binding to
lysosomal proteolysis affects ADC catabolism by targeted interferences. Using a
commercial and a biosimilar ado-trastuzumab emtansine (T-DM1) as model ADCs, we recorded unequivocal catabolites
kinetics for the two T-DM1s in the presence and absence of the targeted
interferences. Their negligible differences in TARSC profiles fitting with
their undifferentiated therapeutic outcomes suggested by <i>in vitro</i> viability assays and <i>in
vivo</i> tumor growth assays, highlighting TARSC analysis as a good indicator
of ADC efficacy and bioequivalency. Lastly, we
demonstrated the use of TARSC in assessing payload release efficiency for a new
Trastuzumab-toxin conjugate. Collectively, we demonstrated the use of TARSC in
characterizing ADC catabolism at (sub)cellular level, and in systematically
depicting whether given target proteins affect ADC payload release and hence
therapeutic efficacy. We anticipate its future use in high-throughput screening,
quality assessment and mechanistic understanding of ADCs for drug R&D
before proceeding to costly <i>in vivo</i>
experiments.</p><br /><p></p> | Hua Sang; Jiali Liu; Fang Zhou; Xiaofang Zhang; Jingwei Zhang; Yazhong Liu; Guangji Wang; Hui Ye | Biochemical Analysis; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752ab842e6501bbdb3dec/original/t-arget-responsive-subcellular-catabolism-analysis-for-early-stage-antibody-drug-conjugates-screening-and-assessment.pdf |
60c74fe69abda2cddff8d91f | 10.26434/chemrxiv.12950309.v1 | Development of a New and Improved Guanidine-based Rac1 Inhibitor with in Vivo Activity against Non-Small Cell Lung Cancer | <p>Rac1 (Ras-related C3 botulinum toxin substrate
1), is a member of the family of Rho GTPases involved in the dynamic control of
cytoskeleton reorganization and other fundamental cellular functions including
growth, motility and survival. Aberrant activity of Rac1 and its regulators is
common in human cancer. In particular, deregulated expression/activity of Rac
Guanine nucleotide Exchange Factors (GEFs), responsible for Rac activation, has
been largely associated to a metastatic phenotype and drug resistance. Thus, the development of novel Rac1-GEF interaction
inhibitors is a promising strategy for finding new preclinical candidates. In
this work, we have studied structure-activity relationships within a new family
of N,N’-disubstituted guanidine as Rac1-GEF protein-protein interaction
inhibitors, starting from our first developed member 1A-116. We found that new
analogue 1D-142, bearing a pyridine ring instead of benzene ring, presents
improved antiproliferative activity in human cancer cell lines and higher
potency as Rac1-GEF interaction inhibitor in vitro. In addition, 1D-142 reduces
TNFα-induced NF-κB nuclear translocation, a mechanisms mediated by Rac1 during
cell proliferation and migration in NSCLC. Notably, 1D-142 was used to show for
the first time the application of a Rac1 inhibitor in a lung cancer animal
model.<br /></p> | Matias S Ciarlantini; Andrea Barquero; diana wetzler; Juan Bayo; Martín M. Dodes Traian; Hernan A. Bucci; Esteban J. Fiore; Lucía Gandolfi-Donadío; Lucas Defelipe; Adrián Turjanski; javier a ramirez; Guillermo Mazzolini; Maria Julieta Comin | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fe69abda2cddff8d91f/original/development-of-a-new-and-improved-guanidine-based-rac1-inhibitor-with-in-vivo-activity-against-non-small-cell-lung-cancer.pdf |
6645151891aefa6ce118b68f | 10.26434/chemrxiv-2024-cnc9w | Ultrafast Dynamics of a Red-Light-Activated Organic Photocatalyst in the Oxidative Hydroxylation of Phenylboronic Acid | Over the past few years, photoredox catalysis has led to significant transformations in modern synthetic chemistry. It has allowed the development of new synthetic pathways for the assembly of complex molecular scaffolds using light as a driving force. However, investigations of the ultrafast light-initiated mechanisms required for these reactions are relatively scarce. Here we follow the ultrafast dynamics of a red-light organic photocatalyst, N,N′-di-n-propyl-1,13-dimethoxyquinacridinium (nPr-DMQA+), in the aerobic oxidative hydroxylation of phenylboronic acid using transient absorption and time correlated single photon counting spectroscopy. Global target analysis supports a reaction mechanism that proceeds through the excited triplet state of nPr-DMQA+, leading to the generation of a superoxide anion and subsequent oxidative hydroxylation. The triplet pathway proposed here has relatively wide application in organic photocatalytic oxidative reactions including those using methylene blue and other organic dyes as catalysts. Observation of the ultrafast dynamics of nPr-DMQA+ as it acts as a catalyst can provide insights to improve the efficiency of oxidative hydroxylation reactions and the mechanisms of photoredox catalysis more broadly. | Anshu Kumar; Benjamin Thompson; Md Mubarak Hossain; Thomas Gianetti; Vanessa Huxter | Physical Chemistry; Catalysis; Photocatalysis; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6645151891aefa6ce118b68f/original/ultrafast-dynamics-of-a-red-light-activated-organic-photocatalyst-in-the-oxidative-hydroxylation-of-phenylboronic-acid.pdf |
60c74851ee301cf516c79844 | 10.26434/chemrxiv.11852040.v2 | A Tale of Seemingly “Identical” Silicon Quantum Dot Families: Structural Insight into Silicon Quantum Dot Photoluminescence | <p>Two
quantum dots, both alike in composition, but differing in structure, where we
lay our scene. From broader classes, to bring deeper understanding, to the
crystalline core that drives the quantum dot's sheen. In this contribution we
examine two families of silicon quantum dots (SiQDs) that bring to mind the
Capulets and the Montagues in Shakespeare’s Romeo and Juliet because of their
stark similarities and differences. SiQDs are highly luminescent,
heavy-metal-free and based upon earth-abundant elements. As such, they have attracted attention for far
reaching applications ranging from biological imaging to luminescent solar
concentrators to light-emitting diodes that rely on their size-dependent
optical response. Unfortunately, correlating SiQD “size” to their photoluminescence
maximum is often challenging. Herein, we provide essential structural insight
into the correlation of SiQD dimension and PL maximum through a direct comparison
of samples that exhibit statistically identical physical dimensions (d<sub>TEM</sub>)
and chemical compositions, but different crystallite size (d<sub>XRD</sub>) and
PL maxima. We then expand the scope of
this investigation and systematically compare groupings of SiQDs: one in which
the d<sub>XRD</sub> and d<sub>TEM</sub> agree and one where d<sub>XRD </sub><
d<sub>TEM</sub>. This latter comparison clearly shows d<sub>XRD</sub> better
predicts SiQD optical response when using the well-established effective mass
approximation. </p> | Alyxandra Thiessen; Lijuan Zhang; Anton Oliynyk; Haoyang Yu; Kevin O'Connor; Alkiviathes Meldrum; Jonathan G.C. Veinot | Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74851ee301cf516c79844/original/a-tale-of-seemingly-identical-silicon-quantum-dot-families-structural-insight-into-silicon-quantum-dot-photoluminescence.pdf |
67566f6bf9980725cf798590 | 10.26434/chemrxiv-2024-5w2q4 | Preparative [3+2] cycloaddition of CH2N2 to acrylate derivatives: revising, scope and synthetic applications | Safe and preparative approaches using flow chemistry technologies were applied to the known [3+2] cycloaddition of diazomethane with a diverse set of substituted methyl acrylates. The initially formed Δ¹-pyrazolines were also subjected to in-flow transformations. DFT modelling of the [3+2] cycloaddition predicts a concerted asynchronous mechanism for the reaction. The observed in the experiment regio- and stereoselectivity of the transformation are kinetically driven. Some of the initially formed Δ1-pyrazolines tend to isomerize spontaneously to Δ2-isomers. However, conditions suitable for isolating Δ¹-pyrazolines, previously considered unstable, have been discovered. Other [3+2] cycloaddition products were found to be stable on isolation and storage. By treatment of the formed Δ1-pyrazolines with strong acid (HCl), hydrochlorides of isomeric Δ2-pyrazolines have been isolated. Photo-induced nitrogen elimination from Δ1-pyrazolines in the flow photo reactor provides an easy approach for the preparative synthesis of a broad series of cyclopropanes, which are valuable motifs in pharmaceuticals and agrochemicals. The reaction proceeds under mild conditions with preservation of configuration of stereocenters. All the reactions are easily scalable at least up to several tens of grams. This work demonstrates that a deep mechanistic understanding of the reaction pathways, combined with the advantages of flow chemistry and photochemical techniques, can transform a classic reaction into a practical and scalable synthetic methodology. | Serhii Shuvakin; Sergiy Ivonin; Vyacheslav Pendyukh; Olexandr Pashenko; Svitlana Shishkina; Andriy Kozytskiy; Alexander Rozhenko; Uwe Manthe; Tobias Spengler; Dmytro Volochnyuk; Serhiy Ryabukhin | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67566f6bf9980725cf798590/original/preparative-3-2-cycloaddition-of-ch2n2-to-acrylate-derivatives-revising-scope-and-synthetic-applications.pdf |
6379a1fbbe365e4e1925d0c4 | 10.26434/chemrxiv-2022-xxpqc | Computational studies of rubber ozonation explain the effectiveness of 6PPD as an antidegradant and the mechanism of its quinone formation | The discovery that the commercial rubber antidegradant 6PPD reacts with ozone (\ce{O3}) to produce a highly toxic quinone (6PPDQ) spurred a significant research effort into non-toxic alternatives. Identification of non-toxic alternatives has been hampered by lack of a detailed understanding of the mechanism of protection that 6PPD affords rubber compounds against ozone. Herein, we report high-level density functional theory studies into early steps of rubber and PPD ($p$-phenylenediamine) ozonation, identifying key steps that contribute to the antiozonant activity of PPDs. In this, we establish that our density functional theory approach can achieve chemical accuracy for many ozonation reactions, which are notoriously difficult to model. Using adiabatic energy decomposition analysis, we examine and dispel the notion that one-electron charge transfer initiates ozonation in these systems, as is sometimes argued. Instead, we find direct interaction between \ce{O3} and PPD carbon atoms is kinetically accessible, and that this motif is more significant than interactions with PPD nitrogens. The former pathway results in a hydroxylated PPD intermediate, which reacts further with \ce{O3} to afford 6PPD hydroquinone and, ultimately, 6PPDQ. This mechanism directly links the toxicity of 6PPDQ to the antiozonant function of 6PPD. These results have significant implications for development of alternative antiozonants, which are discussed. | Elliot Rossomme; William Hart-Cooper; William Orts; Colleen McMahan; Martin Head-Gordon | Theoretical and Computational Chemistry; Organic Chemistry; Earth, Space, and Environmental Chemistry; Physical Organic Chemistry; Wastes; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6379a1fbbe365e4e1925d0c4/original/computational-studies-of-rubber-ozonation-explain-the-effectiveness-of-6ppd-as-an-antidegradant-and-the-mechanism-of-its-quinone-formation.pdf |
6605757f66c138172912e214 | 10.26434/chemrxiv-2024-lbxqn | Novel tetragonal boron pnictides BX (X = N, P, As, Sb, Bi) with square B2X2 motifs from crystal chemistry and first principles | Novel tetragonal (P42/mnm) boron pnictides BX (X = N, P, As, Sb, Bi) with chromium boride (crb) topology exhibiting a square B2X2 motif with resulting edge- and corner-sharing tetrahedra have been predicted from crystal chemistry and extensively characterized by density functional theory (DFT) calculations. All new BX phases were found to be cohesive with decreasing cohesive energy along the series. Mechanically stable with positive sets of elastic constants, all crb phases exhibit slightly lower hardness than other BX polymorphs due to increased openness of the crystal structures. All-positive phonon frequencies characterize the crb BX family except for X = Bi, which shows a slight acoustic instability; also the shape of the phonon spectra changes from band-like for X = N, P, As to flat bands for the heavier elements. The electronic band structures reveal insulating to semiconducting properties for crb BX, depending on the pnictogen nature along the series. | Samir F. Matar; Vladimir L. Solozhenko | Materials Science; Inorganic Chemistry; Materials Chemistry; Crystallography – Inorganic | CC BY 4.0 | CHEMRXIV | 2024-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6605757f66c138172912e214/original/novel-tetragonal-boron-pnictides-bx-x-n-p-as-sb-bi-with-square-b2x2-motifs-from-crystal-chemistry-and-first-principles.pdf |
60c74726469df4a483f4378b | 10.26434/chemrxiv.11542431.v1 | Ultrapermeable Thin Film Composite Membranes Enhanced via Doping MOF Nanosheets | Thin film composite (TFC) membranes have attracted increasing interest to meet the demands of industrial gas separation. However, the development of high performance TFC membranes within their current configuration faces two key challenges: (i) the thickness-dependent gas permeability of polymeric materials (mainly polydimethylsiloxane (PDMS)) and (ii) the geometric restriction effect due to the limited pore accessibility of porous substrates. Here we demonstrate for the first time that the incorporation of trace (~1.8 wt%) amounts of amorphous metal-organic framework (aMOF) nanosheets into the gutter layer of TFC assemblies can simultaneously address these two limitations, with experimental evidence revealing the creation of rapid gas diffusion pathways along horizontal direction. Leveraging this strategy, we successfully fabricated a novel TFC membrane, consisting of a PDMS/aMOF gutter and an ultrathin (~54 nm) poly(ethylene glycol) top selective layer<i> via</i> surface-initiated atom transfer radical polymerization (ATRP). The complete TFC membrane exhibits excellent processability and the highest CO<sub>2</sub> permeance (1,990 GPU with a CO<sub>2</sub>/N<sub>2</sub> ideal selectivity of 39) yet observed for a TFC membrane employing a PDMS gutter layer. This study reveals an avenue for the design and fabrication of a new TFC membrane system with unprecedented gas separation performance. | Min Liu; Ke Xie; MITCHELL NOTHLING; Lianhai Zu; qiang fu; PAUL WEBLEY; GREG QIAO | Composites; Thin Films; Coordination polymers; Nanofabrication; Coordination Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74726469df4a483f4378b/original/ultrapermeable-thin-film-composite-membranes-enhanced-via-doping-mof-nanosheets.pdf |
63315ce50e3c6a66462918b7 | 10.26434/chemrxiv-2022-ggzd3 | An Imbalance in the Force: The Need for Standardised Benchmarks for Molecular Simulation | Force fields (FF) for molecular simulation have been under development for more than half a century. As with any predictive model, rigorous testing and comparisons of models critically depends on the availability of standardized datasets and benchmarks. While such benchmarks are rather common in the fields of quantum chemistry, this is not the case for empirical FFs. That is, few benchmarks are re-used to evaluate FFs and development teams rather use their own test sets. Here we present an overview of currently available tests and benchmarks for computational chemistry, focusing on organic compounds, including halogens and common ions, as FFs for these are the most common ones. We argue that many of the benchmark datasets from quantum chemistry can in fact be re-used for evaluating FFs, but new gas phase data is still needed for compounds containing phosphor and sulfur. In addition, more non- equilibrium energies and forces are needed for compounds with halogens, P and S. For the condensed phases there is a large body of experimental data available and tools to utilise these data in an automated fashion are under development. If FF developers, as well as researchers in artificial intelligence would adopt a number of these datasets it would become easier to compare the relative strengths and weaknesses of different models and to, eventually, restore the balance in the force. | Kristian Kriz; Lisa Schmidt; Alfred Andersson; Marie-Madeleine Walz; David van der Spoel | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63315ce50e3c6a66462918b7/original/an-imbalance-in-the-force-the-need-for-standardised-benchmarks-for-molecular-simulation.pdf |
60c75715bb8c1a57633dc73d | 10.26434/chemrxiv.13250333.v2 | Stacking Disorders in MixedAlkali Honeycomb Layered Oxide NaKNi2TeO6 and Feasibility for Mixed-Cation Transport | <b>We demonstrate the feasibility of using a combination of alkali
atoms (Na and K) to develop a robust mixed-alkali honeycomb layered oxide NaKNi<sub>2</sub>TeO<sub>6</sub>.
Through a series of atomic-resolution transmission electron microscopy in
multiple zone axes, we reveal for the first time the local atomic structural
disorders characterised by aperiodic stackings and incoherency in the
alternating arrangement of Na and K atoms. Our findings indicate great
structural versatility that renders NaKNi<sub>2</sub>TeO<sub>6</sub> an ideal
platform for investigating other fascinating properties such as mixed ionic
transport and intriguing electromagnetic and quantum phenomena amongst honeycomb
layered oxides. Finally, we unveil the possibility of inducing mixed Na- and
K-ion transport electrochemistry of NaKNi<sub>2</sub>TeO<sub>6</sub> at high
voltages (~ 4V), thus epitomising it as a competent cathode candidate for the
emerging dendrite-free batteries based on NaK liquid metal alloy as anodes. The
results not only betoken a new avenue for developing functional materials with
fascinating crystal versatility, but also prefigure a new age of
‘dendrite-free’ energy storage system designs that rely on mixed-cation
electrochemistry.</b> | Titus Masese; Yoshinobu Miyazaki; Josef Rizell; Godwill Mbiti Kanyolo; Chih-Yao Chen; Hiroki Ubukata; Keigo Kubota; Kartik Sau; Tamio Ikeshoji; Zhen-Dong Huang; Kazuki Yoshii; Teruo Takahashi; Miyu Ito; Hiroshi Senoh; Jinkwang Hwang; Abbas Alshehabi; Kazuhiko Matsumoto; Masatomo Yashima; Kotaro Fujii; Toshiyuki Matsunaga; Masahiro Shikano; Yoshiharu Uchimoto; Cedric Tassel; Rika Hagiwara; Hiroshi Kageyama; Tomohiro Saito | Ceramics; Materials Processing; Multilayers; Nanostructured Materials - Materials; Imaging; Microscopy; Nanostructured Materials - Nanoscience; Bonding; Electrochemistry; Solid State Chemistry; Theory - Inorganic; Computational Chemistry and Modeling; Theory - Computational; Quantum Computing; Thermodynamics (Chem. Eng.); Transport Phenomena (Chem. Eng.); Energy Storage; Physical and Chemical Processes; Physical and Chemical Properties; Quantum Mechanics; Structure; Thermodynamics (Physical Chem.); Transport phenomena (Physical Chem.); Materials Chemistry; Crystallography; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75715bb8c1a57633dc73d/original/stacking-disorders-in-mixed-alkali-honeycomb-layered-oxide-na-k-ni2te-o6-and-feasibility-for-mixed-cation-transport.pdf |
630b6a060c5277df29c5db50 | 10.26434/chemrxiv-2022-4hxvt | A database to compare possible MOFs for volumetric hydrogen storage, taking into account the cost of their building blocks | Physical adsorption at cryogenic temperature can increase the density of the stored hydrogen at a lower pressure than conventional compressed gas systems. This mechanism is also reversible and involves faster kinetics than chemical storage. Materials with certain structural and porous properties are necessary for volumetrically efficient hydrogen storage, including large specific surface areas, pore volumes, and appropriated bulk densities. Metal-organic frameworks (MOF) materials are remarkable candidates as adsorbents due to their porous properties and high crystallinity. Large databases like the MOF subset from the CSD or the CoRE-MOF can be used to find the best materials for this application, providing crystallographic information, composition, and porous properties. Herein, we created a database which includes crystallographic and porous properties, metallic and organic composition, and the minimum available cost for their linkers and corresponding suppliers for those for which it was publicly available. The database is also helpful for selecting structures with potential for industrial production and starting material for computational tools like machine learning or artificial intelligence approaches that relate the composition of MOFs with their performance in different applications. A user interface allows for creating customized selections of suitable MOF structures, looking for their porous and crystalline properties, gravimetric and volumetric total uptakes, and metallic and organic composition, as well as properties for the organic linkers like name, molecular mass, price, or presence of specific functional groups. This information was used to select potential structures from up to two metals and two linkers for the volumetric cryostorage of hydrogen. | Jose Antonio Villajos Collado; Martin Bienert; Nikita Gugin; Franziska Emmerling; Michael Maiwald | Materials Science; Energy; Chemical Engineering and Industrial Chemistry; Hybrid Organic-Inorganic Materials; Hydrogen Storage Materials; Industrial Manufacturing | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630b6a060c5277df29c5db50/original/a-database-to-compare-possible-mo-fs-for-volumetric-hydrogen-storage-taking-into-account-the-cost-of-their-building-blocks.pdf |
67422205f9980725cf9ebb4f | 10.26434/chemrxiv-2024-x5btd | Catch & Release of Al(I) at a Zinc Bis-Amide | [(HMDS)(Cp*)Al]2Zn (1) is an intriguing trimetallic zinc aluminyl for which reactivity and quantum chemical studies remain elusive. Through a combined experimental and computational approach 1 is revisited showcasing its reversible formation and reaction chemistry. As revealed computationally, the compound is prone to eliminate and transfer monomeric [AlCp*] – reminiscent of Schnöckels (AlCp*)4. Experimental validation is provided based on NMR studies which showcase the transfer of one and two equivalents of [AlCp*] possible with suitable trapping reagents. Without trapping reagents and thermal treatment of 1, Cp* transfer, Al(HMDS) release and decomposition pathways are induced. Disclosing complementary reactivity, sequential insertion of carbodiimides into 1 yields a series of carbene complexes through one- and twofold insertions. All transformations are followed by state-of-the-art chemical calculations to understand the chemical bonding and bimetallic cooperation between the elements Al and Zn in-depth. | Fabian Dankert; Enric Sabater; Pedro Salvador; Eva Hevia | Inorganic Chemistry; Bonding; Main Group Chemistry (Inorg.); Reaction (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67422205f9980725cf9ebb4f/original/catch-release-of-al-i-at-a-zinc-bis-amide.pdf |
675de65df9980725cf16fe71 | 10.26434/chemrxiv-2024-czx5t-v2 | Drug Binding Modulates Chiral Water Structures in the DNA First Hydration Shell | Knowledge of how intermolecular interactions change hydration structures surrounding DNA will heighten understanding of DNA biology and advance drug development. However, probing changes in DNA hydration structures in response to molecular interactions and drug binding in situ under ambient conditions has remained challenging. Here, we apply a combined experimental and computational approach of chiral-selective vibrational sum frequency generation spectroscopy (chiral SFG) to probe changes of DNA hydration structures when a small-molecule drug, netropsin, binds the minor groove of DNA. Our results show that chiral SFG can detect water being displaced from the minor groove of DNA due to netropsin binding. Additionally, we observe that chiral SFG distinguishes between weakly and strongly hydrogen-bonded water hydrating DNA. Chiral SFG spectra show that netropsin binding, instead of displacing weakly hydrogen-bonded water, preferentially displaces water molecules strongly hydrogen-bonded to thymine carbonyl groups in the DNA minor groove, revealing the roles of water in modulating site-specificity of netropsin binding to duplex DNA rich in adenine-thymine sequences. The results convey the promise of chiral SFG to offer mechanistic insights into roles of water in drug development targeting DNA. | Ty Santiago; Daniel Konstantinovsky; Matthew Tremblay; Ethan A. Perets; Sharon Hammes-Schiffer; Elsa C. Y. Yan | Physical Chemistry; Biological and Medicinal Chemistry; Biophysical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675de65df9980725cf16fe71/original/drug-binding-modulates-chiral-water-structures-in-the-dna-first-hydration-shell.pdf |
669d42fa5101a2ffa84a47be | 10.26434/chemrxiv-2024-4nnkt | Radical mediated deoxygenative alkynylation of Heterocyclic N-oxides under ball milling | Herein, we disclose the first example of stainless steel induced deoxygenative C-2 alkynylation of heterocyclic N-oxides under ball milling via a radical mediated pathway. The current approach showed compatibility to both electron donating and electron withdrawing phenylacetylenes as well as corresponding heterocyclic N-oxides affording the targeted products in moderate to excellent yields including biologically active molecules. Detailed mechanistic investigations based on control experiments and XPS analysis corroborated the significant role of Fe(III) species present in the milling equipment (stainless steel) as well as the mechanical impact of the milling equipment (Fe/Zr-jar/balls), in initiating the reaction via a radical pathway. | Ajay Kumar Dhiya; Manpreet Kaur; Anuj Sharma | Organic Chemistry; Catalysis; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669d42fa5101a2ffa84a47be/original/radical-mediated-deoxygenative-alkynylation-of-heterocyclic-n-oxides-under-ball-milling.pdf |
67d0b68c6dde43c908783ac6 | 10.26434/chemrxiv-2025-mcbt4-v2 | Exploring Vinylidene/Acetylene Isomerization by Photoelectron Spectroscopy of Vibrationally Excited Vinylidene Anions | In order to explore the vibrational levels of vinylidene (H2CC) and their possible couplings with acetylene (HCCH), we investigate the effect of infrared (IR) vibrational pre-excitation on the high-resolution photoelectron spectra of the vinylidene anion (H2CC¯) and its deuterated isotopologue (D2CC¯). The photoelectron spectra are obtained using slow electron velocity-map imaging of cryogenically cooled anions (cryo-SEVI); here, cold anions are vibrationally excited by an IR laser pulse prior to photodetachment (IR cryo-SEVI). Infrared action spectra of the anion CH2 stretching fundamentals are measured by monitoring growth and depletion of features in photoelectron spectra as the IR laser is tuned, yielding excitation frequencies of the symmetric (ν1) and antisymmetric (ν5) CH2 stretching modes of 2590±2 cm-1 and 2658±2 cm-1, respectively. We then use IR cryo-SEVI to explore the effect of vibrational excitation of the two modes on the anion photoelectron spectrum. Interpretation of these spectra is facilitated by quantum calculations performed for each isotopologue on accurate six-dimensional potential energy surfaces of both neutral and anionic vinylidene. IR cryo-SEVI spectra resulting from excitation of these two close-lying anion vibrations are noticeably different. Excitation of the ν1 mode leads to several new features that appear in the photoelectron spectra which closely match the Franck-Condon allowed transitions predicted by theory. Excitation of the ν5 mode in H2CC¯ reveals complicated spectral features in the vicinity of the 5_1^1 sequence band that are not seen for D2CC¯. These are explained by a combination of anharmonic coupling between ν5 and ν6 (CH2 rock) states in neutral H2CC and possible coupling to the HCCH isomer. | Martin DeWitt; Dongzheng Yang; Jascha A. Lau; Korina Vlahos; Hua Guo; Daniel M. Neumark | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2025-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d0b68c6dde43c908783ac6/original/exploring-vinylidene-acetylene-isomerization-by-photoelectron-spectroscopy-of-vibrationally-excited-vinylidene-anions.pdf |
66e20912cec5d6c142cd9765 | 10.26434/chemrxiv-2024-xpq3n | Naphtho[1,2-b][1,4]diazepinedione-based P2X4 Receptor Antagonists from Structure-Activity Relationships Study Towards PET Tracer Development | The P2X4 receptor, a ligand-gated ion channel, is implicated in various pathological conditions, including neuropathic pain and cancer. This study reports the development of 1,4-naphthodiazepinedione-based P2X4 receptor antagonists aimed at both therapeutic applications and potential use as PET tracers for imaging P2X4 receptor expression in cancer and neuroinflammatory diseases. Structure-activity relationship studies aided by docking studies and molecular dynamics simulations led to a series of compounds with potent P2X4 receptor antagonism, promising in vitro inhibition of interleukin-1β release in THP-1 cells and suitability for radiolabeling with fluorine-18. The most potent compounds were further evaluated for their physicochemical properties, metabolic stability, and in vivo biodistribution using PET imaging in mice. While these antagonists exhibited strong receptor binding and serum stability, rapid in vivo metabolism limited their potential as PET tracers, highlighting the need for further structural optimization. This study advances the understanding of P2X4 receptor antagonism and underscores the challenges in developing effective PET tracers for this target. | Katharina Sophie Erlitz; Ann-Kathrin Prinz; Stefan Wagner; Joana Massa; Calvin Dunker; Meike Höhl; Angelika Griep; Róisín M. McManus; Sonja Schelhaas; Oliver Koch; Anna Junker | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e20912cec5d6c142cd9765/original/naphtho-1-2-b-1-4-diazepinedione-based-p2x4-receptor-antagonists-from-structure-activity-relationships-study-towards-pet-tracer-development.pdf |
655197192c3c11ed7147a548 | 10.26434/chemrxiv-2023-sw036 | Synthesis and spectroscopic investigation of substituted piperazine-2,5-dione derivatives | The piperazine-2,5-dione moiety is a useful scaffold for functionalisation to generate bioactive molecules. Synthetic methods for accessing substituted piperazine-2,5-diones involve cyclising dipeptides or building from the already established core. Utilising the latter method, we have developed procedures to condense a variety of methoxylated benzaldehydes to exclusively form (Z,Z)-(benzylidene)piperazine-2,5-diones 7. This methodology can easily be utilised to form both homo- and heterodimeric substituted piperazine-2,5-diones. Subjecting these compounds to hydrogenation affords two isomers. We detail simple NMR analyses that allow for identification of the cis or trans isomers. These analyses, combined with X-ray crystallography have shown that under the hydrogenation conditions used the cis isomer forms as the major product. The synthetic methodology combined with spectral analysis provides a valuable understanding of piperazine-2,5-dione properties. | Craig D. Stuart; Nicholas G. White; Russell A. Barrow; Tristan A. Reekie | Organic Chemistry; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655197192c3c11ed7147a548/original/synthesis-and-spectroscopic-investigation-of-substituted-piperazine-2-5-dione-derivatives.pdf |
621b44cedaa4fbfc1078a6ab | 10.26434/chemrxiv-2022-mqppg | Hidden Heterometallic Interaction Emerges from Resonant Inelastic X-ray Scattering in Luminescent Tb–Pt Molecules | Theoretical calculations are typically utilized for examining intermetallic interactions. However, to validate theory, experimental confirmation of the existence of these interactions is necessary. We synthesized new heterometallic Ln–Pt complexes, NEt4{[Pt(PhSAc)4]Ln[(PhSAc)4Pt]}·2DMF (Ln: lanthanoid = Gd (1), Tb (2), Dy (3), PhSAc = benzothioacetate, NEt4 = tetraethylammonium), in which both diamagnetic Pt(II) ions interact with the central Ln(III) ion. Typically, these interactions are not detected, because the distance between Ln and Pt atoms (~3.6 Å) is much larger than the covalent radius (~3.3 Å) and ionic radius (~3.10 Å). Pt-LIII resonant inelastic X-ray scattering (RIXS) analysis was conducted to experimentally confirm the unique influence of the hidden Ln–Pt interaction on the luminescence of the Tb–Pt molecule, where the interaction induced emission properties in the Tb and Pt ions, with high quantum yield (59%). Quantum theory of atoms in molecules (QTAIM) analysis was also used to confirm the experimental results. RIXS analysis allowed the identification of several distinctive characteristics of the coordination environment, including the existence of heterometallic interactions, that affected the observed luminescence. | Takefumi Yoshida; Ahmed Shabana; David Chukwuma Izuogu; Kentaro Fuku; Tetsu Sato; Haitao Zhang; Yukina Yamamoto; Jun Kamata; Hitomi Ohmagari; Miki Hasegawa; Goulven Cosquer; Shinya Takaishi; Takuma Kaneko; Tomoya Uruga; Yasuhiro Iwasawa; Masahiro Yamashita | Physical Chemistry; Inorganic Chemistry; Spectroscopy (Inorg.); Physical and Chemical Properties; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621b44cedaa4fbfc1078a6ab/original/hidden-heterometallic-interaction-emerges-from-resonant-inelastic-x-ray-scattering-in-luminescent-tb-pt-molecules.pdf |
668c6dc6c9c6a5c07aaf1445 | 10.26434/chemrxiv-2024-s649t | Sterically-Hindered Derivatives of Pentacene and Octafluoropentacene | 6,13-Diethynylpentacene derivatives with sterically bulky substituents (Tr*, tris(3,5-di-tert-butylphenyl)methyl groups) appended to the ethynyl moieties at the 6- and 13-positions have been synthesized, as well as derivatives with electron withdrawing fluorine groups on the eight pro-cata positions. These molecules are designed to investigate relationships between steric and electronic effects on the stability of pentacene toward endoperoxide formation via reaction with photosensitized oxygen in solution under conditions of ambient light (i.e., ‘laboratory’ conditions). It is evident from the study that stabilization through changes to the electronic characteristics of pentacene are more effective than the incorporation of sterically bulky groups at the acetylenic termini. Selected pentacene derivatives have been made into binary, amorphous films with the fullerene derivative PCBM to investigate the stability imparted by substituents against cycloaddition reactions. Overall, the introduction of steric protection through incorporation of Tr* groups is not an efficient strategy for enhancing persistence of pentacenes. Stabilization through fluorination proves successful for extending the lifetime of the pentacene derivatives by an order of magnitude in solution. Notably, the persistence of pentacene derivatives in solution can also be enhanced through the use ethereal solvents stabilized with butylated hydroxy toluene (BHT) and/or an increased number of trialkylsilyl groups as substituents. | Zachary W. Schroeder; Parisa Rezghirami; Matthias Adam; Michael J. Ferguson; Frank Hampel; Rik R. Tykwinski | Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668c6dc6c9c6a5c07aaf1445/original/sterically-hindered-derivatives-of-pentacene-and-octafluoropentacene.pdf |
62fa1737e78f70e6053ba563 | 10.26434/chemrxiv-2022-24svz | Correlation consistent auxiliary basis sets in density fitting Hartree-Fock. The atoms sodium through argon revisited. | We present a series of auxiliary basis sets, for the elements Na to Ar, for use in density-fitted Hartree-Fock calculations with the correlation consistent cc-pV(n+d)Z orbital basis sets. Benchmarking on total molecular energies, reaction energies and the spectroscopic constants of the SO molecule demonstrate that the new sets address the deficiencies of using existing auxiliary sets in combination with these orbital basis sets. We also report auxiliary basis sets for Na and Mg matched to cc-pVnZ, along with recommendations for pairing auxiliary basis sets to the cc-pVnZ-F12 basis sets for Hartree-Fock calculations. | Harry Nash; Robert Shaw; Grant Hill | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fa1737e78f70e6053ba563/original/correlation-consistent-auxiliary-basis-sets-in-density-fitting-hartree-fock-the-atoms-sodium-through-argon-revisited.pdf |
628f376b70432666e047b763 | 10.26434/chemrxiv-2022-54d5q | Exploring the NCS-382 Scaffold for CaMKIIα Modulation: Synthesis, Pharmacology, and Biophysical Characterization of Ph-HTBA as a Novel High-Affinity Brain-Penetrant Stabilizer of the CaMKIIα Hub Domain | Ca2+/calmodulin-dependent protein kinase II alpha (CaMKIIα) is a brain-relevant kinase and an emerging drug target for ischemic stroke and neurodegenerative disorders. Despite various reported CaMKIIα inhibitors, their usefulness is limited by low subtype selectivity and brain permeability. (E)-2-(5-Hydroxy-5,7,8,9-tetrahydro-6H-benzo[7]annulen-6-ylidene)acetic acid (NCS-382) is structurally related to the proposed neuromodulator, γ-hydroxybutyric acid, and is a brain-penetrating high nanomolar-affinity ligand selective for the CaMKIIα hub domain. Herein, guided by in silico approaches, we synthesized the first series of NCS-382 analogs displaying improved affinity and preserved brain permeability. Specifically, we present Ph-HTBA (1i) with enhanced mid-nanomolar affinity for the CaMKIIα binding site and a marked hub thermal stabilization effect along with a distinct CaMKIIα Trp403 flip upon binding. Moreover, Ph-HTBA has good cellular permeability and low microsomal clearance and shows brain permeability after systemic administration to mice, signified by a high Kp,uu value (0.85). Altogether, our study highlights Ph-HTBA as a promising candidate for CaMKIIα-associated pharmacological interventions and future clinical development. | Yongsong Tian; Mohamed Shehata; Stine Gauger; Carolina Veronesi; Louise Hamborg; Louise Thiesen; Jesper Bruus-Jensen; Johanne Schlieper Royssen; Ulrike Leurs; Anne Sofie Larsen; Jacob Krall; Sara Solbak; Petrine Wellendorph; Bente Frølund | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628f376b70432666e047b763/original/exploring-the-ncs-382-scaffold-for-ca-mkii-modulation-synthesis-pharmacology-and-biophysical-characterization-of-ph-htba-as-a-novel-high-affinity-brain-penetrant-stabilizer-of-the-ca-mkii-hub-domain.pdf |
60c747c2842e652ec8db2a19 | 10.26434/chemrxiv.11778390.v1 | Layered High-Entropy Oxide Structures for Reversible Energy Storage | <p>Layered
Li<i><sub>x</sub></i>MO<sub>2</sub>
materials, a new class of high-entropy oxides, have been synthesized by
nebulized spray pyrolysis. Specifically, the lattice structure of Li(Ni<sub>1/3</sub>Mn<sub>1/3</sub>Co<sub>1/3</sub>)O<sub>2</sub>
(NCM111) cathode material has been replicated successfully while increasing the
number of cations in equimolar proportions, thereby allowing transition to
high-entropy oxide materials.</p> | Junbo Wang; Yanyan Cui; Qingsong Wang; Kai Wang; Xiaohui Wang; David Stenzel; Abhishek Sarkar; Subramshu S. Bhattacharya; Robert Kruk; Horst Hahn; Torsten Brezesinski; Ben Breitung | Ceramics; Electrochemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747c2842e652ec8db2a19/original/layered-high-entropy-oxide-structures-for-reversible-energy-storage.pdf |
64d0ae8ddfabaf06ffdae5a9 | 10.26434/chemrxiv-2023-pknnt | Reaction-Agnostic Featurization of Bidentate Ligands for Bayesian Ridge Regression of Enantioselectivity | Chiral ligands are important components in asymmetric homogeneous catalysis, but their synthesis and screening can be both time-consuming and resource-intensive. Data-driven approaches, in contrast to screening procedures based on intuition, have the potential to reduce the time and resources needed for reaction optimization by more rapidly identifying an ideal catalyst. These approaches, however, are often non-transferable and cannot be applied across different reactions. To overcome this drawback, we introduce a general featurization strategy for bidentate ligands that is coupled with an automated feature selection pipeline and Bayesian ridge regression to perform multivariate linear regression modeling. This approach, which is applicable to any reaction, incorporates electronic, steric, and topological features (rigidity/flexibility, branching, geometry, constitution) and is well-suited for early-stage ligand optimization. Using only a limited number of points per dataset, our workflow capably predicts the enantioselectivity of four metal-catalyzed asymmetric reactions. Uncertainty estimates provided by Bayesian ridge regression permit the use of Bayesian optimization to efficiently explore pools of prospective new ligands. Using this procedure, a new library of 312 chiral bidentate ligands was screened to identify promising ligand candidates for a challenging asymmetric oxy-alkynylation reaction. | Alexandre Schoepfer; Ruben Laplaza; Matthew Wodrich; Jerome Waser; Clemence Corminboeuf | Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry; Machine Learning; Homogeneous Catalysis; Ligands (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d0ae8ddfabaf06ffdae5a9/original/reaction-agnostic-featurization-of-bidentate-ligands-for-bayesian-ridge-regression-of-enantioselectivity.pdf |
66860eab5101a2ffa85329d9 | 10.26434/chemrxiv-2024-k5mps | Allylic C‒H Alkylation of Internal and Terminal Alkenes with Alkenes by Rare-Earth Catalysts | Allylic C−H functionalization of simple alkenes presents a step-economical route to access functionalized alkenes. However, current approaches are generally focused on the transformation of α-alkenes, the conversion of internal alkenes was challenging. Herein, we present that rare-earth catalysts enable to activate the allylic C‒H bond, allowing for the atom-efficient allylic alkylation of internal or terminal alkenes with styrene derivatives as well as dimerization of internal or terminal alkenes. In the presence of cationic imidazolin-2-iminato scandium alkyl complexes, various of alkene-coupling products were afforded in moderate to good results (64 examples, 16−99% yield, 1:3.4−>19:1 E/Z ratio). In this process, both catalyst precursors and additives impact on the reactivity and stereoselectivity. Additionally, the newly developed strategy was applied to benzylic C‒H alkylation of toluene derivatives. Mechanistic studies suggested that allylic rare-earth metal species was the key intermediate. A possible catalytic cycle with the participation of Lewis base was provided to understand the reaction mechanism and E/Z selectivity. | Shunxi Dong; Shiyu Wang; Lichao Ning; Tao Mao; Yuqiao Zhou; Maoping Pu; Xiaoming Feng | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Acid Catalysis; Base Catalysis | CC BY 4.0 | CHEMRXIV | 2024-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66860eab5101a2ffa85329d9/original/allylic-c-h-alkylation-of-internal-and-terminal-alkenes-with-alkenes-by-rare-earth-catalysts.pdf |
60c7507b702a9b4ffc18bdb2 | 10.26434/chemrxiv.13011536.v1 | Simplified One-stop Protocols to Extract Collagen from Various Animal Tissues for 3D Cell Cultures | In this manuscript, we present a one-stop protocol to extract collagen from various animal tissues, and apply it to fabricate 3D cell culture scaffolds. | John A. Terrell; Chengpeng Chen | Biocompatible Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7507b702a9b4ffc18bdb2/original/simplified-one-stop-protocols-to-extract-collagen-from-various-animal-tissues-for-3d-cell-cultures.pdf |
671a92581fb27ce1247466ad | 10.26434/chemrxiv-2024-h76ms | Advanced Charge Extended Hückel (CEH) Model and a Consistent Adaptive Minimal Basis Set for the Elements Z=1-103 | The Charge Extended Hückel (CEH) model, initially introduced for adaptive atomic orbital (AO) basis set construction (J. Chem. Phys. 159, 164108 (2023)), has been significantly revised to enhance accuracy and robustness, particularly in challenging electronic situations. This revision includes an extension towards f-elements, covering actinoids with their f-electrons in the valence space. We present a novel non-iterative approximation for the electrostatic contribution to the effective Fock matrix, which substantially improves performance in polar or charged systems. Additionally, the training dataset for elements Z = 1-103 has been expanded to encompass even more chemically diverse reference molecules as well as dipole moments and shell populations in addition to atomic charges. It includes a greater variety of "mindless" molecules (MLMs) as well as more complex electronic structures through open-shell and highly charged species. The revised method achieves mean absolute errors for atomic charges q of approximately 0.02 e- for randomly selected (mostly organic) molecules and 0.09 e- for MLMs, outperforming both classical charge models and established tight-binding methods. Furthermore, the revised CEH model has been validated through density functional theory calculations with the updated adaptive q-vSZP AO basis set on common thermochemical databases. Consistent with the extension of the CEH model, q-vSZP has also been variationally optimized and tested for elements Z = 58-71 and 87-103. The original versions of both CEH and q-vSZP are now considered deprecated. | Marcel Müller; Thomas Froitzheim; Andreas Hansen; Stefan Grimme | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2024-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671a92581fb27ce1247466ad/original/advanced-charge-extended-huckel-ceh-model-and-a-consistent-adaptive-minimal-basis-set-for-the-elements-z-1-103.pdf |
6709ca9751558a15efd11534 | 10.26434/chemrxiv-2024-tk90h-v2 | Synthesis of Chiral δ-Aminoboronic Esters by Enantioselective Hydrogenation of 1,2-Azaborines | We describe herein an iridium-catalyzed highly diastereo- and enantioselective hydrogenation of 1,2-azaborines ac- cessing δ-aminoboronic esters of potential biological importance. This method represents the first enantioselective hydrogenation of boron-containing heteroarene and features a diverse substitution pattern and wide scope. The synthetic utility of our method was demonstrated by the synthesis of (–)-Phenibut and the formal synthesis of (+)-3-PPP and Fluvirucinine A1. | Jiangpeng Liu; Devon Robinson; Bo Li; Shih-Yuan Liu | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6709ca9751558a15efd11534/original/synthesis-of-chiral-aminoboronic-esters-by-enantioselective-hydrogenation-of-1-2-azaborines.pdf |
66fdcfd812ff75c3a13c616f | 10.26434/chemrxiv-2024-tn0bc | Extending Density-Corrected Density Functional Theory to Large Molecular Systems | Practical density-corrected density functional theory (DC-DFT) calculations rely on Hartree-Fock (HF) densities, which can be computationally expensive for systems with over a hundred atoms. We extend the applicability of HF-DFT using the dual-basis method, where the density matrix from a smaller basis set is used to estimate the HF solution on a larger basis set. Benchmarks on many systems, including the GMTKN55 database for main-group chemistry, and the L7 and S6L datasets for large molecular systems demonstrate the efficacy of our approach. We apply the dual-basis method to both DNA and HIV systems, and compare with the literature. A careful reparameterisation of HF-r2SCAN-DC4 eliminates the negative s8 coefficient, with no loss of performance. | Youngsam Kim; Mingyu Sim; Minhyeok Lee; Sehun Kim; Suhwan Song; Kieron Burke; Eunji Sim | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fdcfd812ff75c3a13c616f/original/extending-density-corrected-density-functional-theory-to-large-molecular-systems.pdf |
60c75123567dfe8876ec59db | 10.26434/chemrxiv.13125338.v1 | Evaluation of the Mechanical Properties and Blood Compatibility of Polycarbonate Urethane and Fluorescent Self-Colored Polycarbonate Urethane as Polymeric Biomaterials | <p>Fluorescent polymeric biomaterials have got significant attention
due to their promising applications in biomedical fields such as labeling,
monitoring, diagnostics, imaging and tracking. Polycarbonate urethane (PCU) and
1,8-naphthalimide based fluorescent dyes separately have been studied and shown
great biocompatibility and physical properties. Therefore, in this work we have
taken advantage of excellent fluorescence properties of naphthalimide dye and
biocompatibility of PCU, and covalently attached the fluorescent dye to the PCU
(self-colored PCU). Covalent attachment can increase the stability of the dye
in the biomedical applications especially when biomaterials are in contact with
blood and can inhibit the release of the dye to surrounding media. DMTA, AFM,
and contact angle measurement were used to study the mechanical and
morphological properties of the self-colored PCU and results showed that
incorporation of the dye to the PCU did not change the mechanical and
morphological properties of the PCU. In addition, MTT assay, hemolysis assay,
PT and aPTT assays as well as protein adsorption assay was used to evaluate the
blood compatibility of PCU and self-colored PCU and results indicated great bio
and blood compatibility of these materials. These great mechanical and blood compatibility
properties of the self-colored PCU as well as their excellent fluorescent
properties suggested that, these materials could be an ideal candidates to be use
in biomedical applications in which non-invasive and non-destructive
fluorescent based techniques are required. </p> | Ehsan Zamani; Hossein Yahyaei; Majid Zamani | Dyes and Chromophores; Biopolymers; Polymerization (Polymers); Polymers | CC BY NC 4.0 | CHEMRXIV | 2020-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75123567dfe8876ec59db/original/evaluation-of-the-mechanical-properties-and-blood-compatibility-of-polycarbonate-urethane-and-fluorescent-self-colored-polycarbonate-urethane-as-polymeric-biomaterials.pdf |
60c73fa2842e6570b6db1b55 | 10.26434/chemrxiv.7466591.v1 | Tuning and Mechanistic Insights of Metal Chalcogenide Molecular Catalysts for the Hydrogen-Evolution Reaction | The
production of hydrogen through water splitting using earth-abundant metal
catalysts is a promising pathway for converting solar energy into chemical
fuels. However, existing approaches for fine stoichiometric control, structural
and catalytic modification of materials by appropriate choice of earth abundant
elements are either limited or challenging. Here we explore the tuning of redox
active immobilized molecular metal-chalcoxide electrocatalysts by controlling
the chalcogen or metal stoichiometry and explore critical aspects of the
hydrogen evolution reaction (HER). Linear sweep voltammetry (LSV) shows that
stoichiometric and structural control leads to the evolution of hydrogen at low
overpotential with no catalyst degradation over 1000 cycles. Density functional
calculations reveal the effect of the electronic and structural features and
confer plausibility to the existence of a unimolecular mechanism in the HER
process based on the tested hypotheses. We anticipate these findings to be a
starting point for further exploration of molecular catalytic systems | James McAllister; Nuno Bandeira; Jessica McGlynn; Alexey Ganin; Yu-Fei Song; Carles Bo; Haralampos Miras | Electrocatalysis; Heterogeneous Catalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fa2842e6570b6db1b55/original/tuning-and-mechanistic-insights-of-metal-chalcogenide-molecular-catalysts-for-the-hydrogen-evolution-reaction.pdf |
673297f6f9980725cfe57ed4 | 10.26434/chemrxiv-2024-kqjt2 | A Multipoint Validation of Quantification in Capillary Electrophoresis Mass Spectrometry Proteomics: Isobaric Multiplexing with Tandem Mass Tags | Multiplexing quantification using isobaric barcoding has gained traction in single-cell mass spectrometry (MS), both in nano-flow liquid chromatography (nanoLC) and capillary electrophoresis (CE). In nanoLC-MS, ratio compression from isobaric interferences challenges the accuracy of quantification during tandem MS (MS2); this is remedied at the MS3 level, albeit at the expense of a reduction in proteome coverage. In single-cell capillary electrophoresis (CE) electrospray ionization (ESI) MS, electrophoresis-correlative (Eco) ion sorting practically orders ions into narrow mass-to-charge-dependent trends. Despite pioneering targeted and discovery single-cell MS proteomics, practically nothing is known about how close separation of similar m/z values (Eco-sorting) may affect the fidelity of quantification in CE-MS proteomics. This study is dedicated to bridging this gap in our basic knowledge for the sake of accurate proteome quantification, at a time when CE-MS is emerging into the public domain. Leveraging the mouse–yeast two-proteome model, as validated in nanoLC, we systematically characterize the fidelity of quantification in CE-MS. By employing the strategies of both MS2 and MS3 on the same mass spectrometer, we gain valuable insights to interferences within and between the approaches. Briefly, we found CE-MS to yield ~12-fold sensitivity enhancement than nanoLC. Considering +2 charge state, the driver of protein identifications in this study, we find ratio compression to be severe in MS2 in CE-MS (~66.5% interference free index, IFI), but statistically significantly less than in nanoLC (~63.5% IFI). Simultaneous precursor selection MS3 effectively remedied these interferences in CE-MS (~87.0% IFI), statistically indifferently than nanoLC. CE-MS provides comparable, technically actually slightly and significantly better, quantitative performance than the reference standard nanoLC for limited amounts of proteomes, such as single cells and their subcellular organelles. | Laura Rodriguez; Camille Lombard-Banek; Vi Quach; Sam Choi; M. Chiara Manzini; Peter Nemes | Physical Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673297f6f9980725cfe57ed4/original/a-multipoint-validation-of-quantification-in-capillary-electrophoresis-mass-spectrometry-proteomics-isobaric-multiplexing-with-tandem-mass-tags.pdf |
624aab565ab8df6dfc89ea0f | 10.26434/chemrxiv-2022-dtnbw | The curious case of a sterically crowded Stenhouse salt | We report a peculiar Stenhouse salt. It does not evolve into cyclopentenones upon basification, due to the steric hindrance of its bulky stable carbene patterns. This allowed for the observation and characterization of the transient open-chain neutral derivative, which was isolated as its cyclized form. The latter features an unusually long reactive C–O bond (150 pm) and a rich electrochemistry, including oxidation into an air-persistent radical cation. | Valentin Thery; Florian Molton; selim Sirach; Neven Tillet; Jacques Pecaut; Eder Tomas-Mendivil; David Martin | Organic Chemistry; Organic Compounds and Functional Groups | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624aab565ab8df6dfc89ea0f/original/the-curious-case-of-a-sterically-crowded-stenhouse-salt.pdf |
6269952a1033881573fcfc6c | 10.26434/chemrxiv-2022-75cjp | Simulation of energy-resolved mass spectrometry distributions from surface-induced dissociation | Understanding the relationship between protein structure and experimental data is crucial for utilizing experiments to solve biochemical problems and optimizing the use of sparse experimental data for structural interpretation. Tandem mass spectrometry (MS/MS) can be used with a variety of methods to collect structural data for proteins. One example is surface-induced dissociation (SID), which is used to break apart protein complexes (via a surface collision) into intact subcomplexes and can be performed at multiple laboratory frame SID collision energies. These energy-resolved tandem MS/MS experiments have shown that the profile of the breakages depends on the acceleration energy of the collision. It is possible to extract an appearance energy (AE) from energy-resolved mass spectrometry (ERMS) data, which shows the relative intensity of each type of subcomplex as a function of SID acceleration energy. We previously determined that these AE values for specific interfaces correlated with structural features related to interface strength. In this study, we further examined the structural relationships by developing a method to predict the full ERMS plot from structure, rather than extracting a single value. First, we noted that for proteins with multiple interface types, we could reproduce the correct shapes of breakdown curves, further confirming previous structural hypotheses. Next, we demonstrated that interface size and energy density (measured using Rosetta) correlated with data derived from the ERMS plot (R^2 = 0.71). Furthermore, based on this trend, we used native crystal structures to predict ERMS. The majority of predictions resulted in good agreement, and the average root-mean-square error (RMSE) was 0.20 for the 20 complexes in our dataset. We also show that if additional information on cleavage as a function of collision energy could be obtained, the accuracy of predictions improved further. Finally, we demonstrated that ERMS prediction results were better for the native than for inaccurate models in 17/20 cases. An application to run this simulation has been developed in Rosetta, which is freely available for use. | Justin Seffernick; SM Bargeen Turzo; Sophie Harvey; Yongseok Kim; Árpád Somogyi; Shir Marciano; Vicki Wysocki; Steffen Lindert | Theoretical and Computational Chemistry; Analytical Chemistry; Biochemical Analysis; Mass Spectrometry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6269952a1033881573fcfc6c/original/simulation-of-energy-resolved-mass-spectrometry-distributions-from-surface-induced-dissociation.pdf |
6388a5e604bc667db3033137 | 10.26434/chemrxiv-2021-39n35-v3 | Automated handling of complex chemical structures in Z-matrix coordinates - the chemcoord library
| In this work, we present a fully automated method
for the construction of chemically meaningful sets of non-redundant
internal coordinates (also commonly denoted as Z-matrices)
from the cartesian coordinates of a molecular system.
Particular focus is placed on avoiding ill-definitions
of angles and dihedrals due to linear arrangements of atoms,
to consistently guarantee a well-defined transformation
to cartesian coordinates, even after structural changes.
The representations thus obtained are particularly well suited for
pathway construction in double-ended methods for transition state search and
optimisations with non-linear constraints.
Analytical gradients for the transformation between
the coordinate systems were derived for the first time,
which allows analytical geometry optimizations purely in Z-matrix coordinates.
The geometry optimisation was coupled with
a Symbolic Algebra package to support arbitrary non-linear constraints
in Z-matrix coordinates, while retaining analytical energy gradient conversion.
Sample applications are provided for a number of common chemical
reactions and illustrative examples where these new algorithms
can be used to automatically produce chemically reasonable structure interpolations,
or to perform non-linearly constrained optimisations of molecules.
| Oskar Weser; Björn Hein-Janke; Ricardo Mata | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6388a5e604bc667db3033137/original/automated-handling-of-complex-chemical-structures-in-z-matrix-coordinates-the-chemcoord-library.pdf |
66fab8f7cec5d6c142af71db | 10.26434/chemrxiv-2024-v4c91 | The influence of commercial Ionomers and Membranes on a PGM-free catalyst in the Alkaline Oxygen Reduction | Hitherto, research into alkaline exchange membrane fuel cells (AEMFCs) lacks a commercial benchmark anionomer and membrane, analogue to Nafion™ in proton-exchange membrane fuel cells (PEMFCs). Three commercial alkaline exchange ionomers (AEI) are scrutinized for that role in combination with a commercial platinum-group-metal free (PGM-free) Fe-N-C (Pajarito Powder) catalyst for the cathode. Initial rotating disc electrode (RDE) benchmarking of the Fe-N-C catalyst’s oxygen reduction reaction (ORR) activity using Nafion™ in alkaline electrolyte seems to neglect the restricted oxygen diffusion in the AEIs, and is recommended to be complemented by measurements with the same AEI as used in the AEMFC testing. Evaluation of the catalyst layer in a Gas-Diffusion-Electrode (GDE) setup offers a way to assess the performance in realistic operating conditions, without the additional complications of device-level water management. Blending of a porous Fe-N-C catalyst with different types of AEI yields catalyst layers with different pore size distributions. The catalyst layer with Piperion® retains the highest proportion of the original BET surface area of the Fe-N-C catalyst. The water adsorption capacity is also influenced by the AEI, with Fumion FAA-3® and Piperion® having equal high capabilities surpassing Sustainion®. Finally, the choice of the membrane influences the ORR performance as well, particularly the low hydroxide conductivity of Fumion FAA-3® at the room temperature experiments mitigates the ORR performance irrespective of the AEI in the catalyst layer. The best overall performance at high current densities is shown by Piperion® AEI matched with Sustainion® X37-50 AEM. | Simon Kellner; Ziyang Liu; Francesco D'Acierno; Angus Pedersen; Jesus Barrio; Sandrine Heutz; Ifan Stephens; Silvia Favero; Maria-Magdalena Titirici | Materials Science; Catalysis; Energy; Polyelectrolytes - Materials; Energy Storage; Fuel Cells | CC BY NC 4.0 | CHEMRXIV | 2024-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fab8f7cec5d6c142af71db/original/the-influence-of-commercial-ionomers-and-membranes-on-a-pgm-free-catalyst-in-the-alkaline-oxygen-reduction.pdf |
60c758cebdbb8934d2a3ae1c | 10.26434/chemrxiv.14609670.v1 | Learning Structure Activity Relationship (SAR) of the Wittig Reaction from Genetically-Encoded Substrates | The Wittig reaction can be used for late stage functionalization of proteins and peptides to ligate glycans, pharmacophores, and many other functionalities. In this manuscript, we modified 160,000 N-terminal glyoxaldehyde peptides displayed on phage with the Wittig reaction by biotin labeled ylide under conditions that functionalize only 1% of the library population. Deep-sequencing of the biotinylated and input populations estimated the rate of conversion for each sequence. This “deep conversion” (DC) from deep sequencing correlates with rate constants measured by HPLC. Peptide sequences with fast and slow reactivity highlighted a critical role of primary backbone amides (N-H) in accelerating the rate of the aqueous Wittig reaction. Experimental measurement of reaction rates and density functional theory (DFT) computation of the transition state geometries corroborated this relationship. We also collected deep-sequencing data to build structure activity relationship (SAR) models that can predict DC value of the Wittig reaction. By using this data, we trained two classifier models based on Gradient Boosted trees. These classifiers achieved area under the ROC (Receiver Operating Characteristic) Curve (ROC AUC) of 81.2 ± 0.4 and 73.7 ± 0.8 (90–92% accuracy) in determining whether a sequence belonged to the top 5% or the bottom 5% in terms of its reactivity. We have deployed our learned models as a publicly available web app: <a href="http://44.226.164.95/">http://44.226.164.95/</a> We anticipate that phage-displayed peptides and related mRNA or DNA-displayed substrates can be employed in a similar fashion to study the substrate scope and mechanisms of many other chemical reactions. | Kejia Yan; Vivian Triana; Sunil Vasu Kalmady; Kwami Aku-Dominguez; Sharyar Memon; Alex Brown; Russell Greiner; Ratmir Derda | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758cebdbb8934d2a3ae1c/original/learning-structure-activity-relationship-sar-of-the-wittig-reaction-from-genetically-encoded-substrates.pdf |
60c742d2ee301c20eac78ef5 | 10.26434/chemrxiv.8786129.v1 | Multiscale Morphological Visualization of a Semi-crystalline Polymer by a Polymorphic AIE Marker | <p>Direct spatial mapping of polymer morphologies remains challenging owing to poor imaging contrast across different
microstructures. Now this conundrum is addressed by a polymorphic molecule with
aggregation-induced emission (AIE), capable of selectively lighting up
amorphous and crystalline phases with distinct color. The polymorphic behaviors
of the AIE molecule embedded within polymer network is dependent on the size of
nano-confinement: a thermodynamically stable polymorph of the AIE molecule with
green emission is stabilized in amorphous phase, while a metastable polymorph
with yellow emission is confined in crystalline phase. The information on
polymer crystalline and amorphous phases is transformed into distinct
fluorescence colors, allowing a single AIE molecule as a fluorescent marker for
multiscale visualization of polymer morphologies in terms of amorphous and
crystalline phases distribution, quantitative polymer crystallinity
measurement, and spatial morphological arrangement. The proposed strategy
provides a correlation between microscopic morphologies and macroscopic optical
signals, opens an avenue of fluorescence imaging in materials science.</p> | Michidmaa Khorloo; yanhua Cheng; Haoke Zhang; Ming Chen; Herman H.-Y. Sung; Ian Duncan Williams; Jacky W. Y. Lam; Ben Zhong Tang | Polymer morphology; Imaging | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742d2ee301c20eac78ef5/original/multiscale-morphological-visualization-of-a-semi-crystalline-polymer-by-a-polymorphic-aie-marker.pdf |
62f6370ee78f70510038c91d | 10.26434/chemrxiv-2022-250v6-v2 | Suspended phospholipid bilayers:
a new biological membrane mimetic | Hypothesis: The attractive interaction between a cationic surfactant monolayer at the air-water interface and
vesicles, incorporating anionic lipids, is sufficient to drive the adsorption and deformation of the vesicles. Osmotic rupture of the vesicles produces a continuous lipid bilayer beneath the monolayer.
Experimental: Specular neutron reflectivity has been measured from the surface of a purpose-built laminar
flow trough, which allows for rapid adsorption of vesicles, the changes in salt concentration required for osmotic rupture of the adsorbed vesicles into a bilayer, and for neutron contrast variation of the sub-phase without disturbing the monolayer.
Findings: The neutron reflectivity profiles measured after vesicle addition are consistent with the adsorption
and flattening of the vesicles beneath the monolayer. An increase in the buffer salt concentration results in further
flattening and fusion of the adsorbed vesicles, which are ruptured by a subsequent decrease in the salt concentration. This process results in a continuous, high coverage, bilayer suspended 11A beneath the monolayer. As the bilayer is not constrained by a solid substrate, this
new mimetic is well-suited to studying the structure of lipid bilayers that include transmembrane proteins. | Sophie Ayscough; Maximilian Skoda; Luke Clifton; Simon Titmuss | Physical Chemistry; Biological and Medicinal Chemistry; Nanoscience; Biophysics; Interfaces; Self-Assembly | CC BY NC 4.0 | CHEMRXIV | 2022-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f6370ee78f70510038c91d/original/suspended-phospholipid-bilayers-a-new-biological-membrane-mimetic.pdf |
60c7548f4c89196adcad455f | 10.26434/chemrxiv.13681765.v1 | A Guide to Water Free Lithium Bis(oxalate) Borate (LiBOB) | The use of LiBOB is limited due to slight instability
issues under ambient conditions that might require extra purification steps and
might result in poorer performances in real systems. Here, we address some of
these issues and report the high purity water free LiBOB synthesized with fewer
processing steps employing lithium carbonate, oxalic acid, and boric acid as
low-cost starting materials, and via ceramic processing methods under
protective atmosphere. The physical and chemical characterizations of both
anhydrous and monohydrate phases are performed with X-ray powder diffraction
(XRPD), Fourier-transform infra-red spectroscopy (FTIR), Raman spectroscopy and
scanning electron microscopy (SEM) analyses to determine the degree of the
purity and the formation of impurities like LiBOB.H<sub>2</sub>O, HBO<sub>2 </sub>and
Li<sub>2</sub>C<sub>2</sub>O<sub>4</sub> as a result of the aging
investigations performed. Differential thermal analysis (DTA) is applied to
determine the optimum synthesis conditions for anhydrous LiBOB and to analyze
the water loss and the decomposition of LiBOB.H<sub>2</sub>O. Aging experiments
with the water free LiBOB are carried out to evaluate the effect of humidity in
the phase changes and resulting impurities under various conditions. The
detrimental effect of even slightest humidity conditions is shown, and
protective measures during and after the synthesis of LiBOB are discussed. | Ceren Zor; Yaprak Subaşı; Durata Haciu; Mehmet Somer; Semih Afyon | Ceramics; Solid State Chemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7548f4c89196adcad455f/original/a-guide-to-water-free-lithium-bis-oxalate-borate-li-bob.pdf |
60c745b5337d6ccb0be27016 | 10.26434/chemrxiv.8019527.v3 | A GPU-Accelerated Machine Learning Framework for Molecular Simulation: HOOMD-blue with TensorFlow | <div>
<div>
<div>
<p>As interest grows in applying machine learning force-fields and methods to molecular simulation, there is a need for
state-of-the-art inference methods to use trained models within efficient molecular simulation engines. We have designed and implemented software that enables integration of a scalable GPU-accelerated molecular mechanics engine,
HOOMD-blue, with the machine learning (ML) TensorFlow package. TensorFlow is a GPU-accelerated, scalable,
graph-based tensor computation model building package that has been the implementation of many recent innovations
in deep learning and other ML tasks. TensorFlow models are constructed in Python and can be visualized or debugged
using the rich set of tools implemented in the TensorFlow package. In this article, we present four major examples of
tasks this software can accomplish which would normally require multiple different tools: (1) we train a neural network
to reproduce a force field of a Lennard-Jones simulation; (2) we perform online force matching of methanol; (3) we
compute the maximum entropy bias of a Lennard-Jones collective variable; (4) we calculate the scattering profile of
an ongoing TIP4P water molecular dynamics simulation. This work should accelerate both the design of new neural network based models in computational chemistry research and reproducible model specification by leveraging a
widely-used ML package.</p></div></div></div> | Rainier Barrett; Maghesree Chakraborty; Dilnoza Amirkulova; Heta Gandhi; Andrew White | Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745b5337d6ccb0be27016/original/a-gpu-accelerated-machine-learning-framework-for-molecular-simulation-hoomd-blue-with-tensor-flow.pdf |
6633a40c21291e5d1d4145c0 | 10.26434/chemrxiv-2024-r63tb | Structure-guided discovery of orexin receptor-binding PET ligands | Molecular imaging using positron emission tomography (PET) can serve as a promising tool for visualizing biological targets in the brain. Insights into the expression pattern and the in vivo imaging of the G protein-coupled orexin receptors OX1R and OX2R will further our understanding of the orexin system and its role in various physiological and pathophysiological processes. Guided by crystal structures of our lead compound JH112 and the approved hypnotic drug suvorexant bound to OX1R and OX2R, respectively, we herein describe the design and synthesis of two novel radioligands, [18F]KD23 and [18F]KD10. Key to the success of our structural modifications was a bioisosteric replacement of the triazole moiety with a fluorophenyl group. The 19F-substituted analog KD23 showed high affinity for the OX1R and selectivity over OX2R, while the high affinity ligand KD10 displayed similar Ki values for both subtypes. Radiolabeling starting from the respective pinacol ester precursors resulted in excellent radiochemical yields of 93% and 88% for [18F]KD23 and [18F]KD10, respectively, within 20 minutes. The new compounds will be useful in PET studies aimed at subtype-selective imaging of orexin receptors in brain tissue. | Katharina Distler; Simone Maschauer; Eduard Neu; Harald Hübner; Jürgen Einsiedel; Olaf Prante; Peter Gmeiner | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6633a40c21291e5d1d4145c0/original/structure-guided-discovery-of-orexin-receptor-binding-pet-ligands.pdf |
6436f59808c86922ffdbd59a | 10.26434/chemrxiv-2023-hs7ql | Correlation of binding site properties with chemistries used for generation of ultra-large virtual libraries. | Although the size of virtual libraries of synthesizable compounds is growing rapidly, we are still enumerating only tiny fractions of the drug-like chemical universe. At the same time, our ability to mine these newly generated libraries also lags their growth. That is why fragment-based approaches that utilize on-demand virtual combinatorial libraries are gaining popularity. These à la carte libraries utilize synthetic blocks that have been shown to be effective binders in parts of target protein pockets. There is, however, no data on the potential impact of the chemistries used for making on-demand libraries on the hit rates during virtual screening. There are also no rules to guide in selection of these synthetic methods for libraries production. We have used the SAVI (Synthetically Accessible Virtual Inventory) library, constructed using 53 reliable reaction types (transforms), to test for correlations between these chemistries and docking hit rates for 39 well- characterized protein pockets. The data shows that the hit rate depends on the chemistry used and that chemistry selection can be optimized based on pocket properties. | Robert Song; Marc Nicklaus; Nadya Tarasova | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6436f59808c86922ffdbd59a/original/correlation-of-binding-site-properties-with-chemistries-used-for-generation-of-ultra-large-virtual-libraries.pdf |
656ee0ca29a13c4d47afa2a0 | 10.26434/chemrxiv-2023-kslds | From Organic Fragments to Photoswitchable Catalysts: The OFF-ON Structural Repository for Transferable Kernel-based Potentials | Structurally and conformationally diverse databases are needed to train accurate neural networks or kernel-based potentials capable of exploring the complex free en- ergy landscape of flexible functional organic molecules. Curating such databases for species beyond “simple” drug-like compounds or molecules comprised of well-defined building blocks (e.g., peptides) is challenging, as it requires thorough chemical space mapping and evaluation of both chemical and conformational diversity. Here, we intro- duce the OFF–ON (Organic Fragments From Organocatalysts that are Non-modular) database, a repository of 7,869 equilibrium and 67,457 non–equilibrium geometries of organic compounds and dimers aimed at describing conformationally flexible func- tional organic molecules, with an emphasis on photoswitchable organocatalysts. The relevance of this database is then demonstrated by training a Local Kernel Regres- sion model on a low-cost semiempirical baseline and comparing it with a PBE0-D3 reference for several known catalysts, notably the free energy surfaces of exemplary photoswitchable organocatalysts. Our results demonstrate that the OFF–ON dataset offers reliable predictions for simulating the conformational behavior of virtually any (photoswitchable) organocatalyst or organic compound comprised of H, C, N, O, F, and S atoms, thereby opening a computationally feasible route to explore complex free energy surfaces in order to rationalize and predict catalytic behavior. | Frédéric Célerse; Matthew Wodrich; Sergi Vela; Simone Gallarati; Raimon Fabregat; Veronika Juraskova; Clémence Corminboeuf | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Machine Learning; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656ee0ca29a13c4d47afa2a0/original/from-organic-fragments-to-photoswitchable-catalysts-the-off-on-structural-repository-for-transferable-kernel-based-potentials.pdf |
6480158fe64f843f4171df60 | 10.26434/chemrxiv-2023-b3hf6 | Elucidating Functional Group Presence by Analyzing IR Spectra with 1-Dimensional Convolutional Neural Networks | This paper presents a novel solution to the problem of IR spectrum interpretation by applying a 1-dimensional convolutional neural network to classify molecular spectra as either containing a functional group or not containing a functional group. 16 mod- els were trained using a single general model architecture, and 11 were highly effective with accuracy, precision, recall, F1, and AUC scores, all greater than 90%. Phenome- nal classification performance was achieved on aldehydes and ketones, where previous attempts have struggled. Furthermore, a tool was developed to generate saliency maps for each model, allowing for the analysis and study of how the model interprets the IR spectra to make classifications. Our results have applications in fields such as the pharmaceutical industry and drug development, as well as the rapid assay screening of environmental pollutants while being generalizable to be a competitive option for any high-volume IR spectroscopy screening process. | Ryan Tang | Theoretical and Computational Chemistry; Analytical Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6480158fe64f843f4171df60/original/elucidating-functional-group-presence-by-analyzing-ir-spectra-with-1-dimensional-convolutional-neural-networks.pdf |
630dbd06eadd9a33f186cf29 | 10.26434/chemrxiv-2022-qvbdk | Tailored Charge Transfer Kinetics in Organic Radical Batteries – A Joint Synthetic-Theoretical Approach | The development of sustainable energy storage devices is crucial for the transformation of our energy management. In this scope, organic batteries attracted considerable attention. To overcome the shortcomings of typically applied materials from the classes of redox-active conjugated polymers, i.e., unstable cell voltages, and soft matter embedded stable organic radicals, i.e., low conductivity, we introduce a novel design concept integrating such stable radicals within a conductive polymer backbone. In our present theory-driven design approach redox-active TEMPOs were incorporated in thiophene-based polymer model systems, while structure-property relationships governing the thermodynamic properties as well as the charge transfer kinetics underlying the charging and discharging processes were investigated in a systematical approach. Thereby, the impact of the substitution pattern, the length as well as the nature of the chemical linker and the ratio of TEMPO and thiophene units was studied using state-of-the-art quantum chemical and quantum dynamical simulations for a set of six molecular model systems. Finally, two promising candidates were synthesized and electrochemically characterized – paving the way to applications in the frame of novel organic radical batteries. | Clara Zens; Christian Friebe; Ulrich S. Schubert; Martin Richter; Stephan Kupfer | Theoretical and Computational Chemistry; Polymer Science; Energy; Conducting polymers; Computational Chemistry and Modeling; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630dbd06eadd9a33f186cf29/original/tailored-charge-transfer-kinetics-in-organic-radical-batteries-a-joint-synthetic-theoretical-approach.pdf |
60c7453c567dfe7c25ec441f | 10.26434/chemrxiv.9985496.v1 | Photocontrolled Radical Polymerization from Hydridic C–H Bonds | <p>Given the ubiquity of C–H bonds in biomolecules and polymer backbones, the development of a photocontrolled polymerization from a C–H bond would represent a powerful strategy for selective polymer conjugation precluding several synthetic steps to introduce complex functionality. We have developed a hydrogen-atom abstraction strategy that allows for a controlled polymerization from a C–H bond using a benzophenone photocatalyst, a trithiocarbonate-derived disulfide, and visible light. We perform the polymerization from a variety of ethers, alkanes, unactivated C–H bonds, and alcohols as well as showcase the applicability of the method to several monomer classes. Our method lends itself to photocontrol which has important implications for building advanced macromolecular architectures. Finally, we demonstrate that we can graft polymer chains controllably from poly(ethylene glycol) showcasing the potential application of this method for controlled grafting from C–H bonds of commodity polymers.</p> | Erin Stache; Veronika Kottisch; Brett Fors | Organic Polymers; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7453c567dfe7c25ec441f/original/photocontrolled-radical-polymerization-from-hydridic-c-h-bonds.pdf |
66c38e10f3f4b052905d4e54 | 10.26434/chemrxiv-2024-hrqq9-v2 | Combined physics- and machine-learning-based method to identify druggable binding sites using SILCS-Hotspots | Identifying druggable binding sites on proteins is an important and challenging problem, particularly for cryptic, allosteric binding sites that may not be obvious from X-ray, cryo-EM, or predicted structures. The Site-Identification by Ligand Competitive Saturation (SILCS) method accounts for the flexibility of the target protein using all-atom molecular simulations that include various small molecule solutes in aqueous solution. During the simulations the combination of protein flexibility and comprehensive sampling of the water and solute spatial distributions can identify buried binding pockets absent in experimentally-determined structures. Previously, we reported a method for leveraging the information in the SILCS sampling to identify binding sites (termed Hotspots) of small mono- or bi-cyclic compounds, a subset of which coincide with known binding sites of drug-like molecules. Here we build in that physics-based approach and present a ML model for ranking the Hotspots according to the likelihood they can accommodate drug-like molecules (e.g. molecular weight > 200 daltons). In the independent validation set, which includes various enzymes and receptors, our model recalls 67% and 89% of experimentally-validated ligand binding sites in the top 10 and 20 ranked Hotspots, respectively. Furthermore, we show that the model’s output Decision Function is a useful metric to predict binding sites and their potential druggability in new targets. Given the utility the SILCS method for ligand discovery and optimization the tools presented represent an important advancement in the identification of orthosteric and allosteric binding sites and the discovery of drug-like molecules targeting those sites. | Erik Nordquist; Mingtian Zhao; Anmol Kumar; Alex MacKerell | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c38e10f3f4b052905d4e54/original/combined-physics-and-machine-learning-based-method-to-identify-druggable-binding-sites-using-silcs-hotspots.pdf |
672ee7a87be152b1d080cf26 | 10.26434/chemrxiv-2024-1rfzp | The use of Ni(cod)(dq) (COD: 1,5-cyclooctadiene; DQ: duroqui-none) for the dehalogenative coupling polycondensation to π-conjugated polyarylenes | Ni(cod)(dq) (COD: 1,5-cyclooctadiene; DQ: duroquinone) with an appropriate bipyridine ligand is available for the dehalogenative polycondensation of dihaloarenes to afford -conjugated polymers. The reaction of 2,7-dibromo-9,9-di(n-hexylfluorene) with nickel complex composed of Ni(cod)(dq) and 4,4'-di-tert-butyl-2,2'-bipyridine in DMF/toluene (1:4) proceeded at 120 °C for 72 h. Polyfluorene was obtained in 81% yield with Mn = 13000 (Mw/Mn = 2.0). Ni(cod)(dq) was found to be stored under an ambient atmosphere at room temperature and the use of which after several month vs. a freshly opened nickel complex resulted to afford the corresponding polymer in a comparable yield and molecular weight. Other dihal-oarenes such as fluorene with different alkyl chain structures, 1,4- and 1,3-dihalobenzenes, 5,5'-dibromo-2,2'-bithiophene, and 2,6-dibromo-cyclopentadithiophen also underwent the dehalogenative polymerization to afford the corresponding conjugated polymers in excellent yields with an appropriate degree of polymerization. | Naoki Noda; Maho Umeda; Kentaro Okano; Masaki Horie; Atsunori Mori | Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672ee7a87be152b1d080cf26/original/the-use-of-ni-cod-dq-cod-1-5-cyclooctadiene-dq-duroqui-none-for-the-dehalogenative-coupling-polycondensation-to-conjugated-polyarylenes.pdf |
60c74f7ff96a00c5c0287c73 | 10.26434/chemrxiv.12911156.v1 | Dynamic Real-Time Magnetic Resonance at Very Low Magnetic Fields | The phenomenon of nuclear magnetic resonance (NMR) is widely applied in biomedical and
biological science to study structures and dynamics of proteins and their reactions. Despite
its impact, NMR is an inherently insensitive phenomenon and has driven the field to construct
spectrometers with increasingly higher magnetic fields leading to more detection sensitivity.
Here, we are demonstrating that enzymatic reactions can be followed in real-time at millitesla
fields, 1000-fold lower than state-of-the-art spectrometers. This requires signal-enhancing
samples via hyperpolarization. Within seconds, we have enhanced the signals of 2-
13Cpyruvate, an important metabolite to probe cancer metabolism, in 22 mM concentrations (up
to 10.1%±0.1% polarization) and show that such a large signal allows for the real-time
detection of enzymatic conversion of pyruvate to lactate. This development paves the
pathways for biological studies in portable and affordable NMR systems with a potential for
medical diagnostics. <br /> | Sergey Korchak; Anil P. Jagtap; Stefan Gloeggler | Chemical Kinetics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f7ff96a00c5c0287c73/original/dynamic-real-time-magnetic-resonance-at-very-low-magnetic-fields.pdf |
60c73cc90f50db82113953ba | 10.26434/chemrxiv.14740563.v1 | Linking Chemical Reaction Intermediates of the Click Reaction to Their Molecular Diffusivity | Bipolar reactions have been provoked by reports of boosted diffusion during chemical and enzymatic reactions. To some, it is intuitively reasonable that relaxation to truly Brownian motion after passing an activation barrier can be slow, but to others the notion is so intuitively unphysical that they suspect the supporting experiments to be artifact. Here we study a chemical reaction according to whose mechanism some intermediate species should speed up while others slow down in predictable ways, if the boosted diffusion interpretation holds. Experimental artifacts would do not know organic chemistry mechanism, however. Accordingly, we scrutinize the absolute diffusion coefficient (D) during intermediate stages of the CuAAC reaction (coppercatalyzed azide-alkyne cycloaddition click reaction), using proton pulsed field-gradient nuclear magnetic resonance (PFG-NMR) to discriminate between the diffusion of various reaction intermediates. For the azide reactant, its D increases during reaction, peaks at the same time as peak reaction rate, then returns to its initial value. For the alkyne reagent, its D decreases consistent with presence of the intermediate large complexes formed from copper catalyst and its ligand, except for the 2Cu-alk complex whose more rapid D may signify that this species is the real reactive complex. For the product of this reaction, its D increases slowly as it detaches from the triazolide catalyst complex. These examples of enhanced diffusion for some molecular species and depressed diffusion for others causes us to conclude that diffusion coefficients during these elementary reactions are influenced by two components: hydrodynamic radius increase from complex formation, which slows diffusion, and energy release rate during the chemical reaction, which speeds it up. We discuss possible mechanisms and highlight that too little is yet understood about slow solvent reorganization during chemical reactions.<br /> | Tian Huang; Bo Li; Huan Wang; Steve Granick | Chemical Kinetics; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc90f50db82113953ba/original/linking-chemical-reaction-intermediates-of-the-click-reaction-to-their-molecular-diffusivity.pdf |
66bb009a20ac769e5f71e8f5 | 10.26434/chemrxiv-2024-tk46x | On the Nature of the Out-Of-Plane Distortions in Subporphyrins | The field of subporphyrins has garnered great interest in recent years owing to its unique structure and associated properties. They exhibit spectroscopic features similar to porphyrins and find applications in various optoelectronic devices, photodynamic therapy etc. Most of the synthesized subporphyrins have boron coordination with an axial ligand and exhibits a bowl-shaped geometry. The first isolation of a stable free-base subporphyrin is achieved recently with mesityl groups at two of the meso positions and anthracene at the other. X-ray studies reveal a markedly non-planar structure different from the bowl shape and is attributed to the steric hindrance of the inner N-H bonds. Herein, we report a systematic quantum chemical investigation assisted by symmetry principles on molecular models to characterize the out-of-plane (OOP) distortions observed so far in subporphyrins and unveil the electronic reasons. Correlation of the frontier molecular orbital (FMO) landscape between the D4h porphyrin and D3h subporphyrin gives insight into their electronic structure relative to one another and the nature of OOP distortions. Further the effect of a π-donor cum σ-acceptor substituent at the meso/beta positions of the subporphyrin ring as well as the impact of boron incorporation in the central cavity on the OOP distortions are also discussed. | J Haripriya; A Anjana; J Harikrishnan; Pattath D. Pancharatna | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66bb009a20ac769e5f71e8f5/original/on-the-nature-of-the-out-of-plane-distortions-in-subporphyrins.pdf |
65798da77acf130c32202f7e | 10.26434/chemrxiv-2023-5g600 | Aurones: Unexplored, Highly Efficient Visible-Light Photoswitches for Aqueous Medium | The development of synthetically accessible photoswitches showing an efficient performance in aqueous medium has recently become an urgent task due to the rapid development of photopharmacology and novel biomedical applications. In response to this challenge, in this work, aurone derivatives are introduced for the first time as highly efficient visible-light photoswitches for aqueous medium. In general, aurones exhibit superior performance in water, including significantly higher quantum yields, compared with other indigoid photoswitches (hemithioindigo and hemiindigo). Especially remarkable are the half-lifes of the photoinduced E-isomers of aurones in water, reaching up to 7 years. Further modification of the aurone scaffold with substituents that increase water solubility does not affect most of the photoswitching characteristics and even improves some them. The highly advantageous property profile of the aurone photoswitches in water make them a perfect novel platform for the design of light-controllable molecules for bioapplications. | Daria V. Berdnikova | Organic Chemistry; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65798da77acf130c32202f7e/original/aurones-unexplored-highly-efficient-visible-light-photoswitches-for-aqueous-medium.pdf |
628ac9fed555506367a3d3f7 | 10.26434/chemrxiv-2022-bctjk-v2 | Tuning the Band Gap in the Halide Perovskite CsPbBr3 Through Sr Substitution | The ability to continuously tune the band gap of a semiconductor allows its optical properties to be precisely tailored for specific applications. We demonstrate that the band gap of the halide perovskite CsPbBr3 can be continuously widened through homovalent substitution of Sr2+ for Pb2+ using solid-state synthesis, creating a material with the formula CsPb1-xSrxBr3 (0 ≤ x ≤ 1). Sr2+ and Pb2+ form a solid solution in CsPb1-xSrxBr3. Pure CsPbBr3 has a band gap of 2.29(2) eV, which increases to 2.64(3) eV for CsPb0.25Sr0.75Br3. The increase in band gap is clearly visible in the color change of the materials and is also confirmed by a shift in the photoluminescence. Density-functional theory calculations support the hypothesis that Sr incorporation widens the band gap without introducing mid-gap defect states. These results demonstrate that homovalent B-site alloying can be a viable method to tune the band gap of simple halide perovskites. | Daniel Straus; Robert Cava | Inorganic Chemistry; Solid State Chemistry; Spectroscopy (Inorg.); Theory - Inorganic; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628ac9fed555506367a3d3f7/original/tuning-the-band-gap-in-the-halide-perovskite-cs-pb-br3-through-sr-substitution.pdf |
629846114f43d613992cba4f | 10.26434/chemrxiv-2022-3z6s7-v2 | Nanomechanics and morphology of simulated respiratory particles | The impact of respiratory particle composition on the equilibrium morphology and phase are not well understood. Furthermore, the effects of these different phases and morphologies on the viability of viruses embedded within these particles are equally unknown. Physiologically relevant respiratory fluid analogues were constructed, and their hygroscopic behavior were measured using an ensemble technique. A relationship between hygroscopicity and protein concentration was determined, providing additional validation to the high protein content of respiratory aerosol measured in prior works (>90%). It was found that the salt component of the respiratory particles could crystallize as a single crystal, multiple crystals, or would not crystallize at all. It was found that dried protein particles at indoor-relevant climatic conditions could exist separately in a glassy (~77% of particles) or viscoelastic state (~23% of particles). The phase state and morphology of respiratory particles may influence the viability of embedded pathogens. We recommend that pathogen research aiming to mimic the native composition of respiratory fluid should use a protein concentration of at least 90% by solute volume to improve the representativity of the pathogen’s microenvironment. | Robert Groth; Sadegh Niazi; Graham Johnson; Zoran Ristovski | Physical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629846114f43d613992cba4f/original/nanomechanics-and-morphology-of-simulated-respiratory-particles.pdf |
615575d2aade363f2cc75eda | 10.26434/chemrxiv-2021-9kgn9 | Direct C-H-Sulfonylation of 6-Membered Nitrogen-Heteroaromatics | Heterocyclic sulfones and sulfonamides represent important structural motives in medicinal chemistry and drug development. Therefore, efficient and reliable methods for their construction from simple building blocks are in high demand. Herein we report a novel approach for the direct C-H-sulfonylation of N heteroaromatics via N-activation with triflic anhydride (Tf2O), base-mediated addition of a sulfinate salt and subsequent rearomatization through trifluoromethanesulfinate elimination. This operationally simple one-pot protocol enables direct access to various sulfonylated 6-ring N-heterocycles. It is applicable to the late-stage functionalization of complex, drug-like molecules. The direct incorporation of sulfur dioxide with organometallic reagents as well as the utilization of a rongalite-based sulfonylation reagent provide opportunities for a highly modular synthesis of N-heterocyclic sulfones and sulfonamides from three different building blocks. | Marius Friedrich; Lisa Schulz; Kamil Hofman; Rene Zangl; Nina Morgner; Saad Shaaban; Georg Manolikakes | Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615575d2aade363f2cc75eda/original/direct-c-h-sulfonylation-of-6-membered-nitrogen-heteroaromatics.pdf |
61125c2645805dbdfa849400 | 10.26434/chemrxiv-2021-vcbs9 | Hydroboration of terminal alkenes and trans-1,2-diboration of terminal alkynes catalyzed by a Mn(I) alkyl complex | A Mn(I)-catalyzed hydroboration of terminal alkenes and the 1,2-diboration of terminal alkynes with pinacolborane (HBPin) is described. In the case of alkenes anti-Markovnikov hydroboration takes place, while in the case of alkynes the reaction proceeds with excellent trans-1,2-selectivity. The most active pre-catalyst is the bench-stable alkyl bisphosphine Mn(I) complex fac-[Mn(dippe)(CO)3(CH2CH2CH3)]. The catalytic process is initiated by migratory insertion of a CO ligand into the Mn-alkyl bond to yield an acyl intermediate which undergoes B-H bond cleavage of HBPin (in the case of alkenes) and rapid C-H bond cleavage (in the case of alkynes) forming the active Mn(I) boryl and acetylide catalysts [Mn(dippe)(CO)2(BPin)] and [Mn(dippe)(CO)2(CCR)], respectively, together with liberated butanal. The diboration is accompanied by dihydrogen liberation. A broad variety of aromatic and aliphatic alkenes and alkynes was efficiently and selectively borylated. Mechanistic insights are provided based on experimental data and DFT calculations revealing that an acceptorless reaction pathway involving dihydrogen release is operating. | Stefan Weber; Daniel Zobernig; Berthold Stöger; Luis Veiros; Karl Kirchner | Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61125c2645805dbdfa849400/original/hydroboration-of-terminal-alkenes-and-trans-1-2-diboration-of-terminal-alkynes-catalyzed-by-a-mn-i-alkyl-complex.pdf |
62fe166a8bffee5a75901504 | 10.26434/chemrxiv-2022-bgcqd | High-Pressure promoted Nazarov-like electrocyclization enables access to trans-4,5-Diamino-Cyclopent-2-enones bearing Electron-Poor Anilines | Unlike secondary alkyl amines and electron-rich anilines, secondary electron-poor anilines are challenging amine sources to explore the chemical space of Lewis acid-catalyzed condensation-based transformations with furfural. In this work is reported the efficient synthesis of trans-4,5--diamino cyclopentenones (DCP) using a high-pressure promoted Nazarov-like electrocyclization of Stenhouse salts arising from the Sc(III)-catalyzed condensation of furfural with secondary electron-poor anilines. The reaction enables access to otherwise difficultly accessible DCP and compatibility with a large scope of alkyl and aryl secondary amines. A 2 to 18-fold increase in yields for electron-poor anilines was highlighted by the use of this approach in the synthesis of a pharmacologically active compound. | Carlos Alberto Mateus Afonso; Lídia Cavaca; João Ravasco; Rafael Gomes | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fe166a8bffee5a75901504/original/high-pressure-promoted-nazarov-like-electrocyclization-enables-access-to-trans-4-5-diamino-cyclopent-2-enones-bearing-electron-poor-anilines.pdf |
664215fb21291e5d1d238653 | 10.26434/chemrxiv-2024-ckv1v | Platinum-catalyzed Isomerization of Cyclopropenes to 1,3-Dienes | Herein we report a platinum-catalyzed isomerization of cyclopropenes to 1,3-dienes. Diverse dienylated alcohols were ob-tained in 42-98% yield. The synthetic potential of the products was demonstrated by their use in Diels-Alder cycloadditions with various dienophiles. Isotope labelling studies provide strong support for a mechanism involving pericyclic [1,5]-σ-bond rearrangement of a vinyl platinum carbene intermediate. | Vladyslav Smyrnov; Antonin Homassel; Leander Choudhury; Jerome Waser | Organic Chemistry; Catalysis | CC BY 4.0 | CHEMRXIV | 2024-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664215fb21291e5d1d238653/original/platinum-catalyzed-isomerization-of-cyclopropenes-to-1-3-dienes.pdf |
64ee0bf6dd1a73847fc6bf23 | 10.26434/chemrxiv-2023-98j7g | Binding Modes of High Stoichiometry Guest Complexes with a Co8L12 Cage Uncovered by Mass Spectrometry | We demonstrate how different modes of guest binding to a Co8L12 cubic cage host can be determined using ESI-MS. High stoichiometry guest binding was observed, with binding modes which showed the guests preferentially binding externally, but internal guest inclusion was also seen at higher guest loading. | Daniel L. Stares; Cristina Mozaceanu; Michael D. Ward; Christoph A. Schalley | Inorganic Chemistry; Organometallic Compounds; Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ee0bf6dd1a73847fc6bf23/original/binding-modes-of-high-stoichiometry-guest-complexes-with-a-co8l12-cage-uncovered-by-mass-spectrometry.pdf |
60c741a6bb8c1a2f8f3d9fa3 | 10.26434/chemrxiv.8075105.v1 | Mechanistic Approaches for Modifying the Coordination Sphere of Metal–Amyloid-β Complexes: Covalent Adduct Formation and Oxidation | <p>We report, f<i>or the first time</i>, a novel mechanistic tactic to directly modify the coordination sphere of Cu(II)–Aβ complexes in a metal binding residue-specific manner, which can prevent Cu(II) binding to Aβ, modulate the aggregation of Cu(II)–Aβ, and generate chemically transformed Aβ with less cytotoxicity, to the best of our knowledge.</p> | Jiyeon Han; Hyuck Jin Lee; Kyu Yeon Kim; Junghyun Chae; Mi Hee Lim | Bioinorganic Chemistry; Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741a6bb8c1a2f8f3d9fa3/original/mechanistic-approaches-for-modifying-the-coordination-sphere-of-metal-amyloid-complexes-covalent-adduct-formation-and-oxidation.pdf |
6217808b97f210b060f288ce | 10.26434/chemrxiv-2021-1r1dn-v2 | Development of a NanoBRET assay to validate inhibitors of Sirt2-mediated lysine deacetylation and defatty-acylation that block prostate cancer cell migration | Sirtuin2 (Sirt2) with its NAD+-dependent deacetylase and defatty-acylase activities plays a central role in the regulation of specific cellular functions. Dysregulation of Sirt2 activity has been associated with the pathogenesis of many diseases, thus making Sirt2 a promising target for pharmaceutical intervention. Herein, we present new high affinity Sirt2 selective Sirtuin-Rearranging Ligands (SirReals) that inhibit both Sirt2-dependent deacetylation and defatty-acylation in vitro and in cells. We show that simultaneous inhibition of both Sirt2 activities results in strongly reduced levels of the oncogene c-Myc and an inhibition of cancer cell migration. Furthermore, we describe the development of a NanoBRET-based assay for Sirt2, thereby providing a method to study cellular target engagement for Sirt2 in a straightforward and accurately quantifiable manner. Applying this assay, we could confirm cellular Sirt2 binding of our new Sirt2 inhibitors and correlate their anticancer effects with their cellular target engagement. | Anja Vogelmann; Matthias Schiedel; Nathalie Wössner; Annika Merz; Daniel Herp; Sören Hammelmann; Arianna Colcerasa; Garrison Komaniecki; Jun Young Hong; Manuela Sum; Eric Metzger; Emilia Neuwirt; Lin Zhang; Oliver Einsle; Olaf Groß; Roland Schüle; Hening Lin; Wolfgang Sippl; Manfred Jung | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2022-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6217808b97f210b060f288ce/original/development-of-a-nano-bret-assay-to-validate-inhibitors-of-sirt2-mediated-lysine-deacetylation-and-defatty-acylation-that-block-prostate-cancer-cell-migration.pdf |
6605ebeb66c13817291d78f6 | 10.26434/chemrxiv-2024-p2pvb | Bicyclo[1.1.0]butyl Radical Cations: Synthesis and Application to [2π+2σ] Cycloaddition Reactions | As the chemistry that surrounds the field of strained hydrocarbons, such as bicyclo[1.1.0]butane, continues to expand, it becomes increasingly advantageous to develop alternative reactivity modes that harness their unique properties to access new regions of chemical space. Herein, we report the use of photoredox catalysis to promote the single-electron oxidation of bicyclo[1.1.0]butanes. The synthetic utility of the resulting radical cations is highlighted by their ability to undergo highly regio- and diastereoselective [2π+2σ] cycloaddition reactions. The most notable feature of this transformation is the breadth of alkene classes that can be employed, including non-activated alkenes, which have so far been
elusive for previous strategies. A rigorous mechanistic investigation, in conjunction with DFT computation, was undertaken in order to better understand the physical nature of bicyclo[1.1.0]butyl radical cations and thus provides a platform from which further studies into the synthetic applications of these intermediates can be built upon. | Jasper Tyler; Felix Schäfer; Huiling Shao; Colin Stein; Audrey Wong; Constantin Daniliuc; Ken Houk; Frank Glorius | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Photocatalysis; Bond Activation | CC BY 4.0 | CHEMRXIV | 2024-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6605ebeb66c13817291d78f6/original/bicyclo-1-1-0-butyl-radical-cations-synthesis-and-application-to-2-2-cycloaddition-reactions.pdf |
65eb9cf0e9ebbb4db949711c | 10.26434/chemrxiv-2024-jphgm | Concise Chemoenzymatic Synthesis of 4,5-Dihydroxyisoleucine Fragment of α-Amanitin | The ability of α-amanitin to potently inhibit RNA polymerase II (RNAP II) has elicited further research into its use as a novel payload for antibody-drug conjugates. Despite this promise, the de novo synthesis of α-amanitin is still a major chal-lenge, as it possesses an unusual bicyclic octapeptide structure that contains several oxidized amino acids, most notably 4,5-dihydroxy-L-isoleucine. Here, we report a concise chemoenzymatic synthesis of this key amino acid residue, which features two regio- and diastereoselective enzymatic C–H oxidations on L-isoleucine. | Tsung-Han Chao; Hans Renata | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65eb9cf0e9ebbb4db949711c/original/concise-chemoenzymatic-synthesis-of-4-5-dihydroxyisoleucine-fragment-of-amanitin.pdf |
623c70765c8daecbbef51d95 | 10.26434/chemrxiv-2022-h2rw7 | Deep Learning Models for the Estimation of Free Energy of Permeation of Small Molecules across Lipid Membranes | Calculating the free energy of drug permeation across membranes carries great importance in pharmaceutical and related applications. Traditional methods, including experiments and molecular simulations, are expensive and time-consuming, and existing statistical methods suffer from low accuracy.
In this work, we propose a hybrid approach that combines molecular dynamics simulations and deep learning techniques to predict the free energy of permeation of small drug-like molecules across lipid membranes with high accuracy and at a fraction of the computational cost of advanced sampling methods like umbrella sampling. We have performed several molecular dynamics simulations of molecules in water and lipid bilayers to obtain multidimensional time-series data of features. Deep learning architectures based on Long Short-Term Memory networks, attention mechanisms, and dense layers are built to estimate free energy from the time series data. The prediction errors for the test set and an external validation set are much lower than that of existing data-driven approaches, with R2 of the best model around 0.99 and 0.82 for the two cases. Our approach reduces the time required for free energy calculations by an order of magnitude. This work presents an attractive option for high-throughput virtual screening of molecules based on their membrane permeabilities, demonstrates the applicability of language processing techniques in biochemical problems, and suggests a novel way of integrating physics with statistical learning to great success | Prantar Dutta; Deepak Jain; Rakesh Gupta; Beena Rai | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623c70765c8daecbbef51d95/original/deep-learning-models-for-the-estimation-of-free-energy-of-permeation-of-small-molecules-across-lipid-membranes.pdf |
67bf397f6dde43c9089763e0 | 10.26434/chemrxiv-2025-7pbsd-v2 | Ultrafast laser synthesis of zeolites | Research has demonstrated that zeolite nucleation and growth can be controlled by fine-tuning chemical composition, temperature, and pressure, resulting in structures with diverse porosities and functionalities. Nevertheless, current energy delivery methods lack the finesse required to operate on the femto- and picosecond timescales of silica polymerisation and depolymerisation, limiting their ability to direct synthesis with high precision. To overcome this limitation, we introduce an ultrafast laser synthesis technique capable of delivering energy at these timescales with unprecedented spatiotemporal precision. Unlike conventional or emerging approaches, this method bypasses the need for specific temperature and pressure settings, as nucleation and growth are governed by dynamic phenomena arising from nonlinear light-matter interactions—such as convective flows, cavitation bubbles, plasma formation, and shock waves. These processes can be initiated, paused, and resumed within fractions of a second, effectively “freezing” structures at any stage of self-assembly. Using this approach, we traced the entire nucleation and growth pathway of laser-synthesized TPA-silicate-1 zeolites, from early oligomer formation to fully developed crystals. The unprecedented spatiotemporal control of this technique unlocks new avenues for manipulating reaction pathways and exploring the vast configurational space of zeolites. | Sezin Galioglu; Mehdi Hagverdiyev; Meryem M. Doğan; Özgün Yavuz; Ghaith Makey; Ü. Seleme Nizam; Aladin Şura; Mesut Laçin; Burcu Akata Kurç; Parviz Elahi; F. Ömer Ilday; Serim Ilday | Physical Chemistry; Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Physical and Chemical Processes; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bf397f6dde43c9089763e0/original/ultrafast-laser-synthesis-of-zeolites.pdf |
60c73ed3f96a0002a8285fa7 | 10.26434/chemrxiv.7094297.v1 | Thermally-Triggered Effervescent Mixing for Assay Automation | <div>Meltable barriers are an attractive means to achieve controlled delivery of reagents in a variety of settings, enabling assays to be performed through thermal automation instead of manual addition of reactants. However, mixing kinetics in such systems can be slow due to the lack of active flow or mechanical shaking. We demonstrate a new strategy for hands-free, thermally-automated agitation of biochemical reactions. Reagents for binary effervescent reactions are lyophilized then capped with a phase-change partition, eicosane. This barrier can be melted at moderate temperatures, at which point an aqueous solution dissolves the reactants, generating bubbles that mix the solution through convection. We explore reactions that generate bubbles of carbon dioxide and oxygen gasses, characterizing the induced mixing rate of two aqueous solutions with dissimilar densities. This strategy affords control over the initiation and duration of convective mixing, providing a tool for thermal automation of biochemical reactions with efficient reaction kinetics.</div> | John Goertz; Andrew Lippe; Ian White | Analytical Apparatus; Bioengineering and Biotechnology; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ed3f96a0002a8285fa7/original/thermally-triggered-effervescent-mixing-for-assay-automation.pdf |
65adf5f49138d23161742ae9 | 10.26434/chemrxiv-2024-8wn5c | Direct Synthesisof Pyrroles by Decarboxylative Ethynyl Methylene Cyclic Carbamates (EMCCs) and Amines Catalyzed by a Binuclear Copper Complexe | An efficient, facile and practical one-pot procedure for the synthesis of polysubstituted pyrroles catalyzed by a binuclear copper complexe using EMCCs as precursors for generating 2-aminoallyl cations was firstly demonstrated. A wide variety of poly-substituted pyrroles were obtained in acceptable to good yields under quite mild conditions. | Shi-Wu Li; Yujie Zhao | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2024-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65adf5f49138d23161742ae9/original/direct-synthesisof-pyrroles-by-decarboxylative-ethynyl-methylene-cyclic-carbamates-emc-cs-and-amines-catalyzed-by-a-binuclear-copper-complexe.pdf |
62740cbf3f1e7c0758b28665 | 10.26434/chemrxiv-2022-191l3 | Chemosensitivity–Gene Expression Correlations and Functional Enrichment Analysis Provide Insight into the Mechanism of Action of a Platinum–Acridine Anticancer Agent | Growth inhibition (GI) and gene expression profiles across the 60 cell lines of the NCI-60 screen were analyzed to elucidate mechanistic differences between a nucleolus-targeting platinum-acridine (PA) hybrid anticancer agent (compound 1) and the standard-of-care chemotherapies cisplatin, oxaliplatin, mitomycin c, doxorubicin, and topotecan. The study utilized Pearson correlation and functional enrichment analysis tools (including gene set enrichment analysis, GSEA) in combination with the gene ontology (GO) resource to identify cellular processes that might contribute to the unique spectrum of activity and high potency of compound 1. The GSEA results are consistent with DNA being a major target of compound 1 based on the negative correlation observed between its potency and expression levels of genes implicated in DNA double-strand break (DSB) repair. GO terms related to RNA processing, including ribosome biogenesis and RNA splicing, are also negatively enriched in GSEA for compound 1, suggesting a mechanism by which these processes render cells more resistant to the hybrid agent. The opposite trend is observed for the other DNA-targeted drugs. Significant functional interactions (STRING) exist between genes/gene products involved in ribosome biogenesis and DSB repair in rDNA, including BRCA1, BABAM1, RPA2, MDM2, RAD21, RAD54L, RPL5, and PAK1IP1. The results suggest that high levels of ribosome biogenesis may buffer compound 1’s cytotoxicity by triggering the ribosomal protein (RPL5)-MDM2-p53 surveillance pathway to facilitate downstream repair of DSBs in rDNA as a nucleolar stress response. | Haoqing Wu; Ulrich Bierbach | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62740cbf3f1e7c0758b28665/original/chemosensitivity-gene-expression-correlations-and-functional-enrichment-analysis-provide-insight-into-the-mechanism-of-action-of-a-platinum-acridine-anticancer-agent.pdf |
60f147e7f1a54f9bc0504d79 | 10.26434/chemrxiv-2021-qklc0 | Structure and Biosynthesis of Myxofacyclines: Unique Myxobacterial Polyketides Featuring Varying and Unprecedented Heterocycles | A metabolome-guided screening approach in the novel myxobacterium Corallococcus sp. MCy9072 resulted in the isolation of the unprecedented natural product myxofacycline A featuring a rare isoxazole substructure. Identification and genomic investigation of additional producers alongside targeted gene inactivation experiments and heterologous expression of the corresponding biosynthetic gene cluster in the host Myxococcus xanthus DK1622 confirmed a noncanonical megaenzyme complex as the biosynthetic origin of myxofacycline A. Induced expression of the respective genes led to significantly increased production titers enabling the identification of six further members of the myxofacycline natural product family. Whereas myxofacycline A–D display an isoxazole substructure, myxofacycline E and F intriguingly were found to contain 4 pyrimidinole, a heterocycle unprecedented in natural products. Lastly, myxofacycline G features another rare 1,2 dihydropyrol-3-one moiety. In addition to the full structure elucidation, we report the underlying biosynthetic machinery and present a rationale for the formation of all myxofacyclines. Unexpectedly, an extraordinary polyketide synthase-nonribosomal peptide synthetase hybrid was found to produce all three types of heterocycles in these natural products. | Alexander Popoff; Joachim Hug; Sebastian Walesch; Ronald Garcia; Lena Keller; Rolf Müller | Organic Chemistry; Natural Products | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f147e7f1a54f9bc0504d79/original/structure-and-biosynthesis-of-myxofacyclines-unique-myxobacterial-polyketides-featuring-varying-and-unprecedented-heterocycles.pdf |
60c74dcb567dfe9f43ec53ee | 10.26434/chemrxiv.12661628.v1 | Quantum Chemical Calculations on Locked Nucleic Acid based Antisense Modifications: A Density Functional Theory (DFT) Study at Monomer Level | <p>Antisense technology has been
developed as the next generation drug discovery methodology by which unwanted
gene expression can be inhibited by targeting mRNA specifically with antisense
oligonucleotides. It has been observed that a good number of these molecules
entered into clinical trials at a faster rate and some of them got approved.
The computational studies of antisense modifications based on phosphorothioate
(PS), methoxyethyl (MOE), locked nucleic acids (LNA) may help to design better
novel modifications. In the present study, newer LNA based modifications have
been proposed. The conformational search and density functional theory (DFT)
calculations have been used to investigate the quantum chemical parameters of
PS, LNA, MOE, and novel LNA based proposed modifications. The conformational
search has been done to identify the most and alternative stable conformations.
The geometry optimization followed by single point energy calculation has been
done at B3LYP/6-31G(d,p) level for gas phase and B3LYP/6-311G(d,p) level for
the solvent phase of all modifications. The electronic properties and the
quantum chemical descriptors for the frontier molecular orbitals of all the
antisense modifications were derived and compared. The local and global
reactivity descriptors, such as hardness, chemical potential,
electronegativity, electrophilicity index, Fukui function calculated at DFT
level for the optimized geometries. These are used for understanding the
reactive nature and reactive sites of the modifications. A comparison of global
reactivity descriptors confirmed that LNA based modifications are the most
reactive modifications and prone to the chemical reactions. It may form stable
duplex when it is bound to complementary nucleotides, compared to other modifications.
Therefore, we are proposing that one of our proposed antisense modification
(A3) may show strong binding to the complementary nucleotide as LNA and may
also show reduced toxic effects like MOE.</p> | Mallikarjunachari Uppuladinne V N; Dikshita Dowerah; Uddhavesh Sonavane; Suvendra Kumar Ray; ramesh deka; Rajendra Joshi | Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74dcb567dfe9f43ec53ee/original/quantum-chemical-calculations-on-locked-nucleic-acid-based-antisense-modifications-a-density-functional-theory-dft-study-at-monomer-level.pdf |
60c74b77702a9b339f18b432 | 10.26434/chemrxiv.12307217.v2 | An Alternative Kinetic Model of the Iodide-Iodate Reaction for Its Use in Micromixing Investigations | The Villermaux-Dushman method, one of the most extensively used test reaction systems for micromixing characterization, has been widely criticized for years due to uncertainties regarding the incomplete dissociation of sulfuric acid and the proposed kinetic study by Guichardon et al. In this work, a renewed study of the kinetics of the iodide-iodate reaction is presented, using perchloric acid to avoid issues concerning incomplete acid dissociation. The experimental results are in good agreement with the fifth order rate law for the iodide-iodate reaction. The reaction rate coefficient strongly depends on the ionic strength and can be modeled with a Davies-like equation. When implemented in the incorporation model, the kinetic model presented in this study can be used to estimate micromixing times that are in line with the theoretical engulfment time. This is observed in two different reactors with low and high intensity of mixing: an unbaffled stirred vessel and a rotor-stator spinning disc reactor. The results from the latter are also compared with the second Bourne reaction, giving very similar micromixing times. The use of sulfuric acid in combination with the kinetic model from Guichardon et al. also provides micromixing times of the same order of magnitude; presumably their kinetic model indirectly accounts for the second proton dissociation rate in the overall reaction rate coefficient. The kinetic model presented in this study in combination with perchloric acid is suggested as an alternative to characterize micromixing behavior.
<pre><br /><br /></pre> | Arturo Neissen Manzano Martinez; A. Sander Haase; Melissa Assirelli; John van der Schaaf | Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b77702a9b339f18b432/original/an-alternative-kinetic-model-of-the-iodide-iodate-reaction-for-its-use-in-micromixing-investigations.pdf |
60c745bb702a9b472118aa8b | 10.26434/chemrxiv.10172969.v1 | Boosting Solar Steam Generation by Using AIE Photothermal Molecule-Doped 3D Nanofibrous Aerogel with Self-Pumping Water Function | <p>Utilizing solar
energy to generate clean water by interface solar steam generation is
considered to be a promising strategy to address the challenge of <a></a><a>water
shortage globally.</a> However, <a></a><a>high evaporation rate and
long-term sustainability have rarely been achieved simultaneously</a>,
due to salt accumulation, discontinuous water supply and insufficient
photothermal conversion. Herein, we demonstrate that a three-dimensional nanofibrous
aerogel (3D NA) with Janus layers enables floating on the surface water by
hydrophobic layer and continues pumping water by hydrophilic layer and
interconnected porous structure. <a>More notably, an </a><a></a><a>aggregation-induced emission (AIE)</a> photothermal molecule is doped into
nanofibers for the first time, which was endowed with superior capacity of transferring
solar energy into heat. Combining these unique benefits, the presented 3D NA
exhibits extremely high evaporation rate (1.99 kg m<sup>-2</sup> h<sup>-1</sup>)
and solar-to-vapor conversion efficiency (89%) under irradiation of 1 sun.
Besides, there is no significant change in evaporation performance after 21 cycles
in the case of seawater treatment, suggesting that the designed 3D NA possess
sustainable stability and self-cleaning function to restrain salt deposition. With
highly efficient evaporation rate and long-term sustainable solar steam
generation, such 3D NA can offer new strategy for desalination and sewage
treatment. </p> | Haoxuan Li; Haifei Wen; Jie Li; Jiachang Huang; Dong Wang; Ben Zhong Tang | Hydrology and Water Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745bb702a9b472118aa8b/original/boosting-solar-steam-generation-by-using-aie-photothermal-molecule-doped-3d-nanofibrous-aerogel-with-self-pumping-water-function.pdf |
60c7521f337d6c8f5ee2868d | 10.26434/chemrxiv.13250102.v1 | Viscoelastic Phase Patterning in Artificial Protein Hydrogels | Viscoelastic forces can affect the dynamics of pattern formation during phase separation in polymeric materials. We programmed an artificial protein hydrogel to undergo viscoelastic phase separation above a critical temperature. Highly dynamic phase patterns that coarsened under the influence of viscoelastic stresses spontaneously emerged in these gels. Local oxidative crosslinking promoted by mild photobleaching could be used to initiate phase separation locally, enabling the creation of non-equilibrium patterns that evolved under the influence of surface tension and viscoelastic stresses to yield dynamic structures of controlled size and shape. | Peter Rapp; Bradley Silverman | Biological Materials; Photosensitizers; Biopolymers; Hydrogels; Polymer morphology | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7521f337d6c8f5ee2868d/original/viscoelastic-phase-patterning-in-artificial-protein-hydrogels.pdf |
62cff0f127b1e42fe039c25e | 10.26434/chemrxiv-2022-jg608-v3 | Probing the Stability of SrIrO3 During Active Water Electrolysis via Operando Atomic Force Microscopy | Mechanistic studies of oxide electrocatalysts for heterogeneous water oxidation have been primarily focused on understanding the origins of activity, with fewer studies studying fundamental properties influencing stability. The main challenge is directly observing and quantifying local structural instability under operating conditions. In this work, we provide a dynamic view of the perovskite stability as a function of time and operational voltage using operando electrochemical atomic force microscopy (EC-AFM). Specifically, we study the degradation pathways of SrIrO3, a highly active electrocatalyst, during the oxygen evolution reaction (OER) by tracking the potential-dependent Sr leaching and perovskite dissolution at the nanometer scale. This material serves as a model system for degradation studies of perovskite AMO3 oxides, exhibiting both A-cation leaching and transition metal (M) dissolution. We show that Sr leaching precedes perovskite dissolution by up to 0.8 V, leading to a wide voltage window of stability where water oxidation occurs on a Sr-depleted surface without significant corrosion. Moreover, we reveal that the stability of the perovskite surface is strongly influenced by the electrolytic environment and that corrosion rates differ dramatically as a function of dissolved Sr concentration. Ultimately, our study demonstrates the overall stability of perovskite oxides during electrocatalysis can be substantially improved by suppressing A-site leaching. | Andrew R. Akbashev; Vladimir Roddatis; Christoph Baeumer; Tianchi Liu; J. Tyler Mefford; William C. Chueh | Materials Science; Catalysis; Energy; Thin Films; Electrocatalysis | CC BY NC 4.0 | CHEMRXIV | 2022-07-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62cff0f127b1e42fe039c25e/original/probing-the-stability-of-sr-ir-o3-during-active-water-electrolysis-via-operando-atomic-force-microscopy.pdf |
671f781283f22e42146f2755 | 10.26434/chemrxiv-2024-kxf0x | High-throughput and Automated Anion Transport Assays | Ion transport across biological lipid membranes is crucial for both health and disease, prompting investigation into synthetic ion transporters as potential therapeutics. However, state of the art methods for assessing transporter activity are often time-consuming and resource-intensive, hindering the screening of large compound libraries. In this work we have developed an automated high-throughput assay capable of determining 24 EC50 values in a single day. This assay, adapted from the established lucigenin Cl-/NO3- antiport method, has been optimised for multi-well plates with fully automated liquid handling. Notably, our protocol allows for the use of DMSO as a delivery solvent for target molecules, enhancing its versatility. Validation with six standard ion transporters demonstrated a strong correlation between the EC50 values obtained through our assay and previously reported values, confirming its efficacy and potential for broader applications in the field of ion transport. | Kylie Yang; Lana Lee; Hiral Kotak; Evelyn Morton; Soo Mei Chee; Duy Nguyen; Alvaro Keskküla; Cally Haynes | Biological and Medicinal Chemistry; Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2024-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671f781283f22e42146f2755/original/high-throughput-and-automated-anion-transport-assays.pdf |
60c75613842e654049db4456 | 10.26434/chemrxiv.14215310.v1 | Facile and Selective Conversion of Levulinic Acid into γ-Valerolactone by Low-cost Fe and Ni Catalysts in Water | <p>Renewable chemical production from biomass
is desirable for the sustainable development of the society. Levulinic acid
(LA) is a common biomass-derived building block that furnishes a suitable
source to produce the industrially valuable γ-valerolactone (GVL). In this
work, a low-cost, green and effective catalytic system was developed to
transform LA into GVL in water by using Fe and Ni, in which the hydrogen source
was provided by water splitting. The Fe primarily functioned as the reductant
that transformed into Fe<sub>3</sub>O<sub>4</sub> species after the reaction,
while Ni played the major catalytic role to promote selective LA hydrogenation
into GVL. After optimizations, the GVL yield reached the highest of 99% within
2-3 h at relatively low hydrothermal temperature of 230-250 °C. The recycling
tests of Ni has suggested negligible decrease of product yield after four runs.
This study establishes a green, facile and eco-friendly approach to synthesize
GVL from biomass-derived LA.</p> | Xi Chen; Zhuang Ma; Wubin Yan; Guodong Yao; qiuju li; Binbin Jin; Yaling Guo; yudi wang | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75613842e654049db4456/original/facile-and-selective-conversion-of-levulinic-acid-into-valerolactone-by-low-cost-fe-and-ni-catalysts-in-water.pdf |
60c74ec4842e65330fdb36ed | 10.26434/chemrxiv.12753593.v2 | Elucidating the Structural Evolution of a Highy Porous Responsive Metal-Organic Framework (DUT-49(M)) upon Guests Desorption by Time-Resolved In-Situ Powder X-Ray Diffraction | Variation in the metal centres of M-M
paddle-wheel SBU results in the formation of isostructural DUT-49(M) frameworks.
However, the porosity of the framework was found to be different for each of
the structures. While a high and moderate porosity was obtained for DUT-49(Cu)
and DUT-49(Ni), respectively, other members of the series [DUT-49(M); M= Mn,
Fe, Co, Zn, Cd] show very low porosity and shapes of the adsorption isotherms
which is not expected for op phases of these MOFs. Investigation on those MOFs
revealed that those frameworks undergo structural collapse during the solvent
removal at the activation step. Thus, herein, we aimed to study the detailed
structural transformations that are possibly occurring during the removal of
the subcritical fluid from the framework. | Bikash Garai; Volodymyr Bon; Francesco Walenszus; Azat Khadiev; Dmitri Novikov; Stefan Kaskel | Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Coordination Chemistry (Inorg.); Physical and Chemical Processes; Physical and Chemical Properties; Structure; Surface; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ec4842e65330fdb36ed/original/elucidating-the-structural-evolution-of-a-highy-porous-responsive-metal-organic-framework-dut-49-m-upon-guests-desorption-by-time-resolved-in-situ-powder-x-ray-diffraction.pdf |
Subsets and Splits
No saved queries yet
Save your SQL queries to embed, download, and access them later. Queries will appear here once saved.