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60c74512bdbb895324a38945 | 10.26434/chemrxiv.9961664.v1 | Tuning Second Coordination Sphere Interactions in Polypyridyl–Iron Complexes to Achieve Selective Electrocatalytic Reduction of Carbon Dioxide to Carbon Monoxide | The development of noble metal-free catalysts capable of electrochemically converting carbon dioxide (CO<sub>2</sub>) selectively into value added compounds remains one of the central challenges in sustainable energy science. Here, we present a systematic study of Fe(II) complexes of the functionalized ligands bpy<sup>R</sup>PY2Me (bpyPY2Me = 6-(1,1-di(pyridin-2-yl)ethyl)-2,2′-bipyridine) in pursuit of water-stable molecular Fe complexes that are selective for the catalytic formation of CO from CO<sub>2</sub>. Taking advantage of the inherently high degree of tunability of this ligand manifold, we followed a bio-inspired approach by installing protic functional groups of varying acidities (–H, –OH, –OMe, –NHEt, and –NEt2) into the ligand framework to systematically modify the second coordination sphere of the Fe center. This family of [(bpy<sup>R</sup>PY2Me)Fe(II)] complexes was characterized using single-crystal X-ray analysis, 1H NMR spectroscopy, and mass spectrometry. Comparative catalytic evaluation of this set of compounds via voltammetry and electrolysis experiments identified [(bpy<sup>NHEt</sup>PY2Me)Fe]<sup>2+</sup> in particular as an efficient, iron-based, non-heme CO<sub>2</sub> electro-reduction catalyst that displays significant selectivity for the conversion of CO<sub>2</sub> to CO in acetonitrile solution with 11 M H<sub>2</sub>O. We propose that the NH group acts as a local proton source for cleaving the C–O bond in CO<sub>2</sub> to form CO. Interestingly, the complex with the most acidic functional group in the second coordination sphere, [(bpy<sup>OH</sup>PY2Me)Fe]<sup>2+</sup>, favors formation of H<sub>2</sub> over CO. Our results correlate the selectivity of water versus carbon dioxide reduction to the acidity of the second coordination sphere functional group and emphasize the continued untapped potential that synthetic molecular chemistry offers in the pursuit of next-generation CO<sub>2</sub> reduction electrocatalysts.<br /> | David Zee; Michael Nippe; Amanda King; Christopher Chang; Jeffrey R. Long | Coordination Chemistry (Inorg.); Electrochemistry; Ligands (Inorg.); Small Molecule Activation (Inorg.); Transition Metal Complexes (Inorg.); Electrocatalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74512bdbb895324a38945/original/tuning-second-coordination-sphere-interactions-in-polypyridyl-iron-complexes-to-achieve-selective-electrocatalytic-reduction-of-carbon-dioxide-to-carbon-monoxide.pdf |
60c745ffbb8c1a2a773da7d7 | 10.26434/chemrxiv.10312373.v1 | Discovery of a Small Molecule Probe to Rpn-6, an Essential Subunit of the 26S Proteasome | Rpn-6 is among several essential proteins that facilitate assembly of the 26S proteasome. We were interested in discovering a small molecule binder to Rpn-6 that could be used to further our understanding of the association of the 19S regulatory particle with the 20S core particle and if a small molecule-Rpn-6 interaction could potentially be cytotoxic to cancer cells that heavily rely on proteasome activity for survival. A workflow to utilize a one-bead-one-compound library and a thermal shift assay was developed to discover such a molecule. TXS-8 was discovered to have low micromolar range binding affinity for Rpn-6 and showed with very limited binding to other proteins. Cytotoxicity of TXS-8 was evaluated in several cell lines, revealing increased cytotoxicity to hematological cancers. | Wenzhi Tian; Darci Trader | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745ffbb8c1a2a773da7d7/original/discovery-of-a-small-molecule-probe-to-rpn-6-an-essential-subunit-of-the-26s-proteasome.pdf |
60c74222702a9b268e18a3b5 | 10.26434/chemrxiv.8209349.v1 | Surface Co-Presentation of BMP-2 and Integrin Selective Ligands at the Nanoscale Favors β1 Integrin Adhesion | Here we present the use of surface nanopatterning of covalently immobilized BMP-2 and integrin selective ligands to determine the specificity of their interactions in regulating cell adhesion and focal adhesion assembly. Gold nanoparticle arrays carrying single BMP-2 dimersare prepared by block-copolymer micellar nanolithography and azide-functionalized integrin ligands (RGD peptides or α<sub>5</sub>β<sub>1</sub>integrin peptidomimetics) are immobilized on the surrounding polyethylene glycol alkyne by click chemistry. | Francesca Posa; Elisabeth Baha-Schwab; Qiang Wei; Adriana Di Benedetto; Stefanie Neubauer; Horst Kessler; Joachim P. Spatz; Corinne Albigès-Rizo; Giorgio Mori; Ada Cavalcanti | Nanostructured Materials - Nanoscience; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74222702a9b268e18a3b5/original/surface-co-presentation-of-bmp-2-and-integrin-selective-ligands-at-the-nanoscale-favors-1-integrin-adhesion.pdf |
60c759e2337d6c0fd4e29481 | 10.26434/chemrxiv.13567349.v2 | Understanding the Role of R266K Mutation in Cystathionine β-Synthase (CBS) Enzyme: An in Silico Study | Human cystathionine β-synthase (hCBS) is a Heme containing unique
pyridoxal 5’-phosphate (PLP) dependent enzyme that catalyzes the bio-chemical condensation
reactions in the transsulfuration pathway. The role of Heme in the catalytic
activities of enzyme has not yet been understood completely, even though various
experimental studies have indicated its participation in the bi-directional
electronic communication with the PLP center. Most probably Heme acts as the
electron density reservoir for the catalytic reaction center but not as a redox
electron source. Here, in this work, we investigated <i>In Silico</i> dynamical
aspects of the bi-directional communications by performing classical molecular
dynamics (MD) simulations upon developing the necessary force field parameters
for the cysteine and histidine bound hexa-coordinated Heme. The comparative
aspects of electron density overlap across the communicating pathways are also
explored adopting the density functional theory (DFT) in conjunction with the
hybrid exchange-correlation functional for the CSB<sup>WT</sup> (wild-type) and
CBS<sup>R266K</sup> (mutated) case. The atomistic MD simulations and subsequent
explorations of the electronic structures not only confirm the reported
observations but provide an in-depth mechanistic understating of how the
non-covalent hydrogen bonding interactions with Cys52 control such
long-distance communication. Our study also provides a convincing answer to the
reduced enzymatic activities in the R266K hCBS in comparison to the wild-type
enzymes. We further realized that the difference in hydrogen-bonding patterns,
as well as salt-bridge interactions, play a pivotal role in such long distant
bi-directional communications.<br /> | Aashish Bhatt; Md. Ehesan Ali | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759e2337d6c0fd4e29481/original/understanding-the-role-of-r266k-mutation-in-cystathionine-synthase-cbs-enzyme-an-in-silico-study.pdf |
62ea4f5f04c85faeb582173b | 10.26434/chemrxiv-2022-j0x08-v2 | Copper-Catalyzed Alkynylation of Hydrazides: An Easy Access to Functionalized Azadipeptides | We report a copper-catalyzed alkynylation of azadipeptides using ethynylbenziodoxolone (EBX) reagents. Non-symmetrical ynehydrazides could be obtained in 25-97% yield using azaglycine derivatives as nucleophiles. The transfor-mation is compatible with most functional groups naturally occurring on amino acid side-chains and allows the transfer of silyl-, alkyl- and aryl-substituted alkynes. The obtained α-alkynyl azaglycine products could be further functionalized by nucleophilic attack or cycloaddition on the triple bond. | Eliott Le Du; Julien Borrel; Jerome Waser | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2022-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ea4f5f04c85faeb582173b/original/copper-catalyzed-alkynylation-of-hydrazides-an-easy-access-to-functionalized-azadipeptides.pdf |
60c74ce3842e6590bedb337e | 10.26434/chemrxiv.12555272.v1 | A Fluorogenic Heparan Sulfate Disaccharide for the Measurement of Heparanase Activity | <p>The endo-β-glucuronidase heparanase mediates
mammalian heparan sulfate catabolism, and is of considerable medical interest
due to its prominent role in cancer aggression and metastasis. Biochemical
studies of heparanase are currently hampered by a lack of suitable chromogenic
or fluorogenic assay substrates, instead relying on lengthy multistep
procedures to measure activity. Herein, we demonstrate that
N’,6-O’-bis-sulfated 4-methylumbelliferyl heparan sulfate disaccharide is a
competent fluorogenic heparanase substrate. Despite somewhat slow turnover, the
high sensitivity of 4-methylumbelliferyl fluorescence provides a wide signal
window that enables both enzyme turnover and inhibition kinetics measurements.
Crystal structures with heparanase also provide the first ever observation of a
substrate in an activated <sup>1</sup>S<sub>3</sub> conformation, highlighting
previously unknown interactions involved in turnover. Our results pave the way
for the design of further improved HPSE substrates that may enable rapid
assessment of enzyme activity, which in turn will drive development of new
heparanase inhibitors for therapeutic use.</p> | Liang Wu; Norbert Wimmer; Vito Ferro; Gideon J. Davies | Organic Compounds and Functional Groups; Biochemistry; Chemical Biology; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ce3842e6590bedb337e/original/a-fluorogenic-heparan-sulfate-disaccharide-for-the-measurement-of-heparanase-activity.pdf |
649da4baba3e99daef3fa74a | 10.26434/chemrxiv-2023-gkx45 | On-Surface Synthesis and Determination of the Open-Shell Singlet Ground State of Tridecacene | The character of the electronic structure of acenes has been the subject of the longstanding discussion. However, convincing experimental evidence of their open-shell character has so far been missing. Here, we present on surface synthesis of tridecacene molecule by thermal annealing of octahydrotridecacene on Au(111) surface. We characterized the electronic structure of the tridecacene by scanning probe microscopy, which reveals presence of the inelastic signal at 126 meV. We attribute the inelastic signal to the spin excitation from the singlet biradical ground state to triplet excited state. To rationalize the experimental findings we carried out many-body ab-initio calculations as well as model Hamiltonian to take into account the effect of metallic substrate. Moreover, we provide a detailed analysis how the dynamical electron correlation and virtual charge fluctuation between molecule and metallic surface reduces the singlet-triplet band gap. Therefore, this work provides first experimental confirmation of the magnetic character of tridecacene. | Rafal Zuzak; Manish Kumar; Otilia Stoica; Diego Soler; Jiri Brabec; Katarzyna Pernal; Libor Veis; Remi Blieck; Antonio Echavarren; Pavel Jelinek; Szymon Godlewski | Nanoscience; Nanofabrication | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649da4baba3e99daef3fa74a/original/on-surface-synthesis-and-determination-of-the-open-shell-singlet-ground-state-of-tridecacene.pdf |
671b587e1fb27ce1248e3ec0 | 10.26434/chemrxiv-2024-cm4xr-v3 | Phase coexistence in Hamiltonian hybrid particle--field theory using a Multi-Gaussian approach | This study introduces an implementation of multiple Gaussian filters within the Hamiltonian hybrid particle-field (HhPF) theory, aimed at capturing phase coexistence phenomena in mesoscopic molecular simulations. By employing a linear combination of two Gaussians, we demonstrate that HhPF can generate potentials with attractive and steric components analogous to Lennard-Jones potentials, which are crucial for modeling phase coexistence. We compare the performance of this method with the Multi-Gaussian Core Model (MGCM) in simulating liquid-gas coexistence for a single-component system across various densities and temperatures. Our results show that HhPF effectively captures detailed information on phase coexistence and interfacial phenomena, including micro-configuration transitions and increased interfacial fluctuations at higher temperatures. Notably, the phase boundaries obtained from HhPF simulations align more closely with those of Lennard-Jones systems compared to the MGCM results. This work advances the hybrid particle-field methodology to address phase coexistence without requiring modifications to the equation of state or introducing additional interaction energy functional terms, offering a promising approach for mesoscale molecular simulations of complex systems. | Samiran Sen; Henrique Musseli Cezar; Morten Ledum; Xinmeng Li; Michele Cascella | Physical Chemistry; Physical and Chemical Properties; Statistical Mechanics; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671b587e1fb27ce1248e3ec0/original/phase-coexistence-in-hamiltonian-hybrid-particle-field-theory-using-a-multi-gaussian-approach.pdf |
6675902fc9c6a5c07a08d68a | 10.26434/chemrxiv-2024-1nrql | Ultra-Efficient Electrolytic Ocean Carbon Removal Through Capacitive Decarbon Reactors | Direct ocean capture (DOC) is a promising technique for mitigating residual anthropogenic CO2 levels. However, the existing DOC methods are energy-intensive and may have unforeseen effects on marine ecosystems due to the chemical processes involved. We introduce a capacitive decarbon (CDC) reactor that converts carbonate ions into CaCO3, a construction material, using only calcium ions (Ca2+) from seawater and renewable electricity. After optimizations of the electrode and electrolytic reactor, the CDC reactor achieves ocean carbon removal with an exceptionally low energy consumption of 16 kJ mol−1 CO2, which is one order of magnitude lower than previously reported values. This energy requirement increases to 107 kJ mol−1 CO2 when factoring in the seawater intake and pre-treatment. We then used a global integrated analysis model to evaluate the carbon mitigation potential of this approach and found that it can remove about 360 to 1,670 million tonnes of CO2 in 2050 and 2100, respectively, which corresponds to 4.55% and 14.82% of the global carbon sequestration capacity for those years. Given the high efficiency of the CDC reactor, we anticipate it may become a viable solution for sequestering oceanic carbon.
| Yifang Zhu; Yang Ou; Jay Fuhrman; Meng Lin; Kuichang Zuo; Huazhang Zhao; Zishuai Zhang | Energy; Chemical Engineering and Industrial Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6675902fc9c6a5c07a08d68a/original/ultra-efficient-electrolytic-ocean-carbon-removal-through-capacitive-decarbon-reactors.pdf |
676aed8efa469535b9aa00a4 | 10.26434/chemrxiv-2024-r2qq0 | A Low-Spin Manganese (II) Complex with an Emissive Charge-Transfer Excited State | Manganese is an attractive earth-abundant metal for chromophores because it has multiple oxidation states, making it well-suited for photochemical applications involving electron transfer reactivity. Unfortunately, the tendency of manganese (II) to form high-spin complexes with metal-centered excited states has limited its viability. Herein, we disclose an air-stable S = ½ Mn(II) complex with (N)-heterocyclic carbene ligands. Spectroscopy revealed panchromatic absorption with two main bands in the visible region (with maxima at 480 nm and 580 nm), which have mixed charge-transfer and metal-centered character. Each band produces a unique emission spectrum in the range of 600-800 nm upon excitation. In both cases, time-resolved emission spectroscopy revealed biphasic kinetics for the ground state recovery, with a lifetime of 1 ns at 620 nm. | Maxwell Rhames; Nora Burnett; William Tocco; Ahshabibi Ahmed; Annemarie Lee; Alexander Ruhren; Claire Besson; Julien Panetier; John Swierk; Daniela Arias-Rotondo | Inorganic Chemistry; Coordination Chemistry (Inorg.); Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676aed8efa469535b9aa00a4/original/a-low-spin-manganese-ii-complex-with-an-emissive-charge-transfer-excited-state.pdf |
60c7470a842e65a4e0db2903 | 10.26434/chemrxiv.11502486.v1 | Two Cycling Centers in One Molecule: Communication by Through-Bond Interactions and Entanglement of the Unpaired Electrons | <div>
<div>
<div>
<p>Many applications in quantum information science (QIS) rely on the ability to
laser-cool molecules. The scope of applications can be expanded if laser-coolable
molecules possess two or more cycling centers, i.e., moieties capable of scattering
photons via multiple absorption-emission events. Here we employ equation-of-motion
coupled-cluster method for double electron attachment (EOM-DEA-CCSD) to study
electronic structure of hypermetallic molecules with two alkaline earth metals con-
nected by an acetylene linker. We demonstrate that the interaction between two
unpaired electrons is weak yet non-negligible, and is reflected in the underlying
wavefunction. The electronic structure of the molecules is similar to that of two
separated alkali metals, however the interaction between two electrons is largely
dominated by through-bond interactions. The communication between the two cycling centers is quantified by the extent of the entanglement of the two unpaired
electrons associated with each center. This contribution highlights rich electronic
structure of hypermetallic molecules that may advance various applications in QIS
and beyond.
</p>
</div>
</div>
</div> | Maxim Ivanov; Sahil Gulania; Anna I. Krylov | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7470a842e65a4e0db2903/original/two-cycling-centers-in-one-molecule-communication-by-through-bond-interactions-and-entanglement-of-the-unpaired-electrons.pdf |
60c750d1ee301c239bc7a937 | 10.26434/chemrxiv.13087553.v1 | On the Use of Aqueous Metal-Aqua pKa Values as a Descriptor of Lewis Acidity | The behavior of Lewis acidic metal ions in multimetallic
systems has become a subject of intense interest in recent years. Parametrizing the behavior of these ions in non-aqueous conditions, commonly used in the field, is challenging due to the lack of direct measures
of the Lewis acidity of metal ions in polar organic solvents. Here, we report the use of triphenylphosphine oxide (TPPO) as a 31P nuclear magnetic resonance (NMR) probe to quantify the Lewis acidity of a library
of metal triflate salts using the Gutmann-Beckett method. A plot of the
pKa values of the corresponding metal-aqua species, [M(H2O)m]n+,
measured in H2O, vs. the 31P NMR shifts of TPPO in the presence of
these metals in deuterated acetonitrile (d3-MeCN) and deuterated dichloromethane (CD2Cl2) displays a tightly co-linear relationship, suggesting similar behavior for these ions in water, d3-MeCN, and CD2Cl2.
This collinearity reinforces the utility of the common approach of using
the aqueous pKa values as a descriptor of Lewis acidity, regardless of the
solvent used in the immediate experiments, and provides an insight into
the usefulness of this descriptor in wide-ranging applications. Titration
studies in d3-MeCNsuggest 1:1 binding of TPPO with monovalent ions,
greater than 1:1 binding with divalent ions, and formation of multiple
species with the highly Lewis acidic trivalent ions. Together, these data
suggest that both aqueous pKa values and other single-measurement descriptors, while useful, provide only a snapshot of the influence of Lewis
acidity on multimetallic chemical systems. | Amit Kumar; James Blakemore | Inorganic Acid/Base Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750d1ee301c239bc7a937/original/on-the-use-of-aqueous-metal-aqua-p-ka-values-as-a-descriptor-of-lewis-acidity.pdf |
60c74333702a9b421818a594 | 10.26434/chemrxiv.8964776.v1 | Copper-mediated selenazolidine deprotection enables one-pot chemical synthesis of challenging proteins | <p>While chemical protein synthesis (CPS) has granted access to challenging proteins, synthesis of longer proteins is often limited by low abundance or non-strategic placement of cysteine (Cys) residues, essential for native chemical ligations (NCL), as well as multiple purification and isolation steps. Selective deselenization and one-pot CPS serve as key technologies to circumvent these issues. Herein, we describe the one-pot total synthesis of human thiosulfate: glutathione sulfurtransferase (TSTD1), a 115-residue protein with a single Cys residue at its active site, and its seleno-analogue. WT-TSTD1 was synthesized in a C-to-N synthetic approach employing multiple NCL reactions, Cu(II)-mediated deprotection of selenazolidine (Sez), and chemoselective deselenization, all in one-pot. In addition, the protein’s seleno analogue (Se-TSTD1), in which the active site Cys is replaced with selenocysteine, was synthesized with a kinetically controlled ligation in a one-pot, N-to-C synthetic approach. TSTD1’s one-pot synthesis was made possible by the newly reported, rapid, and facile copper-mediated selenazolidine deprotection that can be accomplished in one minute. Finally, catalytic activity of the two proteins indicated that Se-TSTD1 possessed only four-fold lower activity than WT-TSTD1 as a thiosulfate: glutathione sulfurtransferase, suggesting that selenoproteins can have physiologically comparable sulfutransferase activity as their cysteine counterparts. </p> | Zhenguang Zhao; Norman Metanis | Bioorganic Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74333702a9b421818a594/original/copper-mediated-selenazolidine-deprotection-enables-one-pot-chemical-synthesis-of-challenging-proteins.pdf |
62c70903cd7a994dc9bcb043 | 10.26434/chemrxiv-2022-4wj4j | Organelle-selective membrane labeling through PLD-mediated transphosphatidylation | The specialized functions of eukaryotic organelles have motivated chemical approaches for their selective tagging and visualization. Here we develop non-genetically encoded tools using metabolic labeling of abundant membrane lipids for selective visualization of organelle compartments. Synthetic choline analogs with three N-methyl substituents replaced with 2-azidoethyl and additional alkyl groups enabled generation of corresponding analogs of phosphatidylcholine, a ubiquitous and abundant membrane phospholipid. Subsequent click chemistry tagging with a single cyclooctyne-fluorophore reagent enabled differential labeling of the endoplasmic reticulum, the Golgi complex, mitochondria, and lysosomes depending upon the substitution pattern at the choline ammonium center. Key to the success of this strategy were the harnessing of both the organic cation transporter OCT1 to enable cytosolic delivery of these cationic metabolic probes and endogenous phospholipase D enzymes for rapid, one-step metabolic conversion of the choline analogs to the desired lipid products. The remarkably stable localizations of these azidolipids, even after fluorophore conjugation, suggests their application not only for organelle-selective imaging but also for local modulation of physiological events with organelle-level precision by tethering of bioactive small molecules, via click chemistry, within defined subcellular membrane environments. | Din-Chi Chiu; Jeremy M. Baskin | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c70903cd7a994dc9bcb043/original/organelle-selective-membrane-labeling-through-pld-mediated-transphosphatidylation.pdf |
6707ecc5cec5d6c142c9885f | 10.26434/chemrxiv-2024-pzf57 | Organophotocatalytic Reduction of Benzenes to Cyclohexenes | The reduction of abundant benzene rings to scarce C(sp3)-rich motifs is invaluable for drug design as C(sp3) content is known to correlate with clinical success. Cyclohexenes are attractive targets as they can be rapidly elaborated into large product libraries and are stable against rearomatization. However, partial reduction reactions of benzenes to cyclohexenes are rare and have a very narrow scope. Herein, we report a broadly applicable method that converts electron-poor benzenes to cyclohexenes and tolerates Lewis-basic functional groups like triazoles and thioethers, as well as reducible groups like cyanides, alkynes, and sulfones. The reaction utilizes an organic donor that induces mild arene reduction by pre-association to a photo-excitable electron-donor-acceptor (EDA) complex and mild isomerization of redox-inert 1,4-cyclohexadienes to reducible 1,3-cyclohexadienes without a strong base in its oxidized thioquinone methide form. | Kirti Devi; Asad Shehzad; Mario Patrick Wiesenfeldt | Organic Chemistry; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6707ecc5cec5d6c142c9885f/original/organophotocatalytic-reduction-of-benzenes-to-cyclohexenes.pdf |
622b97b8968f529045b788f0 | 10.26434/chemrxiv-2022-jtchd-v2 | HADOKEN: An Open-Source Software Package for Predicting Electron Confinement Effects in Various Nanowire Geometries and Configurations | We present an open-source software package, HADOKEN (High-level Algorithms to Design, Optimize, and Keep Electrons in Nanowires), for predicting electron confinement/localization effects in nanowires with various geometries, arbitrary number of concentric shell layers, doping densities, and external boundary conditions. The HADOKEN code is written in the MATLAB programming environments to aid in its readability and general accessibility to both users and practitioners. We provide several examples and outputs on a variety of different nanowire geometries, boundary conditions, and doping densities to demonstrate the capabilities of the HADOKEN software package. As such, the use of this predictive and versatile tool by both experimentalists and theorists could lead to further advances in both understanding and tailoring electron confinement effects in these nanosystems. | Bryan Wong; Cameron Chevalier | Theoretical and Computational Chemistry; Materials Science; Nanoscience; Core-Shell Materials; Nanostructured Materials - Nanoscience; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622b97b8968f529045b788f0/original/hadoken-an-open-source-software-package-for-predicting-electron-confinement-effects-in-various-nanowire-geometries-and-configurations.pdf |
60c74b18f96a0020e1287568 | 10.26434/chemrxiv.12286376.v1 | Optimization of the Reaction Conditions for the Synthesis of Dihydrobenzofuran Neolignans | We
have optimized the experimental conditions for the silver(I)-promoted oxidative
coupling of methyl <i>p</i>-coumarate (<b>I</b>) and methyl ferulate (<b>II</b>),
which is the most frequently used methodology to synthesize the bioactive dihydrobenzofuran
neolignans <b>1</b> ((±)-<i>trans</i>-dehydrodicoumarate dimethyl
ester) and <b>2</b> ((±)-<i>trans</i>-dehydrodiferulate
dimethyl ester). Most of the tested conditions affected the conversion (i.e.,
the consumption of <b>I</b> and <b>II</b>) and the selectivity (i.e., the
percentage of <b>I</b> and <b>II</b> that was converted into <b>1</b> and <b>2</b>,
respectively), so the optimized conditions were the conditions that afforded
the best balance between conversion and selectivity. Silver(I) oxide (0.5 eq) is the most efficient
oxidant agent amongst the silver(I) reagents that were tested to convert methyl
esters <b>I </b>and <b>II </b>into compounds <b>1</b> and <b>2</b>,
respectively. Acetonitrile, which has not yet been reported as a solvent for
this reaction, provided the best balance between conversion and selectivity,
besides being “greener” than other solvents that are more often employed (e.g.,
dichloromethane and benzene). Under the optimized conditions, the reaction time
decreased from 20 h to 4 h without significantly impacting the conversion and
selectivity. However, the relation between the results obtained by adding a radical
initiator (AIBN) or a radical inhibitor (isoquinoline) and the previously
reported involvement of radical intermediate species in the silver(I)-promoted
oxidative coupling of <b>I</b> and <b>II</b> is not clear and deserves further investigation. | Herbert Dias; Matheus Rodrigues; Antônio Eduardo Crotti | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b18f96a0020e1287568/original/optimization-of-the-reaction-conditions-for-the-synthesis-of-dihydrobenzofuran-neolignans.pdf |
639df138e9d0fd23b320876a | 10.26434/chemrxiv-2022-j051p | Poly(Heptazine Imide) Ligand Exchange Enables Remarkable Low Catalyst Loadings in Heterogeneous Metallaphotocatalysis | The development of heterogeneous metallaphotocatalysis is of great interest for sustainable organic synthesis. The rational design and controllable preparation of well-defined (site-isolated) metal/photo bifunctional solid catalysts to meet such goals remain a critical challenge. Herein, we demonstrate the incorporation of privileged homogeneous bipyridyl-based Ni-catalysts into highly ordered and crystalline potassium poly(heptazine imide) (K-PHI). A variety of PHI-supported cationic bipyridyl-based Ni catalysts (LnNi-PHI) have been prepared and fully characterized by various techniques, including NMR, ICP-OES, XPS, HAADF-STEM, and XAS. The LnNi-PHI catalysts exhibit exceptional chemical stability and recyclability in diverse C−P, C−S, C−O, and C−N cross-coupling reactions. The proximity and cooperativity effects in LnNi-PHI significantly enhance the photo/Ni dual catalytic activity, thus resulting in low catalyst loadings and high turnover numbers. | Liuzhuang Xing; Qian Yang; Chen Zhu; Yilian Bai; Yurong Tang; Magnus Rueping; Yunfei Cai | Organic Chemistry; Inorganic Chemistry; Catalysis; Organic Synthesis and Reactions; Photochemistry (Org.); Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639df138e9d0fd23b320876a/original/poly-heptazine-imide-ligand-exchange-enables-remarkable-low-catalyst-loadings-in-heterogeneous-metallaphotocatalysis.pdf |
674b14bcf9980725cf96f3bd | 10.26434/chemrxiv-2024-74pzh-v2 | Are Grignard Reactions in Deep Eutectic Solvents Interface-Driven? | Organolithium and organomagnesium addition reactions to ketones are important and versatile processes used in synthetic organic chemistry. However, due to the high reactivity of these species, the reactions are usually done under an inert atmosphere at low temperature. Recent work has demonstrated the possibility to carry out these procedures safely on the benchtop, in air at room temperature using deep eutectic solvents (DES) to dissolve the organic substrate. Surprisingly the organometallic reagent, added in an organic solution, is compatible with these unconventional conditions, and instead of undergoing fast decomposition by the DES, better yields and selectivities are observed than when working under standard conditions. Earlier it was posited that the choline chloride component of the DES might chemically activate the ketone substrate making it more amenable to reaction. Here we probe this hypothesis with experiments; liquid diffraction, neutron reflectometry, NMR and interfacial tension measurements for acetophenone in DES and with all-atom molecular dynamics simulations. We show instead that the role of the choline chloride is to reduce the solubility of the ketone, forcing it to accumulate at the air-solvent (or organic solvent/DES) interface. Molecular dynamics simulations for isopropyl magnesium chloride in the same DES/tetrahydrofuran bi-phase system also indicate a preference to localize at the interface. These results suggest that surface accumulation promotes the addition reaction and account for these remarkable experimental conditions. Accumulation of the organic non-protic substrate at the interface could also protect the organometallic species from rapid decomposition by the protons of the DES. | Iva Manasi; Marco Bortoli; Daniel Bowron ; Mario Campana; Oliver Hammond; Tom Headen; Jake Hooton; Eva Hevia; Michele Cascella; Odile Eisenstein; Karen Edler | Theoretical and Computational Chemistry; Physical Chemistry; Organometallic Chemistry; Main Group Chemistry (Organomet.); Physical and Chemical Processes; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674b14bcf9980725cf96f3bd/original/are-grignard-reactions-in-deep-eutectic-solvents-interface-driven.pdf |
60c741e8f96a0080c02864ea | 10.26434/chemrxiv.7629467.v3 | Intrinsic doping limit and defect-assisted luminescence in Cs4PbBr6 | Cs<sub>4</sub>PbBr<sub>6 </sub>is a member of the halide perovskite family that is built from isolated (zero-dimensional) PbBr<sub>6</sub><sup>4-</sup> octahedra with Cs<sup>+</sup> counter ions. The material exhibits anomalous optoelectronic properties: optical absorption and weak emission in the deep ultraviolet (310 - 375 nm) with efficient luminescence in the green region (~ 540 nm). Several hypotheses have been proposed to explain the giant Stokes shift including: (i) phase impurities; (ii) self-trapped exciton; (iii) defect emission. We explore, using first-principles theory and self-consistent Fermi level analysis, the unusual defect chemistry and physics of Cs<sub>4</sub>PbBr<sub>6</sub>. We find a heavily compensated system where the room-temperature carrier concentrations (< 10<sup>9</sup> cm<sup>-3</sup>) are more than one million times lower than the defect concentrations. We show that the low-energy Br-on-Cs antisite results in the formation of a polybromide (Br<sub>3</sub>) species that can exist in a range of charge states. We further demonstrate from excited-state calculations that tribromide moieties are photoresponsive and can contribute to the observed green luminescence. Photoactivity of polyhalide molecules is expected to be present in other halide perovskite-related compounds where they can influence light absorption and emission. <br /> | Young-Kwang Jung; Joaquin Calbo; Ji-Sang Park; Lucy D. Whalley; Sunghyun Kim; Aron Walsh | Optical Materials; Computational Chemistry and Modeling; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741e8f96a0080c02864ea/original/intrinsic-doping-limit-and-defect-assisted-luminescence-in-cs4pb-br6.pdf |
6621d76b21291e5d1d23d57e | 10.26434/chemrxiv-2024-l21qz | Machine learning photodynamics beyond the Frenkel exciton model: Intermolecular vibrations trigger ultrafast singlet fission in pentacene crystal | Crystalline pentacene is a model solid-state light-harvesting material because its quantum efficiencies exceed 100% via ultrafast singlet fission (SF). The SF mechanism in pentacene crystals is unresolved due to insufficient electronic information in time-resolved experiments and intractable quantum mechanical calculations for simulating realistic crystal dynamics. We combine multiscale multiconfigurational approach and machine learning (ML) photodynamics to understand SF in pentacene crystals. Our simulations identify two competing SF channels in the herringbone and parallel dimers, underpinning the high efficiency of SF in pentacene crystal. The predicted SF time constants (61 and 33 fs) are in excellent agreement with experiments (78 and 35 fs). The trajectories highlight the essential role of intermolecular stretching between monomers in generating the multi-exciton state. The ML-photodynamics resolved the elusive interplay between electronic structure and vibrational relations in the SF dynamics, enabling fully atomistic excited-state dynamics for the solid state with multiconfigurational quantum mechanical calculations. | Zhendong Li; Federico Hernández; Christian Salguero; Steven Lopez; Rachel Crespo-Otero; Jingbai Li | Theoretical and Computational Chemistry; Physical Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6621d76b21291e5d1d23d57e/original/machine-learning-photodynamics-beyond-the-frenkel-exciton-model-intermolecular-vibrations-trigger-ultrafast-singlet-fission-in-pentacene-crystal.pdf |
60c74f41ee301c2e73c7a68c | 10.26434/chemrxiv.12869651.v1 | Lessons from the USMA Faculty Development Workshop in Teaching STEM Courses During COVID-19 | <p>Prior to the start of every academic year, the Department of Chemistry and Life Science in the United States Military Academy at West Point conducts a four-week Faculty Development Workshop (FDW). The purpose of FDW is to develop new faculty such that they are prepared to effectively educate students, and a critical hallmark of this program is in-depth feedback and mentorship from senior faculty. With nationwide uncertainty regarding the method of instruction for the upcoming semester, ranging from remote to in-person, and the possibility that schools may need to transition to exclusively remote learning during the semester due to health concerns from Coronavirus disease (COVID-19), this year’s FDW incorporated different modes of instruction. Using classrooms with a maximum capacity of 20 students, new instructors conducted lessons fully remote, in-person with modified classroom paradigms, and through a hybrid approach where half of the students attended class synchronously online and the other half attended class in-person to facilitate social distancing requirements. In the process of preparing new instructors for the upcoming semester and equipping them with tools to teach under varied conditions, numerous lessons were learned on best practices for teaching this fall. In this manuscript, we describe our implementation of FDW and review the aforementioned teaching modalities, with a critical focus on the advantages and disadvantages of each teaching approach during COVID-19 and faculty perceptions on the difficulty and efficacy of each format of instruction.</p> | Eric Mowles; Chi Nguyen; Lam Nguyen; Jared E Hollows; Melissa Eslinger; Eileen Kowalski; F John Burpo; Ryan Limbocker | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f41ee301c2e73c7a68c/original/lessons-from-the-usma-faculty-development-workshop-in-teaching-stem-courses-during-covid-19.pdf |
60c75495337d6c9535e28a81 | 10.26434/chemrxiv.13679083.v1 | A Rearrangement of Allylic Silanols | <div>
<p><a>We show that
1M aq. HCl/THF or NaBH<sub>4</sub>/DMF allows for demercurative ring-opening of
cyclic organomercurial synthons into secondary silanol products bearing
terminal alkenes. We had previously demonstrated that primary allylic silanols
are readily transformed into cyclic organomercurials using Hg(OTf)<sub>2</sub>/NaHCO<sub>3</sub>
in THF. Overall, this amounts to a facile two-step protocol for the
rearrangement of primary allylic silanol substrates. Computational
investigations suggest that this rearrangement is under </a>thermodynamic control and that the di-tert-butylsilanol protecting
group is essential for product selectivity.</p>
</div>
<br /> | Shyam Sathyamoorthi; Ranjeet Dhokale; Frederick Seidl | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75495337d6c9535e28a81/original/a-rearrangement-of-allylic-silanols.pdf |
60c75338bb8c1ae9993dbfd6 | 10.26434/chemrxiv.13431158.v1 | Visible-Light Induced Singlet Nucleophilic Carbenes: Rapid and Mild Access to Fluorinated Tertiary Alcohol Derivatives | Singlet nucleophilic carbenes (SNCs) that
contain only one heteroatom donor remain underexplored and underutilized in chemical
synthesis. To discover new synthetic strategies that harness these SNCs as
reactive intermediates, aromatic or aliphatic siloxy carbenes represent
excellent model substrates as they can be readily generated photochemically
from stable acyl silane precursors. We herein report the discovery that photochemically
generated siloxy carbenes undergo 1,2-carbonyl addition to trifluoromethyl
ketones, followed by a silyl transfer process to afford benzoin-type products.
This new transformation is a rare example of the use of ketones as trapping reagents
for SNC intermediates and delivers an efficient, user-friendly and scalable process
to access fluorinated tertiary alcohol derivatives driven by only light, circumventing
the use of catalysts or additives. | Daniel Priebbenow; Rowan Pilkington; Anastasios Polyzos | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75338bb8c1ae9993dbfd6/original/visible-light-induced-singlet-nucleophilic-carbenes-rapid-and-mild-access-to-fluorinated-tertiary-alcohol-derivatives.pdf |
66378eaf21291e5d1d7e0c52 | 10.26434/chemrxiv-2024-89cw5 | Discovering Neuraminidase Inhibitors via Computational and Experimental Studies | Influenza A viruses spread out worldwide causing several global concerns. Discovering neuraminidase inhibitors to prevent the influenza A virus is thus of great interests. In this work, a machine learning model was trained and tested to evaluate the ligand-binding affinity to neuraminidase. The model was then used to predict the possibility of compounds from the CHEMBL database, which is manually curated database of bioactive molecules with drug-like properties. The physical insights into the binding process of ligands to neuraminidase were clarified via molecular docking and molecular dynamics simulations. Experimental studies on enzymatic and antiviral activity as well as cytotoxicity have validated our computational results and suggested that 2 compounds were potential inhibitors of neuraminidase of the influenza A virus. | Trung Hai Nguyen; Ngoc Quynh Anh Pham; Quynh Mai Thai; Van V. Van; Son Tung Ngo; Jim-Tong Horng | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66378eaf21291e5d1d7e0c52/original/discovering-neuraminidase-inhibitors-via-computational-and-experimental-studies.pdf |
66913826c9c6a5c07a16eeee | 10.26434/chemrxiv-2024-6rn7j | Rational exploration of 2,4-diaminopyrimidines as DHFR inhibitors active against Mycobacterium abscessus and Mycobacterium avium, two emerging human pathogens | Nontuberculous mycobacteria (NTM) are emerging human pathogens linked to severe pulmonary diseases. Current treatments involve the prolonged use of multiple drugs and are often ineffective. Bacterial dihydrofolate reductase (DHFR) is a key enzyme targeted by antibiotics in Gram-negative bacterial infections. However, existing DHFR inhibitors designed for Gram-negative bacteria often fail against mycobacterial DHFRs. Here, we detail the rational design of NTM DHFR inhibitors based on P218, a malarial DHFR inhibitor. We identified 8, a 2,4-diaminopyrimidine exhibiting improved pharmacological properties and activity against purified DHFR and whole cell cultures of two predominant NTM species: Mycobacterium avium and Mycobacterium abscessus. This study underscores the potential of 8 as a promising candidate for the in vivo validation of DHFR as an effective treatment against NTM infections. | Matheus Meirelles; Vitor Almeida; Jaryd Sullivan; Ian de Toledo; Caio dos Reis; Micael Cunha; Rachael Zigweid; Abraham Shim; Banumathi Sankaran; Elijah Woodward; Steve Seibold; Lijun Liu; Mohammad Mian; Kevin Battaile; Jennifer Riley; Christina Duncan; Frederick Simeons; Liam Ferguson; Kevin Read; Scott Lovell; Bart Staker; Marcel Behr; Ronaldo Pilli; Rafael Couñago | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66913826c9c6a5c07a16eeee/original/rational-exploration-of-2-4-diaminopyrimidines-as-dhfr-inhibitors-active-against-mycobacterium-abscessus-and-mycobacterium-avium-two-emerging-human-pathogens.pdf |
672893cff9980725cf0ad212 | 10.26434/chemrxiv-2024-s0kks-v6 | Exploring Magnesium- and Calcium-Ion Conductors Via Solid-State Metathesis Reactions | Magnesium and calcium batteries offer promising energy storage solutions characterised by cost-effectiveness, safety, and high energy density. However, the scarcity of viable electrode and electrolyte materials vastly hinders their advancement. This study utilises solid-state metathetical reactions involving predominantly chalcogen- and pnictogen-based honeycomb layered oxides with alkaline-earth halides/nitrates to synthesise Mg- and Ca-based materials previously achievable only under high-temperature/high-pressure conditions, as well as new metastable materials with unique crystal versatility. Particularly, we employ metathetical reactions involving Li4MgTeO6, Na2Mg2TeO6, and Na4MgTeO6 with MgCl/Mg(NO3)2 or Ca(NO3)2 at temperatures not exceeding 773 K to produce Mg3TeO6 polymorphs, ilmenite-type CaMg2TeO6 (Mg2CaTeO6), and double perovskite Ca2MgTeO6. Thus, we demonstrate that these materials, conventionally requiring gigascale pressures and high temperatures (>1273 K) for their proper synthesis, are now readily accessible at ambient pressure and considerably lower temperatures. Meanwhile, despite sub-optimal pellet densities, the synthesised ilmenite-type Mg3TeO6 and double perovskite Ca2MTeO6 (M=Mg,Ca,Zn) materials exhibit remarkable bulk ionic conductivity at room temperature, marking them as promising compositional spaces for exploring novel Mg2+ and Ca2+ conductors. Furthermore, this study extends the applicability of metathetical reactions to attain Mg- or Ca-based antimonates, bismuthates, ruthenates, tungstates, titanates, phosphates, and silicates, thus opening avenues to novel multifunctional nanomaterial platforms with utility in energy storage and beyond.
| Titus Masese; Godwill Kanyolo; Yoshinobu Miyazaki; Shintaro Tachibana; Keigo Kubota; Naoya Ishida; Kohei Tada; Hiroyuki Ozaki; Toyoki Okumura; Sahori Takeda; Sachio Komori; Tomoyasu Taniyama; Yuki Orikasa; Tomohiro Saito | Materials Science; Energy; Materials Processing; Nanostructured Materials - Materials; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672893cff9980725cf0ad212/original/exploring-magnesium-and-calcium-ion-conductors-via-solid-state-metathesis-reactions.pdf |
60c75304bdbb89cd0ba3a3c1 | 10.26434/chemrxiv.13379957.v1 | Sialylation Fine-Tunes Glycoprotein Structural Microheterogeneity Associated with Alzheimer’s Disease as Captured by Native Ion Mobility-Mass Spectrometry | Protein sialylation has
been closely linked to many diseases including Alzheimer’s disease (AD) and is
broadly implicated in therapeutics in a terminal structure-sensitive manner.
However, how sialylation structurally affects mature glycoproteins and how such
effect is linked biochemically to AD progression largely remain ill-defined and
are, likely beset with the lack of appropriate strategies capable of rapid and
in situ manipulation of sialic acids on mature glycoproteins. Herein, we report
the use of native ion mobility-mass spectrometry (IM-MS)-based structural probing
methodology, enabling well-controlled, synergistic and in situ manipulation of mature
glycoproteins and attached sialic acids. Cell viability experiments and IM-MS
suggest that the dysregulating effects of transferrin sialylation on the
iron-enhanced Aβ cytotoxicity acts through sialylation-dependent Aβ and iron
co-importing pathway. Meanwhile, native gel electrophoresis and IM-MS reveal
the sialylation-regulated transferrin dimerization tendency. Collectively, IM-MS
is adapted to capture key sialylation intermediates involved in fine-tuning
AD-associated glycoprotein structural micoheterogeneity. Our results may shed
new lights on AD-modifying strategies based on sialylation-regulated
glycoprotein functions and cytotoxicity. | Gongyu Li; Ashley Phetsanthad; Min Ma; Qinying Yu; Ashita Nair; Zhen Zheng; Kellen DeLaney; Fengfei Ma; Seungpyo Hong; Lingjun Li | Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75304bdbb89cd0ba3a3c1/original/sialylation-fine-tunes-glycoprotein-structural-microheterogeneity-associated-with-alzheimer-s-disease-as-captured-by-native-ion-mobility-mass-spectrometry.pdf |
64de382900bbebf0e65486d8 | 10.26434/chemrxiv-2023-96k5d | Pure Hydrolysis of Polyamides: A Comparative Study | Nylon, also known as polyamides (PAs), undergoes local environmental degradation, leading to a decline in its mechanical properties over time. The degradation process is strongly influenced by the surrounding environment in which the polymer is utilized. PAs can experience various forms of degradation, such as thermal degradation, oxidation, hydrothermal oxidation, UV oxidation, and hydrolysis. It is crucial to understand each of these degradation mechanisms individually to better comprehend the degradation process of nylon. Although extensive research has been conducted on hydrolysis over the past few decades, there is currently no comprehensive review that consolidates the latest findings. This review analyzes the available characterization data and evaluates the changes in molecular weight, crystallinity, chemical structure, and mechanical properties of PAs that have aged in oxygen-free water at high temperatures. The primary objective is to gain a comprehensive understanding of the aging process of PAs in water without oxygen. Additionally, secondary information is provided, including the influence of fibers and additives in the polymer, hydrolysis susceptibility among PAs with longer aliphatic chains, correlation between different parameters, impact of acids, and important factors for determining the point at which PAs become brittle when subjected solely to hydrolysis. | Mathis Mortensen Brette; Allan Hjarbæk Holm; Aleksey D. Drozdov; Jesper De Claville Christiansen | Materials Science; Polymer Science; Chemical Engineering and Industrial Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64de382900bbebf0e65486d8/original/pure-hydrolysis-of-polyamides-a-comparative-study.pdf |
633157b0fee74e27a84acfd2 | 10.26434/chemrxiv-2022-s4jw1-v2 | Non-Gaussian distributions of absolute free energies in ensemble molecular dynamics simulations | Significantly more ‘outliers’ can be produced from a non-Gaussian distribution than one would anticipate were the statistics to conform to a normal distribution. Using ensemble simulations consisting of 25 replicas, we have previously identified a considerable percentage of ligand-protein systems which present non-Gaussian distributions in calculated binding free energies. Here we report on the statistics of much larger ensemble and find that the free energy distributions are definitively non-Gaussian for these systems. | Peter Coveney; Shunzhou Wan | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633157b0fee74e27a84acfd2/original/non-gaussian-distributions-of-absolute-free-energies-in-ensemble-molecular-dynamics-simulations.pdf |
668c469301103d79c56929af | 10.26434/chemrxiv-2024-z9rgh | Zigzag Graphene Nanoribbons with Periodic Porphyrin
Edge Extensions | Graphene nanoribbons (GNRs) with zigzag edges are promising materials for spintronic devices due to tunable bandgaps and spin-polarized edge states. Porphyrins offer complementary benefits such as desirable optoelectronic properties. Here, we combine these features in a hybrid
system via the on-surface synthesis of zigzag-edge GNRs embedded with porphyrins laterally fused along the ribbon backbone. Using scanning probe methods, we show that this design achieves strong electronic coupling between porphyrin and GNR. For transition metal porphyrins, significant exchange coupling between distant metal centers is mediated by the π-electron system. Such hybrid d- and π-electron ribbon system introduces spin-orbit coupling and magnetic anisotropy to carbon nanomaterials, and holds great promise for the fabrication of one-dimensional spin qubit arrays. | Feifei Xiang; Yanwei Gu; Amogh Kinikar; Nicolò Bassi; Andres Ortega-Guerrero; Zijie Qiu; Oliver Gröning; Pascal Ruffieux; Carlo Pignedoli; Klaus Müllen; Roman Fasel | Materials Science; Nanoscience; Carbon-based Materials; Magnetic Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668c469301103d79c56929af/original/zigzag-graphene-nanoribbons-with-periodic-porphyrin-edge-extensions.pdf |
65eb66e39138d231610a8598 | 10.26434/chemrxiv-2024-r2tw8 | Characterizing Discrete Binding Conformations of T4 L99A via Markov State Modeling | As a model system, the binding pocket of the L99A mutant of T4 lysozyme has been the subject of numerous computational free energy studies. However, some previous studies have failed to fully sample and account for the observed changes in the binding pocket of T4 L99A upon binding of a congeneric ligand series, limiting the accuracy of results. In this work, we establish definitions for the conformational states of the T4 L99A binding pocket based on the dynamics of the system rather than from experimental crystal structures. Using these definitions, we estimate the timescales for the transitions between states in this protein, which will have important implications for future binding studies in this system. We also discuss the need to develop enhanced sampling methods to generally account for significant changes in protein conformation due to relatively small ligand perturbations. | Chris Zhang; Meghan Osato; David Mobley | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65eb66e39138d231610a8598/original/characterizing-discrete-binding-conformations-of-t4-l99a-via-markov-state-modeling.pdf |
642e9c97736114c96301544d | 10.26434/chemrxiv-2023-q5rvm-v2 | On the Automatic Optimization of Lipid Models in the Martini Force Field using SwarmCG | After two decades of continued development of the Martini coarse-grained force field (CG FF), further refining the already rather accurate Martini lipid models has become a demanding task that could benefit from integrative data-driven methods. Automatic approaches are increasingly used in the development of accurate molecular models, but they typically make use of specifically-designed interaction potentials that transfer poorly to molecular systems or conditions different than those used for model calibration. As a proof of concept here we employ SwarmCG, an automatic multi-objective optimization approach facilitating the development of lipid force fields, to refine specifically the bonded interaction parameters in building blocks of lipid models within the framework of the general Martini CG FF. As targets of the optimization procedure, we employ both experimental observables (top-down references: area per lipid & bilayer thickness) and all-atom molecular dynamics simulations (bottom-up reference), respectively informing on the supra-molecular structure of the lipid bilayer systems and on their sub-molecular dynamics. In our training sets we simulate at different temperatures in the liquid and gel phases up to 11 homogeneous lamellar bilayers, composed of phosphatidylcholine lipids spanning various tail lengths and degrees of (un)saturation. We explore different CG representations of the molecules and evaluate improvements a posteriori using additional simulation temperatures and a portion of the phase diagram of a DOPC/DPPC mixture. Successfully optimizing up to ~80 model parameters within still limited computational budgets, we show that this protocol allows to obtain improved transferable Martini lipid models. In particular, the results of this study demonstrate how a fine tuning of the representation and parameters of the models may improve their accuracy, and how automatic approaches such as SwarmCG may be very useful to this end. | Charly Empereur-mot; Kasper B. Pedersen; Riccardo Capelli; Martina Crippa; Cristina Caruso; Mattia Perrone; Paulo C.T. Souza; Siewert J. Marrink; Giovanni M. Pavan | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2023-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642e9c97736114c96301544d/original/on-the-automatic-optimization-of-lipid-models-in-the-martini-force-field-using-swarm-cg.pdf |
65c613099138d23161c026c3 | 10.26434/chemrxiv-2024-3n41t | Decoupling strategy-enabled radical generality via an asymmetric SH2 path | Reaction generality is essential for evaluating the value and impact of a synthetic method. However, asymmetric catalysis, particularly that involving highly reactive species such as radicals, typically prioritizes enantioselectivity at the expense of generality. Selectivity and reactivity often conflict because the bond-forming step is usually also stereodetermining. If these two steps were separated, the reaction selectivity and generality issues could then be addressed independently. Herein we report a catalytic asymmetric radical coupling with great generality by merging the copper-catalyzed enantioselective S(IV) center formation and copper-mediated enantiospecific SH2 radical coupling. This decoupling strategy has enabled the successful coupling of over 30 different carbon-, nitrogen-, and oxygen-based radicals having a broad range of reactivity with N-acyl sulfenamides, leading to diverse S-chiral compounds with exceptional enantioselectivity. Thus, it offers a holistic approach to accessing a rich portfolio of S(IV) and S(VI) chiral centers, which is anticipated to have a transformative impact on the synthesis of S-chiral compounds and benefit medicinal chemistry and other related fields. Furthermore, this decoupling strategy via SH2 processes has promising potential to enable a comprehensive single-electron methodology for forging other chiral centers with heteroatoms such as phosphorous(III) and silicon(IV), and eventually also carbon atoms. | Li-Wen Fan; Jun-Bin Tang; Li-Lei Wang; Ji-Ren Liu; Zhong-Liang Li; Yu-Shuai Zhang; Dai-Lei Yuan; Li Qin; Cheng Luan; Qiang-Shuai Gu; Xin Hong; Zhe Dong; Xin-Yuan Liu | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c613099138d23161c026c3/original/decoupling-strategy-enabled-radical-generality-via-an-asymmetric-sh2-path.pdf |
6134c9e165db1e3fcbacf591 | 10.26434/chemrxiv-2021-gl4s5-v3 | PhotothermalPhage: A Virus-Based Photothermal Therapeutic Agent | ABSTRACT: Virus-like particles (VLPs) are multifunctional nanocarriers that mimic the architecture of viruses. They can serve as a safe platform for specific functionalization and immunization, which provides benefits in a wide range of biomedical applications. In this work, a new generation immunophotothermal agent is developed that adjuvants photothermal ablation using a chemically modified VLP called bacteriophage Qβ. The design is based on the conjugation of near-infrared absorbing croconium dyes to lysine residues located on the surface of Qβ, which turns it to a powerful NIR-absorber called Photothermal Phage. This system can generate more heat upon 808 nm NIR laser radiation than free dye and possesses a photothermal efficiency comparable to gold nanostructures, yet it is biodegradable and acts as an immunoadjuvant combined with the heat it produces. The synergistic combination of thermal ablation with the mild immunogenicity of the VLP leads to effective suppression of primary tumors, reduced lung metastasis, and increased survival time. | Arezoo Shahrivarkevishahi; Michael A. Luzuriaga; Fabian C. Herbert; Alisia C. Tumac; Olivia R. Brohlin; Yalini H. Wijesundara; Abhinay V. Adlooru; Candace Benjamin; Hamilton Lee; Perouza Parsamian; Jashkaran Gadhvi; Nicole J. De Nisco; Jeremiah J. Gassensmith | Nanoscience; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6134c9e165db1e3fcbacf591/original/photothermal-phage-a-virus-based-photothermal-therapeutic-agent.pdf |
627d794843d1f01c5a2a81f2 | 10.26434/chemrxiv-2022-gh1x3-v2 | Polymer-Induced Biofilms for Enhanced Biocatalysis | The intrinsic resilience of biofilms to environmental conditions makes them an attractive plat-form for biocatalysis, bioremediation, agriculture or consumer health. However, one of the main challenges in these areas is that beneficial bacteria are not necessarily good at biofilm formation. Currently, this problem is solved by genetic engineering or experimental evolution, techniques that can be costly and time consuming, require expertise in molecular biology and/or microbiolo-gy and, more importantly, are not suitable for all types of microorganisms or applications. Here we show that synthetic polymers can be used as an alternative, working as simple additives to nucleate the formation of biofilms. Using MC4100, a strain of Escherichia coli that forms bio-films poorly, we demonstrate that hydrophobic polymers induce clustering and promote biofilm formation in this bacterium, with increasingly hydrophobic polymers outperforming less hydro-phobic polymers. Moreover, we compare the effect of the polymers on MC4100 against PHL644, an E. coli strain that forms biofilms well due to a single point mutation which increases expres-sion of the adhesin curli. In the presence of selected polymers MC4100 can reach levels of bio-mass production and curli expression similar or higher than PHL644, demonstrating that syn-thetic polymers promote similar changes in microbial physiology than those introduced following genetic modification. Finally, we demonstrate that these polymers can be used to improve the performance of MC4100 biofilms in the biocatalytic transformation of 5-fluoroindole into 5-fluorotryptophan. Our results show that incubation with these synthetic polymers helps MC4100 match and even outperform PHL644 in this biotransformation, demonstrating that synthetic polymers can underpin the development of beneficial applications of biofilms. | Pavan Adoni; Andrey Romanyuk; Tim Overton; Paco Fernandez-Trillo | Catalysis; Polymer Science; Biocatalysis | CC BY NC 4.0 | CHEMRXIV | 2022-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627d794843d1f01c5a2a81f2/original/polymer-induced-biofilms-for-enhanced-biocatalysis.pdf |
65801d2066c1381729796f32 | 10.26434/chemrxiv-2023-33j02 | One chiral fingerprint to find them all | Background: Molecular fingerprints are indispensable tools in cheminformatics. However, stereochemistry is generally not considered, which is problematic for large molecules which are almost all chiral.
Results: Herein we report MAP4C, a chiral version of our previously reported fingerprint MAP4, which lists MinHashes computed from character strings containing the SMILES of all pairs of circular substructures up to a diameter of four bonds and the shortest topological distance between their central atoms. MAP4C includes the Cahn-Ingold-Prelog (CIP) annotation (R, S, r or s) whenever the chiral atom is the center of a circular substructure, a question mark for undefined stereocenters, and double bond cis-trans information if specified. MAP4C performs as good as the achiral MAP4, ECFP and AP fingerprints in non-stereoselective virtual screening benchmarks. Furthermore, it readily distinguishes between thousands of stereoisomers in complex natural products and peptides.
Conclusion: MAP4C is recommended as a generally applicable chiral molecular fingerprint.
| Markus Orsi; Jean-Louis Reymond | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65801d2066c1381729796f32/original/one-chiral-fingerprint-to-find-them-all.pdf |
67459da85a82cea2faf147c6 | 10.26434/chemrxiv-2024-fxwm3 | A Study on the Allylic Oxidation of Some beta -Rose Ketones | A study on the allylic oxidation of some beta-rose ketones was conducted. The oxo-derivatives of three representative rose ketones beta-damascone, beta-damascenone and beta-ionone were synthesized by using Rh-catalyzed allylic oxidation in good yields at room temperature in the presence of tert-butyl hydroperoxide. Some typical oxidants for allylic oxidation were screened to compare with the Rh-catalyzed reaction by using HPLC analysis (external standard method). The conventional oxidants, i.e. CrO3 and SeO2 with different modified conditions gave generally inferior yields. These results indicated that this method exhibited high efficiency and good selectivity in the oxidation of beta-rose ketones. The presence of water played an important role in promoting the oxidation reaction. The Rh-catalyzed reactions can be conducted under mild, environment friendly reaction conditions, very low loading of catalyst and the possibility of repeated use of Rh-catalyst, making it a competitive method for large scale preparations of such fragrances. | Deshou Mao; Shihua Zhu; Yafen Zhao; Wenwen Zhang; Ruilin Hu; Bingbiao Cai; Cenming Zhu; Jianfeng Li | Agriculture and Food Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67459da85a82cea2faf147c6/original/a-study-on-the-allylic-oxidation-of-some-beta-rose-ketones.pdf |
664280c1418a5379b02c7a22 | 10.26434/chemrxiv-2024-dmpdd | Plasma-Structured Molybdenum Oxycarbides Enabling Ultrastable Acidic Hydrogen Evolution up to 10 A cm-2 | Fabricating electrocatalysts capable of stable operation at high current densities is crucial for the industrial proton exchange membrane water electrolysis. However, current catalysts suffer from high overpotentials and rapid degradation when working in acid electrolytes at high current densities. In this paper, we report the design of vertical-standing, nanoedge-enriched molybdenum oxycarbide electrocatalysts via plasma-enhanced chemical vapor deposition (PECVD) with salts as precursors to achieve outstanding acidic electrocatalytic hydrogen evolution performance. Benefiting from their unique structural features and chemical compositions, the plasma-grown molybdenum oxycarbide catalysts exhibit a low overpotential of 415 mV at industrial-level high current densities up to 10 A cm-2 for 1,000 h, corresponding to an ultrahigh hydrogen throughput of 4,477.4 L cm-2 and substantially surpassing the performance of state-of-the-art transition metal- and even noble metal-based catalysts. This work paves the way for the development of new transition metal-based catalysts for practical industrial electrocatalytic hydrogen evolution. | Shiwen Wu; Taesoon Hwang; Amirarsalan Mashhadian; Tianyi Li; Kyeongjae Cho; Guoping Xiong | Catalysis; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2024-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664280c1418a5379b02c7a22/original/plasma-structured-molybdenum-oxycarbides-enabling-ultrastable-acidic-hydrogen-evolution-up-to-10-a-cm-2.pdf |
654bf307dbd7c8b54bdfbd0e | 10.26434/chemrxiv-2023-4m3rt-v2 | Applying Large Graph Neural Networks to Predict Transition Metal Complex Energies Using the tmQM_wB97MV Dataset | Machine learning (ML) methods have shown promise for discovering novel catalysts, but are often restricted to specific chemical domains. Generalizable ML models require large and diverse training datasets, which exist for heterogeneous catalysis but not for homogeneous catalysis. The tmQM dataset, which contains properties of 86,665 transition metal complexes calculated at the TPSSh/def2-SVP level of density functional theory (DFT), provided a promising training dataset for homogeneous catalyst systems. However, we find that ML models trained on tmQM consistently underpredict the energies of a chemically distinct subset of the data. To address this, we present the tmQM_wB97MV dataset, which filters out several structures in tmQM found to be missing hydrogens and recomputes the energies of all other structures at the wB97M-V/def2-SVPD level of DFT. ML models trained on tmQM_wB97MV show no pattern of consistently incorrect predictions and much lower errors than those trained on tmQM. The ML models tested on tmQM_wB97MV were, from best to worst, GemNet-T > PaiNN ~ SpinConv > SchNet. Performance consistently improves when using only neutral structures instead of the entire dataset. However, while models saturate with only neutral structures, more data continues to improve the models when including charged species, indicating the importance of accurately capturing a range of oxidation states in future data generation and model development. Furthermore, a fine-tuning approach where weights were initialized from models trained on OC20 led to drastic improvements in model performance, indicating transferability between ML strategies of heterogeneous and homogeneous systems. | Aaron Garrison; Javier Heras-Domingo; John Kitchin; Gabriel Gomes; Zachary Ulissi; Samuel Blau | Theoretical and Computational Chemistry; Machine Learning | CC BY 4.0 | CHEMRXIV | 2023-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654bf307dbd7c8b54bdfbd0e/original/applying-large-graph-neural-networks-to-predict-transition-metal-complex-energies-using-the-tm-qm-w-b97mv-dataset.pdf |
60c7467bee301c7f63c79516 | 10.26434/chemrxiv.11328242.v1 | A Comonomer Strategy for Triggered Degradation and Re/Upcycling of High-Performance Thermoset Plastics | Thermosets play a key role in the modern plastics and rubber industries, comprising ~18% of polymeric materials with a worldwide annual production of 65 million tons. The high density of crosslinks that give these
materials their useful properties comes at the expense of facile degradability
and re/upcyclability. Here, using the high-performance industrial thermoset plastic poly-dicyclopentadiene (pDCPD) as a model system, we show that when a small number of cleavable bonds are selectively installed within the strands of thermoset plastics using a low-cost comonomer approach, the resulting materials display the same exceptional properties as the native material yet they can undergo triggered degradation to yield soluble, re/upcyclable products of controlled size and functionality. In contrast, installation of cleavable crosslinks, even at comparably high loadings, does not produce degradable materials. These findings shed new light on the topology of polymer networks, revealing cleavable bond location as a universal design principle for controlled thermoset degradation and re/upcycling.<br /> | Peyton Shieh; Wenxu Zhang; Keith Husted; Samantha Kristufek; Boya Xiong; David Lundberg; Jet Lem; David Veysset; Yuchen Sun; Keith Nelson; Desiree Plata; Jeremiah Johnson | Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7467bee301c7f63c79516/original/a-comonomer-strategy-for-triggered-degradation-and-re-upcycling-of-high-performance-thermoset-plastics.pdf |
66fe8b2acec5d6c14207c8d8 | 10.26434/chemrxiv-2024-ff58v | Metal Halide Perovskite-based Heterojunctions for Green Ammonia Production: Material Engineering and Mechanistic Features | Designing innovative photocatalysts for nitrogen photofixation is becoming crucial for the development of carbon neutral ammonia production. Metal halide perovskites (MHPs) have been demonstrated to be effective materials to run a wide range of photoredox reactions mediated by solar light. Herein, we develop an innovative heterojunction based on the vacancy-ordered double perovskite Cs2SnBr6 and carbon nitride nanosheets and demonstrate its ability in running the nitrogen photofixation reaction to produce ammonia. We explore the full compositional range for the Cs2SnBr6/g-C3N4 system and identify an optimal range providing an ammonia evolution rate up to 260 μmol g-1 h-1, the highest value reported to date for a MHP-containing catalyst. Mechanistic insight into the photofixation reaction promoted by the heterojunction was obtained through a combination of advanced spectroscopy and computational modelling. Efficient ammonia production stems from an effective charge transfer from the perovskite to the nitrogen vacancies on the carbon nitride enabled by the absence of self-trapped excitons in Cs2SnBr6 which also provides additional reactive sites through bromide vacancies. This work, reporting an efficient MHP-based heterojunction for nitrogen photofixation and a clear definition of the underlying reaction mechanism, provides a catalyst design strategy that may pave the way for sustainable ammonia production. | Lorenzo Malavasi; Costanza Tedesco; Angelica Simbula; Riccardo Pau; Michele Saba; Andrea Speltini; Antonella Profumo; Francesca Merlo; Vincenza Armenise; Andrea Listorti; Asma Alothman; Luca Gregori; Edoardo Mosconi | Materials Science; Catalysis | CC BY 4.0 | CHEMRXIV | 2024-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fe8b2acec5d6c14207c8d8/original/metal-halide-perovskite-based-heterojunctions-for-green-ammonia-production-material-engineering-and-mechanistic-features.pdf |
65d63cfb66c13817292ef917 | 10.26434/chemrxiv-2024-f1mxj | Spectral and dynamical properties of multiexcitons in semiconductor nanorods | Understanding multiple charge carrier relaxation dynamics in semiconductor nanocrystals is crucial for utilizing their full potential, as it allows to guide the design of optimized structures. Multiple excitons dynamics often are characterized via the observation of additional fast exponential kinetics at band edge in transient absorption spectroscopy data with increasing excitation intensities. However, these investigations are complicated by the formation of surface localized excitons which also introduce additional fast decay components which could falsely be interpreted as multiexciton kinetics in semiconductor nanocrystals. Another challenge presents the generation of a distribution of species in dependence of the excitation intensity not only including single and double excited systems, but even higher-order multiple excitons. In this study we used intensity dependent transient absorption spectroscopy with broadband probing spanning the whole visible range to identify characteristic spectroscopic signatures for the presence of multiple excitons of varying order in seeded and non-seeded CdS nanorods. Applying an MCMC sampling approach for global target analysis enables us to determine contributions of multiple exciton decay via Auger recombination and population of surface exciton states to the observed transient dynamics. The influence of surface chemistry, i.e., the nature of the surface ligands on multiexciton dynamics of nanorods is studied. | Krishan Kumar; Maria Wächtler | Physical Chemistry; Nanoscience; Energy; Nanostructured Materials - Nanoscience; Quasiparticles and Excitations; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d63cfb66c13817292ef917/original/spectral-and-dynamical-properties-of-multiexcitons-in-semiconductor-nanorods.pdf |
6491cdc3853d501c00338984 | 10.26434/chemrxiv-2022-c6npj-v3 | Intrinsic Bond Strength Index as a halogen bond interaction energy predictor | Halogen bonds (XBs) have become increasingly popular over the past few years with numerous applications in catalysis, material design, anion recognition, and medicinal chemistry. To avoid a \textit{post factum} rationalization of XB trends, descriptors can be tentatively employed to predict the interaction energy of potential halogen bonds. These typically comprise the electrostatic potential maximum at the tip of the halogen, ${V_{S, max}}$, or properties based on the topological analysis of the electronic density. However, such descriptors either can only be used with confidence for specific families of halogen bonds or require intense computations and, therefore, are not particularly attractive for large datasets with diverse compounds or biochemical systems. Therefore, the development of a simple, widely applicable, and computationally cheap descriptor remains a challenge as it would facilitate the discovery of new XB applications while also improving the existing ones. Recently, the Intrinsic Bond Strength Index (IBSI) has been proposed as a new tool to evaluate any bond strength, however, it has not been extensively explored in the context of halogen bonding. In this work, we show that IBSI values linearly correlate with the interaction energy of diverse sets of closed-shell halogen-bonded in the ground state, and therefore, can be used to quantitatively predict this property. Although the linear fit models that use quantum-mechanics-based electron density provided MAEs typically below 1~kcal~mol$^{-1}$, this type of calculation might still be computationally heavy in large sets or systems. Therefore, we also explored the exciting possibility to use a promolecular density approach (\pro{}), which only requires the geometry of the complex as an input, being computationally cheap. Surprisingly, the performance was comparable to the QM-based methods, thus opening the door for the usage of \pro{} as a fast, yet accurate, XB energy descriptor in large datasets but also in biomolecular systems such as protein--ligand complexes. We also show that $\delta g^{pair}$ descriptor emerging from the Independent Gradient Model that leads to IBSI can be seen as a term proportional to the overlapping van der Waals volume of the atoms at a given interaction distance. Overall ISBI can be thought of as a complementary descriptor to ${V_{S, max}}$ for situations when the geometry of the complex is available and QM calculations are not feasible whereas the latter still remains a hallmark of XB descriptors | Ona Šivickytė; Paulo J. Costa | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6491cdc3853d501c00338984/original/intrinsic-bond-strength-index-as-a-halogen-bond-interaction-energy-predictor.pdf |
6630fcff21291e5d1d176e4a | 10.26434/chemrxiv-2023-4s67j-v2 | Synthesis of zirconium(IV) and hafnium(IV) isopropoxide, sec-butoxide and tert-butoxide | We revisited the synthesis of zirconium(IV) and hafnium(IV) alkoxides, namely the metal isopropoxide isopropanol complex (M(OiPr)4.iPrOH, M = Zr, Hf) and the metal sec- and tert-butoxide (M(OsBu)4 and M(OtBu)4, M = Zr, Hf). We optimized the most convenient synthesis methods and compared the products with commercial sources. En route to the metal sec- and tert-butoxides, we synthesized the metal diethylamido complex (M(NEt2)4, M = Zr, Hf). | Evert Dhaene; Carlotta Seno; Jonathan De Roo | Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Organometallic Compounds; Transition Metal Complexes (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6630fcff21291e5d1d176e4a/original/synthesis-of-zirconium-iv-and-hafnium-iv-isopropoxide-sec-butoxide-and-tert-butoxide.pdf |
60c74e64567dfe3d57ec54ef | 10.26434/chemrxiv.12746558.v1 | Structure-Based Screening of Potential Triterpenoids for Anti-Viral Activity Against SARS-CoV-2 and Related Coronaviruses | <p>Triterpenoids possess valuable medicinal
properties ranging from anti-microbial to anti-cancer. Some of them were known
for their activity against HIV, Ebola and Influenza viruses. In this study, 108
triterpenoids were screened for its potential usage as anti-viral drug against
SARS-CoV-2, MERS and SARS coronaviruses, using molecular docking calculation
against their main proteases (M<sup>pro</sup>) and ADME based drug-likeliness parameters.<br /></p> | Vijaya sundar Jeyaraj; Thiagarayaselvam Aarthy | Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e64567dfe3d57ec54ef/original/structure-based-screening-of-potential-triterpenoids-for-anti-viral-activity-against-sars-co-v-2-and-related-coronaviruses.pdf |
6710c53bcec5d6c14266377c | 10.26434/chemrxiv-2024-hs3gv-v2 | Template-assisted electrospinning and 3D printing of multilayered hierarchical vascular grafts | Fabricating complex hierarchical structures mimicking natural vessels and arteries is pivotal for addressing problems of cardiovascular diseases. Various fabrication strategies have been explored to achieve this goal, each contributing unique advantages and challenges to the development of functional vascular grafts. In this study, a three-layered tubular structure resembling vascular grafts was fabricated using biocompatible and biodegradable copolymers of poly(butylene succinate)(PBS) using advanced manufacturing techniques. The outer layer was fabricated by template-assisted electrospinning utilizing 3D printed scaffold with a precise hexagonal pore design as the template, and the inner layer was coated with gelatin through perfusion. Cellulose nanocrystals (CNC) were incorporated into electrospun fibers to enhance mechanical properties. Gelatin coating was applied to the lumen using perfusion coating, resembling inner layer. Integration of 3D printed structures with electrospun fibers via template-assisted electrospinning, and gelatin coating resulted in a seamless multilayered scaffold. Mechanical testing demonstrated robustness, surpassing natural arteries in some aspects, while gelatin coating significantly reduced liquid leakage, ensuring leak-free functionality. Cytotoxicity assessment confirmed biocompatibility of processed materials with fibroblast cells, supporting potential for medical applications. | Moein Zarei; Marek J. Żwir; Beata Michalkiewicz; Jarosław Gorący; Miroslawa El Fray | Materials Science; Biocompatible Materials; Materials Processing | CC BY 4.0 | CHEMRXIV | 2024-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6710c53bcec5d6c14266377c/original/template-assisted-electrospinning-and-3d-printing-of-multilayered-hierarchical-vascular-grafts.pdf |
60c73dd4702a9b287d189c3f | 10.26434/chemrxiv.6149204.v1 | Mobilising Ion Mobility Mass Spectrometry in a Synthetic Biology Analytics Workflow | <p>Chromatography based mass spectrometry approaches (xC-MS)
are commonly used in untargeted metabolomics, providing retention time, m/z
values and metabolite specific-fragments all of which are used to identify and validate
an unknown analyte. Ion mobility-mass spectrometry (IM-MS) is emerging as an
enhancement to classic xC-MS strategies, by offering additional separation as
well as collision cross section (CCS) determination. In order to apply such an
approach to a synthetic biology workflow, verified data from metabolite
standards is necessary. In this work we present experimental <sup>DT</sup>CCS<sub>N2</sub>
values for a range of metabolites in positive and negative ionisation modes
using drift time-ion mobility-mass spectrometry (DT-IM-MS) with nitrogen as the
buffer gas. Creating a useful database containing <sup>DT</sup>CCS<sub>N2</sub>
measurements for application in metabolite identification relies on a robust
technique that acquires measurements of high reproducibility. We report that 86%
of the metabolites measured in replicate have a relative standard deviation
lower than 0.2 %. Examples of
metabolites with near identical mass are demonstrated to be separated by ion
mobility with over 4% difference in <sup>DT</sup>CCS<sub>N2</sub> values. We conclude
that the integration of ion mobility into current LC-MS workflows can aid in
small molecule identification for both targeted and untargeted metabolite
screening which is commonly performed in synthetic biology.</p> | Eleanor Sinclair; Katherine A. Hollywood; Cunyu Yan; Richard Blankley; Rainer Breitling; Perdita Barran | Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2018-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd4702a9b287d189c3f/original/mobilising-ion-mobility-mass-spectrometry-in-a-synthetic-biology-analytics-workflow.pdf |
60c7468d4c8919e265ad2b87 | 10.26434/chemrxiv.11352101.v1 | Light-Activatable, 2,5-Disubstituted Tetrazoles for the Proteome-Wide Profiling of Aspartates and Glutamates in Living Bacteria | Covalent inhibitors have recently seen a
resurgence of interest in drug development. Nevertheless, compounds, that do
not rely on an enzymatic activity, have almost exclusively been developed to
target cysteines. Expanding the scope to other amino acids would be largely
facilitated by the ability to globally monitor their engagement by covalent
inhibitors. Here, we present the use of light-activatable 2,5-disubstituted
tetrazoles that allow quantifying 8971 aspartates and glutamates in the
bacterial proteome with excellent selectivity. Using these probes, we
competitively map the binding sites of two isoxazolium salts and introduce
hydrazonyl chlorides as a new class of carboxylic acid-directed covalent
protein ligands. As the probes are unreactive prior to activation, they allow global
profiling even in living Gram-positive and Gram-negative bacteria. Taken
together, this method to monitor aspartates and glutamates proteome-wide will
lay the foundation to efficiently develop covalent inhibitors targeting these
amino acids | Kathrin Bach; Bert L. H. Beerkens; Patrick R. A. Zanon; Stephan M. Hacker | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7468d4c8919e265ad2b87/original/light-activatable-2-5-disubstituted-tetrazoles-for-the-proteome-wide-profiling-of-aspartates-and-glutamates-in-living-bacteria.pdf |
60c746b09abda2ea54f8c7a8 | 10.26434/chemrxiv.11367698.v1 | Assessment of 2,4-Dinitroanisole Transformation Using Compound-Specific Isotope Analysis After in Situ Chemical Reduction of Iron Oxides | A study of isotope fractionation upon reaction of the insensitive munitions compounds 2,4-dintroanisole with natural minerals in the presence of ferrous iron or treated with dithionite to produce reducing equivalents. | Matthew J. Berens; Thomas Hofstetter; Jakov Bolotin; William Arnold | Environmental Science; Geochemistry; Wastes | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746b09abda2ea54f8c7a8/original/assessment-of-2-4-dinitroanisole-transformation-using-compound-specific-isotope-analysis-after-in-situ-chemical-reduction-of-iron-oxides.pdf |
60c74a27567dfedbc7ec4cfe | 10.26434/chemrxiv.12159945.v1 | The Effect of ACE2 Inhibitor MLN-4760 on the Interaction of SARS-CoV-2 Spike Protein with Human ACE2: A Molecular Dynamics Study | <p>A previous study shows that an ACE2 enzymatic activity inhibitor efficiently blocks the interaction of SARS-CoV spike protein with human ACE2 and may be effective in preventing the coronavirus membrane fusion and entry to human cells. The report suggests that potent ACE2 inhibitors can be used to treat hypertension as well as for controlling SARS-CoV infection. We here studied the effect of a selective and highly potent ACE2 inhibitor (MLN-4760) on the interaction of the SARS-CoV-2 spike receptor-binding domain (RBD) with human ACE2 by molecular dynamics (MD) simulation. To this end, we docked the RBD of SARS-CoV-2 to the human native ACE2 and the ACE2 complexed with MLN-4760, and analyzed the dynamics, protein-protein and ligand-protein interactions of the complexes by MD simulation in a simulated biological condition for 100 ns. Analyzing crystallographic structures of SARS-CoV-2 and SARS-CoV RBDs in the complexes with human ACE2 showed that RBD of SARS-CoV-2 binds to ACE2 with a higher affinity than that of SARS-CoV. Results also revealed that MLN-4760 binds to ACE2 at the enzymatic active site with a high affinity and significantly alters the ACE2 protein conformation. MLN-4760 also changes the binding site and the residues involved in hydrogen and hydrophobic binding between RBD and ACE2, however, it had no major effect on the binding affinity of the interaction between RDB and ACE2. Interestingly, binding RBD to the ACE2 complexed with MLN-4760 abrogated the inhibitory effect of MLN-4760 and rescued the conformation of the ACE2 enzymatic site by reforming the closed conformation to the open native conformation. This was due to the disassociation of MLN-4760 from the enzymatic active site of the ACE2 in the result of RBD binding. Overall, these results show that MLN-4760 does neither block nor increase the binding of SARS-CoV-2 spike RBD to human ACE2 and probably had no effect on the viral entry. However, binding the spike protein to ACE2 can rescue the enzymatic function of ACE2 from its inhibitor.</p> | Babak Nami; Avrin Ghanaeian; Kasra Ghanaeian; Negin Nami | Bioinformatics and Computational Biology; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a27567dfedbc7ec4cfe/original/the-effect-of-ace2-inhibitor-mln-4760-on-the-interaction-of-sars-co-v-2-spike-protein-with-human-ace2-a-molecular-dynamics-study.pdf |
60c74506337d6cdc50e26eef | 10.26434/chemrxiv.7982456.v2 | Rapid Deconvolution of Low-Resolution Time-of-Flight Data using Bayesian Inference | Deconvolution of low-resolution time-of-flight data has numerous advantages including the ability to extract additional information from the experimental data. We augment the well-known Lucy-Richardson deconvolution algorithm by various Bayesian prior distributions and show that a prior of second-differences of the signal outperforms the standard Lucy-Richardson algorithm, accelerating the rate of convergence by more than a factor of four, while preserving the peak amplitude ratios of a similar fraction of the total peaks. A novel stopping criterion and boosting mechanism is implemented to ensure these methods converge to a similar entropy, and that local minima are avoided, respectively. Improvement by a factor of two in mass resolution allows more accurate quantification of the spectra. The general method is demonstrated in this paper by the deconvolution of fragmentation peaks of the DHB matrix, as well as the BTP thermometer ion, following femtosecond ultraviolet laser desorption. | Cornelius Pieterse; Michiel B. De Kock; Wesley D. Robertson; Hans C. Eggers; R. J. Dwayne Miller | Imaging; Mass Spectrometry; Biophysical Chemistry; Photochemistry (Physical Chem.); Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74506337d6cdc50e26eef/original/rapid-deconvolution-of-low-resolution-time-of-flight-data-using-bayesian-inference.pdf |
67baeb0e81d2151a02a991ba | 10.26434/chemrxiv-2025-j5g73 | MlCOFSyn: A Machine Learning Framework to Facilitate the Synthesis of 2D Covalent Organic Frameworks | Two-dimensional covalent organic frameworks (2D COFs) have been historically synthesized empirically, often resulting in uncontrolled crystallization and inferior crystal sizes, which limit their performance in various applications. Recently, crystallization models tailored for 2D COFs have been developed, which demonstrate great potential in facilitating their rational synthesis. Nevertheless, effective strategies to leverage these models for 2D COF synthesis remain underdeveloped, and the specialized expertise required, combined with the high computational costs of exploring the vast chemical space, poses additional barriers to their practical application. In this work, we present a machine learning framework, named MlCOFSyn, designed to assist in the synthesis of 2D COFs. This framework explores the application of 2D COF crystallization models by implementing three pivotal functionalities: predicting crystal sizes based on the input monomer addition sequence, reverse-engineering monomer addition sequences to achieve desired crystal sizes, and optimizing monomer addition sequences to produce larger crystals. These functionalities are critical for the controlled synthesis of 2D COFs but have been largely underexplored due to the lack of accessible theoretical tools. The MlCOFSyn framework leverages efficient machine-learning algorithms and features an intuitive graphical interface, enabling its use on consumer-grade computers by non-experts. By addressing these gaps, the MlCOFSyn framework represents a substantial advancement in facilitating 2D COF research and synthesis. | Yue Shi; Jiaxin Tian; Haoyuan Li | Theoretical and Computational Chemistry; Materials Science; Theory - Computational; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67baeb0e81d2151a02a991ba/original/ml-cof-syn-a-machine-learning-framework-to-facilitate-the-synthesis-of-2d-covalent-organic-frameworks.pdf |
63d003b610cb6a3727e4f3ca | 10.26434/chemrxiv-2023-g8gd7 | Impact of Sodium Pyruvate on the Electrochemical Reduction of NAD+ Biomimetics | Biomimetics of nicotinamide adenine dinucleotide (mNADH) are promising cost-effective alternatives to their natural counterpart for biosynthetic applications; however, attempts to recycle mNADH often rely on coenzymes or precious metal catalysts. Direct electrolysis is an attractive approach for recycling mNADH, but electrochemical reduction of the oxidized mimetic (mNAD+) primarily results in the formation of an enzymatically inactive dimer. Herein, we find that aqueous electrochemical reduction of an NAD+ mimetic, 1-n-butyl-3-carbamoylpyridinium bromide (1+), to its enzymatically active form, 1,4-dihydro-1-n-butyl nicotinamide (1H), is favored in the presence of sodium pyruvate as a supporting electrolyte. Maximum formation of 1H is achieved in the presence of a large excess of pyruvate in combination with a large excess of a co-supporting electrolyte. Formation of 1H is found to be favored at pH 7, with an optimized product ratio of ~50/50 dimer/1H observed by cyclic voltammetry. Furthermore, sodium pyruvate is shown to promote electroreductive generation of the 1,4-dihydro form of several additional mNADH as well as NADH itself. This method provides a general strategy for regenerating 1,4-dihydro-nicotinamide mimetics of NADH from their oxidized forms. | Chase Bruggeman; Karissa Gregurash; David Hickey | Organic Chemistry; Catalysis; Analytical Chemistry; Electrochemical Analysis; Biocatalysis; Electrocatalysis | CC BY NC 4.0 | CHEMRXIV | 2023-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d003b610cb6a3727e4f3ca/original/impact-of-sodium-pyruvate-on-the-electrochemical-reduction-of-nad-biomimetics.pdf |
66fc776c12ff75c3a11aa430 | 10.26434/chemrxiv-2024-vfrzg | Strain-Promoted, Visible Light Triggerable CO Releasing Micelles | Carbon monoxide (CO), along with nitric oxide and hydrogen sulfide, is one of a trinity of known gasotransmitters, or endogenously produced gaseous molecules that signal and regulate a panoply of physiological functions. CO releasing molecules (CORMs) are chemical tools that enable the study and application of this ephemeral gas, that, ideally, release CO on-demand when externally stimulated. Surveying the available triggers, photolysis is optimal: it is contactless and grants practitioners unparalleled spatial and temporal control. However, current photo-triggered CORMs are capricious and do not meet current needs. Presented here is a highly efficient platform for the visible light triggered release of CO gas. This platform is built on a unique CO containing functionality, the cyclopropenone, which undergoes facile decar-bonylation through visible light (470 nm) mediated photoredox catalysis. Due to the exothermic strain-release that oc-curs upon formation of CO, this photoreaction is rapid, quantitative, and has tunable release rates. To render this photo-CORM water soluble, deliverable, and to keep reactants in proximity, necessary components were polymerized into block copolymers that self-assemble into CO releasing micelles (CORMIs). This platform was compared directly to other state-of-the-art CORMs, showing significantly improved CO production efficiency, lower toxicity, tunable release rates, and con-sistent efficacy in ex vivo and in vitro settings. | Mckenna Hanson; Ram Ambre; Riya Joshi; Jeffrey Amidon; Jackson Snow; Vivian Lawless; Brady Worrell | Biological and Medicinal Chemistry; Catalysis; Polymer Science; Organic Polymers; Chemical Biology; Photocatalysis | CC BY NC 4.0 | CHEMRXIV | 2024-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fc776c12ff75c3a11aa430/original/strain-promoted-visible-light-triggerable-co-releasing-micelles.pdf |
60c751549abda2b487f8dbd5 | 10.26434/chemrxiv.13150820.v1 | Reduced Scaling Formulation of CASPT2 Analytical Gradients Using the Supporting Subspace Method | We present a reduced scaling and exact reformulation of state specific CASPT2 analytical gradients in terms of the MP2 and Fock derivatives using the supporting subspace method. This work follows naturally from the supporting subspace formulation of the CASPT2 energy in terms of the MP2 energy using dressed orbitals and Fock builds. For a given active space configuration, the terms corresponding to the MP2-gradient can be evaluated with O(N<sup>5</sup>) operations, while the rest of the calculations can be computed with O(N<sup>3</sup>) operations using Fock builds, Fock gradients, and linear algebra. When tensor-hyper-contraction is applied simultaneously, the computational cost can be further reduced to O(N<sup>4</sup>) for a fixed active space size. The new formulation enables efficient implementation of CASPT2 analytical gradients by leveraging existing GPU-based MP2 and Fock routines. We present benchmark results that demonstrate the accuracy and performance of the new method. Example applications of the new method in ab initio molecular dynamics simulation and constrained geometry optimization are given. | Chenchen Song; Jeffrey B. Neaton; Todd J. Martínez | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751549abda2b487f8dbd5/original/reduced-scaling-formulation-of-caspt2-analytical-gradients-using-the-supporting-subspace-method.pdf |
6338631a08470080b7906b55 | 10.26434/chemrxiv-2022-bzg9v | The potential energy minima of nH2O (n=4,8...,24) in relation to their hydrogen bond cycles | Hydrogen bonded water has a multitude of possible configurations and energies. By treating networks of hydrogen bonded water molecules as directed graphs, and by using a program for reversing cycles in the graphs, significant portions of the energy terrain can be systematically mapped out with relative ease. Configurations that are mutual cycle reversals of each other, or hydrogen bonding families, are observed to have similar energies. Therefore, in the determination of the lowest energy configuration, it would be sufficient to find one member of its hydrogen bonding family. | Mihali Felipe | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2022-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6338631a08470080b7906b55/original/the-potential-energy-minima-of-n-h2o-n-4-8-24-in-relation-to-their-hydrogen-bond-cycles.pdf |
628e225059f0d6fa839d0aa8 | 10.26434/chemrxiv-2022-j4h2f | Diffusion coefficient measurement inconsistency as a parameter to monitor structural conformational changes in biomolecules | Residue specific measurement of translational diffusion coefficient involving labile amide protons of a protein
molecule is known to give inconsistent result due to multiple solute-solvent exchange events during the
diffusion encoding period. The residues accessible to solvent often overestimates the diffusion coefficient due
to the contribution by fast diffusing solvent molecules to the measured values. It has been, however, shown
that this apparent drawback of overestimation can become a valuable source of information about the
exchange rates. An associated exchange related drawback that has never been perceived in a similar positive
manner is the high repetition inaccuracy. The exchanging residues not only overestimate, they do so in an
inconsistent way as the contribution of exchange differs from one measurement to the next. We show here
how measurement uncertainty can become another useful tool in recognizing the sections of the polypeptide
chain that are exposed to solvent. Additionally, we show that the uncertainty is more sensitive a marker than
the overestimation in detecting small changes in solvent accessibility of a residue due to structural changes of
a protein molecule. | Subhayan Chakraborty; Shalini Pandey; Arindam Ghosh | Analytical Chemistry; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628e225059f0d6fa839d0aa8/original/diffusion-coefficient-measurement-inconsistency-as-a-parameter-to-monitor-structural-conformational-changes-in-biomolecules.pdf |
60c751e59abda27c1af8dce4 | 10.26434/chemrxiv.13227881.v1 | Identifying Molecules as Biosignatures with Assembly Theory and Mass Spectrometry | <p><b>The search for evidence of life elsewhere
in the universe is hard because it is not obvious what signatures are unique to
life. Here we postulate that complex molecules found in high abundance are
universal biosignatures as they cannot form by chance. To explore this, we
developed the first intrinsic measure of molecular complexity that can be
experimentally determined, and this is based upon a new approach called
assembly theory which gives the molecular assembly number (MA) of a given
molecule. MA allows us to compare the intrinsic complexity of molecules using
the minimum number of steps required to construct the molecular graph starting
from basic objects, and a probabilistic model shows how the probability of any
given molecule forming randomly drops dramatically as its MA increases. To map
chemical space, we calculated the MA of <i>ca.</i> 2.5 million compounds, and
collected data which showed the complexity of a molecule can be experimentally determined
by using three independent techniques including infra-red spectroscopy, nuclear
magnetic resonance, and by fragmentation in a mass spectrometer, and this data
has an excellent corelation with the values predicted from our assembly theory.
We then set out to see if this approach could allow us to identify molecular
biosignatures with a set of diverse samples from around the world, outer space,
and the laboratory including prebiotic soups. <a>The
results show that </a><a>there
is a non-living to living threshold in MA complexity and the higher the MA for
a given molecule, the more likely that it had to be produced by a biological
process</a>. This work demonstrates it is possible to use this approach
to build a life detection instrument that could be deployed on missions to
extra-terrestrial locations to detect biosignatures, map the extent of life on
Earth, and be used as a molecular complexity scale to quantify the constraints
needed to direct prebiotically plausible processes in the laboratory. Such an
approach is vital if we are going to find new life elsewhere in the universe or
create <i>de-novo</i> life in the lab. </b></p> | stuart Marshall; Cole Mathis; Emma Carrick; Graham Keenan; Geoffrey Cooper; Heather Graham; Jessica Bame; Matthew Craven; Nicola Bell; Piotr S. Gromski; Marcel Swart; Douglas G. Moore; Sara Walker; Leroy Cronin | Combinatorial Chemistry; Natural Products; Space Chemistry; Analytical Chemistry - General; Analytical Apparatus; Chemoinformatics; Environmental Analysis; Mass Spectrometry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751e59abda27c1af8dce4/original/identifying-molecules-as-biosignatures-with-assembly-theory-and-mass-spectrometry.pdf |
60c73d919abda28e0ff8b711 | 10.26434/chemrxiv.5887243.v1 | Rigid and concave, 2,4-cis-substituted azetidine derivatives: A platform for asymmetric catalysis | A series of single enantiomer, 2,4-<i>cis</i>-disubstituted amino azetidines were synthesised and used as ligands for copper-catalysed Henry reactions of aldehydes with nitromethane. Optimisation of ligand substituents and the reaction conditions was conducted. The enantiomeric excess of the formed products was highest when alkyl aldehydes were employed in the reaction (>99% e.e.). The absolute stereochemistry of one representative azetidine derivative salt was determined by analysis of the Flack parameter of an XRD single crystal structure. The origin of selectivity in catalysis was investigated computationally, revealing the importance of the amino-substituent in determining the stereochemical outcome. A racemic platinum complex of a <i>cis</i>-disubstituted azetidine is examined by XRD single crystal structure analysis with reference to its steric parameters, and analogies to the computationally determined copper complex catalyst are drawn.<br /> | Akina Yoshizawa; Antonio Feula; Louise Male; Andrew G. Leach; John Fossey | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d919abda28e0ff8b711/original/rigid-and-concave-2-4-cis-substituted-azetidine-derivatives-a-platform-for-asymmetric-catalysis.pdf |
66e9854851558a15ef40b9e6 | 10.26434/chemrxiv-2024-78n0x | Non-Innocent Role of Sacrificial Anodes in Electrochemical Nickel-Catalyzed C(sp2)-C(sp3) Cross-Electrophile Coupling | Sacrificial anodes composed of inexpensive metals such as Zn, Fe and Mg are widely used to support electrochemical nickel-catalyzed cross-electrophile coupling (XEC) reactions, in addition to other reductive electrochemical transformations. Such anodes are appealing because they provide a stable counter-electrode potential and typically avoid interference with the reductive chemistry. The present study outlines development of an electrochemical Ni-catalyzed XEC reaction that streamlines access to a key pharmaceutical intermediate. Metal ions derived from sacrificial anode oxidation, however, directly contribute to homocoupling and proto-dehalogenation side products that are commonly formed in chemical and electrochemical Ni-catalyzed XEC reactions. Use of a divided cell limits interference by the anode-derived metal ions and supports high product yield with negligible side product formation, introducing a strategy to overcome one of the main limitations of Ni-catalyzed XEC. | Luana Cardinale; Gregory L. Beutner; Christopher Y. Bemis; Daniel J. Weix; Shannon Stahl | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e9854851558a15ef40b9e6/original/non-innocent-role-of-sacrificial-anodes-in-electrochemical-nickel-catalyzed-c-sp2-c-sp3-cross-electrophile-coupling.pdf |
6304f8d0d858fb496759779f | 10.26434/chemrxiv-2022-w800h | Untargeted metabolomics based prediction of therapeutic potential for apigenin and chrysin | Flavonoids belong to the polyphenol superfamily and present in our foods derived from natural sources including fruits and vegetables. Apigenin and Chrysin, prominent flavonoids have been demonstrated to have systemic benefits. Our previous work was first to establish the impact of apigenin and chrysin on cellular transcriptome. In the current study, we have revealed the ability of apigenin and chrysin to alter cellular metabolome based on untargeted metabolomics. Based on our metabolomics data, both these structurally related flavonoids demonstrate diverging and converging properties. Apigenin demonstrated the potential to possess anti-inflammatory and vasorelaxant properties through the upregulation of alpha-linolenic acid and linoleic acid metabolism intermediates. Chrysin on the other hand exhibited abilities to inhibit protein and pyrimidine synthesis along with downregulation of gluconeogenesis pathways based on the metabolites obtained. These metabolic effects were due to the impact of chrysin to modulate L-alanine metabolism and urea cycle. On the other hand, both the flavonoids demonstrated converging effects by their ability to downregulate metabolites involved in cholesterol biosynthesis and uric acid synthesis namely 7-dehydrocholesterol and xanthosine respectively. Our work could provide understanding regarding the various therapeutic potential of these naturally occurring flavonoids which are food constituents to treat metabolic complications in conditions like obesity, diabetes, cancer, and cardiovascular diseases. Further investigation of these natural agents for targeted diseases using whole animal and translational approaches will validate their therapeutic ability and help in curbing an array of metabolic complications.
| Cole Cochran; Katelyn Martin; Daniel Rafferty; Jennifer Choi; Angela Leontyev; Akanksh Shetty; Sonali Kurup; Prasanth Puthanveetil | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6304f8d0d858fb496759779f/original/untargeted-metabolomics-based-prediction-of-therapeutic-potential-for-apigenin-and-chrysin.pdf |
64a95d666e1c4c986b07597f | 10.26434/chemrxiv-2023-27ndz-v2 | On the interactions between RNA and titrateable
lipid layers: Implications for RNA delivery with lipid
nanoparticles | Characterising the interaction between cationic ionisable lipids (CIL) and nucleic acids (NA) is key to
understand the process of RNA lipid nanoparticle (LNP) formation and release of NAs from LNPs.
Here, we have used different surface techniques to reveal the effect of pH and NA type on the
interaction with a model system of DOPC and the CIL DLin-MC3-DMA (MC3). At only 5 % MC3,
differences in the structure and dynamics of the lipid layer were observed. Both pH and %MC3
were shown to affect the absorption behaviour of erythropoietin mRNA, polyadenylic acid (polyA)
and polyuridylic acid (polyU). The adsorbed amount of all studied NAs was found to increase with
decreasing pH and increasing %MC3 but with different effects on the lipid layer, which could be
linked to the NA secondary structure. For polyA at pH 6, adsorption to the surface of the layer was
observed, whereas for other conditions and NAs, penetration of the NA into the layer resulted in the
formation of a multilayer structure. By comparison to simulations excluding the secondary structure,
difference in adsorption behaviours between polyA and polyU could be observed, indicating that also
the NA’s secondary structure affected the MC3-NA interactions. | Jennifer Gilbert; Inna Ermilova; Marco Fornasier; Maximilian Skoda; Giovanna Fragneto; Jan Swenson; Tommy Nylander | Physical Chemistry; Biological and Medicinal Chemistry; Nanoscience; Biophysics; Biophysical Chemistry; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a95d666e1c4c986b07597f/original/on-the-interactions-between-rna-and-titrateable-lipid-layers-implications-for-rna-delivery-with-lipid-nanoparticles.pdf |
67a3a07d6dde43c908b5a7b6 | 10.26434/chemrxiv-2025-r004t | Stereogenesis in Organic Addition Reactions: Cram’s Steric Control vs Charge-Transfer Control. A Natural Bond Orbital Analysis | In a rudimentary setting of asymmetric induction in the syntheses of acyclic systems, the competing addition reactions may occur at different rates on account of a stereogenic center placed in the immediate vicinity of the addition site. Coming from one side of the mirror, we would usually like one of the competing reactions to be much faster than the other and so the question what features of transition state impede or facilitate bond formation in such settings is a matter of great interest. To address this issue, we have proposed in the past that two effects determine relative stability of the alternative transition states in π-facial selection: Cram’s steric strain, and charge transfer into intrinsically electron deficient incipient bond. Here we model the donor-acceptor interactions of the incipient bond by introducing in common diastereoselection probes a low-lying, vacant NBO orbital that defines two stereogenic parameters, charge-transfer differentials and electron-affinity differentials. To test the model, we examine its explanatory and predictive power vis-à-vis effects of EWG/EDG substitution on the stereochemistry of (i) alkylation and metal hydride reduction of ketones, (ii) oxygenation of alkane C-H bonds, (iii) oxidations and 1,3dipolar cycloadditions of olefins, and (iv) cycloadditions of dienes. Depending on the extent of electronic perturbation of the probe, variation in the available log[Z]/[E] data is a linear function of charge-transfer differentials, a cubic function of electron-affinity differentials, or a function of system’s electron affinity. Thus, the two transition state effects, charge-transfer stabilization and steric-strain destabilization, are indeed necessary and sufficient to account for πfacial selection results in all examined reactions, including nucleophilic addition to C=O. Accordingly, an interplay of vicinal electron donation and steric strain is expected to underlie 1,2-asymmetric induction in related processes. | Andrzej Cieplak | Organic Chemistry; Physical Organic Chemistry; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a3a07d6dde43c908b5a7b6/original/stereogenesis-in-organic-addition-reactions-cram-s-steric-control-vs-charge-transfer-control-a-natural-bond-orbital-analysis.pdf |
629e6a0b6057b17ae293debf | 10.26434/chemrxiv-2022-n214g | Low humidity dependence of proton conductivity in modified zirconium (IV)-hydroxy ethylidene diphosphonates | Proton conducting materials play an essential role in various fields of science and many applications, such as polymer electrolyte fuel cells (PEFCs). However, their proton conductivities suffer from the strong dependence on relative humidity (RH) and severely decrease at low RH conditions. Here, we synthesized zirconium (IV)-hydroxy ethylidene diphosphonates (ZrHEDP), which have phosphonic acid groups at a close distance. As the acidic groups are more concentrated in ZrHEDP, the proton conductivity exhibits lower dependence on the RH. In particular, the ZrHEDP with the largest amount of phosphonic acid groups among the examined samples showed the lowest RH dependence; the proton conductivity at 40% RH remained 2/3 of the conductivity at 95% RH, whereas a representative electrolyte, Nafion, at 40 % RH showed 1/5-1/20 of its conductivity at 95% RH. | Takaya Ogawa; Gopinathan M. Anilkumar; Takanori Tamaki; Hidenori Ohashi; Takeo Yamaguchi | Materials Science; Polyelectrolytes - Materials; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629e6a0b6057b17ae293debf/original/low-humidity-dependence-of-proton-conductivity-in-modified-zirconium-iv-hydroxy-ethylidene-diphosphonates.pdf |
6565d8facf8b3c3cd750bb2a | 10.26434/chemrxiv-2023-hb73w | Mineral fusion via dehydration-induced residual stress: from gels to ceramic monoliths | Man-made ceramics generally undergo harsh manufacturing conditions (e.g., high-temperature sintering). In contrast, mineral structures with superior mechanical strength (e.g., teeth) are generated in organisms under mild biocompatible conditions. Herein, we report that ceramic objects can be directly produced and strengthened by drying purely inorganic gels (PIGs), mimicking the biological tactic of fabricating continuous monoliths from hydrated amorphous precursors. The overall process is easy and biocompatible in that solutions of common iron and molybdate salts are mixed to generate a PIG, which, upon drying under mild temperature, turns into a strengthened ceramic block that displays a high mechanical performance. Analogous to the well-known Prince Rupert’s drop reinforced by residual stress upon quenching, the uneven volume shrinkage from the outside inwards during dehydration builds up residual stress that enables amorphous mineral fusion and strengthening. Furthermore, a dramatic bandgap reduction is achieved in the dried objects due to local structural changes of the Fe atoms under residual stress. This PIG-dehydration approach holds promise for green ceramic manufacturing and offers insights into biomineralization puzzles. | Bo Li; Jie Yan; Hongkun Li; Haikun Wu; Jialun Gu; Weixia Dong; Peiyu Wang; Lanxi Li; Xinxue Tang; Xunli Wang; Yang Ren; Jian Lu; YangYang Li | Materials Science; Biocompatible Materials; Ceramics | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6565d8facf8b3c3cd750bb2a/original/mineral-fusion-via-dehydration-induced-residual-stress-from-gels-to-ceramic-monoliths.pdf |
60c7547f0f50db55dc397d2a | 10.26434/chemrxiv.13667729.v1 | Design of Pure Heterodinuclear Lanthanoid Cryptate Complexes | Heterolanthanide complexes are difficult to synthesize owing to the similar chemistry of the lanthanide ions. Conse-quently, very few purely heterolanthanide complexes have been synthesized. This is despite the fact that such complexes hold inter-esting optical and magnetic properties. To fine-tune these properties, it is important that one can choose complexes with any given combination of lanthanides. Herein we report a synthetic procedure which yields pure heterodinuclear lanthanide cryptates LnLn*LX3 (X = NO3- or OTf-) based on the cryptand H3L = N[(CH2)2N=CH-R-CH=N-(CH2)2]3N (R = m-C6H2OH-2-Me-5). In the synthesis the choice of counter ion and solvent prove crucial in controlling the Ln-Ln*composition. Choosing the optimal solvent and counter ion affords pure heterodinuclear complexes with any given combination of Gd(III)-Lu(III) including Y(III). To demon-strate the versatility of the synthesis all dinuclear combinations of Y(III), Gd(III), Yb(III) and Lu(III) were synthesized resulting in 10 novel complexes of the form LnLn*L(OTf)3 with LnLn* = YbGd 1, YbY 2, YbLu 3, YbYb 4, LuGd 5, LuY 6, LuLu 7, YGd 8, YY 9 and GdGd 10. Through the use of 1H, 13C NMR and mass spectrometry the heterodinuclear nature of YbGd, YbY, YbLu, LuGd, LuY and YGd was confirmed. Crystal structures of LnLn*L(NO3)3 reveal short Ln-Ln distances of ~3.5 Å. Using SQUID magnetometry the exchange coupling between the lanthanide ions was found to be anti-ferromagnetic for GdGd and YbYb while ferromagnetic for YbGd. | Christian Dirk Buch; Steen Hansen; Dmitri Mitcov; Camilla Mia Tram; Gary Nichol; Euan Brechin; Stergios Piligkos | Coordination Chemistry (Inorg.); Lanthanides and Actinides; Ligands (Inorg.); Magnetism | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7547f0f50db55dc397d2a/original/design-of-pure-heterodinuclear-lanthanoid-cryptate-complexes.pdf |
662bcaec418a5379b0ccc7c0 | 10.26434/chemrxiv-2024-lpfs9 | Dielectric properties of strongly coupled hybridized light-matter states | The Lorentz oscillator model is applied to a strongly coupled hybridized light-matter state. It is noted that the real part of the index undergoes rapid change in the area of the so-called “dark states.” This property of hybridized light-matter states could allow them to function as unorthodox materials in which their absorptive and refractive properties are selectively manipulated. In this manuscript, basic properties of hybrid light-matter states are reviewed. The Lorentz oscillator model is then applied to two types of light-matter states, one formed from a coupling of a single exciton and a single cavity photon, and one formed from coupling two excitons to a cavity photon. | Aleksandr Avramenko | Physical Chemistry; Optics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662bcaec418a5379b0ccc7c0/original/dielectric-properties-of-strongly-coupled-hybridized-light-matter-states.pdf |
63b70bbf4ba573626c6bf1c3 | 10.26434/chemrxiv-2023-26xd8 | A Computational Physics-based Approach to Predict Unbound Brain-to-Plasma Partition Coefficient, Kp,uu | The blood-brain barrier (BBB) plays a critical role in preventing harmful endogenous and exogenous substances from penetrating the brain. Optimal brain penetration of small molecule CNS drugs is characterized by a high unbound brain/plasma ratio (Kp,uu). While various medicinal chemistry strategies and in silico models have been reported to improve BBB penetration, none were developed to predict Kp,uu directly. We describe a physics-based computational approach, solvation free energy calculations (energy of solvation or E-sol), to predict Kp,uu. Prospective application of this method to internal CNS drug discovery programs highlighted the utility and accuracy of this new method, which showed a categorical accuracy of 79% and a R2 of 0.61 from a linear regression model. | Morgan Lawrenz; Mats Svensson; Mitsunori Kato; Karen Dingley; Jackson Chief Elk; Zhe Nie; Yefen Zou; Zachary Kaplan; H. Rachel Lagiakos; Hideyuki Igawa; Eric Therrien | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b70bbf4ba573626c6bf1c3/original/a-computational-physics-based-approach-to-predict-unbound-brain-to-plasma-partition-coefficient-kp-uu.pdf |
61d9d48ef51b2210f40dfea6 | 10.26434/chemrxiv-2022-xrgnf | Sooting tendencies of diesel fuel component mixtures follow a linear mixing rule | With the growing importance of climate change, soot emissions from engines have been receiving increasing attention since black carbon is the second largest source of global warming. A sooting tendency can be used to quantify the extent of soot formation in a combustion device for a given fuel molecule, and therefore to quantify the soot reduction benefits of alternative fuels. However real fuels are complex mixtures of multiple components. In this work, we have used experimental methods to investigate how the sooting tendency of a blended fuel mixture is related to the sooting tendencies of the individual components. A test matrix was formulated that includes sixteen mixtures of six components that are representative of the main categories of hydrocarbons in diesel (eicosane (ECO) for alkanes, isocetane (ICE) for isoalkanes, butylcyclohexane (BCH) for cycloalkanes, 1-methylnaphthalene (1MN) for aromatics, tetralin for naphthoaromatics, and methyl-decanoate (MDC) for oxygenates). Most of the mixtures contain three to five components. The sooting tendency of each mixture was characterized by yield sooting index (YSI), which is based on the soot yield when a methane/air nonpremixed flame is doped with 1000 ppm of the test fuel. The YSIs were measured experimentally. The results show that the blending behavior is linear, i.e., the YSI of the mixtures is the mole-fraction-weighted average of the component YSIs. Experimental results have shown that the sooting tendency of a fuel mixture can be accurately estimated as the linear combination of the individual components. In addition, mass density of the mixtures is also measured, and a linear blending rule is applied to test whether mixing rules exist for mass density of diesel mixtures in this study. Results also have shown that the mixing rule tested in this study is valid and mass density of a mixture can be accurately estimated from the linear combination of the individual components. | Zhanhong Xiang; Karnsiree Chen; Charles McEnally; Lisa Pfefferle | Energy; Fuels - Energy Science | CC BY 4.0 | CHEMRXIV | 2022-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d9d48ef51b2210f40dfea6/original/sooting-tendencies-of-diesel-fuel-component-mixtures-follow-a-linear-mixing-rule.pdf |
6426abb891074bccd095c32b | 10.26434/chemrxiv-2023-hlk3f | Biocompatible lysine protecting groups for the chemoenzymatic synthesis of K48/K63 heterotypic and branched ubiquitin chains
| The elucidation of emerging biological functions of heterotypic and branched ubiquitin (Ub) chains requires new strategies for their preparation with defined length and connectivity. While in vitro enzymatic assembly using expressed E1 activating and E2 conjugating enzymes can deliver homotypic chains, the synthesis of branched chains typically requires extensive mutations of lysines or other sequence modifications. The combination of K48 and K63 biased E2 conjugating enzymes and two new carbamate protecting groups – pyridoxal 5’-phosphate (PLP) cleavable aminobutanamide carbamate (Abac group) and periodate cleavable aminobutanol carbamate (Aboc group) – provides a strategy for the synthesis of heterotypic and branched Ub trimers, tetramers, and pentamers. The Abac- and Aboc-protected lysines are readily prepared and incorporated into synthetic ubiquitin monomers. As these masking groups contain a basic amine, they preserve the overall charge and properties of the Ub structure, facilitating folding and enzymatic conjugations. These protecting groups can be chemoselectively removed from folded Ub chains and monomers with buffered solutions of PLP or NaIO4. Through the incorporation of a cleavable C-terminal His tag on the Ub acceptor, the entire process of chain building, iterative Abac deprotections, and global Aboc cleavage can be conducted on a resin-support, obviating the need for handling and purification of the intermediate oligomers. Simple modulation of the Ub monomers affords various K48/K63 branched chains, including tetramers and pentamers not previously accessible by synthetic or biochemical methods. | Toshiki Mikami; Sohei Majima; Haewon Song; Jeffrey Bode | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2023-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6426abb891074bccd095c32b/original/biocompatible-lysine-protecting-groups-for-the-chemoenzymatic-synthesis-of-k48-k63-heterotypic-and-branched-ubiquitin-chains.pdf |
65184274ade1178b2469ee95 | 10.26434/chemrxiv-2023-6ngm1 | Network Polymer Properties Engineered through Polymer Backbone Dispersity and Structure | Dispersity (Ɖ or Mw/Mn) is an important parameter in material design and as such can significantly impact the properties of polymers. Here polymer networks with independent control over the molecular weight and dispersity of the linear chains that form the material are developed. Using a RAFT polymerization approach a library of polymers with dispersity ranging from 1.2-1.9 for backbone chain-length (DP) 100, and 1.4-3.1 for backbone chain-length 200 were developed and transformed to networks through post-polymerization crosslinking to form disulfide linkers. The tensile, swelling, and adhesive properties were explored, finding that both at DP 100 and DP 200 the swelling ratio, tensile strength, and extensibility were superior at intermediate dispersity (1.3-1.5 for DP 100 and 1.6-2.1 for DP 200) compared to materials with either substantially higher or lower dispersity. Furthermore, adhesive properties for materials with chains of intermediate dispersity at DP 200 revealed enhanced performance compared to the very low or high dispersity chains. | Ibrahim O. Raji; Obed J. Dodo; Nirob K. Saha; Mary Eisenhart; Kevin M. Miller; Richard Whitfield; Athina Anastasaki; Dominik Konkolewicz | Polymer Science; Polymer chains; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65184274ade1178b2469ee95/original/network-polymer-properties-engineered-through-polymer-backbone-dispersity-and-structure.pdf |
614c375ab1d4a6c2ea917354 | 10.26434/chemrxiv-2021-601d3 | Reducing the irreducible: Dispersed metal atoms facilitate reduction of irreducible oxides. | Oxide reducibility is a central concept quantifying the role of the support in catalysis. While reducible oxides are often considered catalytically active, irreducible oxides are seen as inert supports. Enhancing the reducibility of irreducible oxides has, however, emerged as an effective way to increase their catalytic activity while retaining their inherent thermal stability. In this work, we focus on the prospect of using single metal atoms to increase the reducibility of a prototypical irreducible oxide, zirconia. Based on extensive self-consistent DFT+U calculations, we demonstrate that single metal atoms significantly improve and tune the surface reducibility of zirconia. Detailed analysis of the observed single atom induced reducibility allows us to attribute the enhanced reducibility to strong interactions between the metal atom and the electrons trapped in the vacancy, and d-p orbital interactions between the metal atom and oxygen. This analysis enables transferring the obtained theoretical understanding to other irreducible oxides as well. The detailed understanding of how oxide reducibility can be tuned offers precise control over the catalytic properties of metal--oxides. | Ville Korpelin; Marko M. Melander; Karoliina Honkala | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis; Redox Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614c375ab1d4a6c2ea917354/original/reducing-the-irreducible-dispersed-metal-atoms-facilitate-reduction-of-irreducible-oxides.pdf |
63e21f1bcdb6a7f57b46e5bf | 10.26434/chemrxiv-2023-kbtf5 | Multifunctional nanomicelles constructed by aggregation and de-aggregation strategy for magnetic resonance/NIR II fluorescence imaging guided Type I photodynamic therapy | Fluorescence and magnetic resonance imaging (FL/MRI) has received much attention from their complementary characteristics. However, the simultaneous enhancement of fluorescence and MR signals plus the efficacy of the treatment is still a major challenge. To solve this problem, we put forward a strategy of aggregation and de-aggregation based on aggregation-induced emission (AIE). NIR II photosensitizer TQ-TPA with Type I reactive oxygen species (ROS) generation ability and an amphiphilic 2TPE-Gd were firstly synthesized, and both of them showed the AIE property. Depending on the hydrophilic properties, hydrophobic TQ-TPA spontaneously aggregated into the core of nanomicelles formed by DSPE-PEG. Meanwhile, the aggregated 2TPE-Gd in aqueous solution could de-aggregate and insert in the interface, and formed TGdTT NMs. Based on this strategy and AIE property, TGdTT NMs exhibited strong NIR II fluorescence emission and Type I ROS generation ability, and enhanced T1 relaxivity (r1). Moreover, in vitro, in vivo, and pharmacokinetics results demonstrated these nanomicelles had good biosafety and long blood circulation time. Finally, they successfully realized complementary MR/NIR II fluorescence dual-modal imaging guided photodynamic therapy (PDT) to inhibit tumor growth. This work demonstrated that aggregation and de-aggregation strategy of AIEgens in the core-shell nanomicelle exudes infinite charm for constructing the multifunctional theranostic probes. | Lirong Wang; Ji Qi; Ke Zhang; zeyan Zhuang; Keke Ding; Xu Chen; Hong Shan; Dan Ding; Anjun Qin; Ben Zhong Tang | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e21f1bcdb6a7f57b46e5bf/original/multifunctional-nanomicelles-constructed-by-aggregation-and-de-aggregation-strategy-for-magnetic-resonance-nir-ii-fluorescence-imaging-guided-type-i-photodynamic-therapy.pdf |
60c7426b0f50dbc7b2395cd8 | 10.26434/chemrxiv.8280464.v1 | Visualization and Manipulation of Molecular Motion in Solid State through Photo-Induced Clusteroluminescence | <p>Building molecular machine has long been a dream of scientists as it is expected to revolutionize many aspects of technology and medicine. Implementing the solid-state molecular motion is the prerequisite for a practical molecular machine. However, few works on solid-state molecular motion have been reported and it is almost impossible to “see” the motion even if it happens. Here the light-driven molecular motion in solid state is discovered in two non-conjugated molecules <i>s</i>-DPE and <i>s</i>-DPE-TM, resulting in the formation of excited-state though-space complex (ESTSC). Meanwhile, the newly formed ESTSC generates an abnormal visible emission which is termed as clusteroluminescence. Notably, the original packing structure can recover from ESTSC when the light source is removed. These processes have been confirmed by time-resolved spectroscopy and quantum mechanics calculation. This work provides a new strategy to manipulate and “see” solid-state molecular motion and gains new insights into the mechanistic picture of clusteroluminescence.<br /></p> | Haoke Zhang; Lili Du; Lin Wang; Junkai Liu; Qing Wan; Ryan Tsz Kin Kwok; Jacky W. Y. Lam; David Lee Phillips; Ben Zhong Tang | Physical and Chemical Properties; Quantum Mechanics; Radiation; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7426b0f50dbc7b2395cd8/original/visualization-and-manipulation-of-molecular-motion-in-solid-state-through-photo-induced-clusteroluminescence.pdf |
66490977418a5379b0a9e2ce | 10.26434/chemrxiv-2024-5bbbm | Fluorescent Polymers for Environmental Monitoring: Targeting Pathogens and Metal Contaminants with Naphthalimide Derivatives | The continuous monitoring of Hg2+ levels in aqueous environments is crucial to assess a potential indication of methylmercury contamination via bacterial conversion, yet existing methods often require extensive sample treatment, expensive equipment, and transportation to a specialized facility. To mitigate this issue, this study introduces the synthesis and application of three naphthalimide-based compounds with significant fluorescent and solvatochromic behaviour (C1, C2 and C3) for the detection of mercury ions, with an inherent associated antibacterial activity, creating a dual-functionality material. The incorporation of these compounds into polymers, such as polyvinyl chloride (PVC), poly (methyl methacrylate-co-methacrylic acid) (PUMA), and starch, allowed for the development of solid-support sensors/surfaces with a strong antibacterial profile, highlighting the inherent dual-functionality of the compounds. Most interestingly, the C2-doped starch biopolymer allowed for the detection of Hg2+ ions at concentrations as low as 2 ppm in an aqueous environment through a rapid, on-site evaluation without the need for sample treatment. This biopolymer was constructed following a sustainable, green-chemistry-oriented, temperature-dependent water/starch synthetic route, without the addition of plasticizers, and without any associated ecotoxicity. The study promotes the use of sustainable methods for environmental monitoring and antibacterial applications, advancing material science to offer effective, accessible, and eco-friendly solutions for detecting and mitigating mercury pollution and bacterial contaminations, enhancing environmental and health safety. | Joana Galhano; Atanas Kurutos; Georgi Dobrikov; Maria Paula Duarte; Hugo M. Santos; José Luis Capelo Martínez; Carlos Lodeiro; Elisabete Oliveira | Organic Chemistry; Materials Science; Analytical Chemistry; Physical Organic Chemistry; Dyes and Chromophores; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66490977418a5379b0a9e2ce/original/fluorescent-polymers-for-environmental-monitoring-targeting-pathogens-and-metal-contaminants-with-naphthalimide-derivatives.pdf |
60c747cdf96a000246286fc9 | 10.26434/chemrxiv.11799705.v1 | Homology Models of the Papain-Like Protease PLpro from Coronavirus 2019-nCoV | The December 2019 outbreak of pneumonia in Wuhan, Hubei Province of China was rapidly linked to a novel coronavirus 2019-nCoV. The rapid spread and severity of the virus has led the World Health Organization to declare it a Public Health Emergency of International Concern. We recently described the first homology models of the main 3CL protease from 2019-nCoV, and now present models of the other viral protease, the papain-like protease or PLpro. Whilst the overall viral genome is most closely associated with bat coronaviruses, no bat PLpro crystal structures are known. Wuhan 2019-nCoV PLpro is most closely related to a bat coronavirus PLpro (97% identity), then SARS (80 %) and MERS (29%) and the most promising models presented here are prepared from SARS crystal structure templates. | Martin Stoermer | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2020-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747cdf96a000246286fc9/original/homology-models-of-the-papain-like-protease-p-lpro-from-coronavirus-2019-n-co-v.pdf |
65cd7c349138d23161255c65 | 10.26434/chemrxiv-2024-m6716 | BIOMX-DB: A web application for the BIOFACQUIM natural product database | Natural product databases (NPDBs) are an integral part of chemoinformatics and computer-aided drug design. Despite their pivotal role, a distinct scarcity of projects in Latin America, particularly in Mexico, provides accessible tools of this nature. Herein, we introduce BIOMX-DB, an open and freely accessible web-based database designed to address this gap. BIOMX-DB enhances the features of the existing Mexican natural product database, BIOFACQUIM, by incorporating advanced search, filtering, and download capabilities. The user-friendly interface of BIOMX-DB aims to provide an intuitive experience for researchers. For seamless access, BIOMX-DB is freely available at www.biomx-db.com | Fernando Martínez-Urrutia; José L. Medina-Franco | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cd7c349138d23161255c65/original/biomx-db-a-web-application-for-the-biofacquim-natural-product-database.pdf |
6170af0664e2afd3eb0ba328 | 10.26434/chemrxiv-2021-712mq | Colorimetric quantification of linking in thermoreversible nanocrystal gel assemblies | Nanocrystal gel networks can be responsive, tunable materials, but deliberately designing their structure and controlling their properties have been challenging. By employing reversibly bonded molecular linkers, gelation can be realized under conditions predicted by thermodynamics. But, simulations have offered the only microscopic insights, with no experimental means to monitor linking leading to gelation. Here, we introduce a metal coordination linkage with a distinct optical signature allowing us to quantify linking in situ and establish the structural and thermodynamic basis for assembly. Due to coupling between linked indium tin oxide nanocrystals, their infrared absorption shifts abruptly at a chemically tunable gelation temperature. We quantify bonding spectroscopically and use molecular dynamics simulations to understand bonding motifs as a function of temperature, revealing that gel formation is governed by reaching a critical number of effective links that extend the nanocrystal network. Microscopic insights from our colorimetric linking chemistry enable switchable gels based on equilibrium thermodynamic principles, opening the door to rational design of programmable nanocrystal net-work assemblies. | Jiho Kang; Stephanie Valenzuela; Emily Lin; Manuel Dominguez; Zachary Sherman; Thomas Truskett; Eric Anslyn; Delia Milliron | Materials Science; Aggregates and Assemblies | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6170af0664e2afd3eb0ba328/original/colorimetric-quantification-of-linking-in-thermoreversible-nanocrystal-gel-assemblies.pdf |
60c741ce842e653d57db1f81 | 10.26434/chemrxiv.8139194.v1 | Debiasing Algorithms for Protein Ligand Binding Data do not Improve Generalisation | The structured nature of chemical data means machine learning models trained to predict protein-ligand binding risk overfitting the data, impairing their ability to generalise and make accurate predictions for novel candidate ligands. To address this limitation, data debiasing algorithms systematically partition the data to reduce bias. When models are trained using debiased data splits, the reward for simply memorising the training data is reduced, suggesting that the ability of the model to make accurate predictions for novel candidate ligands will improve. To test this hypothesis, we use distance-based data splits to measure how well a model can generalise. We first confirm that models perform better for randomly split held-out sets than for distant held-out sets. We then debias the data and find, surprisingly, that debiasing typically reduces the ability of models to make accurate predictions for distant held-out test sets. These results suggest that debiasing reduces the information available to a model, impairing its ability to generalise. | Vikram Sundar; Lucy Colwell | Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741ce842e653d57db1f81/original/debiasing-algorithms-for-protein-ligand-binding-data-do-not-improve-generalisation.pdf |
60d8940e67d4915cb1962c4b | 10.26434/chemrxiv-2021-r04pc-v2 | A Convenient Synthesis and Spectral Studies of Diamines Derivatives | <div>A new series of substituted anthranilic esters derivatives linked with a 1,3-dithiolane and</div><div>benzyloximino moiety was synthesized using the simple esterfication reaction and products were</div><div>fully characterized. The isolated yields of these compounds range from 59 to 96%. 1,3-</div><div>dithiolane ester and the benzyloxy substituted diamine derivatives are white solids and stable to</div><div>air and moisture. The synthesized compounds can be exhibits UV-vis absorption properties by</div><div>their structures with a amine or amide group, It is observed that absorption maximum is excellent</div><div>for 2,6-disubstituted benzyloxy esters which can be explained by electron transfer or conjugation</div><div>is steric effect in ortho substitution from the amino group and the amide group.</div> | Sudershan Reddy Gondi; Michael B. Jacobsson; Christiana Julia Rissing; DAVID Y SON | Organic Chemistry; Organic Synthesis and Reactions; Crystallography – Organic | CC BY 4.0 | CHEMRXIV | 2021-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d8940e67d4915cb1962c4b/original/a-convenient-synthesis-and-spectral-studies-of-diamines-derivatives.pdf |
61bc85ea203b40e5ee90a2d8 | 10.26434/chemrxiv-2021-rttkf | Application of LFER to pKas and Dipole Moments of 1H and 2H Tautomers of Tetrazole: Mimicking Structure-Function Relation as a Chemical Education Perspective | Structure-function relation is a 155 year old concept to explain the dependence of biological activity of a drug molecule on its structure put forward by Crum-Brown and Fraser*. Similar line of interest is followed in the present work, and it stimulates the understanding of structure-activity relation (SAR) among the graduate students. An attempt is made for the first time from our laboratory to apply the Hammett and Taft equations to a five membered ring system with four nitrogens as heteroatoms viz. tetrazole to identify the aqueous medium 1H and 2H Tautomers. For this purpose experimentally determined aqueous medium pKa values of NH-acidities of a total of fifteen 5-X-1,2,3,4-tetrazoles and DFT/B3LYP method at the 6-31G* level calculated dipole moments of seven 1H and 2H tautomers of 5-X-1,2,3,4-tetrazoles are used to correlate with Hammett para and meta, and Taft _ortho^* values. Good correlations are obtained. The promising response of more abundant and more polar 1H tautomer with less susceptibility (* = -1.38 in pKa correlations and * = -0.55 in dipole moments correlation) to Taft equation and less abundant and less polar 2H tautomer with more susceptibility (para = 6.56, meta = 7.79 in pKa correlations, and para = 2.69, meta = 3.26 in dipole moments correlation) to Hammett equation of the tetrazole is well distinguished. Thus it mimics a principle of structure-function study on a chemical property like the ionization of NH proton of tetrazole and on a physical property like dipole moment for the first time. Therefore finding a way is achieved to get the equilibrium identification of 1H and 2H tautomers without using any expensive and time consuming experimental techniques. | Sanjeev Rachuru; Jagannadham Vandanapu | Chemical Education; Chemical Education - General | CC BY 4.0 | CHEMRXIV | 2021-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61bc85ea203b40e5ee90a2d8/original/application-of-lfer-to-p-kas-and-dipole-moments-of-1h-and-2h-tautomers-of-tetrazole-mimicking-structure-function-relation-as-a-chemical-education-perspective.pdf |
64f1d26779853bbd78dca5ab | 10.26434/chemrxiv-2023-0hgbc | Benchmarking machine-readable vectors of chemical re- actions on computed activation barriers | In recent years, there has been a surge of interest in predicting computed activation barriers, to enable the acceleration of the automated exploration of reaction networks. Consequently, various predictive approaches have emerged, ranging from graph-based models to methods based on the three-dimensional structure of reactants and products. In tandem, many representations have been developed to predict experimental targets, which may hold promise for barrier prediction as well. Here, we bring together all of these efforts and benchmark various methods (CGR, SLATMd , B2R2l , MFPs, DRFP and RXNFP) for the prediction of computed activation barriers on three diverse datasets | Puck van Gerwen; Ksenia R. Briling; Yannick Calvino Alonso; Malte Franke; Clemence Corminboeuf | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f1d26779853bbd78dca5ab/original/benchmarking-machine-readable-vectors-of-chemical-re-actions-on-computed-activation-barriers.pdf |
6551f8442c3c11ed714c1299 | 10.26434/chemrxiv-2023-136wn | Improving the gas sorption capacity in lantern-type metal-organic polyhedra by a scrambled cage method. | The synthesis of multivariate metal-organic frameworks (MOFs) is a well-known method for increasing the complexity of porous frameworks. In these materials, the structural differences of the ligands used in the synthesis are sufficiently subtle that they can each occupy the same site in the framework. However, multivariate or ligand scrambling approaches are rarely used in the synthesis of porous metal-organic polyhedra (MOPs) – the molecular equivalent of MOFs – despite the potential to retain a unique intrinsic pore from the individual cage while varying the extrinsic porosity of the material. Herein we directly synthesise scrambled cages across two families of lantern-type MOPs and find contrasting effects on their gas sorption properties. In one family, the scrambling approach sees a gradual increase in the BET surface area with the maximum and minimum uptakes associated with the two pure homoleptic cages. In the other, the scrambled materials display improved surface areas with respect to both of the original, homoleptic cages. Through analysis of the gas sorption isotherms, we attribute this effect to the balance of micro- and mesoporosity with the materials. The gas uptake of the materials presented here underscores the tunability of cages that springs from their combination of intrinsic, extrinsic, micro- and meso- porosities. | Beatriz Doñagueda Suso; Zaoming Wang; Alan Kennedy; Ashleigh Fletcher; Shuhei Furukawa; Gavin Craig | Inorganic Chemistry; Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6551f8442c3c11ed714c1299/original/improving-the-gas-sorption-capacity-in-lantern-type-metal-organic-polyhedra-by-a-scrambled-cage-method.pdf |
6323697808470084f27cebed | 10.26434/chemrxiv-2022-l5hp1 | Double Paddle-Wheel Enhanced Sodium Ion Conduction in an Antiperovskite Solid Electrolyte | Antiperovskite (AP) structure compounds (X3AB, where X is an alkali cation and A and B are anions) have the potential for highly correlated motion between the cation and a cluster anion on the A or B site. This so-called “paddle-wheel” mechanism may be the basis for enhanced cation mobility in solid electrolytes. Here we show, through combined experiments and modeling, the first instance of a double paddle-wheel mechanism, leading to fast sodium ion conduction in the antiperovskite Na3-xO1-x(NH2)x(BH4). As the concentration of amide (NH2-) cluster anions is increased, large positive deviations in ionic conductivity above that predicted from a vacancy diffusion model are observed. Using EIS, PXRD, synchrotron XRD, neutron diffraction, AIMD, and NMR, we characterize the cluster anion rotational dynamics, and find that cation mobility is influenced by the rotation of both NH2- and BH4- species, resulting in sodium ion conductivity a factor of 102 higher at x = 1 than expected for the vacancy mechanism alone. Generalization of this phenomenon to other compounds could accelerate fast ion conductor exploration and design. | Ping-Chun Tsai; Sunil Mair; Jeffrey Smith; David Halat; Po-Hsiu Chien; Kwangnam Kim; Duhan Zhang; Yiliang Li; Liang Yin; Jue Liu; Saul Lapidus; Jeffrey Reimer; Nitash Balsara; Donald Siegel; Yet-Ming Chiang | Materials Science; Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6323697808470084f27cebed/original/double-paddle-wheel-enhanced-sodium-ion-conduction-in-an-antiperovskite-solid-electrolyte.pdf |
630cba8bd858fb248c608bdf | 10.26434/chemrxiv-2022-wqr91 | Eliminative Nucleophilic Aromatic Substitution of Hydrogen (SNArH): An Alternative Mechanism Explaining Reactivity of N-heterocyclic Carbene (NHC) toward Tritylium | Despite a recent proposal on the mechanism of a single-electron transfer (SET) process between tritylium and 2,6-bis(diisopropylphenyl)imidazol-2-ylidene (IPr) based on evidence of transient IPr radical cation intermediate ([IPr]●+) formation, such oxidation is still contentious because of the high oxidation potential of N-heterocyclic carbenes. Our experimental analysis indicates that the appearance of a deep purple color, previously considered to be from transient [IPr]●+, originates from a zwitterionic intermediate (3a), not a radical cation. Here, we propose an alterna-tive mechanism for the reaction involving tritylium and IPr: the eliminative nucleophilic aromatic substitution of hydrogen (SNArH). This mechanism is noteworthy in two respects: (1) for showing the first example of SNArH without any vicarious leaving group and (2) for explaining how [NHC–H]+ can be generated without the formation of tran-sient [NHC]●+, which has been frequently proposed as an intermediate for the reaction between NHC and oxidants. These results also show that a transient strong single-electron donor (3a) could be generated by the eliminative SNArH mechanism for oxidants using NHCs, which is a more feasible explanation for the reactivity of NHCs with oxidants. | Hayoung Song; Eunsung Lee | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630cba8bd858fb248c608bdf/original/eliminative-nucleophilic-aromatic-substitution-of-hydrogen-sn-ar-h-an-alternative-mechanism-explaining-reactivity-of-n-heterocyclic-carbene-nhc-toward-tritylium.pdf |
6562637f5bc9fcb5c95f0cac | 10.26434/chemrxiv-2023-93jq8 | Rational Molecular Design of Efficient Yellow-Red Dendrimer TADF for Solution-Processed OLEDs: A Combined Effect of Substitution Position and Strength of the Donors | The development of high-performance solution-processed red organic light-emitting diodes remains a challenge, particularly in terms of maintaining efficiency at high luminance. Here, we designed and synthesized four novel orange-red solution-processable TADF dendrimers, 2GCzBP, 2DPACzBP, 2FBP2GCz and 2FBP2DPACz. We systematically investigated the effect of substitution position and strength of donors on the opto-electronic properties. The reverse intersystem crossing rate constant (kRISC) of the emitters having donors substituted at positions 11 and 12 of the dibenzo[a,c]phenazine (BP) is more than 10-times faster than that of compounds substituted having donors substituted at positions 3 and 6. Compound 2DPACzBP, containing stronger donors than 2GCzBP, exhibits a red-shifted emission and smaller singlet−triplet energy splitting, EST, of 0.01 eV. The solution-processed OLED with 10 wt% 2DPACzBP doped in mCP emitted at 640 nm and showed a maximum external quantum efficiency (EQEmax) of 7.8%, which was effectively maintained out to a luminance of 1000 cd m−2. Such a device performance at relevant display luminance is among the highest for solution-processed red TADF OLEDs. The efficiency of the devices was improved significantly by using 4CzIPN as an assistant dopant in a hyperfluorescence (HF) configuration, where the 2DPACzBP HF device shows an EQEmax of 20.0% at EL of 605 nm and remains high at 11.8% at a luminance of 1000 cd m−2, which makes this device one of the highest efficiency orange-to-red HF SP-OLEDs to date. | Changfeng Si; Dianming Sun; Tomas Matulaitis; David Cordes; Alexandra Slawin; Eli Zysman-Colman | Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6562637f5bc9fcb5c95f0cac/original/rational-molecular-design-of-efficient-yellow-red-dendrimer-tadf-for-solution-processed-ole-ds-a-combined-effect-of-substitution-position-and-strength-of-the-donors.pdf |
63de62583067856f18aa2c7e | 10.26434/chemrxiv-2023-fl2wp | Wrapping up Metal-Organic Framework Crystals with Carbon Nanotubes | The presence of tetrazine units in the organic nodes of UiO- 68-TZCD controls the formation of ultrathin coatings of single wall nanotubes that decorate the surface of the crystal. These crystal hybrids can be prepared straightforwardly in one step and are extraordinarily respectful with the properties of the framework for combination of mesoporosity and surface areas near 4.000 m·g-1 ,with excellent stability in water, and conductivities at room temperature of 4·10-2 S·cm-1 even at very low carbon weight contents (2.3 wt%). | Belén Lerma-Berlanga; Natalia M. Padial; Marta Galbiati; Isaac Brotons-Alcazar; Josep Albero; Hermenegildo García; Alicia Forment-Aliaga; Carolina R. Ganivet; Carlos Martí-Gastaldo | Inorganic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63de62583067856f18aa2c7e/original/wrapping-up-metal-organic-framework-crystals-with-carbon-nanotubes.pdf |
661d11f491aefa6ce199789a | 10.26434/chemrxiv-2024-1l52c | Optical Diffusion-Ordered Spectroscopy:
A Simultaneous Probe of Molecular Size and
UV/Visible Absorption | Based on concepts from nuclear magnetic resonance, we have developed UV/Vis Diffusion-Ordered Spectroscopy, which simultaneously probes the size and the electronic
spectrum of molecules and particles. We use simple flow technology to create a step-function concentration profile inside an optical sample cell, and by measuring the time-dependent absorption spectrum in an initially solvent-filled part of the sample volume, we obtain the diffusion coefficients and the UV/Vis spectra of the species present in the sample solution. From this data, we construct a two-dimensional spectrum with absorption wavelength on one axis and diffusion coefficient (or equivalently, size) on the other, in which the UV/Vis spectrum of a mixture with different molecular sizes is separated into the spectra of the different species, sorted by size. We demonstrate this method on mixed aqueous solutions of fluorescent dyes,
biomolecules, and the UV-absorbing components of coffee, caffeine and chlorogenic acid, all with concentrations in the μM range. By using UV/Vis-DOSY, we can simultaneously determine the diffusion coefficient and the electronic spectrum of molecular species in a solution. | Giulia Giubertoni; Marina Gomes Rachid; Carolyn Moll; Michiel Hilbers; Saer Samanipour; Sander Woutersen | Physical Chemistry; Analytical Chemistry; Biochemical Analysis; Spectroscopy (Anal. Chem.); Optics | CC BY 4.0 | CHEMRXIV | 2024-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661d11f491aefa6ce199789a/original/optical-diffusion-ordered-spectroscopy-a-simultaneous-probe-of-molecular-size-and-uv-visible-absorption.pdf |
671a20d098c8527d9e30dfb0 | 10.26434/chemrxiv-2024-n5r4n | 1 min synthesis of phase-pure nanocrystalline high-entropy sulphides for efficient water electrolysis | The development of noble-metal free electrocatalysts with low production cost is of utmost importance for sustainable water electrolysis. Herein, we present a fast, flexible synthesis pathway for the preparation of a variety of different medium- and high-entropy spinel sulphides of various compositions, using a non-aqueous microwave-assisted synthesis without any H2S. Nanoparticulate high-entropy sulphides containing up to 8 different metal cations can be obtained after an extremely short synthesis time of only 1 min and comparatively low temperatures of 200-230 °C. We further demonstrate the high activity of the obtained sulphides for both the hydrogen evolution reaction (HER) and the oxygen evolution reaction (OER). | Judith Zander; Roland Marschall | Catalysis; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671a20d098c8527d9e30dfb0/original/1-min-synthesis-of-phase-pure-nanocrystalline-high-entropy-sulphides-for-efficient-water-electrolysis.pdf |
60c7478cf96a00e4cf286f50 | 10.26434/chemrxiv.11702439.v1 | WS2/MoS2 Heterostructures via Thermal Treatment of MoS2 Layers Electrostatically Functionalized with W3S4 Molecular Clusters | The preparation of 2D stacked layers that combine flakes of different nature, gives rise
to countless number of heterostructures where new band alignments, defined at the interfaces,
control the electronic properties of the system. Among the large family of 2D/2D heterostructures,
the one formed by the combination of the most common semiconducting transition metal
dichalcogenides WS2/MoS2, has awaken great interest due to its photovoltaic and
photoelectrochemical properties. Solution as well as dry physical methods have been developed
to optimize the synthesis of these heterostructures. Here a suspension of negatively charged MoS2
flakes is mixed with a methanolic solution of a cationic W3S4-core cluster, giving rise to a
homogeneous distribution of the clusters over the layers. In a second step, a calcination under N2
of this molecular/2D heterostructure leads to the formation of clean WS2/MoS2 heterostructures
where the photoluminescence of both counterparts is quenched, proving an efficient interlayer
coupling. Thus, this chemical method combines the advantages of a solution approach (simple,
scalable and low-cost) with the good quality interfaces reached by using more complicated
traditional physical methods. | Marc Morant-Giner; Isaac Brotons-Alcazar; Nikita Y. Shmelev; Artem L. Gushchin; Luke Norman; Andrei N. Khlobystov; Antonio Alberola; Sergio tatay; J. Canet-Ferrer; Alicia Forment-Aliaga; Eugenio Coronado | Multilayers | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7478cf96a00e4cf286f50/original/ws2-mo-s2-heterostructures-via-thermal-treatment-of-mo-s2-layers-electrostatically-functionalized-with-w3s4-molecular-clusters.pdf |
60d897aefca490c937c95556 | 10.26434/chemrxiv-2021-6h6kj-v2 | Regioselective and Water-Promoted Surface Esterification of Never-Dried Cellulose Fibers Towards Nanofibers with Adjustable Surface Energy | A new regioselective route is introduced for surface modification of biological colloids in the presence of water. Taking the case of cellulose nanofibers (CNFs), we demonstrate a site-specific (93% selective) reaction between the primary surface hydroxyl groups (C6-OH) of cellulose and acyl imidazoles. Cellulose nanofibers bearing C6-acetyl and C6-iso-butyl groups, with a degree of substitution of up to 1 mmol·g–1 are obtained upon surface esterification, affording CNFs of adjustable surface energy. The morphological and structural features of the nanofibers remain largely unaffected, but the regioselective surface reactions enable tailoring the interfacial interactions, as demonstrated in oil/water Pickering emulsions. Our method precludes the need for drying or exchange with organic solvents for surface esterification, otherwise needed in the synthesis of esterified colloids and polysaccharides. Moreover, the method is well suited for application at high-solid content, opening the possibility for implementation in reactive extrusion and compounding. The proposed acylation is introduced as a sustainable approach that benefits from the presence of water and affords a high chemical substitution selectivity. | Marco Beaumont; Caio G. Otoni; Bruno
D. Mattos; Tetyana V. Koso; Roozbeh Abidnejad; Bin Zhao; Anett Kondor; Alistair W. T. King; Orlando J. Rojas | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d897aefca490c937c95556/original/regioselective-and-water-promoted-surface-esterification-of-never-dried-cellulose-fibers-towards-nanofibers-with-adjustable-surface-energy.pdf |
65d78dcf66c1381729448fc1 | 10.26434/chemrxiv-2024-mfpkx | Rapid Flow-Based Synthesis of Post-Translationally Modified Peptides and Proteins: A Case Study on MYC’s Transactivation Domain | Protein-protein interactions of c-Myc (MYC) are often regulated by post-translational modifications (PTMs), such as phosphorylation, and crosstalk thereof. Studying these interactions requires proteins with unique PTM patterns, which are challenging to obtain by recombinant methods. Standard peptide synthesis and native chemical ligation can produce such modified proteins, but are time-consuming and therefore typically limited to the study of individual PTMs. Herein, we report the development of flow-based methods for the rapid synthesis of phosphorylated MYC sequences (up to 84 AA), and demonstrate the versatility of this approach for the incorporation of other PTMs (Nε methylation, sulfation, acetylation, glycosylation) and combinations thereof. Peptides containing up to seven PTMs and five phosphorylations were successfully prepared and isolated in high yield and purity. Our methodology was then applied in the production of ten PTM-decorated analogues of the MYC Transactivation Domain (TAD) to screen for binding to the tumor suppressor protein, Bin1, using heteronuclear NMR and native mass spectrometry. We determined the effects of phosphorylation and glycosylation on the strength of the MYC:Bin1 interaction, and reveal an influence of MYC sequence length on binding. Our platform for the rapid synthesis of MYC sequences up to 84 AA with distinct PTM patterns thereby enables the systematic study of PTM function at a molecular level, and offers a convenient way for an expedited screening of constructs. | Elyse T. Williams; Kevin Schiefelbein; Matthias Schuster; Ikhlas M. M. Ahmed; Marije De Vries; Rebecca Beveridge; Oliver Zerbe; Nina Hartrampf | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Biophysics; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d78dcf66c1381729448fc1/original/rapid-flow-based-synthesis-of-post-translationally-modified-peptides-and-proteins-a-case-study-on-myc-s-transactivation-domain.pdf |
653302c887198ede07eac7e4 | 10.26434/chemrxiv-2023-gnxgj | Synthesis and Characterization of a Series of U(IV) trans-bis(Wittig) Adducts Across the UX4 Halide Series | Addition of 2 equiv. of the Wittig reagents CH2PAr3 (Ar = Ph; 3,5-di-tert-butylphenyl (tBuAr)) to the tetravalent uranium halides, UX4(solvent)n (X = Cl, n = 0; X = Br, solvent = THF, n = 2; X = I, solvent = 1,4-dioxane, n = 2), generates the trans-bis(Wittig) adducts UX4(CH2PAr3)2 (Ar = Ph, X = Cl (1Ph-Cl), I (1Ph-I); Ar = tBuAr, X = Cl (2tBu-Cl), Br (2tBu-Br), I (2tBu-I)) in low to good yields. Complexes 1Ph-X exhibit poor solubility in aromatic solvents but are partially soluble in 1,2-difluorobenzene, while 2tBu-X possesses greatly improved solubility in these solvents. In all cases, 1Ph-X and 2tBu-X are sensitive to polar coordinating solvents, such as THF or DME, decomposing in these solutions to intractable products. The solid-state molecular structures of 1Ph-XꞏC7H8 and 2tBu-Xꞏn(o-DFB), reveal U-CWittig bonds that range from = 2.506(3) – 2.58(1) Å, generally shorter than those found in other uranium-Wittig (2.60(1) – 2.71(1) Å) and untethered, monodentate U-CNHC (2.62(1) – 2.79(1) Å) complexes. Notably, a general contraction of the U-CWittig bond is observed in the UX4(CH2PAr3)2 as the halide series is descended, which may be attributable to the poorer π-donation of the heavier halides that gives rise to increased Lewis acidity at the uranium center that results in contraction of the U-CWittig bond. Attempts to oxidize 2tBu-Cl with Ag+ or Fc+ salts leads to complicated product mixtures from which a few crystals of {[(tBuAr)3PCH2]UCl3(μ-Cl)}2·C7H8 can be isolated, whereas addition of the reductant Cp*2Co to 2tBu-I, in the presence of an extra equiv. of CH2P(tBuAr)3, leads to the formation of the highly encumbered U(III) tris(Wittig) adduct UI3[CH2P(tBuAr)3]3 (3tBu-I). Preliminary experiments show these complexes are amenable to substitution reactions as treatment of 2tBu-Cl with 2 equiv. of LiCH2SiMe3 generates the thermally sensitive bis(alkyl) bis(Wittig) complex trans-UCl2[CH2P(tBuAr)3]2(CH2SiMe3)2 (4tBu-TMS), a mixed ylide-alkyl system featuring distinct U-CWittig and U-Calkyl σ-bonds. This chemistry demonstrates that untethered, neutral Wittig ligands, when coordinated to uranium, are compatible with redox transformations and metathesis reactions. The report of these UX4(CH2PAr3)2 complexes significantly expands the library of known uranium-Wittig compounds and contributes to the relatively small collection of uranium complexes featuring neutral C-donor ligands. | Frank MacGregor; Alejandro Metta; Skye Fortier | Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Organometallic Compounds | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653302c887198ede07eac7e4/original/synthesis-and-characterization-of-a-series-of-u-iv-trans-bis-wittig-adducts-across-the-ux4-halide-series.pdf |
60c9e3b279801879d2c766fb | 10.26434/chemrxiv.14776965.v1 | Momentum Removal to Obtain the Position-Dependent Diffusion Constant in Constrained Molecular Dynamics Simulation | <div>The position-dependent diffusion coefficient along with free energy profile are important parameters needed to study mass transport in heterogeneous systems such as biological and polymer membranes, and molecular dynamics (MD) calculation is a popular tool to obtain them. Among many methodologies, the Marrink-Berendsen (MB) method is often employed to calculate the position-dependent diffusion coefficient, in which the autocorrelation function of the force on a fixed molecule is related to the friction on the molecule. However, the diffusion coefficient is shown to be affected by the period of the removal of the center-of-mass velocity, which is necessary when performing MD calculations using the Ewald method for Coulombic interaction. We have clarified theoretically in this study how this operation affects the diffusion coefficient calculated by the MB method, and the theoretical predictions are proven by MD calculations. Therefore, we succeeded in providing guidance on how to select an appropriate the period of the removal of the center-of-mass velocity in estimating the position-dependent diffusion coefficient by the MB method. This guideline is applicable also to the Woolf-Roux method.</div> | Kazushi Fujimoto; Tetsuro Nagai; Tsuyoshi Yamaguchi | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c9e3b279801879d2c766fb/original/momentum-removal-to-obtain-the-position-dependent-diffusion-constant-in-constrained-molecular-dynamics-simulation.pdf |
60c7586c0f50dbd2bc398435 | 10.26434/chemrxiv.14544213.v1 | Discovery of the Class I Antimicrobial Lasso Peptide Arcumycin | <p>Lasso peptides are a structurally diverse superfamily of</p><p>conformationally-constrained peptide natural products, of which a</p><p>subset exhibits broad antimicrobial activity. Although advances in</p><p>bioinformatics have increased our knowledge of strains harboring</p><p>the biosynthetic machinery for lasso peptide production, relating</p><p>peptide sequence to bioactivity remains a continuous challenge.</p><p>Towards this end, a structure-driven genome mining investigation</p><p>of Actinobacteria-produced antimicrobial lasso peptides was</p><p>performed to correlate predicted primary structure with antibiotic</p><p>activity. Bioinformatic evaluation revealed eight putative novel</p><p>class I lasso peptide sequences. This subset is predicted to</p><p>possess antibiotic activity as characterized members of this class</p><p>have both broad spectrum and potent activity against Gram positive</p><p>strains. Fermentation of one of these hits, Streptomyces</p><p>NRRL F-5639, resulted in the production of a novel class I lasso</p><p>peptide, arcumycin, named for the Latin word for bow or arch,</p><p>arcum. Arcumycin exhibited antibiotic activity against Gram positive</p><p>bacteria including <i>Bacillus subtilis</i> (4 μg/mL),</p><p><i>Staphylococcus aureus </i>(8 μg/mL), and <i>Micrococcus luteus</i> (8</p><p>μg/mL). Arcumycin treatment of <i>B. subtilis</i> liaI-β-gal promoter</p><p>fusion reporter strain resulted in upregulation of the system liaRS</p><p>by the promoter liaI, indicating arcumycin interferes with lipid II</p><p>biosynthesis. Cumulatively, the results illustrate the relationship</p><p>between phylogenetically related lasso peptides and their</p><p>bioactivity as validated through the isolation, structural</p><p>determination, and evaluation of bioactivity of the novel class I</p><p>antimicrobial lasso peptide arcumycin.</p> | Lydia Stariha; Dewey G. McCafferty | Natural Products; Bioinformatics and Computational Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7586c0f50dbd2bc398435/original/discovery-of-the-class-i-antimicrobial-lasso-peptide-arcumycin.pdf |
65b969869138d231611267bc | 10.26434/chemrxiv-2023-c04wz-v2 | DFT-based characterization of double β-B-Bagostic interaction in model Ti-borane complexes | Simultaneous activation of two intramolecular B-H bonds in Ti-borane complexes, designated as double β-B-agostic interaction, has been investigated using state-of-the-art DFT techniques and further tuned by coordination number, systematic substitution, and conformational changes. A series of (L)y(M)zTi-NH2BH3 [L=Cl-, M=H2O, y+z=3-6] compounds have been considered to investigate the electronic and structural properties of double β-B-agostic interaction. Our analysis infers that the strength, pattern, and symmetricity of the B-H bond activation depend on each tuning parameter mentioned above; in extreme cases, a few complexes show single B-H activation. It has been noticed that the extent of activation of B-H bonds has a proportional relationship with B-H bond distance and an inversely proportional relationship with Ti-H bond distance, which is further confirmed through QTAIM analysis. The formation of partial covalent character between Ti and H centers illustrates the impact of metal on the generation of double β-B-agostic interaction. Overall, the concept of double β-B-agostic interactions encourages the researcher to study novel catalytic activities related to metal-borane complexes through more than one B-H bonds activation. | Tamalika Ash; Soumadip Banerjee; Avik Ghosh; Tanay Debnath; Abhijit K. Das | Theoretical and Computational Chemistry; Organometallic Chemistry; Bond Activation; Theory - Organometallic | CC BY NC 4.0 | CHEMRXIV | 2024-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b969869138d231611267bc/original/dft-based-characterization-of-double-b-bagostic-interaction-in-model-ti-borane-complexes.pdf |
66df0773cec5d6c14299d70d | 10.26434/chemrxiv-2024-k4vjd | Frontal Polymerization of Covalent Adaptable Networks | Frontal polymerization is a curing method that is known for its high conversion, short reaction times and low energy consumption. However, the resulting materials are typical thermosets, allowing no reprocessing, reshaping nor recycling. Herein, a new approach is pursued, which combines the energy efficiency of frontal polymerization with the unique post-processability of covalent adaptable networks. Thus, selected thiol-acrylate resins, bearing a sufficiently high number of ester linkages and free hydroxyl groups, were investigated, using phosphate esters as transesterification catalysts. The amount of phosphate ester and thiol was varied and its influence on material properties and frontal polymerization kinetics were analyzed. The reaction kinetics were studied with FTIR and photo-DSC measurements, showing a trend towards lower reactivity and higher conversions with an increased thiol content. The obtained networks exhibited tunable bond exchange rates by varying either the amount of thiol or of the catalyst. DMA measurements reveal a higher network homogeneity with increasing thiol content. Moreover, reprocessing, recycling as well as reshaping of the material was successfully demonstrated. Concludingly, these findings could significantly lower energy consumption and increase circularity in future thermoset production. | Christoph Schmidleitner; Matthias Udo Kriehuber; Sandra Schlögl; Elisabeth Rossegger | Polymer Science; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66df0773cec5d6c14299d70d/original/frontal-polymerization-of-covalent-adaptable-networks.pdf |
60c74fb0bb8c1a0c0d3db9a1 | 10.26434/chemrxiv.12888296.v2 | Design of Metal-Organic Framework Templated Materials using High-Throughput Computational Screening | <p>The ability to crosslink Metal-Organic Frameworks (MOFs) has recently been discovered as a flexible approach towards synthesizing MOF-templated “ideal network
polymers”. Crosslinking MOFs with rigid cross-linkers would allow the synthesis of
crystalline Covalent-Organic Frameworks (COFs) of so far unprecedented flexibility
in network topologies, far exceeding the conventional direct COF synthesis approach.
However, to date only flexible cross-linkers were used in the MOF crosslinking approach, since a rigid cross-linker would require an ideal fit between the MOF structure
and the cross-linker, which is experimentally extremely challenging, making in silico design mandatory. Here, we present an effective geometric method to find an ideal
MOF cross-linker pair by employing a high-throughput screening approach. The algorithm considers distances, angles, and arbitrary rotations to optimally match the
cross-linker inside the MOF structures. In a second, independent step, using Molecular Dynamics (MD) simulations we quantitatively confirmed all matches provided by
the screening. Our approach thus provides a robust and powerful method to identify
ideal MOF/Cross-linker combinations, which helped to identify several MOF-to-COF
candidate structures by starting from suitable libraries. The algorithms presented here
can be extended to other advanced network structures, such as mechanically interlocked
materials or molecular weaving and knots<br /></p> | Manuel Tsotsalas; Alexander Schug; Momin Ahmad; Christof Wöll; Yi Luo | Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fb0bb8c1a0c0d3db9a1/original/design-of-metal-organic-framework-templated-materials-using-high-throughput-computational-screening.pdf |
67a045d9fa469535b9e05429 | 10.26434/chemrxiv-2025-1kzz4 | Stereoselective Generation and Use of α-Fluorovinyl Radicals via Mesolytic Cleavage of C(sp2)–S Bond of α-Fluorovinyl Sulfoximines | An unusual configurational stability of α-fluorovinyl radical holds significant potential to synthesize valuable monofluoroalkenes, bioisosteres of amides, in a stereoselective fashion. However, the lack of a suitable precursor for this radical, generated in a stereoselective manner, has hindered its application to the stereoselective synthesis of monofluoroalkenes. Herein, we report the stereoselective generation of the α-fluorovinyl radical, which reacts with disulfide to form α-fluorovinyl sulfides. This method hinges on two key reactions: stereoselective condensation of N-pivaloyl fluoromethyl sulfoximine with an aldehyde to form α-fluorovinyl sulfoximine, and substitution radical-nucleophilic unimolecular (SRN1)-type reaction involving the nontrivial mesolytic cleavage of the C(sp2)–S bond of the resulting α-fluorovinyl sulfoximines. The generation of the α-fluorovinyl radical was supported by density functional theory (DFT) calculation, the Arrhenius equation, and the stereospecificity of the substitution with retention of its original stereochemistry. | Kosuke Yasui; Masayuki Miyaoka; Yuichiro Tomishima; Koji Hirano | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a045d9fa469535b9e05429/original/stereoselective-generation-and-use-of-fluorovinyl-radicals-via-mesolytic-cleavage-of-c-sp2-s-bond-of-fluorovinyl-sulfoximines.pdf |
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