id
stringlengths 24
24
| doi
stringlengths 28
32
| title
stringlengths 8
495
| abstract
stringlengths 17
5.7k
| authors
stringlengths 5
2.65k
| categories
stringlengths 4
700
| license
stringclasses 3
values | origin
stringclasses 1
value | date
stringdate 1970-01-01 00:00:00
2025-03-24 00:00:00
| url
stringlengths 119
367
⌀ |
|---|---|---|---|---|---|---|---|---|---|
63eef4cefcfb27a31fe9d30e | 10.26434/chemrxiv-2023-g2zdc | Unusual Flexibility of Transparent Poly(methylsilsesquioxane) Aerogels by Surfactant-Induced Mesoscopic Fiber Assembly | We report a new synthetic strategy to realize highly transparent aerogels with outstanding bending flexibility. Taking poly(methylsilsesquioxane) (PMSQ) aerogels as an example, surfactant-induced fiber-like mesoscopic assembly of PMSQ and poly(ethylene oxide)-block-poly(propylene oxide)-block-poly(ethylene oxide) (PEO-b-PPO-b-PEO, so-called Pluronics) has been demonstrated. The obtained PMSQ aerogels possessed a characteristic branched fibrous structure in the mesoscale. With employing various kinds of PEO-b-PPO-b-PEO as the structure determining agent, optimization of the mesoscale structure of PMSQ gels has realized highly transparent aerogels with outstanding bendability compared to those reported in previous works. This approach provides a novel way to thermally superinsulating flexible devices with glasslike transparency. | Ryota Ueoka; Yosuke Hara; Ayaka Maeno; Hironori Kaji; Kazuki Nakanishi; Kazuyoshi Kanamori | Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63eef4cefcfb27a31fe9d30e/original/unusual-flexibility-of-transparent-poly-methylsilsesquioxane-aerogels-by-surfactant-induced-mesoscopic-fiber-assembly.pdf |
667400c601103d79c5a982a0 | 10.26434/chemrxiv-2024-3z367 | “Hexagonal” Perovskites – From Stacking Sequence to Space Group Symmetry and New Opportunities | The term hexagonal perovskite has been widely used in literature to discuss the structure of perovskite-type compounds with composition ABX3-y with partial h-type stacking of AX3 layers. Though the local surrounding of these AX3 layers resembles a hexagonal close packing, the space group symmetries reported for some of these materials are not belonging to the hexagonal crystal system, but are trigonal or orthorhombic instead. Though reports and books with lists of hexagonal perovskites exist which assign stacking sequences and list a corresponding space group together with them, a concise guideline on how the symmetry of the perovskite type material is related to the stacking sequence has not been reported. Clearly, such a systematization of space group symmetry and stacking notations would be desirable – for distortion or ordering variants of the cubic perovskite, the whole research community benefits from concepts of group-subgroup relations or classification of tilting via the Glazer notation.
In this article, we derive a fully consistent guideline on how the aristotype space group symmetry can be determined for any stacking sequence (e.g., cchhchcch…) in the Jagodzinski notation and provide a computer program which can do this analysis. By this, one can narrow down the possible aristotype space group symmetries for any perovskite stacking sequence with h-type layers to seven space groups in total (R-3m, P-3m, P63/mmc, P-6m2, R3m, P3m, and P63mc), and the space groups can be directly derived from the Jagodzinski sequence. Remarkably, the possibility to obtain polar perovskites with h-type layers by stacking has not been recognized in literature so far, and provides the opportunity to develop new multiferroic materials by design of stacking.
| Sylvia L. Kunz; Michael Haefner; Oliver Clemens | Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667400c601103d79c5a982a0/original/hexagonal-perovskites-from-stacking-sequence-to-space-group-symmetry-and-new-opportunities.pdf |
6753ff4d7be152b1d0374d13 | 10.26434/chemrxiv-2024-1hrrp | Unravelling antisymmetric exchange in a coordination polymer made of copper chloride and triazole | The present work reports the synthesis, structure, and magnetic properties of a one-dimensional coordination polymer made of copper(II) chloride and 1,2,4- triazole. The coordination polymer is synthesized in hydrochloric acid at room temperature. The structure determination by single crystal X-ray diffraction reveals an array of copper atoms bridged via two chlorine and a triazole. Magnetisation data show no hysteresis at temperatures down to 2 K, but suggest antisymmetric exchange and antiferromagnetic coupling between the neighbouring spins of Cu(II) ions. This work gives impetus for the synthesis of large crystals of coordination polymers based on which magnetic properties can be studied in depth. | Hidetsugu Shiozawa; Shiraz Ahmed Siddiqui; Alexander Prado-Roller; Michael Eisterer | Materials Science; Inorganic Chemistry; Magnetism; Organometallic Compounds; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6753ff4d7be152b1d0374d13/original/unravelling-antisymmetric-exchange-in-a-coordination-polymer-made-of-copper-chloride-and-triazole.pdf |
60c73dd2bdbb89c66ba37cf4 | 10.26434/chemrxiv.6135389.v1 | Basis Set Effects in the Description of the Cl-O Bond in ClO and XClO Isomers (X=H,O,Cl) Using DFT and CCSD(T) Methods | <p>The
performance of a group of density functional methods of progressive complexity
for the description of the ClO bond in a series of chlorine oxides was
investigated. The simplest ClO radical species as well as the two isomeric
structures XClO/ClOX for each X=H, Cl and O were studied using the PW91, TPSS,
B3LYP, PBE0, M06, M06-2X, BMK and B2PLYP functionals. Geometry optimizations as
well as reaction enthalpies and enthalpies of formation for each species were
calculated using Pople basis sets and the (aug)-cc-pVnZ Dunning sets, with
n=2-6. For the calculation of enthalpies of formation, atomization as well as
isodesmic reactions were employed. Both the precision of the methods with
respect to the increase of the basis sets, as well as their accuracy, were
gauged by comparing the results with the more accurate CCSD(T) calculations,
performed using the same basis sets as for the DFT methods. The results
obtained employing composite chemical methods (G4, CBS-QB3 and W1BD) were also
used for the comparisons, as well as the experimental results when they are
available. The results obtained show that error compensation is the key for
successful description of molecular properties (geometries and energies) by
carefully selecting method and basis sets. In general, expansion of the
one-electron basis set to the limit of completeness does not improve results at
the DFT level, but just the opposite. The enthalpies of formation calculated at
the CCSD(T)/aug-cc-pV6Z for the species
considered are generally in agreement with experimental determinations, and the
most accurate derived theoretically up to present. Different sources of error
in the calculations are discussed in detail.</p> | Oscar Ventura; Kenneth Irving; Martina Kieninger | Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2018-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd2bdbb89c66ba37cf4/original/basis-set-effects-in-the-description-of-the-cl-o-bond-in-cl-o-and-x-cl-o-isomers-x-h-o-cl-using-dft-and-ccsd-t-methods.pdf |
60c740e60f50db267a395a2d | 10.26434/chemrxiv.7588214.v3 | Mesoscopic Ordering of Water Dynamics in Self-Assembled Materials Revealed by Transient VSFG Microscopy | <b>We report, for the first time, observations of mesoscopically
homogeneous but macroscopically heterogenous water dynamics in self-assembled
materials by a new, spatially resolved infrared (IR) pump vibrational sum
frequency generation (VSFG) probe microscope. Using this new technique, we spatially
resolved dynamics of water bounded by host-guest, self-assembled sheets comprised
of sodium dodecyl sulfate (SDS) and β-cyclodextrin (β-CD). We found that the strong hydrogen-bond interactions
between β-CD
and nearby water not only template nearby water networks to adopt the chirality
of β-CD,
but also allow resonant energy transfer from β-CD to nearby water. More interestingly, the resonant
energy transfer dynamics are heterogeneous among domains, while remaining
uniform within domains. This surprising result indicates that the water near
self-assembled materials can be templated uniformly across micron domains. Because
SDS@2β-CD is a synthetic analogue that parallels the morphology, rigidity and
crystallinity of protein assemblies, similar mesoscopic ordering of water
structure and dynamics could also exist in biological soft materials. The
advancement of adding spatial resolution to ultrafast molecular vibrational
spectroscopy opens a new way to probe mesoscopic molecular structure ordering
and relaxation dynamics in biological systems, and hydro-responsive
self-assembly materials for micro-optics and electronics. </b> | Haoyuan Wang; Wenfan Chen; Jackson Wagner; Wei Xiong | Interfaces; Optics; Self-Assembly; Spectroscopy (Physical Chem.); Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e60f50db267a395a2d/original/mesoscopic-ordering-of-water-dynamics-in-self-assembled-materials-revealed-by-transient-vsfg-microscopy.pdf |
67915080fa469535b952c823 | 10.26434/chemrxiv-2025-kw811 | High-throughput computational analysis of kinetic barriers to ring-closing depolymerization for aliphatic polycarbonates | The chemical reversion of polymers via ring-closing depolymerization (RCD) to their monomeric constituents is a highly promising avenue to enable end of life-cycle recycling and reuse. However, most reported systems using RCD revolve around bespoke monomer designs to facilitate facile depolymerization and there exists relatively few investigations into influence of functional groups on the ability of a particular monomer to cleanly undergo depolymerization. Here, we perform computational investigations into the energy barriers for RCD of 6-membered aliphatic carbonates in different solvents. The results demonstrate highlight clear trends observed in prior experimental studies, validating the utility of computational investigations towards understanding RCD. Experimental evaluation of thermal depolymerization of two monomers confirmed the ability of the computationally investigated monomers to cleanly undergo RCD. Overall, this work highlights the utility of high-throughput energy barrier computations to provide meaningful insight into broad reactivity trends that would be highly laborious to access experimentally. | Brandi Ransom; Riccardo Bosio; Dmitry Zubarev; James Hedrick; Nathaniel Park | Theoretical and Computational Chemistry; Organic Chemistry; Polymer Science; Organic Synthesis and Reactions; Polymerization (Polymers); Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2025-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67915080fa469535b952c823/original/high-throughput-computational-analysis-of-kinetic-barriers-to-ring-closing-depolymerization-for-aliphatic-polycarbonates.pdf |
60c757b1469df40be8f45502 | 10.26434/chemrxiv.14449620.v1 | Exploring Aliovalent Substitutions in the Lithium Halide Superionic Conductor Li3-xIn1-xZrxCl6 (0 ≤ X ≤ 0.5) | <p>In recent years, ternary halides Li<sub>3</sub><i>MX</i><sub>6</sub> (<i>M</i> = Y, Er, In; <i>X</i> = Cl, Br, I) have garnered attention as solid electrolytes due to their wide electrochemical stability window and favorable room-temperature conductivities. In this material class, the influences of iso- or aliovalent substitutions are so far rarely studied in-depth, despite this being a common tool for correlating structure and transport properties. In this work, we investigate the impact of Zr substitution on the structure and ionic conductivity of Li<sub>3</sub>InCl<sub>6</sub> (Li<sub>3-<i>x</i></sub>In<sub>1-<i>x</i></sub>Zr<i><sub>x</sub></i>Cl<sub>6</sub> with 0 ≤ <i>x</i> ≤ 0.5) using a combination of neutron diffraction, nuclear magnetic resonance and impedance spectroscopy. Analysis of high-resolution diffraction data shows the presence of an additional tetrahedrally coordinated lithium position together with cation site-disorder, both of which have not been reported previously for Li<sub>3</sub>InCl<sub>6</sub>. This Li<sup>+</sup> position and cation disorder lead to the formation of a three-dimensional lithium ion diffusion channel, instead of the expected two-dimensional diffusion. Upon Zr<sup>4+</sup> substitution, the structure exhibits non-uniform volume changes along with an increasing number of vacancies, all of which lead to an increasing ionic conductivity in this series of solid solutions.</p> | Bianca Helm; Roman Schlem; Bjöern Wankmiller; Ananya Banik; Ajay Gautam; Justine Ruhl; Cheng Li; Michael Ryan Hansen; Wolfgang Zeier | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757b1469df40be8f45502/original/exploring-aliovalent-substitutions-in-the-lithium-halide-superionic-conductor-li3-x-in1-x-zrx-cl6-0-x-0-5.pdf |
61df2f89db4d9f6bb196c855 | 10.26434/chemrxiv-2022-zdr2h | Real-Space Interpretation of Interatomic Charge Transfer and Electron Exchange Effects by Combining Static and Kinetic Potentials and Associated Vector Fields | Intricate behavior of one-electron potentials from the Euler equation for electron density and corresponding gradient force fields in crystals was studied. Bosonic and fermionic quantum potentials were utilized in bonding analysis as descriptors of the localization of electrons and electron pairs. Channels of locally enhanced kinetic potential and the corresponding saddle Lagrange points were found between chemically bonded atoms linked by the bond paths. Superposition of electrostatic φ_es (r) and kinetic φ_k (r) potentials and electron density ρ(r) allowed partitioning any molecules and crystals into atomic ρ- and potential-based φ-basins; the φ_k-basins explicitly account for electron exchange effect, which is missed for φ_es-ones. Phenomena of interatomic charge transfer and related electron exchange were explained in terms of space gaps between ρ- and φ-zero-flux surfaces. The gap between φ_es- and ρ-basins represents the charge transfer, while the gap between φ_k- and ρ-basins is proposed to be a real-space manifestation of sharing the transferred electrons. The position of φ_k-boundary between φ_es- and ρ-ones within an electron occupier atom determines the extent of electron sharing. The stronger an H‧‧‧O hydrogen bond is, the deeper hydrogen atom’s φ_k-basin penetrates oxygen atom’s ρ-basin. For covalent bonds, a φ_k-boundary closely approaches a φ_es-one indicating almost complete sharing the transferred electrons, while for ionic bonds, the same region corresponds to electron pairing within the ρ-basin of an electron occupier atom. | Sergey A. Shteingolts; Adam I. Stash; Vladimir G. Tsirelson; Robert R. Fayzullin | Physical Chemistry; Quantum Mechanics; Structure; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61df2f89db4d9f6bb196c855/original/real-space-interpretation-of-interatomic-charge-transfer-and-electron-exchange-effects-by-combining-static-and-kinetic-potentials-and-associated-vector-fields.pdf |
60cc0b84403d995d07bb222c | 10.26434/chemrxiv-2021-vtf0r-v2 | The Ferric-superoxo Intermediate of the TxtE Nitration Pathway Resists Reduction, Facilitating Its Reaction with Nitric Oxide | TxtE is a cytochrome P450 (CYP) homolog that mediates the nitric oxide (NO)-dependent direct nitration of L-tryptophan (Trp) to form 4-nitro-L-tryptophan (4-NO2-Trp). A recent report showed evidence that TxtE activity requires NO to react with a ferric-superoxo intermediate. Given this minimal mechanism, it is not clear how TxtE avoids Trp hydroxylation, a mechanism that also traverses the ferric-superoxo intermediate. Our combined results suggest 1) autoxidation is the sole TxtE uncoupling pathway and 2) the TxtE ferric-superoxo intermediate cannot be reduced by these electron transfer partners. We conclude that resistance of the ferric-superoxo intermediate to reduction is a key feature of TxtE that increases the lifetime of the intermediate and enables its reaction with NO and efficient nitration activity. | Christopher Martin; Manyun Chen; Maria Martinez; Rosemary Loria; Yousong Ding; Jonathan Caranto | Biological and Medicinal Chemistry; Inorganic Chemistry; Bioinorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60cc0b84403d995d07bb222c/original/the-ferric-superoxo-intermediate-of-the-txt-e-nitration-pathway-resists-reduction-facilitating-its-reaction-with-nitric-oxide.pdf |
642dde71736114c963f9eacc | 10.26434/chemrxiv-2023-n3dlw | Cu(II), Zn(II), Cd(II) and Hg(II) Complexes of Omeprazole (PPZH): Synthesis and Characterization | Omeprazole is a widely used proton pump inhibitor. This is used for the treatment of gasteo-oesophageal reflux diseases as well as acid induced inflammation disorders of the stomach and duodenum. In the scheme of gradual release and extended acting drugs, metal complexes of the parent drugs are achieving growing importance. Complexes of metallic salts with PPI are known to be more effective and lower in toxicity in numerous circumstances as compared to the original drug itself. In this report, compounds of omeprazole with several metal salts such as copper, zinc, cadmium and mercury have been synthesized. The powders were analyzed applying different characterization techniques such as elemental analysis, infrared and ultraviolet-visible spectroscopy, thermal analysis including both TGA and DSC (differential scanning calorimetric), and finally magnetic susceptibility measurement. Omeprazole (OPZ) behaves as a bidentate ligand forming coordination compounds with metal ions having +2 charge. Anionic imidazolyl nitrogen (N-) and oxygen atom of sulfinyl >S=O group participate in coordination bond formation. Prepared compounds show tetrahedral structure. | Salma Begum; Humaira Yeasmin; Md Akteruzzaman; Md Motiur Mazumder | Inorganic Chemistry; Bioinorganic Chemistry | CC BY 4.0 | CHEMRXIV | 2023-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642dde71736114c963f9eacc/original/cu-ii-zn-ii-cd-ii-and-hg-ii-complexes-of-omeprazole-ppzh-synthesis-and-characterization.pdf |
66057e5be9ebbb4db9ca1b34 | 10.26434/chemrxiv-2024-bn5sm-v2 | Self-assembly of Tyrosine-containing Peptides into Injectable Hydrogels with Distinct Nanostructures is Key in Determining Inflammatory Response of Macrophages | Self-assembling peptides (SAPs) are fully defined nanobiomaterials offering unprecedented opportunities to control nanostructure and chemical attributes to investigate and manipulate cellular signals. To investigate the influence of chemical and morphological characteristics on inflammatory signalling in native immunity, we designed five Beta-sheet SAPs: EFEFKFEFK (EF8), YEFEFKFEFK (YEF8), EFEFKFEFKY (EF8Y), YEFEFKFEFKY (YEF8Y) and EYEFKFEFK (EYF8) (F: phenylalanine; E: glutamic acid; K: lysine, Y: tyrosine). The position of tyrosine in the peptide sequence dictated the distinct self-assembly into nanostructures, with sequences EF8Y, YEF8Y, EYF8 self-assembling into thin nanofibers d≈3.8 ± 0.2 nm, YEF8 self-assembling into rod-like flat ribbons d>20 nm and EF8 (control) consisting of both types of self-assembled nanostructures. These distinct nanostructures induced contrasting inflammatory response of monocytic model THP-1 cells-derived macrophages (MΦs). Presence of soluble EF8 nanofibers (at 2 mM) induced anti-inflammatory response and polarization towards an M2 state, whereas YEF8 displayed tendency for inducing pro-inflammatory response and polarization towards M1 state. The EF8Y, YEF8Y, EYF8 SAPs did not induce an inflammatory response in our models. These results were validated using peripheral blood mononuclear cells (PBMCs)-derived MΦs from human donors, confirming the critical role of the EF8 and YEF8 SAPs as possible orchestrators of the repair of tissues or inducers of pro-inflammatory state, respectively. The same MΦs polarization responses from THP-1 derived cells cultured on 20 mM hydrogels. These findings will facilitate the utilization of this family of SAPs as immunomodulatory nanobiomaterials potentially changing the course of inflammation during the progression of various diseases. | Jacek K. Wychowaniec; Ezgi Irem Bektas; Marcia Mürner; Jiranuwat Sapudom; Martin Šrejber; Marielle Airoldi; Roland Schmidt; Andrea J. Vernengo; Charlotte J.C. Edwards-Gayle; Paul Sean Tipay; Michal Otyepka; Jeremy Teo; David Eglin; Matteo D'Este | Physical Chemistry; Biological and Medicinal Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Bioengineering and Biotechnology; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66057e5be9ebbb4db9ca1b34/original/self-assembly-of-tyrosine-containing-peptides-into-injectable-hydrogels-with-distinct-nanostructures-is-key-in-determining-inflammatory-response-of-macrophages.pdf |
62eccdbf659a3f49c434f960 | 10.26434/chemrxiv-2022-8st2h | The Newton-X platform: new software developments for surface hopping and nuclear ensembles | Newton-X is an open-source computational platform to perform nonadiabatic molecular dynamics based on surface hopping and spectrum simulations using the nuclear ensemble approach. Both are among the most common methodologies in computational chemistry for photophysical and photochemical investigations. This paper describes the main features of these methods and how they are implemented in Newton-X. It emphasizes the newest developments, including zero-point-energy leakage correction, dynamics on complex-valued potential energy surfaces, dynamics induced by incoherent light, dynamics based on machine-learning potentials, exciton dynamics of multiple chromophores, and supervised and unsupervised machine learning techniques. Newton-X is interfaced with several third-party quantum-chemistry programs, spanning a broad spectrum of electronic structure methods. | Mario BARBATTI; Mattia Bondanza; Rachel Crespo-Otero; Baptiste Demoulin; Pavlo Dral; Giovanni Granucci; Fabris Kossoski; Hans Lischka; Benedetta Mennucci; Saikat Mukherjee; Marek Pederzoli; Maurizio Persico; Max Pinheiro Jr; Jiri Pittner; Felix Plasser; Eduarda Sangiogo Gil; Lijljana Stojanovic | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62eccdbf659a3f49c434f960/original/the-newton-x-platform-new-software-developments-for-surface-hopping-and-nuclear-ensembles.pdf |
60c7591cf96a002167288f5f | 10.26434/chemrxiv.14648526.v1 | A Catalytic Highly Enantioselective Synthesis of Spirooxazolines | A catalytic highly enantioselective synthesis of spirooxazolines is presented. Starting from readily available 2-naphthol-substituted benzamides and using catalytic amounts of a chiral triazole-substituted iodoarene catalyst, a variety of spirooxazolines can be isolated through an enantioselective oxidative dearomatization in up to 92% yield and 97% ee. The further synthetic utility of the optically enriched spirooxazolines was examined providing a corresponding 2-naphthalenole and an oxepin.<br /> | Ayham Abazid; Boris Nachtsheim | Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7591cf96a002167288f5f/original/a-catalytic-highly-enantioselective-synthesis-of-spirooxazolines.pdf |
65e8b2dce9ebbb4db914d1c6 | 10.26434/chemrxiv-2024-b2651 | RNA-directed Peptide Synthesis Across a Nicked Loop | Ribosomal translation at the origin of life requires controlled aminoacylation to produce mono-aminoacyl esters of tRNAs. Herein, we show that transient annealing of short RNA oligo:amino acid mixed anhydrides to an acceptor strand enables the sequential transfer of aminoacyl residues to the diol of an overhang, first forming aminoacyl esters then peptidyl esters. Using N-protected of aminoacyl esters prevents unwanted peptidyl ester formation in this manner. However, N-acylaminoacyl transfer is not stereospecific. | Meng Su; Samuel Roberts; John Sutherland | Biological and Medicinal Chemistry | CC BY 4.0 | CHEMRXIV | 2024-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e8b2dce9ebbb4db914d1c6/original/rna-directed-peptide-synthesis-across-a-nicked-loop.pdf |
65b9a239e9ebbb4db95170e3 | 10.26434/chemrxiv-2024-xj25g | Under-representativeness of Physical Chemistry Journals | In the contemporary landscape of scientific publishing, the categorization and ranking of journals significantly influence academic research and scholarly careers [1-2]. Particularly in chemistry with numerous research fields, the issue of misclassification of journals has emerged as a notable concern. In this comment, we aim to examine the misclassification of physical chemistry journals in the Web of Science (WOS) and how this impacts their ranking in the Journal Citation Reports (JCR). We highlight that due to the erroneous categorization of physical chemistry journals within other fields, they are forced to compete with journals possessing much higher impact factors, adversely affecting their standings in the JCR rankings. This not only undermines the reputation of physical chemistry journals but also negatively impacts the academic research and scholars within the field. Through our analysis, we seek to illuminate the severity of this issue and propose recommendations for a more equitable and accurate evaluation of physical chemistry journals. | Zhesi Shen; Jiandong Zhang; An Zeng | Physical Chemistry; Chemical Education | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b9a239e9ebbb4db95170e3/original/under-representativeness-of-physical-chemistry-journals.pdf |
60c7531a702a9ba3bc18c2f4 | 10.26434/chemrxiv.13386758.v1 | Coupling Miniaturized Free-Flow Electrophoresis to Mass Spectrometry via a Multi-Emitter ESI Interface | We present a novel multi-emitter electrospray ionization interface for the coupling of microfluidic<br />free-flow electrophoresis (μFFE) with mass spectrometry. 15 sample streams coming from 15 μFFE outlets were continuously analyzed in quick succession to monitor the electrophoretic<br />separation in the microchip. | Matthias Jender; Stefan Höving; Pedro Novo; Erik Freier; Dirk Janasek | Analytical Apparatus; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7531a702a9ba3bc18c2f4/original/coupling-miniaturized-free-flow-electrophoresis-to-mass-spectrometry-via-a-multi-emitter-esi-interface.pdf |
64761ddabe16ad5c572ef05c | 10.26434/chemrxiv-2023-z3bkm-v2 | Electrostatic Potential Maps on Molecular Surfaces Using Least Squares Reconstruction | Biomolecular surface electrostatic potential maps (EPMs) are routinely used to infer biological function, binding sites, and qualitative guidance (and subsequent quantitative assessment) of the geometric and electrostatic properties of receptor-drug complexes. A major challenge in Poisson-Boltzmann (PB) modeling and generation of EPMs is accurately accounting for the dielectric discontinuity at the molecular surface and associated jump in normal electrostatic field. One option for accommodating such solutions is to develop a surface conforming grid such that no element or mesh edge intersects the molecular surface. Given the complex shapes of biomolecules, unstructured tetrahedral grids are usually necessary to develop such grids. Here an alternate approach is presented that first develops an adaptive Cartesian grid with no attempt to align it with the molecular surface. Next each mesh edge that intersects the surface is processed by identifying the intersection point and then using a least squares-based reconstruction (LSR) method to estimate the surface potentials and their gradients. The LSR incorporates the analytical surface matching constraints, satisfies the PBE locally, accounts for surface curvature, and is combined with the finite difference scheme used at off-surface points to solve the PB equation. This results in a global set of equations that solves the governing equations at all interior and exterior points, and couples then at the edge intersection points. The LSR is implemented in the adaptive Cartesian grid PB solver (from herein called CPB) and applied to a variety of biomolecular systems ranging from small to very large-scale (e.g., viruses) assemblies to compute electrostatic energies, forces, and high-quality estimates of the surface EPM. Using LSR within CPB allows additional memory savings and proper visualization and rationalization of electrostatic complementarity/recognition features of protein-drug and nucleic acid-ligand complexes, with the latter requiring inclusion of nonlinear screening effects. In addition to detailing the LSR method, the article provides several recommendations for producing accurate, reliable, and reproducible biomolecular EPMs. The importance of performing grid convergence tests to ensure converged predictions is emphasized along with the need to properly account for nonlinear effects in highly charged systems and provide sufficient details of the biomolecular geometry, grid size, environmental conditions, and choice of contour levels to facilitate comparison against other EPM generation software. | Alexander Boschitsch; marcia fenley | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64761ddabe16ad5c572ef05c/original/electrostatic-potential-maps-on-molecular-surfaces-using-least-squares-reconstruction.pdf |
60c75019f96a00bfce287d67 | 10.26434/chemrxiv.12991601.v1 | Mechanistic Understanding of Surface Migration Dynamics with DNA Walkers | <p>Dynamic
DNA walkers can move cargoes on a surface through various mechanisms including
enzymatic reactions and strand displacement. While they have demonstrated high
processivity and speed, their motion dynamics are not well understood. Here, we
utilize an enzyme-powered DNA walker as a model system and adopt a random walk
model to provide new insight on migration dynamics. Four distinct migration modes
(ballistic, Lévy, self-avoiding, and diffusive motions) are identified. Each mode
shows unique step time and velocity distributions which are related to mean squared
displacement (MSD) scaling. Experimental results are in excellent agreement
with the theoretical predictions. With a better understanding of the dynamics, we
performed a mechanistic study, elucidating the effects of cargo types and
sizes, walker sequence designs, and environmental conditions. Finally, this
study provides a set of design principles for tuning the behaviors of DNA
walkers. The DNA walkers from this work could serve as a versatile platform for
mathematical studies and open new opportunities for bioengineering.</p> | yancheng Du; Jing Pan; Hengming Qiu; Chengde Mao; Jong Hyun Choi | Nanodevices | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75019f96a00bfce287d67/original/mechanistic-understanding-of-surface-migration-dynamics-with-dna-walkers.pdf |
65e2056666c1381729f63f92 | 10.26434/chemrxiv-2024-9r9hl | Metal-free Electrochemical Desulfurative Borylation of Thioethers | Herein, we present an electrochemical desulfurative protocol for the formation of alkyl boronic esters from thioethers. The paired electrolytic transformation utilizes HBpin as coupling partner and proceeds with inert electrodes. The transformation features mild conditions, broad substrate scope and excellent functional group tolerance, as illustrated by late-stage functionalization of pharmaceutical compounds and natural products. Furthermore, the protocol is scalable, successfully producing gram quantities of borylated product. | Julius Kuzmin; Helena Lundberg | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2024-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e2056666c1381729f63f92/original/metal-free-electrochemical-desulfurative-borylation-of-thioethers.pdf |
6230f749d6d3ed3d2f931fe1 | 10.26434/chemrxiv-2022-s60mx | Cost and performance targets for fully electrochemical ammonia production under flexible operation | Methods to produce ammonia from air, water, and renewable electricity are necessary to transition ammonia production away from the CO2-emitting Haber-Bosch process. In this vein, a fully electric process in which water-splitting-derived hydrogen and air-separation-derived nitrogen are reacted in an electrochemical process to produce ammonia is attractive. Such a process has the potential to be highly flexible and utilize intermittent renewable energy well. Here, we evaluated the cost-effectiveness of large-scale fully electric ammonia production relying on renewable electricity sources in conjunction with different types of storage and flexible operation, using a mixed-integer linear programming framework. The approach incorporates a first-principle, chemistry-independent representation of reactor power consumption and its dependence on reactor sizing and electrochemical parameters, the impact of product separation and recycling unconverted reactants, and plant dynamics in response to temporal variability in renewable energy availability. Given the emerging nature of electrochemical ammonia synthesis from nitrogen and hydrogen, we used the model to identify the reaction descriptors and their threshold values that enable cost parity between fully electric ammonia production with commercially viable production using thermochemical synthesis coupled with electrolytic hydrogen powered by renewable energy. We found that ammonia can be produced in an economically competitive manner, i.e. at costs <1 $/kg, at large scales if the electrochemical reactor can produce ammonia at partial currents exceeding 400 mA cm-2, energy efficiencies exceeding 30%, and process lifetimes of several years. In light of this, novel chemistries that can reduce nitrogen at high rates and moderate (<2.5 V) overpotentials are necessary for economic, large-scale ammonia production. | Nikifar Lazouski; Aditya Limaye; Abhishek Bose; Michal L Gala; Karthish Manthiram; Dharik Mallapragada | Energy; Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Energy Storage; Fuels - Energy Science | CC BY NC 4.0 | CHEMRXIV | 2022-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6230f749d6d3ed3d2f931fe1/original/cost-and-performance-targets-for-fully-electrochemical-ammonia-production-under-flexible-operation.pdf |
612ca91eb817b4f52d0e7802 | 10.26434/chemrxiv-2021-9t07w | Employing artificial neural networks to find reaction coordinates and pathways for self-assembly | Capturing the autonomous self-assembly of molecular building blocks in computer simulations is a persistent challenge, requiring to model complex interactions and to access long time scales. Advanced sampling methods allow to bridge these time scales but typically require to construct accurate low-dimensional representations of the transition pathways. In this work, we demonstrate for the self-assembly of two single-stranded DNA fragments into a ring-like structure how autoencoder architectures based on unsupervised neural networks can be employed to reliably expose transition pathways and to provide a suitable low-dimensional representation. The assembly occurs as a two-step process through two distinct half-bound states, which are correctly identified by the neural net. We exploit this latent space representation to construct a Markov state model for predicting the four molecular conformations and transition rates. Our work opens up new avenues for the computational modeling of multi-step and hierarchical self-assembly, which has proven challenging so far. | Jörn Appeldorn; Simon Lemcke; Thomas Speck; Arash Nikoubashman | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Polymer Science; Biopolymers; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612ca91eb817b4f52d0e7802/original/employing-artificial-neural-networks-to-find-reaction-coordinates-and-pathways-for-self-assembly.pdf |
67b88a6ffa469535b950ce48 | 10.26434/chemrxiv-2025-59c10 | Unleashing the Power of Potassium 2-Ethylhexanoate as a Mild and Soluble Base for Pd-catalyzed C-N Cross-Coupling | The formation of C-N bonds by Pd-catalyzed cross-coupling is one of the most widely practiced reactions in chemical synthesis. Typical reaction conditions involve either a strong base, which limits the scope of substrates, or an insoluble, inorganic base, which complicates running reactions on large scale. Reaction conditions are needed that can facilitate C-N couplings using a base that is both mild and soluble. We report the discovery of a combination of a phosphorinane ligand and a soluble carboxylate base, potassium 2-ethylhexanoate (K-2-EH) that, together, facilitate the coupling of base-sensitive reactants. To explore the enhanced substrate scope of reaction with this base and catalyst, we performed a scope evaluation using representative reactants selected from the chemical literature using chemical descriptors and clustering to ensure their chemical diversity. These results show that this phosphorinane ligand and K-2-EH couple primary aliphatic amines, amides, sulfonamides, and heteroaromatic nucleophiles, as well as acidic secondary nitrogen nucleophiles, such as secondary arylamines, heteroarylamines, and amides, with a range of electrophiles. The stabilities of several coupling products in the presence of a range of previously reported bases show that other soluble bases de-compose those products under standard reaction conditions, while K-2-EH did not. Finally, quantitative structure-reactivity relationship models, trained on ligand screening data, were developed to understand the structural features that engender reactivity. | William Lambert; Stephanie Felten; Nicholas Hadler; N. Ian Rinehart; Rafal Swiatowiec; Gregory Storer; Jeremy Henle; Mark Servos; Cassie Yang; Anna Bay; Pascal Eyimegwu; Shashank Shekhar; John Hartwig | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b88a6ffa469535b950ce48/original/unleashing-the-power-of-potassium-2-ethylhexanoate-as-a-mild-and-soluble-base-for-pd-catalyzed-c-n-cross-coupling.pdf |
60c74799bdbb89f042a38e34 | 10.26434/chemrxiv.11743071.v1 | A Practical Approach to Large Scale Electronic Structure Calculations in Electrolyte Solutions via Continuum-Embedded Linear-Scaling DFT | We present the implementation of a hybrid continuum-atomistic model for including the effects of surrounding electrolyte in large-scale density functional theory (DFT) calculations within the ONETEP linear-scaling DFT code, which allows the simulation of large complex systems such as electrochemical interfaces. The model represents the electrolyte ions as a scalar field and the solvent as a polarisable dielectric continuum, both surrounding the quantum solute. The overall energy expression is a grand canonical functional incorporating the electron kinetic and exchange correlation energies, the total electrostatic energy, entropy and chemical potentials of surrounding electrolyte, osmotic pressure, and the effects of cavitation, dispersion and repulsion. The DFT calculation is performed fully self-consistently in the electrolyte model, allowing the quantum mechanical system and the surrounding continuum environment to interact and mutually polarize. A bespoke parallel Poisson-Boltzmann solver library, DL_MG, deals with the electrostatic problem, solving a generalized Poisson-Boltzmann equation. Our model supports open boundary conditions, which allows the treatment of molecules, entire biomolecules or larger nanoparticle assemblies in electrolyte. We have also implemented the model for periodic boundary conditions, allowing the treatment of extended systems such as electrode surfaces in contact with electrolyte. A key feature of the model is the use of solute-size and solvation-shell-aware accessibility functions that prevent the unphysical accumulation of electrolyte charge near the quantum solute boundary. The model has a small number of parameters: here we demonstrate their calibration against experimental mean activity coefficients. We also present an exemplar simulation of a 1634-atom model of the interface between a graphite anode and LiPF<sub>6</sub> electrolyte in ethylene carbonate solvent. We compare the cases where Li atoms are intercalated at opposite edges of the graphite slab and in solution, demonstrating a potential application of the model in simulations of fundamental processes in Li-ion batteries. | Jacek Dziedzic; Arihant Bhandari; Lucian Anton; Chao Peng; James Womack; marjan famili; Denis Kramer; Chris-Kriton Skylaris | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74799bdbb89f042a38e34/original/a-practical-approach-to-large-scale-electronic-structure-calculations-in-electrolyte-solutions-via-continuum-embedded-linear-scaling-dft.pdf |
60c741e80f50dbad5f395bd7 | 10.26434/chemrxiv.8158013.v1 | Investigations into the Effects of Linker Length Elongation on the Behaviour of Calcium-responsive MRI Probes | Understanding the relationship between chemical structure and the effectiveness of bioresponsive magnetic resonance imaging contrast agents can offer help to identify key components required for the future development of such probes. Here, we report the development and characteristion of two novel monomeric bifunctional chelators, whose paramagnetic metal complexes can serve as calcium-responsive smart contrast agent (SCA). Specifically, relaxometric titrations, luminescence lifetime measurements, NMR studies and NMR diffusion experiments were carried out to assess the behaviour of each system. Overall, our findings demonstrate the impact of subtle changes to the structure of such probes, affecting a range of properties and their coordination behaviour. Through the understanding of such changes, fine tuning of future SCA designs which show optimal changes in relaxivity can be achieved. | Liam Connah; Vincent Truffault; Goran Angelovski | Imaging; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741e80f50dbad5f395bd7/original/investigations-into-the-effects-of-linker-length-elongation-on-the-behaviour-of-calcium-responsive-mri-probes.pdf |
60c74843bdbb89a4dfa38f58 | 10.26434/chemrxiv.11871501.v1 | Catalytic Synthesis of 8-Membered Ring Compounds via Cobalt(III)-Carbene Radicals | The metalloradical activation of o-aryl aldehydes with cobalt(II) porphyrin complexes as catalysts produces cobalt(III)-carbene radical intermediates, providing a novel and powerful strategy for the synthesis of medium-sized ring structures. Herein we make use of the intrinsic radical-type reactivity of cobalt(III)-carbene radical intermediates in the [Co<sup>II</sup>(TPP)]-catalyzed (TPP = tetraphenylporphyrin) synthesis of two types of 8 membered ring compounds; novel dibenzocyclooctenes and unique monobenzo-cyclooctadienes. The method was successfully applied to a variety of substrates, producing several 8-membered ring compounds in good yields and with excellent substituent tolerance. DFT calculations and experimental results suggest that the reactions proceed via initial hydrogen atom transfer from the bis-allylic/benzallylic C-H bond to the carbene radical moiety, followed by two divergent processes for ring-closure to the two different types of 8-membered ring products. While the dibenzocyclooctenes are formed by dissociation of o quinodimethanes (o-QDMs) from the catalyst that undergo an uncatalyzed ring-closure reaction involving 8-pi-cyclisation, DFT calculations suggest that ring-closure to the monobenzocyclooctadienes involves a radical-rebound step in the coordination sphere of cobalt. The latter mechanism implies that unprecedented enantioselective ring-closure reactions to chiral benzocyclooctadienes should be possible, as was confirmed for reactions mediated by a chiral cobalt-porphyrin catalyst. | M. Zhou; J.I. van der Vlugt; Bas de Bruin | Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74843bdbb89a4dfa38f58/original/catalytic-synthesis-of-8-membered-ring-compounds-via-cobalt-iii-carbene-radicals.pdf |
67ace81e6dde43c9089ce052 | 10.26434/chemrxiv-2025-0nx8j | Ultrasound-Driven Radical Expansion: Unlocking Novel Chemical
Pathways | This study investigates the potential of ultrasound-induced radical generation to
accelerate chemical reactions, focusing on the decomposition of hydrogen peroxide (H₂O₂).
High-frequency ultrasound creates cavitation bubbles that collapse to produce hydroxyl radicals
(•OH), significantly enhancing reaction rates. Our results demonstrate that this approach
increases the decomposition rate of H₂O₂ by 400% compared to conventional methods. The
implications extend to various applications, including optimizing chemotherapy drug activation
and improving wastewater treatment through advanced oxidation processes. Given its scalability
and cost-effectiveness, ultrasound-driven radical chemistry has the potential to transform
industrial and scientific processes. | Rand Ranj Adil | Organic Chemistry; Materials Science; Earth, Space, and Environmental Chemistry; Hydrology and Water Chemistry; Space Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ace81e6dde43c9089ce052/original/ultrasound-driven-radical-expansion-unlocking-novel-chemical-pathways.pdf |
613e1b7aac32190c6678f2f1 | 10.26434/chemrxiv-2021-r48w8 | Hydrogen peroxide disproportionation: time-resolved optical measurements of spectra, scattering and imaging combined with correlation analysis and simulations | We study how time-dependent optical measurements of spectra, scattering, and imaging can be used to add to the understanding of heterogeneous reactions, compared to work performed using tools developed for homogeneous reactions. Using hydrogen peroxide disproportionation by potassium permanganate as a model reaction, we measure the entire spectrum over reaction time, enabling a clear and useful correlation analysis and assignment of chemical species in heterogeneous conditions. We measure time-dependent dynamic light scattering to study oxygen nanobubble product formation kinetics and equilibrium. We perform macroscopic video-rate reaction imaging and information-theoretic analysis to characterize reaction and transport contributions to the observed signal. To illustrate the differences arising from measuring sample subsets vs the entire system, we integrate stochastic and macroscopic numerical simulations of reaction-diffusion to study homogeneous and heterogeneous reaction conditions. We hope the tools presented here may help understanding other chemical reactions in heterogeneous conditions. | Mohamed Ibrahim; Rene Nome | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613e1b7aac32190c6678f2f1/original/hydrogen-peroxide-disproportionation-time-resolved-optical-measurements-of-spectra-scattering-and-imaging-combined-with-correlation-analysis-and-simulations.pdf |
6374229921b45c373a1cf5c0 | 10.26434/chemrxiv-2022-wrmhg | Impact of Large Gate Voltages and Ultra-thin Polymer Electrolytes on Carrier Density in Electric-double-layer-gated Two-dimensional Crystal Transistors | Electric double layer (EDL) gating can induce large capacitance densities (∼1−10 μF/cm^2) in two-dimensional (2D) semiconductors; however, several properties of the electrolyte limit performance. One property is the electrochemical activity which limits the gate voltage (VG) that can be applied and therefore the maximum extent to which carriers can be modulated. A second property is electrolyte thickness, which sets the response speed of the EDL gate, and therefore the timescale over which the channel can be doped. Typical thicknesses are on the order of microns, but thinner electrolytes (nanometers) are needed for very-large-scale-integration (VLSI) both in terms of physical thickness and the speed that accompanies scaling. In this study, finite element modeling of an EDL-gated field-effect transistor (FET) is used to self-consistently couple ion transport in the electrolyte to carrier transport in the semiconductor, in which density of states, and therefore, quantum capacitance is included. The model reveals that 50 to 65% of the applied potential drops across the semiconductor, leaving 35 to 50% to drop across the two EDLs. Accounting for the potential drop in the channel suggests that higher carrier densities can be achieved at larger applied VG without concern for inducing electrochemical reactions. This insight is tested experimentally via Hall measurements of graphene FETs for which VG is extended from ±3 to ±6 V. Doubling the gate voltage increases the sheet carrier density by an additional 2.3×10^13 cm^−2 for electrons and 1.4×10^13 cm^−2 for holes without inducing electrochemistry. To address the need for thickness scaling, the thickness of the solid polymer electrolyte, polyethylene oxide (PEO):CsClO_4, is decreased from 1 μm to 10 nm and used to EDL- gate graphene FETs. Sheet carrier density measurements on graphene Hall bars prove that the carrier densities remain constant throughout the measured thickness range (10 nm−1 μm). The results indicate promise for overcoming the physical and electrical
limitations to VLSI while taking advantage of the ultrahigh carrier densities induced by EDL gating. | Shubham Sukumar Awate; Brendan Mostek; Shalini Kumari; Chengye Dong; Joshua Robinson; Ke Xu; Susan Fullerton-Shirey | Materials Science; Nanoscience; Polyelectrolytes - Materials; Nanodevices; Nanofabrication | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6374229921b45c373a1cf5c0/original/impact-of-large-gate-voltages-and-ultra-thin-polymer-electrolytes-on-carrier-density-in-electric-double-layer-gated-two-dimensional-crystal-transistors.pdf |
60c74cf4469df46567f441d2 | 10.26434/chemrxiv.12573701.v1 | Probing Multivalent Lectin-Carbohydrate Binding via Multifunctional Glycan-Gold Nanoparticles: Implications for Blocking Virus Infection | Multivalent lectin-glycan interactions are widespread
in biology and are often exploited by pathogens to bind and infect host cells.
Glycoconjugates can block such interactions and thereby prevent infection. The
inhibition potency strongly depends on matching the spatial arrangement between
the multivalent binding partners. However, the structural details of some key
lectins remain unknown and different lectins may exhibit overlapping glycan
specificity. This makes it difficult to design a glycoconjugate that can
potently and specifically target a particular multimeric lectin for therapeutic
interventions, especially under the challenging <i>in vivo</i> conditions. Conventional techniques such as surface plasmon
resonance (SPR) and isothermal titration calorimetry (ITC) can provide
quantitative binding thermodynamics and kinetics. However, they cannot reveal
key structural information, <i>e.g.</i>
lectin’s binding site orientation, binding mode, and inter-binding site
spacing, which are critical to design specific
multivalent inhibitors. Herein we report that gold nanoparticles (GNPs)
displaying a dense layer of simple glycans are powerful mechanistic probes for
multivalent lectin-glycan interactions. They can not only quantify the
GNP-glycan-lectin binding affinities <i>via</i>
a new fluorescence quenching method, but also reveal drastically different
affinity enhancing mechanisms between two closely-related tetrameric lectins,
DC-SIGN (simultaneous binding to one GNP) and DC-SIGNR (inter-crosslinking with
multiple GNPs), <i>via</i> a combined
hydrodynamic size and electron microscopy analysis. Moreover, a new term,
potential of assembly formation (PAF) has been proposed to successfully predict
the assembly outcomes based on the binding mode between GNP-glycans and lectins.
Finally, the GNP-glycans can potently and completely inhibit DC-SIGN-mediated
augmentation of Ebola virus glycoprotein-driven cell entry (with IC<sub>50</sub>
values down to 95 pM), but only partially block DC-SIGNR-mediated virus
infection. Our results suggest that the ability of a glycoconjugate to
simultaneously block all binding sites of a target lectin is key to robust
inhibition of viral infection. | Darshita Budhadev; Emma Poole; Inga Nehlmeier; Yuanyuan Liu; James Hooper; Elizabeth Kalverda; Uchangi Satyaprasad Akshath; Nicole Hondow; W. Bruce Turnbull; Stefan Pöhlmann; Yuan Guo; Dejian Zhou | Biological Materials; Nanostructured Materials - Materials; Optical Materials; Nanostructured Materials - Nanoscience; Bioengineering and Biotechnology; Biophysics; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cf4469df46567f441d2/original/probing-multivalent-lectin-carbohydrate-binding-via-multifunctional-glycan-gold-nanoparticles-implications-for-blocking-virus-infection.pdf |
61893e998ac7a21a0f6c8f5b | 10.26434/chemrxiv-2021-q4319-v2 | PASSer2.0: Accurate Prediction of Protein Allosteric Sites Through Automated Machine Learning | Allostery is a fundamental process in regulating proteins’ activity. The discovery, design and development of allosteric drugs demand for better identification of allosteric sites. Several computational methods have been developed previously to predict allosteric sites using static pocket features and protein dynamics. Here, we present a computational model using automated machine learning for allosteric site prediction. Our model, PASSer2.0, advanced the previous results and performed well across multiple indicators with 89.2% of allosteric pockets appeared among the top 3 positions. The trained machine learning model has been integrated with the Protein Allosteric Sites Server (https://passer.smu.edu) to facilitate allosteric drug discovery. | Sian Xiao; Hao Tian; Peng Tao | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence | CC BY NC 4.0 | CHEMRXIV | 2021-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61893e998ac7a21a0f6c8f5b/original/pas-ser2-0-accurate-prediction-of-protein-allosteric-sites-through-automated-machine-learning.pdf |
60c73e5a0f50dbc17139564a | 10.26434/chemrxiv.6962813.v1 | Environmental Control Programs the Emergence of Distinct Product Ensembles from Unconstrained Chemical Reaction Networks | <p><b>Harnessing and then controlling </b><b>combinatorial explosions</b><b> in </b><b>uncontrolled condensation reactions of simple building
blocks is a key problem to many hypotheses on the origin</b><b> of </b><b>life. Much has been achieved in understanding how the
building blocks of biopolymers may be formed, and in understanding how
macromolecules may produce functional and increasingly life-like systems. How</b><b> these </b><b>steps can be joined, and how defined populations</b><b> of </b><b>macromolecules can form from mixtures</b><b> of </b><b>simple building blocks, instead of an undifferentiated
</b><b>mess</b><b>, remain open questions.</b><b> Herein, we show </b><b>how</b><b> unconstrained </b><b>condensation</b><b> reactions of both amino acids, and prebiotic soup mixtures
produced by spark discharge, can be steered</b><b> by changes in the reaction environment, such as order
of reactant addition (mixing history), and addition of salts or minerals. Using
</b><b>techniques akin to
untargeted metabolomics</b><b>
to survey product distributions we</b><b> demonstrate that while these reactions do produce a large range of
species, there are distinct, significant, and reproducible differences between the
product ensembles</b><b>.
Furthermore, we observe that differences in composition </b><b>are </b><b>demonstrated through</b><b> clearly different structural and functional properties. </b><b>Using this approach, we
demonstrate for the first time that simple variations in environmental
parameters can mediate the differentiation of distinct ensembles from both
amino acid mixtures and a classic primordial soup model (products of a ‘Miller
Urey’ type spark discharge reaction). </b><b>This shows that </b><b>the
synthetic complexity produced by such unconstrained reactions is not as
intractable as often suggested, when viewed through a chemically agnostic lens.
An open</b><b> approach
to complexity can generate compositional, structural, and functional diversity
from fixed sets of simple starting materials, suggesting that differentiation
of product mixtures can occur in the wider environment without the need for
biological machinery.</b><b></b></p> | Andrew J. Surman,; Marc Rodriguez Garcia; Yousef Abul-Haija; Geoffrey Cooper; Piotr S. Gromski; Rebecca Turk-MacLeod; Margaret Mullin; Cole Mathis; Sara Walker; Leroy Cronin | Combinatorial Chemistry; Environmental Analysis; Mass Spectrometry; High-throughput Screening; Minerals | CC BY NC ND 4.0 | CHEMRXIV | 2018-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e5a0f50dbc17139564a/original/environmental-control-programs-the-emergence-of-distinct-product-ensembles-from-unconstrained-chemical-reaction-networks.pdf |
60c744c3702a9b73a718a8d7 | 10.26434/chemrxiv.9914378.v1 | A Diversified Machine Learning Strategy for Predicting and Understanding Molecular Melting Points | <p>The ability to predict multi-molecule processes, using only knowledge of single molecule structure, stands as a grand challenge for molecular modeling. Methods capable of predicting melting points (MP) solely from chemical structure represent a canonical example, and are highly desirable in many crucial industrial applications. In this work, we explore a data-driven approach utilizing machine learning (ML) techniques to predict and understand the MP of molecules. Several experimental databases are aggregated from the literature to design a low-bias dataset that includes 3D structural and quantum-chemical properties. Using experimental and polymorph-induced uncertainties, we derive a tenable lower limit for MP prediction accuracy, and apply graph neural networks and Gaussian processes to predict MP competitive with these error bounds. To further understand how MP correlates with molecular structure, we employ several semi-supervised and unsupervised ML techniques. First, we use unsupervised clustering methods to identify classes of molecules, their common fragments, and expected errors for each data set. We then build molecular geometric spaces shaped by MP with a semi-supervised variational autoencoder and graph embedding spaces, and apply graph attribution methods to highlight atom-level contributions to MP within the datasets. Overall, this work serves as a case study of how to employ a diversified ML toolkit to predict and understand correlations between molecular structures and thermophysical properties of interest.</p> | ganesh sivaraman; Nicholas Jackson; Benjamin Sanchez-Lengeling; Alvaro Vazquez-Mayagoitia; Alan Aspuru-Guzik; Venkatram Vishwanath; Juan de Pablo | Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry; Thermodynamics (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744c3702a9b73a718a8d7/original/a-diversified-machine-learning-strategy-for-predicting-and-understanding-molecular-melting-points.pdf |
6585c26d9138d23161456a21 | 10.26434/chemrxiv-2023-53g68-v2 | A turn-off fluorescent sensor for metal ions quantifies corrosion in an organic solvent | We demonstrate that the corrosion of AISI 1045 medium carbon steel and pure aluminum can be quantified by the turn-off fluorescent sensor Phen Green-SK (PGSK) in ethanol-based solutions. We first evaluate the dependence of the chelation enhanced quenching of PGSK on iron and aluminum ion concentrations. Subsequently, we apply PGSK to examine the anodic dissolution of metal corrosion. The observed time-dependent PGSK-quenching quantifies the corrosion rates of two metals over 24-hours of immersion in ethanol-based solutions. The PGSK-based quantification of corrosion is compared to scanning electron microscopy and electrochemical techniques, including open circuit potential and Tafel extrapolation. The corrosion rates calculated from PGSK-quenching and Tafel extrapolation are in agreement, and both indicate a decrease in corrosion rates over 24-hours. Our work shows PGSK can efficiently sense and quantify anodic corrosion reactions at metal interfaces, especially in organic solvents or other non-aqueous environments where the application of electrochemical techniques can be limited by the poor conductivity of the surrounding medium. | Lianlian Liu; Zechariah Pfaffenberger; Mark Seigel; Anuj Saini; Lydia Kisley | Organic Chemistry; Materials Science; Alloys; Dyes and Chromophores; Imaging Agents; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6585c26d9138d23161456a21/original/a-turn-off-fluorescent-sensor-for-metal-ions-quantifies-corrosion-in-an-organic-solvent.pdf |
677ca74efa469535b9083a46 | 10.26434/chemrxiv-2025-x59s5 | Computational Insights into Hydrogen Interaction with the Ru (101 ̅1) and Ru (101 ̅0) Surfaces: Implications for Alkane and Polyolefin Hydrogenolysis | Hydrogen interaction with transition metal surfaces such as those exposed by ruthenium (Ru) nanoparticles is critical in applications like hydrogen storage and catalytic processes such as Fischer-Tropsch, Haber-Bosch, and plastic waste hydrogenolysis. While the Ru (0001) surface is well-studied, hydrogen interaction with the Ru (101 ̅1) and Ru (101 ̅0) facets remains mostly underexplored. In this contribution, we use density functional theory calculations to investigate hydrogen adsorption and dissociation and provide insights into the adsorbed hydrogen role in catalytic polyolefin plastic hydrogenolysis. We start our investigation by exploring all the unique surface and subsurface sites for hydrogen adsorption and dissociation and identify hcp and higher hollow as the most favorable atomic hydrogens adsorption sites on the Ru (101 ̅1) and Ru (101 ̅0) surfaces, respectively. We find that atomic hydrogen can easily migrate on these surfaces to achieve the most stable arrangement at different coverages. We then combine these findings with ab-initio thermodynamics and microkinetic modeling to build surface phase diagrams, which show that both surfaces are fully hydrogenated under typical catalytic conditions. We then study how the presence of the full hydrogen coverage affects the adsorption and dehydrogenation of butane as a proxy for polyethylene, as these are the initial steps in the catalytic hydrogenolysis of polyolefin plastic waste. We find that the adsorption energy of butane decreases when the two surfaces are fully hydrogenated but adsorption remains favorable. We then investigate two possible mechanisms for the dehydrogenation step. The most favorable dehydrogenation mechanism involves the reaction of a surface hydrogen with an alkane hydrogen to produce H2 gas and an adsorbed alkyl radical. However, both mechanisms have positive reaction free energies suggesting that polyolefin dehydrogenation will be slow on these surfaces. | Fabio Colasuonno; Sohaib Umer; Martina Lessio | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677ca74efa469535b9083a46/original/computational-insights-into-hydrogen-interaction-with-the-ru-101-1-and-ru-101-0-surfaces-implications-for-alkane-and-polyolefin-hydrogenolysis.pdf |
67174e2d83f22e4214c6cc2c | 10.26434/chemrxiv-2024-8ktc2 | A Glycosylation Mechanism Case Study: Unraveling the Mechanism of Stereospecific Self-promoted N -Glycosylations | In this study, the mechanism of self-promoted N-glycosylations is extensively investigated through kinetic experiments, computational studies, and nucleophilic competition experiments. Based on the findings, the mechanism is proposed to be initiated by proton transfer from the acidic sulfonyl carbamate to the trichloroacetimidate, upon formation of an associated contact ion pair. This ion pair then collapses in an SN 1-like fashion, forming an oxocarbeniumion-like intermediate. According to the proposed mechanism, stereospecificity arises from the associated nature of all intermediates formed throughout the reaction. During the mechanistic study, it was also found that the sulfonyl carbamates have catalytic properties if a competing nucleophile is present. | Natasha Videcrantz Faurschou; Stephan P. A. Sauer; Christian Marcus Pedersen | Theoretical and Computational Chemistry; Organic Chemistry; Natural Products; Organic Compounds and Functional Groups; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67174e2d83f22e4214c6cc2c/original/a-glycosylation-mechanism-case-study-unraveling-the-mechanism-of-stereospecific-self-promoted-n-glycosylations.pdf |
60c75300842e657668db3e7c | 10.26434/chemrxiv.13377173.v1 | Role of Macrocyclic Conformational Steering in a Kinetic Route toward Bielschowskysin | Macrocyclic furanobutenolide-derived cembranoids (FBCs)
are the biosynthetic precursors to a wide variety of highly congested and
oxygenated polycyclic (nor)diterpenes (<i>e.g.</i>
plumarellide, verrillin or bielschowskysin). These architecturally complex
metabolites are thought to originate from site-selective oxidation of the
macrocycles’ backbone and a series of intricate transannular reactions. Yet the
development of a common biomimetic route has been hampered by a lack of synthetic
methods for the pivotal furan dearomatization in a regio- and stereoselective
manner. To address these shortcomings, a concise strategy of chemo- and stereoselective
epoxidation followed by a kinetically-controlled furan dearomatization is reported. The
surprising switch of facial <i>a</i>:<i>b</i>-discrimination observed in the epoxidations of the most strained <i>E</i>-acerosolide
<i>versus</i> <i>E</i>-deoxypukalide
and <i>E</i>-bipinnatin
J derived macrocycles has been rationalized by the 3D-conformational
preferences of the macrocyclic scaffolds. The downstream
functionalization of FBC-macrocycles was also studied, and how the C-7 epoxide configuration was retentively translated
to the C-3 stereogenicity in dearomatized products under kinetic control to
secure the requisite (3<i>S</i>,7<i>S</i>,8<i>S</i>)-configurations
for the bielschowskysin synthesis. Unlike previously
speculated, our results suggest that the most strained FBC-macrocycles bearing a
<i>E</i>-(D<sup>7,8</sup>)-alkene moiety may stand as the true
biosynthetic precursors to bielschowskysin and several other polycyclic natural
products of this class. | Paul Scesa; Lyndon M. West; Stephane Roche | Bioorganic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75300842e657668db3e7c/original/role-of-macrocyclic-conformational-steering-in-a-kinetic-route-toward-bielschowskysin.pdf |
66e56f4fcec5d6c142097352 | 10.26434/chemrxiv-2024-8vf25 | Hexafluorophosphate-Triggered Hydrogen Isotope Exchange (HIE) in Fluorinated Environments: A Platform for the Deuteration of Aromatic Compounds via Strong Bond Activation | There is a perpetual need for efficient and mild methods to integrate deuterium atoms into carbon frameworks through late-stage modifications. We have developed a simple and highly effective synthetic route for hydrogen isotope exchange (HIE) in aromatic compounds under ambient conditions. This method utilizes catalytic amounts of hexafluorophosphate (PF6−) in deuterated 1,1,1,3,3,3-hexafluoroisopropanol (HFIP-d1) and D2O. Phenols, anilines, anisoles, and heterocyclic compounds were converted with high yields and excellent deuterium incorporations, which allows for the synthesis of a wide range of deuterated aromatic compounds. Spectroscopic and theoretical studies show that an interactive H-bonding network triggered by HFIP-d1 activates the typically inert P-F bond in PF6 for D2O addition. The thus in-situ formed DPO2F2 triggers then HIE, offering a new way to deuterated building blocks, drugs, and natural-product derivatives with high deuterium incorporation via the activation of strong bonds. | Yang Ni; Jonathan Lebelt; Milena Barb; Florian Kreuter; Hannah Buttkus; Jiaye Jin ; Martin Kretzschmar; Ralf Tonner-Zech; Knut Asmis; Tanja Gulder | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e56f4fcec5d6c142097352/original/hexafluorophosphate-triggered-hydrogen-isotope-exchange-hie-in-fluorinated-environments-a-platform-for-the-deuteration-of-aromatic-compounds-via-strong-bond-activation.pdf |
61fb14a9c0a8686dfd3b88c5 | 10.26434/chemrxiv-2022-bb2bt | Synthesis of 4-Imidazolidinones from Diamides and Ethynyl Benzio- doxolones vis Double Michael Addition: Ethynyl Benziodoxolones as Electrophilic Ynol Synthons | The moiety of 4-imidazolidinone is an important structural motif in organic synthesis and medicinal chemistry. We achieved the efficient synthesis of 4-imidazolidinones from a variety of diamides by double Michael addition, a novel reaction mode for hypervalent alkynyl iodine compounds, and a formal reductive elimination sequence using in situ-generated EBX from TMS-EBX or EBX-MeCN. The highly reactive EBX enabled chemoselective intermolecular N- alkenylation of the sulfonamide moiety and intramolecular cyclization of the amide moiety under mild basic conditions. The reaction diastereoselectively gave cis-2,5-disubstituted 4-imidazolidinones from amino acid-derived diamides. Furthermore, 2-[(2-iodobenzoyloxy)methyl]-4-imidazolidinone was derivatized by solvolysis and Sonogashira coupling. DFT calculations indicated that the double Michael addition mechanism is plausible. Thus, the potential of an unsubstituted EBX reagent for the synthesis of heterocycles from complex molecules and their functionalization with mild nucleophiles was demonstrated. | Ayaka Shimizu; Atsushi Shibata; Hiroyoshi Esaki; Kazuaki Fukushima; Norihiro Tada; Akichika Itoh | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61fb14a9c0a8686dfd3b88c5/original/synthesis-of-4-imidazolidinones-from-diamides-and-ethynyl-benzio-doxolones-vis-double-michael-addition-ethynyl-benziodoxolones-as-electrophilic-ynol-synthons.pdf |
674d2d115a82cea2faab7579 | 10.26434/chemrxiv-2024-lnz4f-v3 | Viologen-radical-driven Hydrogen Evolution from Water Catalyzed by Co-NHC Catalysts: Radical Scavenging by Nitrate and Volmer-Heyrovsky-like CPET Pathway | The factors controlling the catalytic activity in photochemical hydrogen evolution reaction (HER) are studied in detail for two macrocyclic cobalt compounds bearing two N-heterocyclic carbenes and two pyridyl donors (Co-NHC1 and Co-NHC2, where Co-NHC2 has a methoxy substituent on each pyridyl ligand). The present study adopts an aqueous photosystem consisting of EDTA, [Ru(bpy)3]2+ (bpy = 2,2’-bipyridine), and MV2+ (MV2+ = methylviologen) at pH = 5. Both catalysts are shown to promote HER in a similar efficiency (TON = 12-13 in 6 h), revealing a minor contribution of the electron-donating methoxy substituents. The catalyst degradation is shown to proceed during the photocatalysis, leading to afford [Co(edta)]− (EDTA = H4edta) as a dead-end species. The lack of any heterogeneous species was evidenced by DLS (dynamic light scattering). It was also found that nitrate involved as a counter anion in the photocatalysis components substantially inhibits the photocatalytic HER, giving rise to a large diminishment in TON from 12.7 to 7.2. The Griess test was used to confirm that NO3− serves as a scavenger deactivating the reduced form of MV2+ (i.e., MV+•). The detailed spectroscopic study reveals that the radical dimer (MV+•)2 species plays a key role in promoting the one-step two-electron process: (MV+•)2 + NO3− + 2H+ → 2MV2+ + NO2− + H2O. Experimental and DFT results also reveal that a unique double CPET (concerted proton-electron transfer) pathway is taken to evolve H2 by the Co-NHC catalysts with substantially minimized reorganization energies: Co(II)-NHC → Co(III)(H)-NHC → Co(II)-NHC + H2. This pathway can be viewed as related to the so-called Volmer-Heyrovsky mechanism adopted by some metals and is quite unique to the Co-NHC catalysts. | Kosei Yamauchi; Ken Kawano; Koichi Yatsuzuka; Kaori Kawamura; Masanori Kan; Ken Sakai | Inorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674d2d115a82cea2faab7579/original/viologen-radical-driven-hydrogen-evolution-from-water-catalyzed-by-co-nhc-catalysts-radical-scavenging-by-nitrate-and-volmer-heyrovsky-like-cpet-pathway.pdf |
620374e70aec1a1705177465 | 10.26434/chemrxiv-2021-mz6j8-v2 | Thermal atomic layer deposition of In2O3 thin films using a homoleptic indium triazenide precursor and water | Indium oxide (In2O3) is an important transparent conducting material widely used in optoelectronic applications. Herein, we study the deposition of In2O3 by thermal atomic layer deposition (ALD) using our recently reported indium(III) triazenide precursor and H2O. A temperature interval with self-limiting growth was found between ~270–385°C with a growth per cycle of ~1.0 Å. The deposited films were polycrystalline cubic In2O3 with In:O ratios of 1:1.20, and low levels of C and no detectable N impurities. The transmittance of the films was found to be >70% in visible light and the resistivity was found to be 0.2 mΩcm. The high growth rates, low impurities, high optical transmittance, and low resistivity of these films give promise to this process being used for ALD of In2O3 films that are good candidates for potential display and touch-screen applications. | Pamburayi Mpofu; Polla Rouf; Nathan O'Brien; Urban Forsberg; Henrik Pedersen | Materials Science; Inorganic Chemistry; Coating Materials; Thin Films; Organometallic Compounds; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620374e70aec1a1705177465/original/thermal-atomic-layer-deposition-of-in2o3-thin-films-using-a-homoleptic-indium-triazenide-precursor-and-water.pdf |
6627e1fb21291e5d1d802657 | 10.26434/chemrxiv-2024-66gtp | Mechanism of Nucleic Acid Phosphodiester Bond Cleavage by Human Endonuclease V: MD and QM/MM Calculations Reveal a Versatile Metal Dependence | Human endonuclease V (EndoV) catalytically removes deaminated nucleobases by cleaving the phosphodiester bond as part of RNA metabolism. Despite being implicated in several diseases (cancers, cardiovascular diseases, and neurological disorders) and potentially being a useful tool in biotechnology, details of the human EndoV catalytic pathway remain unclear due to limited experimental information beyond a crystal structure of the apo-enzyme and select mutational data. Since a mechanistic understanding is critical for further deciphering the central roles and expanding applications of human EndoV in medicine and biotechnology, molecular dynamics (MD) simulations and quantum mechanics-molecular mechanics (QM/MM) calculations were used to unveil the atomistic details of the catalytic pathway. Due to controversies surrounding the number of metals required for nuclease activity, enzyme–substrate models with different numbers of active site metals and various metal–substrate binding configurations were built based on structural data for other nucleases. Subsequent MD simulations revealed the structure and stability of the human EndoV–substrate complex for a range of active site metal binding architectures. Four unique pathways were then characterized using QM/MM that vary in metal number (one versus two) and modes of substrate coordination (direct versus indirect (water-mediated)), with several mechanisms being fully consistent with experimental structural, kinetic, and mutational data for related nucleases, including members of the EndoV family. Beyond uncovering key roles for several active site amino acids (D240 and K155), our calculations highlight that, while one metal is essential for human EndoV activity, the enzyme can benefit from using two metals due to the presence of two suitable active site binding sites. By directly comparing one versus two-metal-mediated P–O bond cleavage reactions within the confines of the same active site, our work brings a fresh perspective to the ‘number of metals’ controversy. | Rajwinder Kaur; Stacey Wetmore | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Biophysical Chemistry; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6627e1fb21291e5d1d802657/original/mechanism-of-nucleic-acid-phosphodiester-bond-cleavage-by-human-endonuclease-v-md-and-qm-mm-calculations-reveal-a-versatile-metal-dependence.pdf |
60c74d60337d6c17dee27dac | 10.26434/chemrxiv.12587537.v1 | Non-Covalent Interactions Atlas Benchmark Data Sets 2: Hydrogen Bonding in an Extended Chemical Space | The Non-Covalent Interactions Atlas (www.nciatlas.org) aims to provide a new generation of benchmark data sets for non-covalent interactions. The HB300SPX data set presented here extends the coverage of hydrogen bonds to phosphorus, sulfur and halogens up to iodine. It is again complemented by a set of dissociation curves, HB300SPX×10. The new data make it possible to analyze the transferability of the parametrization of e.g. dispersion corrections for DFT from simple organic molecules to a broader chemical space. The HB300SPX×10 has also been used for the extension of the parametrization of hydrogen-bonding corrections in the semiempirical PM6-D3H4X and DFTB3-D3H5 methods to additional elements.<br /> | Jan Řezáč | Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d60337d6c17dee27dac/original/non-covalent-interactions-atlas-benchmark-data-sets-2-hydrogen-bonding-in-an-extended-chemical-space.pdf |
60c757eb0f50db57c2398351 | 10.26434/chemrxiv.14483067.v1 | Thermosensitive Fluorescent Liposomes | Liposomes are versatile nanomaterials
used in a variety of applications such as drug
delivery and bioimaging. In this study, three
asymmetrical squaraine dyes were synthesized
and embedded in liposomes in the efforts to find a
suitable dye that can be used for bioimaging
procedures involving liposomes. The optical
properties of the synthesized dyes as well as their
liposomes were studied and compared to the
previously synthesized asymmetrical squaraine
dye SQR22 and its liposome form. <br /> | Jin Heng Lim; Ken Chi Lik Lee | Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757eb0f50db57c2398351/original/thermosensitive-fluorescent-liposomes.pdf |
62e2a0e1dc4c78326243900e | 10.26434/chemrxiv-2022-339fz | Selective Reductive Cleavage of the Threonine 2 Peptide Bond of Penta-N-Boc-Polymyxin B with Sodium Borohydride | Sodium borohydride surprisingly cleaves the Threonine2 (Thr2) peptide bond in N-protected Polymyxin B. Occurring at 20 ºC, the mild reductive cleavage is novel; and it facilitates the synthesis of PMB-derived antibiotics. The reaction fails when both Threonine2,10 hydroxyls are protected. The reaction can be performed on all therapeutic peptides containing Threonine. | Jay Weinstein; Adriano Afonso | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e2a0e1dc4c78326243900e/original/selective-reductive-cleavage-of-the-threonine-2-peptide-bond-of-penta-n-boc-polymyxin-b-with-sodium-borohydride.pdf |
643829da73c6563f14cc68cc | 10.26434/chemrxiv-2023-bbq0j-v2 | Computational Insights into the Inhibition Mechanism of Xanthine Oxidoreductase by Oxipurinol | Xanthine oxidoreductase (XOR) is a molybdopterin-containing enzyme found in many living organisms. Its function is to convert hypoxanthine to xanthine and subsequently to urate, which are the final steps in purine elimination in humans. Elevated uric acid levels in the human body can cause gout and hyperuricemia. Therefore, drug development efforts targeting this enzyme are a primary focus not only to treat these conditions but also for other diseases. Oxipurinol, an analog of xanthine, was the drug that emerged as a “gold standard” inhibitor of XO in the late sixties. Crystallographic studies have shown direct coordination of oxipurinol to the molybdenum cofactor (MoCo). The proposed inhibition mechanism based on available crystal structures posits that the oxipurinol’s nitrogen replaces a water-exchangeable OH ligand of the Mo atom. However, the detailed steps involved in the inhibition mechanism remain undefined, which would provide important insights for designing more efficacious drugs with similar inhibition functions. In this study, the inhibition mechanism of XOR by oxipurinol is investigated via molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations. The structural and dynamical effects of oxipurinol on the pre-catalytic structure of the metabolite-bound system are presented, as well as the modeled reaction mechanism catalyzed by the MoCo center in the active site. The kinetics and thermodynamics of the proposed reaction mechanism as well as the non-covalent interactions with the binding cavity align with experimental findings. Our results also suggest the suitability of the inhibition reaction via another tautomer of oxipurinol other than the experimentally predominant tautomer. This might suggest possible routes for designing new analogs of oxipurinol with a similar coordination mode to the latter tautomer, which could lead to more energetically favorable inhibitors. | Yazdan Maghsoud; Chao Dong; G. Andrés Cisneros | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643829da73c6563f14cc68cc/original/computational-insights-into-the-inhibition-mechanism-of-xanthine-oxidoreductase-by-oxipurinol.pdf |
67db8f13fa469535b9e7405e | 10.26434/chemrxiv-2025-kf4rt | Crosslink Dynamics Control Injection Force and Flow Profiles of Non-Covalent Gels | Dynamically crosslinked hydrogels have found remarkable utility in 3D bioprinting and injectable slow-release delivery of pharmaceutics and vaccines, applications which take advantage of their ability to flow through needles or extrusion devices with relative ease. Predicting the force required to inject or extrude dynamic hydrogel materials is paramount to their application. Here, we report an injectable dynamic hydrogel with facile tunability of crosslink exchange rate using a small-molecule surfactant. We found surprising non-monotonic trends in injection force with respect to crosslink dynamics not explained by traditional flow rheology measurements. By using an optical in-situ capillary rheometer, we found that wall slip is the dominant mechanism influencing flow profiles, rather than shear banding, as has been reported in previous studies of dynamically crosslinked hydrogels. We hypothesize that the main driver of flow rheology and injection force for these materials is the combination of a lower slip distance and bulk stiffness with increasing dynamicity, balancing bulk cohesive force with adhesive forces to the wall. Finally, by developing new models which describe the flow behavior of non-covalent gels, we present new criteria for extrudability, enabling better predictions for operating conditions of downstream applications of dynamic hydrogels. | Noah Eckman; Eric Appel | Materials Science; Polymer Science; Chemical Engineering and Industrial Chemistry; Biopolymers; Cellulosic materials; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67db8f13fa469535b9e7405e/original/crosslink-dynamics-control-injection-force-and-flow-profiles-of-non-covalent-gels.pdf |
60fd0de07bf0c920d4609fa9 | 10.26434/chemrxiv-2021-j5wbd | Protonation States of Molecular Groups in the Chromophore-Binding Site Modulate Properties of the Reversibly Switchable Fluorescent Protein rsEGFP2 | The role of protonation states of the chromophore and its neighboring amino acid side chains of the reversibly switching fluorescent protein rsEGFP2 upon photoswitching is characterized by molecular modeling methods. Numerous conformations of the chromophore-binding site in computationally derived model systems are obtained using the quantum chemistry and QM/MM approaches. Excitation energies are computed using the extended multiconfigurational quasidegenerate perturbation theory (XMCQDPT2). The obtained structures and absorption spectra allow us to provide interpretation of the observed structural and spectral properties of rsEGFP2 in the active ON- and inactive OFF-states. To identify intermediates along the routes of chromophore transformations between the ON- and OFF-states, molecular dynamics trajectories with the QM/MM potentials are examined. The results demonstrate that in addition to the dominating anionic and neutral forms of the chromophore, the cationic and zwitterionic forms may participate in the photoswitching of rsEGFP2. Conformations and protonation forms of the Glu223 and His149 side chains in the chromophore-binding site play an essential role in stabilizing specific protonation forms of the chromophore. | Bella Grigorenko; Tatiana Domratcheva; Igor Polyakov; Alexander Nemukhin | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Biophysical Chemistry; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60fd0de07bf0c920d4609fa9/original/protonation-states-of-molecular-groups-in-the-chromophore-binding-site-modulate-properties-of-the-reversibly-switchable-fluorescent-protein-rs-egfp2.pdf |
64d4b501dfabaf06ff0a2533 | 10.26434/chemrxiv-2023-6tv1z-v3 | Preparation of 3,5-methanobenzo[b]azepines: a novel sp3-rich Quinolone Isostere. | The replacement of the aromatic ring in bioactive compounds with saturated bioisosteres has become a popular tactic to obtain novel structures with improved physicochemical profiles. In this communication, we describe an efficient synthesis of 3,5-methanobenzo[b]azepine analogs and suggest them as isosteres of quinolones. Quinolones are heteroaromatic, flat rings and considered as privileged scaffolds. An isosteric version of this scaffold with more 3D character would offer new options to expand their use. | Loic Herter; Timothé Perrin; Thomas Fessard; christophe Salome | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d4b501dfabaf06ff0a2533/original/preparation-of-3-5-methanobenzo-b-azepines-a-novel-sp3-rich-quinolone-isostere.pdf |
66cc52aaf3f4b0529024ef5c | 10.26434/chemrxiv-2024-zw0sp | Chloride, Alkoxide or Silicon: The Bridging Ligand Dictates the Spin-state in Dicobalt Expanded Pincer Complexes | We report the synthesis and characterization of a series of high andnlow spin dicobalt complexes of the tBuPNNP expanded pincer ligand. Reacting this dinucleating ligand in its neutral form with two equivalents of CoCl2(THF)1.5 yields a high-spin dicobalt complex featuring one Co inside and one Co outside of the dinucleating pocket. Performing the same reaction in the presence of two equivalents of KOtBu provides access to a high-spin dicobalt complex wherein both Co centers are bound within the PNNP pocket
and this complex also features a bridging OtBu ligand. Reacting either of the high-spin complexes with excess diethyl silane affords a low-spin dicobalt complex containing two unusual bridging Si-based ligands. These complexes were investigated using NMR spectroscopy, XAS, single crystal X-ray structure determination and computational methods, showing that the Si-based ligands are best described as base-stabilized silylenes. | Roel L. M. Bienenmann; Arun S. Asundi; Martin Lutz; Ritimukta Sarangi; Daniel L. J. Broere | Inorganic Chemistry; Organometallic Chemistry | CC BY 4.0 | CHEMRXIV | 2024-08-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cc52aaf3f4b0529024ef5c/original/chloride-alkoxide-or-silicon-the-bridging-ligand-dictates-the-spin-state-in-dicobalt-expanded-pincer-complexes.pdf |
60c74127337d6c1514e2685b | 10.26434/chemrxiv.7977518.v1 | High-Resolution Tip-Enhanced Raman Scattering Probes Sub-Molecular Density Changes | <div><div><div><p>Tip-enhanced Raman spectroscopy (TERS) exhibits new selection rule and sub- nanometer spatial resolution, which is attributed to the plasmonic near-field confinement. Despite recent advances in simulations of TERS spectra under highly confined fields, a simply physical mechanism has remained elusive. In this work we show that single-molecule TERS images can be explained by local sub-molecular density changes induced by the confined near-field during the Raman process. The local sub-molecular density changes determine the spatial resolution in TERS and the gradient-based selection rule. Using this approach we find that the four-fold symmetry of meso-tetrakis(3,5- di-tert-butylphenyl)porphyrin (H2TBPP) TERS images observed in experiments arises from the combination of degenerate normal modes localized in the functional side groups rather than the porphyrin ring as previously considered. As an illustration of the potential of the method, we demonstrate how this new theory can be applied to microscopic structure characterization.</p></div></div></div> | Xing Chen; Pengchong Liu; Zhongwei Hu; Lasse Jensen | Plasmonic and Photonic Structures and Devices; Theory - Computational; Interfaces; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74127337d6c1514e2685b/original/high-resolution-tip-enhanced-raman-scattering-probes-sub-molecular-density-changes.pdf |
60c75653ee301cae34c7b329 | 10.26434/chemrxiv.13153112.v2 | Reducing hERG Toxicity Using hERG Classification Model and Fragment-growing Network | Drug-induced
cardiotoxicity has become one of the major reasons leading to drug withdrawal in
past decades, which is closely related to the blockade of human
Ether-a-go-go-related gene (hERG) potassium channel. Developing reliable hERG predicting
model and optimizing model can greatly reduce the risk faced in drug discovery.
In this study, we constructed eight hERG classification models, the best of which
shows desirable generalization ability on low-similarity clinical compounds, as
well as advantages in perceiving activity gap caused by small structural
changes. Furthermore, we developed a hERG optimizer based on fragment grow
strategy and explored its usage in four cases. After reinforcement learning, our
model successfully suggests same or similar compounds as chemists’
optimization. Results suggest that our model can provide reasonable optimizing
direction to reduce hERG toxicity when hERG risk is corresponding to
lipophilicity, basicity, the number of rotatable bonds and pi-pi interactions. Overall,
we demonstrate our model as a promising tool for medicinal chemists in hERG optimization
attempts. | Yan Yang; Yanmin Zhang; Xingye Chen; Yi Hua; Guomeng Xing; Chenglong Deng; Li Liang; Tao Lu; Yadong Chen; Haichun Liu | Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75653ee301cae34c7b329/original/reducing-h-erg-toxicity-using-h-erg-classification-model-and-fragment-growing-network.pdf |
6165e8718b620d5b134d6018 | 10.26434/chemrxiv-2021-4fpw4 | Carbene Character in a Series of Neutral PCcarbeneP Cobalt(I) Complexes – Radical Carbenes Versus Nucleophilic Carbenes | Cobalt(I) complexes supported by a series of PCcarbeneP pincer ligands of varying donicity, differing in the aryl group linking the phosphine arms with the anchoring carbon donor, are described. Addition of the proligands to cobalt bromide results in the formation of a series of cobalt(II) tetrahedral complexes, Ln-1, which serve as excellent precur-sors to the corresponding PCalkylP and PCcarbeneP complexes. Square planar cobalt PCcarbeneP complexes, L2R-3-X (X = Cl, Br), are readily synthesized by addition of a bulky aryloxide radical to the corresponding PCalkylP complex, L1-2-Br or via addition of L2R to ClCo(PPh3)3 in the presence of trityl radical or by addition of NaHBEt3 and trityl radical to iso-lated L2R-1. For the L2NMe2 PCcarbeneP complexes, salt metathesis reactions with either CsOH·H2O, LiCH2TMS, or LiNH2 result in the corresponding hydroxo, alkyl, and amine complexes, L2NMe2-3-R (R = OH, CH2TMS, NH2). Reaction of L2NMe2-3-OH with benzoic acid affords the 2-O2CPh derivative The nature of the carbene bond in either ligand plat-form as well as the effects of the X-type capping ligand on the Co=C bond are explored computationally and show that triplet structures are relatively more stable in for the less electron donating ligand L1 while singlet Co(I) carbenes dominate for the more electron rich L2 derivatives. For L2NMe2 complexes, the effect of the trans ligand X was also probed. Pi donors imbue the carbene with singlet character while the strongly donating alkyl derivative exhibits significant triplet character. | Marissa Clapson; Justin Kirkland; Warren Piers; Daniel Ess; Benjamin Gelfand; Jian-Bin Lin | Inorganic Chemistry; Organometallic Chemistry; Bonding; Organometallic Compounds; Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6165e8718b620d5b134d6018/original/carbene-character-in-a-series-of-neutral-p-ccarbene-p-cobalt-i-complexes-radical-carbenes-versus-nucleophilic-carbenes.pdf |
66fd4b9112ff75c3a12d36d8 | 10.26434/chemrxiv-2023-913g7-v2 | Exploration of bioinformatic domain based on data mining, reaction and enzyme promiscuity predictions | Biochemical transformations may allow significant improvements in synthetic efficiency of complex functional molecules through reduction in the number of synthetic steps or avoidance of harsh conditions and/or toxic solvents/reactants. Yet, there is a limited access to biochemical reaction data, which reduces the opportunities of finding alternatives and discovering synergies with organic synthesis. We propose a workflow to explore the sparse synthetic biological domain. Using a molecular graph method we predict feasible biosynthetic reactions. The products of biosyntheses are learned from the functional transformations of the literature-excerpted reactions recorded in KEGG database. Through this approach we expanded the KEGG reaction dataset of biochemical transformations by approximately four times. To catalyse the novel reactions, we proposed a transformer model that learns from reaction SMILES and amino acid sequences of native enzymes and predicts promiscuous enzymes for potential substrates. The proposed transformer model calibrates the feasibility of the predicted reactions and reduces the search scope for promiscuous enzymes in the pool. A populated biological reaction space is eventually visualised in a two-dimensional t-SNE diagram. | Chonghuan Zhang; Qianyue Zhang; Alexei Lapkin | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fd4b9112ff75c3a12d36d8/original/exploration-of-bioinformatic-domain-based-on-data-mining-reaction-and-enzyme-promiscuity-predictions.pdf |
60c7417cee301cbf12c78ca3 | 10.26434/chemrxiv.5901226.v3 | The Mce3R stress-resistance pathway is vulnerable to small-molecule targeting that improves tuberculosis drug activities | <p>One-third of the world’s population carries <i>Mycobacterium tuberculosis </i>(<i>Mtb</i>), the infectious agent that causes tuberculosis (TB), and every 17 seconds someone dies of TB. After infection, <i>Mtb</i>can live dormant within macrophages for decades in a granuloma structure arising from the host immune response; and cholesterol is important for this persistence of <i>Mtb</i>. Current treatments require long-duration drug regimens with many associated toxicities, which are compounded by the high doses required. We phenotypically screened 35 6-azasteroid analogues against <i>Mtb</i>and found that at low micromolar concentrations, a subset of the <a>analogues sensitized <i>Mtb</i></a>to multiple TB drugs. Two analogues were selected for further study to characterize the bactericidal activity of bedaquiline and isoniazid under normoxic and low-oxygen conditions. These two 6-azasteroids <a>showed strong synergy with bedaquiline</a>(fractional inhibitory concentration index = 0.21, bedaquiline minimal inhibitory concentration = 16 nM at 1 μM 6-azasteroid). The rate at which spontaneous resistance to one of the 6-azasteroids arose in the presence of bedaquiline was approximately 10<sup>−9</sup>, and the 6-azasteroid-resistant mutants retained their isoniazid and bedaquiline sensitivity. Genes in the cholesterol-regulated Mce3R regulon were required for 6-azasteroid activity, whereas genes in the cholesterol catabolism pathway were not. Expression of a subset of Mce3R genes was down-regulated upon 6-azasteroid treatment. The Mce3R regulon is implicated in stress resistance and is absent in saprophytic mycobacteria. This regulon encodes a cholesterol-regulated stress-resistance pathway that we conclude is important for pathogenesis and contributes to drug tolerance, and that this pathway is vulnerable to small-molecule targeting in live mycobacteria.</p> | Xinxin Yang; Tianao Yuan; Rui Ma; Kieran Chacko; Melissa Smith; Gintaras Deikus; Robert Sebra; Andrew Kasarskis; Harm van Bakel; Scott
G. Franzblau; Nicole Sampson | Chemical Biology; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7417cee301cbf12c78ca3/original/the-mce3r-stress-resistance-pathway-is-vulnerable-to-small-molecule-targeting-that-improves-tuberculosis-drug-activities.pdf |
61dd5d8f90fc8a7a22f33eba | 10.26434/chemrxiv-2022-jwv10 | Identifying the "true" repeat unit of a copolymer using time-resolved electron paramagnetic resonance spectroscopy: a case study involving PNDIT2, NDI-T2 and T-NDI-T | Semiconducting polymers promise to revolutionise the way electronic devices can be built and deployed for a vast array of applications ranging from light-energy conversion to sensors to thermoelectric generators. Conjugated push-pull copolymers consisting of alternating donor and acceptor moieties are at the heart of these applications, due to the large tunability of their electronic structure. Hence, knowing the repeat unit and thus the chromophore of these materials is essential for a detailed understanding of the structure--function relationship of conjugated polymers used in organic electronics applications. Therefore, spectroscopic tools providing the necessary molecular resolution that allows to discriminate between different building blocks and to decide which one actually resembles the electronic structure of the polymer are of utmost importance. Time-resolved electron paramagnetic resonance (TREPR) spectroscopy is both, perfectly suited for this task and clearly superior to optical spectroscopy, particularly when supported by quantum-chemical calculations. This is due to its molecular resolution and unique capability of using light-induced triplet states to probe the electronic structure as well as the impact of the local environment. Here, we demonstrate the power of this approach for the polymer PNDIT2 (poly{[N,N'-bis(2-octyldodecyl)-naphthalene-1,4,5,8-bis(dicarboximide)-2,6-diyl]-alt-5,5'-(2,2'-bithiophene)}) revealing NDI-T2 unambiguously as the "true" repeat unit of the polymer, representing the chromophore. The alternative building block T-NDI-T has a markedly different electronic structure. These results are of high importance for the rational design of conjugated polymers for organic electronics applications. | Clemens Matt; Rukiya Matsidik; Deborah L. Meyer; Mirjam Schröder; Michael Sommer; Till Biskup | Physical Chemistry; Polymer Science; Organic Polymers; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61dd5d8f90fc8a7a22f33eba/original/identifying-the-true-repeat-unit-of-a-copolymer-using-time-resolved-electron-paramagnetic-resonance-spectroscopy-a-case-study-involving-pndit2-ndi-t2-and-t-ndi-t.pdf |
66f5ac5ecec5d6c1425113a3 | 10.26434/chemrxiv-2024-0h6rl | Carbon-Centered Reactivity in Carbodiphosphorane-Based Ligands Allowing for Redox-Non-Innocent Ligand-Ligand Cooperative- and Catalytic Dual Bond-Activation | A pronounced nucleophilicity in combination with a distinct redox non-innocence is a unique feature of a coordinated ligand, which in the current case, leads to unprecedented carbon-centered reactivity patterns: A carbodiphosphorane-based (CDP) pincer-type rhodium complex allows to cleave two C–Cl-bonds of geminal dichlorides via two consecutive SN2-type oxidative additions resulting in the formation of a stabilized carbene fragment. In the presence of a suitable reductant the carbene fragment can even be converted into olefines or hydrodehalogenation products in a catalytic reaction. The developed method can also be used to convert chlorofluorocarbons (CFCs) such as CH2ClF to fluoromethane and methane. The strong nucleophilic character of coordinated CDPs is also reflected in the low potential for oxidation, which favors radical reactivity and gives rise to an unique cationic C-centered radical CDP ligand, which is capable of a carbon-centered dihydrogen activation, following an unprecedented radical mechanism involving ligand-ligand-cooperativity (LLC). | Philipp Schatz; Weiqin Xu; Sebastian Rynek; Leon Maser; Niels Heise; Olaf Fuhr; Dieter Fenske; Haleh Hashemi Haeri; Dariush Hinderberger; Matthias Vogt; Robert Langer | Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Bond Activation; Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f5ac5ecec5d6c1425113a3/original/carbon-centered-reactivity-in-carbodiphosphorane-based-ligands-allowing-for-redox-non-innocent-ligand-ligand-cooperative-and-catalytic-dual-bond-activation.pdf |
623203d1658bc02e68ad08d4 | 10.26434/chemrxiv-2022-fwdr1 | Mechanistic study of the mechanochemical PdII-catalyzed bromination of aromatic C–H bonds by experimental and computational methods | An environmentally friendly approach was applied to the palladium-catalyzed halogenation of aromatic C–H bonds by N-halosuccinimide. Neat grinding and liquid-assisted grinding of the Pd(OAc)2 precatalyst in the presence of p-toluenesulfonic acid in a ball mill led to the in situ formation of active palladium species that catalyzed the halogenation of azobenzene. Detailed insight into the mechanism of this process was obtained by in situ Raman monitoring, which revealed the nature of the catalytically active PdII species and intermediates and confirmed the crucial role of p-toluenesulfonic acid and acetonitrile as additives in the catalytic halogenation of azobenzene. By quantum-chemical (DFT) modelling of bromination of cyclopalladated azobenzene three reaction mechanisms were characterized: oxidative addition followed by reductive elimination, with neutral or protonated N-bromosuccinimide (NBS), and electrophilic cleavage with neutral NBS. All three mechanisms seem to be operative, with relative participation depending on the reaction conditions. Two mechanistic features were recognized in the oxidative addition of bromine to palladium atom: the biradical singlet character in the transition state realized with neutral NBS as the active species, and the barrierless migration of Br+ with protonated NBS. | Dajana Barišić; Ivan Halasz; Alen Bjelopetrović; Darko Babić; Manda Ćurić | Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry; Bond Activation; Kinetics and Mechanism - Organometallic Reactions; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623203d1658bc02e68ad08d4/original/mechanistic-study-of-the-mechanochemical-pd-ii-catalyzed-bromination-of-aromatic-c-h-bonds-by-experimental-and-computational-methods.pdf |
67b3fc8b6dde43c90858815a | 10.26434/chemrxiv-2025-5kf7z-v2 | Multi-objective Bayesian optimization for experimental design in copolymerization and revealing chemical mechanism of Pareto fronts | The chemical properties of copolymers are strongly influenced by a number of intrinsic characteristics such as their molecular weight and their monomer composition ratio. Identifying the optimal conditions for the copolymerization process that results in a synthesized copolymer with the desired characteristics is a major challenge. Optimization of the copolymerization process has traditionally been based on trial-and-error approaches by humans relying on em-pirical rules. Thus, the design space that can be explored experimentally is severely limited under time and economic constraints. In addition, solving problems such as nonuniformity of both temperature and the concentration of chemi-cals in the reaction field is also challenging. In this study, we established multi-objective Bayesian optimization and flow copolymerization systems to explore optimal copolymerization conditions for synthesizing copolymers that sim-ultaneously exhibit multiple target characteristics. Finally, we visualized Pareto fronts representing trade-offs be-tween polymer characteristics and employed quantum chemical calculations to reveal chemical origins of Pareto fronts. | Hiromu Yamada; Shogo Takasuka; Shunto Oikawa; Yosuke Harashima; Tomoaki Takayama; Aniruddha Nag; Araki Wakiuchi; Tsuyoshi Ando; Tetsunori Sugawara; Miho Hatanaka; Tomoyuki Miyao; Takamitsu Matsubara; Yu-ya Ohnishi; Hiroharu Ajiro; Mikiya Fujii | Polymer Science; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b3fc8b6dde43c90858815a/original/multi-objective-bayesian-optimization-for-experimental-design-in-copolymerization-and-revealing-chemical-mechanism-of-pareto-fronts.pdf |
60c75397337d6cd14ae288b0 | 10.26434/chemrxiv.13489899.v1 | Synthesis of Dipeptides and Ruthenium-Phenanthroline Derivative for Photo Redox Studies | <p><b>Abstract:</b>
This paper describes the synthesis and characterization of a dipeptides and ruthenium
phenanthroline-amine
for the study of photoinitiated electron
transfer (ET) in dipeptides
were described. <b></b></p> | Sudershan Reddy Gondi | Organic Synthesis and Reactions; Physical Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2021-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75397337d6cd14ae288b0/original/synthesis-of-dipeptides-and-ruthenium-phenanthroline-derivative-for-photo-redox-studies.pdf |
60c754984c891959edad4567 | 10.26434/chemrxiv.13671268.v1 | Quasi-3D Modeling of Li-ion Batteries Based on Single 2D Image | In this work, we developed an advanced electrochemical physics-based simulation method for Li-ion batteries that enabled a quasi-3D simulation of charge/discharge using only a single 2D slice image. The governing equations are based on typical theories of electrochemical reactions and ion transport. From referencing the 2D plane, the model was able to simulate both the Li concentration in the active material and the Li-ion concentration in the electrolyte for their subsequent consideration in a virtual 3D structure. To confirm the validity of our proposed model, a full 3D discharge simulation with randomly packed active material particles was performed and compared with the results of the quasi-3D model and a simple-2D model. Results indicated that the quasi-3D model properly reproduced the sliced Li and Li-ion concentrations simulated by the full 3D model in the charge/discharge process, whereas the simple-2D simulation partially overestimated or underestimated these concentrations. Finally, we applied the model to an actual Scanning Electron Microscopy equipped with a Focused Ion Beam (FIB-SEM) image of a positive electrode. | Yoichi Takagishi; Tatsuya Yamaue; Takumi Yamanaka | Computational Chemistry and Modeling; Transport Phenomena (Chem. Eng.); Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754984c891959edad4567/original/quasi-3d-modeling-of-li-ion-batteries-based-on-single-2d-image.pdf |
639741f704bc666083133b2e | 10.26434/chemrxiv-2022-9b3s1 | Development of Adagrasib’s Commercial Manufacturing Route | A commercial route to MRTX849 (adagrasib) was developed to support clinical and commercial needs. Yield was improved to 32% over six chemical steps. A doubly regioselective SNAr reduced consumption of an expensive chiral intermediate, reaction optimization led to parts per million palladium catalysis, and a new method to deprotect Cbz-groups were developed to mitigate risk associated with benzyl iodide. | David Snead; Yonghong Gan; Thomas Scattolin; Dinesh Paymode; Michal Achmatowicz; Duane Rudisill; Ephraim Vidal; Tawfik Gharbaoui; Phil Roberts; Jianbo Yang; Zhangbing Shi; Wei Liu; Joshua Bolger; Zhen Qiao; Cheng-yi Chen | Organic Chemistry; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Process Chemistry; Industrial Manufacturing | CC BY 4.0 | CHEMRXIV | 2022-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639741f704bc666083133b2e/original/development-of-adagrasib-s-commercial-manufacturing-route.pdf |
60c74de7337d6c1178e27e8b | 10.26434/chemrxiv.12666470.v1 | Unambiguous Identification of Key Molecular Species in Deposits Responsible for Increased Pollution from Internal Combustion Engines | <p>Clean and efficient internal
combustion engine performance will play a significant role in the move to a decarbonized energy
system. Currently, fuel deposit formation on engine components negatively impacts CO2
and pollutant emissions, where previous attempts at deposit characterization afforded
non-diagnostic chemical assignments. Here, we uncover the identity and 3D spatial
distribution of molecular species from gasoline, diesel injector and filter deposits with the 3D
OrbiSIMS technique. Alkylbenzyl sulfonates, derived from lubricant oil contamination in the
engine fuel cycle, were common to samples, we evidence transformation of the
native sulfonate to longer chain species by reaction with fuel fragments in the gasoline
deposit. Inorganic salts, identified in both diesel deposits, were prevalent throughout the
injector deposits depth. We identified common polycyclic aromatic hydrocarbons up to
C66H20, these were prevalent in the gasoline deposits lower depths. This work
will enable deposit mitigation by unravelling their chemical composition,
spatial distribution, and origins.</p> | Max K. Edney; Joseph S. Lamb; Matteo Spanu; Emily F. Smith; Elisabeth Steer; Edward Wilmot; Jacqueline Reid; Jim Barker; Morgan R. Alexander; Colin E. Snape; David J. Scurr | Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74de7337d6c1178e27e8b/original/unambiguous-identification-of-key-molecular-species-in-deposits-responsible-for-increased-pollution-from-internal-combustion-engines.pdf |
60c7486b469df45f2cf43a1a | 10.26434/chemrxiv.11907060.v1 | A Simple and Cost-Effective Synthesis of Sulfated β-Cyclodextrin and Its Application as Chiral Mobile Phase Additive in the Separation of Cloperastine Enantiomers | A new, simple and cost-effective
method for the synthesis of sulfated beta-cyclodextrin (S-β-CD), one of the
most widely used chiral mobile phase additive, using sulfamic acid as
sulfonating agent has been described. The method was optimized and the acquired
product was characterized and compared with a marketed Sigma Aldrich sulfated
beta-cyclodextrin (S-β-CD1). Beta cyclodextrin (β-CD), hydroxypropyl beta-cyclodextrin
(HP-β-CD), S-β-CD1 and S-β-CD2 were evaluated as chiral mobile phase additives
(CMPAs) for the enantiomeric separation of cloperastine, an antitussive agent,
using reversed-phase HPLC. Under the optimized conditions, a resolution of 3.14
was achieved within 15 minutes on an achiral Kromasil C<sub>8</sub> (150 x 4.6
mm, 5 µ) column with a mobile phase of 5mM monopotassium phosphate containing
10mM S-β-CD3 pH 3 and 45% methanol with a run time of 15 min. The method
utilizing S-β-CD3 as CMPA was validated as per ICH guidelines and applied for the
quantitative determination of cloperastine enantiomers in active pharmaceutical
ingredients and pharmaceutical formulations. The selectivity changes imparted
by S-β-CD were proven to be beneficial for chiral separation. The chiral recognition mechanism and elution order
of the reported enantiomers were determined by simulation studies. It was
observed that inclusion complex formation and hydrogen bonding are the major
forces for the chiral resolution. | Krishna Deshpande; Pranav Pathak; Vishvas Joshi; Stephen barton; Krishnapriya Mohanraj | Analytical Chemistry - General; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7486b469df45f2cf43a1a/original/a-simple-and-cost-effective-synthesis-of-sulfated-cyclodextrin-and-its-application-as-chiral-mobile-phase-additive-in-the-separation-of-cloperastine-enantiomers.pdf |
6677522e01103d79c5e2c436 | 10.26434/chemrxiv-2024-m536q | Identification of remnant OCT media artifacts after tissue washing by MALDI mass spectrometry imaging | RATIONALE
Universally, the most common method of embedding dissected or resected fresh frozen (FF) tissues is within optimal cutting temperature (OCT) media. Unfortunately, OCT is not ideal for mass spectrometry (MS) assays. The media perfuses through tissues, resulting in persistent polymer contamination causing issues for sensitive analyses. Complete removal of all OCT media background would enable techniques such as MS imaging (MSI) to be bridged to clinically relevant samples stored in biobanks which possess extensive medical histories. Even though methods have been outlined for spatial lipidomics and proteomics, many still avoid these tissues despite vast potential for biological discoveries applying MS or MSI.
METHODS
Reference FF human pancreas was prepared within OCT media and cryosectioned for matrix-assisted laser desorption/ionization (MALDI)-MSI. Sample preparation protocols using aqueous ammonium formate for spatial lipidomics, and a variety of solutions for fixation, delipidation, and salt removal enabled spatial proteomics as well. MSI was performed on a UHMR HF Orbitrap MS detected broad classes of lipids and intact proteins, enabling an assessment of polymer perfusion and signal delocalization over a broad mass range to evaluate any deleterious artifacts.
RESULTS
We observe lower polymer contamination from OCT tissues with ammonium formate washes as expected, with several caveats. This was most effective in negative ion mode, where in tandem with the boosted lipid signal positive results were achieved for phospholipids (600-900 Da) and higher mass lipids (>1250 Da). Positive ion mode analyses can be completed for phospholipids, but the condensation of alkali adducts to protonated forms not only increased lipid signals, but also increased signals of larger, persistent PEG oligomers (>1250 Da) which were not previously reported. Even with extensive tissue washing completing a spatial proteomics protocol, the removal of all remnant artifacts of OCT media was not feasible.
CONCLUSIONS
The finding of these persistent remnant polymers from the OCT embedding process has several consequences for MSI, directly effecting primary performance of the MALDI source and lipid and protein analyses. This does not mean OCT tissues should not be or cannot be used for spatial omics by MSI, but several quality control and quality assurance measures should be implemented, and we discuss paths forward and several considerations. | Kevin Zemaitis; Rashmi Kumar; Marija Veličković; Dušan Veličković; Wei-Jun Qian; Ljiljana Paša-Tolić | Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Imaging; Mass Spectrometry | CC BY NC 4.0 | CHEMRXIV | 2024-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6677522e01103d79c5e2c436/original/identification-of-remnant-oct-media-artifacts-after-tissue-washing-by-maldi-mass-spectrometry-imaging.pdf |
63590093ecdad54aaaed9777 | 10.26434/chemrxiv-2022-1d5x8-v2 | GaTewAY : Graph theory-based software for automatic analysis of molecular conformers generated over time | GaTewAY is a post-processing tool for molecular dynamics (MD) simulation databased on graph theoretical techniques.
The main idea is to construct 2D graphs from the 3D structures. Then, GaTewAY identifies the conformations over time based on the dynamics of bonds and the isomorphism test.
The use of graph theory methods/tools does not only provide a direct and fast methodology to identify conformers,
but also allows following in time the interconversion reactions between the different conformers as shown by graphs of transitions.
In this paper, we describe the methodology used to develop GaTeWAY. Then, we describe the code with its different modules.
We present the inputs of GaTeWAY, the threshold values, the usage of the code and the main outputs.
Our software has been tested and validated on DFT-MD and QM-MM trajectories of gas phase molecules and clusters.
We will, in particular, illustrate results for peptides to have an idea about the outputs.
The algorithm's transferability is further demonstrated on a more complex air/liquid water interface.
We designed our algorithm so that it can be extended and consider any types of bonds/interactions and parameters; hence, GaTeWAY can be applied to any molecular system.
Ongoing work aims to analyze reaction networks in clusters for catalysis.
The results are promising. Another manuscript has just been submitted, which illustrates the performance of GateWAY for these systems. | Sana Bougueroua; Franck Quessette; Dominique Barth; Marie-Pierre Gaigeot | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63590093ecdad54aaaed9777/original/ga-tew-ay-graph-theory-based-software-for-automatic-analysis-of-molecular-conformers-generated-over-time.pdf |
60c74430842e651473db23d2 | 10.26434/chemrxiv.9755543.v1 | Inhibition of the Nrf2-TrxR Axis Sensitizes the Drug-Resistant Chronic Myelogenous Leukemia Cell Line K562/G01 to Imatinib Treatments | Nuclear factor erythroid 2-related factor 2 (Nrf2) is involved in tumor drug resistance, but its role in imatinib-resistance of chronic myeloid leukemia (CML) remains elusive. We aimed to investigate the effects of Nrf2 on drug sensitivity, thioredoxin reductase (TrxR) expression, reactive oxygen species (ROS) production, apoptosis induction in imatinib-resistant CML K562/G01 cells and explored their potential mechanisms. Stable K562/G01 cells with knockdown of Nrf2 were established by infection of siRNA-expressing lentivirus. The mRNA and protein expression levels of Nrf2 and TrxR were determined by real-time quantitative polymerase chain reaction and western blot, respectively. ROS generation and apoptosis were assayed by flow cytometry, while drug sensitivity was measured by Cell Counting Kit-8 assay. Imatinib-resistant K562/G01 cells had higher levels of Nrf2 expression than the parental K562 cells at both mRNA and protein levels. Expression levels of Nrf2 and TrxR were positively correlated in K562/G01 cells. Knockdown of Nrf2 in K562/G01 cells enhanced the intracellular ROS level, suppressed cell proliferation and increased apoptosis in response to imatinib treatments. Nrf2 expression contributes to the imatinib-resistance of K562/G01 cells, and is positively correlated with TrxR expression. Targeted inhibition of the Nrf2-TrxR axis represents a potential therapeutic approach for imatinib-resistant CML.<a></a> | Lianrong Xu; Yan Zhao; Fei Pan; Mengxia Zhu; Liqin Yao; Yan Liu; Jiangfang Feng; Jie Xiong; Xiuhua Chen; Fanggang Ren; Yanhong Tan; Hongwei Wang | Bioengineering and Biotechnology; Cell and Molecular Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74430842e651473db23d2/original/inhibition-of-the-nrf2-trx-r-axis-sensitizes-the-drug-resistant-chronic-myelogenous-leukemia-cell-line-k562-g01-to-imatinib-treatments.pdf |
617883e30f3eeb18ee723587 | 10.26434/chemrxiv-2021-5l2f8-v3 | DiSCoVeR: a Materials Discovery Screening Tool for High Performance, Unique Chemical Compositions | We present Descending from Stochastic Clustering Variance Regression (DiSCoVeR), a Python tool for identifying high-performing, chemically unique compositions relative to existing compounds using a combination of a chemical distance metric, density-aware dimensionality reduction, and clustering. We introduce several new metrics for materials discovery and validate DiSCoVeR on Materials Project bulk moduli using compound-wise and cluster-wise validation methods. We visualize these via multiobjective Pareto front plots and assign a weighted score to each composition where this score encompasses the trade-off between performance and density-based chemical uniqueness. We explore an additional uniqueness proxy related to property gradients in chemical space. We demonstrate that DiSCoVeR can successfully screen materials for both performance and uniqueness in order to extrapolate to new chemical spaces. | Sterling Baird; Tran Diep; Taylor Sparks | Materials Science; Elastic Materials | CC BY 4.0 | CHEMRXIV | 2021-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617883e30f3eeb18ee723587/original/di-s-co-ve-r-a-materials-discovery-screening-tool-for-high-performance-unique-chemical-compositions.pdf |
645a439ba32ceeff2d597f2b | 10.26434/chemrxiv-2023-w4lmg | High-Yielding Synthesis of Cyclometallated Iridium Complexes with Hydrogen Bond-Rich Ligands | A library of cyclometallated iridium (III) complexes with a strong H-bonding motif in their ancillary ligand was synthesized, characterized and their photophysical properties measured. Demonstrated herein is a general synthetic high yield procedure for these compounds. We ascribe these yields to the use of an intermediary primer ligand. This de novo strategy circumnavigates the standard synthetic issues of H-bond rich ligand precursors (self-aggregation and poor solubility in organic solvents). Alternative and greener synthetic pathways were also explored to realize the intermediate iridium primer complex. | Marta Tomás Piqueras; Holly Howe; Robert Williamson; Barry Blight | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645a439ba32ceeff2d597f2b/original/high-yielding-synthesis-of-cyclometallated-iridium-complexes-with-hydrogen-bond-rich-ligands.pdf |
60c747879abda24378f8c90a | 10.26434/chemrxiv.11629068.v1 | Tuning Mechanism through Buffer Dependence of Hydrogen Evolution Catalyzed by a Cobalt Mini-enzyme | Cobalt-mimochrome VI*a (CoMC6*a) is a synthetic mini-protein that catalyzes aqueous proton reduction to hydrogen (H<sub>2</sub>). In buffered water, there are multiple possible proton donors, complicating the elucidation of mechanism. We have found that buffer pKa and sterics have significant effects on activity, evaluated through cyclic voltammetry (CV). Protonated buffer is proposed to act as the primary proton donor to the catalyst, specifically through the protonated amine of the buffers that were tested. At a constant pH of 6.5, catalytic H<sub>2</sub> evolution in the presence of buffer acids of pK<sub>a</sub> ranging from 5.8 to 11.6 was investigated, giving rise to a potential-pK<sub>a</sub> relationship that can be divided into two regions. For acids of pK<sub>a</sub> ≤ 8.7, the half-wave catalytic potential (E<sub>h</sub>) changes as a function of pKa with a slope of –128 mV/pK<sub>a</sub> unit, and for acids of pK<sub>a</sub> ≥ 8.7, Eh changes as a function of pKa with a slope of –39 mV/pKa unit. In addition, a series of buffer acids was synthesized to explore the influence of steric bulk around the acidic proton on catalysis. The catalytic current in CV shows a significant decrease in the presence of the sterically hindered buffer acids compared to their parent compounds, also consistent with the added buffer acid acting as the primary proton donor to the catalyst and showing that acid structure in addition to pK<sub>a</sub> impacts activity. These results demonstrate that buffer acidity and structure are important considerations when optimizing and evaluating systems for proton-dependent catalysis in water. | Jennifer Le; Georgios Alachouzos; Alison Frontier; Angela Lombardi; Kara Bren | Bioinorganic Chemistry; Electrochemistry; Kinetics and Mechanism - Inorganic Reactions; Biochemistry; Biocatalysis; Electrocatalysis; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747879abda24378f8c90a/original/tuning-mechanism-through-buffer-dependence-of-hydrogen-evolution-catalyzed-by-a-cobalt-mini-enzyme.pdf |
66a33fa401103d79c5ba9597 | 10.26434/chemrxiv-2024-zwx80 | Prioritization of Novel Anti-infective Stilbene derivatives by Combining Metabolomic Data Organization and a Stringent 3R-infection Model in a Knowledge Graph | The rising threat of Multidrug-Resistant Tuberculosis (MDR-TB), caused by Mycobacterium tuberculosis (Mtb), underscores the urgent need for new therapeutic solutions to tackle the challenge of antibiotics resistance. The current study utilized an innovative 3R infection model featuring the amoeba Dictyostelium discoideum infected with Mycobacterium marinum, serving as stand-ins for macrophages and Mtb, respectively. This high-throughput phenotypic assay allowed for the evaluation of more specific anti-infective activities that may be less prone to resistance mechanisms. To discover novel anti-infective compounds, a diverse collection of 1,600 plant extracts from the Pierre Fabre Library (PFL) was screened using the latter assay. Concurrently, these extracts underwent untargeted UHPLC-HRMS/MS analysis. The biological screening flagged the extract from Stauntonia brunoniana as one of the anti-infective hit extracts. High-resolution HPLC micro-fractionation coupled with bioactivity profiling was employed to highlight the natural products (NPs) driving this bioactivity. Stilbenes were eventually identified as the primary active compounds in the bioactive fractions. A knowledge graph (KG) was then used to leverage the heterogeneous data integrated into it to make a rational selection of stilbene-rich extracts. Using both CANOPUS chemical classes and Jaccard similarity indices (JSIs) to compare features within the metabolome of the 1600 NEs set, 14 extracts rich in stilbenes were retrieved. Among those, the roots of Gnetum edule were flagged as possessing broader chemo-diversity in their stilbene content, along with the corresponding extract also being a strict anti-infective. Eventually, a total of 11 stilbene oligomers were isolated from G. edule and fully characterized by NMR with their absolute stereochemistry established through electronic circular dichroism (ECD). Six of these compounds are new since they possess a stereochemistry which was never described in the literature to the best of our knowledge. All of them were assessed for their anti-infective activity and (-)-Gnetuhainin M was reported as having the highest anti-infective activity with an IC50 of 22.22 μM. | Olivier Auguste Kirchhoffer; Luis Quiros-Guerrero; Jahn Nitschke; Louis-Félix Nothias; Frédéric Burdet; Laurence Marcourt; Nabil Hanna; Florence Mehl; Bruno David; Antonio Grondin; Emerson Ferreira Queiroz; Marco Pagni; Thierry Soldati; Jean-Luc Wolfender | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Mass Spectrometry; Separation Science; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a33fa401103d79c5ba9597/original/prioritization-of-novel-anti-infective-stilbene-derivatives-by-combining-metabolomic-data-organization-and-a-stringent-3r-infection-model-in-a-knowledge-graph.pdf |
65af957466c1381729138665 | 10.26434/chemrxiv-2024-4mthm | Accelerated Analysis of the Electrochemical Production Route for Biomass-derived Adiponitrile | Electrochemical transformation of biomass feedstocks offers a promising route for sustainable production of fuels and chemicals, enhancing integration with renewable energy sources. Adiponitrile, a key intermediate in Nylon 6,6 production, is mainly produced through thermochemical processes or methods relying fossil fuel feedstocks. Alternatively, it can be produced through Kolbe coupling of biomass-derived 3-cyanopropanoic acid, with its practical implementation hinging on understanding and controlling factors that dictate reaction selectivity. In this study, we establish relationships between electrolyte composition, electrochemical conditions, and performance metrics in this approach, achieving a maximum Faradaic efficiency of 40% towards adiponitrile at current densities up to 500 mA cm-2. Implementing a semi- autonomous high-throughput electrochemical workflow, we tested hundreds of reaction conditions, accelerating the exploration of reaction parameters. Limitations and guidelines obtained from this study apply to a range of electrochemical decarboxylation reactions, and the accelerated research approach shows potential for speeding the development of sustainable electrochemical processes. | Ricardo Mathison; Elina Rani; Meera K. Patel; Casey K. Bloomquist; Antonio Lopez Cerrato; Miguel A. Modestino | Organic Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Reaction Engineering; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65af957466c1381729138665/original/accelerated-analysis-of-the-electrochemical-production-route-for-biomass-derived-adiponitrile.pdf |
64b43017b605c6803bd58a5a | 10.26434/chemrxiv-2023-0s2tq | The development of the MiniXtruder: a low-cost laboratory scale filament extruder with reduced internal dead volume for 3D Printing | OBJECTIVES: To develop a simple small-footprint, single-screw Hot Melt Extrusion device that can combine with existing laboratory equipment to facilitate rapid generation of 3D-printable HME filaments and benchtop quantities of 3D-printed filament for scale-up processes.
METHODS: Design and development of the low-cost device which we call the MiniXtruder was carried out in silico and was manufactured using conventional laboratory tools, machining and 3D printing. To compare its capability, identical filament was produced on a commercial twin-screw extruder and compared with filament from the MiniXtruder. Extrudates from plain-PCL/PCL-caffeine loaded pellets were analysed by TGA, DSC and SEM. 3D printing of the was carried out on a MakerBot Replicator 2X Desktop 3D-printer.
KEY FINDINGS: Realisation of the MiniXtruder as a small footprint/low-cost HME device that can produce 3D printable filaments. Different materials can be used with the device, resulting in facile extrudate production. The MiniXtruder shows versatility and decreased time/material consumption with low internal volumes and replicable filament production.
CONCLUSION: The MiniXtruder’s potential to produce 3D-printable filament has shown that it is suitable for use in a laboratory setting and that it can replicate the production of 3D-printable filament from more expensive extruders whilst minimising the internal dead volume.
| Bruno C. Sil; John Frost; Zaid Muwaffak; Queenie Wong; Matthew R. Penny; Stephen Hilton | Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Pharmaceutical Industry; Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b43017b605c6803bd58a5a/original/the-development-of-the-mini-xtruder-a-low-cost-laboratory-scale-filament-extruder-with-reduced-internal-dead-volume-for-3d-printing.pdf |
6249caa65ab8df5a0189749f | 10.26434/chemrxiv-2022-5qpv9 | Bayesian Sequential Stacking Algorithm for Concurrently Designing Molecules and Synthetic Reaction Networks | In the last few years, de novo molecular design using machine learning has made great technical progress but its practical deployment has not been as successful. This is mostly owing to the cost and technical difficulty of synthesizing such computationally designed molecules. To overcome such barriers, various methods for synthetic route design using deep neural networks have been studied intensively in recent years. However, little progress has been made in designing molecules and their synthetic routes simultaneously. Here, we formulate the problem of simultaneously designing molecules with the desired set of properties and their synthetic routes within the framework of Bayesian inference. The design variables consist of a set of reactants in a reaction network and its network topology. The design space is extremely large because it consists of all combinations of purchasable reactants, often in the order of millions or more. In addition, the designed reaction networks can adopt any topology beyond simple multistep linear reaction routes. To solve this hard combinatorial problem, we present a powerful sequential Monte Carlo algorithm that recursively designs a synthetic reaction network by sequentially building up single-step reactions. In a case study of designing drug-like molecules based on commercially available compounds, compared with heuristic combinatorial search methods, the proposed method shows overwhelming performance in terms of computational efficiency and coverage and novelty with respect to existing compounds. | Qi Zhang; Chang Liu; Stephen Wu; Ryo Yoshida | Theoretical and Computational Chemistry; Machine Learning | CC BY 4.0 | CHEMRXIV | 2022-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6249caa65ab8df5a0189749f/original/bayesian-sequential-stacking-algorithm-for-concurrently-designing-molecules-and-synthetic-reaction-networks.pdf |
6322951abe03b232b0f6c7db | 10.26434/chemrxiv-2022-xpz37 | CRIPT: A Scalable Polymer Material Data Structure | Polymeric materials are integral components of nearly every aspect of modern life. Today, polymer scientists and engineers devote significant resources to the design and development of these materials to meet growing societal needs. However, developing cheminformatic solutions for polymers has been difficult since they are large stochastic molecules with hierarchical structures spanning multiple length scales from chemical bonds to large molecular assemblies. Here we present the design for a general material data model that underpins the Community Resource for Innovation in Polymer Technology (CRIPT) data ecosystem. Among the key challenges that the data model addresses are the high complexity in defining a polymer structure and the intricacies involved with characterizing material properties. The core design of the data model is graph-based which provides flexibility, robustness, and scalability to support the community-driven mission. This approach to structuring material data provides the key advancements that the community needs to bring cheminformatics to polymer science and accelerate the development of new materials. | Dylan Walsh; Weizhong Zou; Ludwig Schneider; Reid Mello; Michael Deagen; Joshua Mysona; Tzyy-Shyang Lin; Juan de Pablo; Klavs Jensen; Debra Audus; Bradley Olsen | Materials Science; Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6322951abe03b232b0f6c7db/original/cript-a-scalable-polymer-material-data-structure.pdf |
60df22fee0330e52ce13443a | 10.26434/chemrxiv-2021-wx9kh | A Broadly Applicable Alkyl-Alkyl Suzuki-Miyaura Cross-Coupling Reaction Catalyzed by an Iron-Based Complex | An iron-based catalyst for the Suzuki-Miyaura reaction between two sp3-hybridized substrates has been developed for a broad range of unactivated alkyl halides and alkyl boranes. Key to success was using a Cs-symmetric beta-diketiminate ligand that contained a tert-butyl and trifluoromethyl functionalized backbone. The breadth of the cross-coupling reaction was demonstrated with high yields of cross-coupled products observed from reactions using primary and secondary alkyl bromides as well as primary alkyl boranes and even some secondary alkyl boranes. Complementary methylation reactions using methyl iodide or methyl-9-BBN was also possible. The facile diversification of a steroid derivative using these reactions demonstrated the synthetic utility of such complementary cross coupling reactions. | Chet Tyrol; Jeffery Byers | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Homogeneous Catalysis; Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60df22fee0330e52ce13443a/original/a-broadly-applicable-alkyl-alkyl-suzuki-miyaura-cross-coupling-reaction-catalyzed-by-an-iron-based-complex.pdf |
64788819be16ad5c57488e23 | 10.26434/chemrxiv-2023-n1x1n | Unexpected single ligand occupancy and negative cooperativity in the SARS-CoV-2 Main protease | Many homodimeric enzymes tune their function by exploiting either negative or positive cooperativity between subunits. In the SARS-CoV-2 Main protease (Mpro) homodimer, the latter has been suggested by symmetry in most of the 500 reported protease/ligand complex structures solved by macromolecular crystallography. Here we apply the latter to both covalent and non-covalent ligands in complex with Mpro. Strikingly, our experiments show that occupation of both active sites of the dimer originates from an excess of ligands. Indeed, co-crystals obtained using a 1:1 ligand/protomer stoichiometry leads to single occupation only. The empty binding site exhibits a catalytic-inactive geometry in solution, as suggested by molecular dynamics simulations. Thus, Mpro operates through negative cooperativity, with asymmetric activity of the catalytic sites. This allows it to function with a wide range of substrate concentrations, making it resistant to saturation and potentially difficult to shut down - all properties advantageous for the virus’ adaptability and resistance. | Simone Albani; Elisa Costanzi; Gia Linh Hoang; Maria Kuzikov; Marcus Frings; Narjes Ansari; Nicola Demitri ; The Toan Nguyen; Valerio Rizzi; Jörg Bernhard Schulz; Carsten Bolm; Andrea Zaliani ; Paolo Carloni; Paola Storici ; Giulia Rossetti | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry | CC BY 4.0 | CHEMRXIV | 2023-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64788819be16ad5c57488e23/original/unexpected-single-ligand-occupancy-and-negative-cooperativity-in-the-sars-co-v-2-main-protease.pdf |
60c74481ee301c6010c79191 | 10.26434/chemrxiv.9849647.v1 | Controlling the Polymorphism and Topology Transformation in Porphyrinic Zirconium Metal-Organic Frameworks via Mechanochemistry | The mechanochemical approach has been used here for preparation and polymorph resolution in porphyrinic MOF-525/PCN-223 zirconium metal-organic frameworks system, achieving pure target MOF phases in 30-60 minutes milling. In specific reaction condition, MOF-525 forms rapidly by milling but transforms into PCN-223, confirming it to be the kinetic phase in this polymorphic system. ESR measurements showed a strong effect of internal MOF structure on the spin structure of paramagnetic cations coordinated into porphyrin linkers, which show potential for these polymorphic MOFs in spintronics application. | Bahar Karadeniz; Dijana Žilić; Igor Huskić; Luzia S. Germann; Athena M. Fidelli; Senada Muratović; Ivor Lončarić; Martin Etter; Robert E. Dinnebier; Dajana Barišić; Nikola Cindro; Timur Islamoglu; Omar
K. Farha; Tomislav Friscic; Krunoslav Uzarevic | Aggregates and Assemblies; Hybrid Organic-Inorganic Materials; Magnetic Materials; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74481ee301c6010c79191/original/controlling-the-polymorphism-and-topology-transformation-in-porphyrinic-zirconium-metal-organic-frameworks-via-mechanochemistry.pdf |
660f96ac21291e5d1d1c83d7 | 10.26434/chemrxiv-2024-chrkx | Identifying the Active Site on ZnxCryOz for HC-O Bond Cleavage in Syn-gas Conversion | The excellent performance of ZnxCryOz catalysts, used in the process of converting CO/H2 to methanol and light olefins, is highly attractive, but the microstructure of ZnxCryOz structure under the syngas conversion conditions remains elusive experimentally and theoretically because of the limitation of the detecting facilities/methods. By using the genetic-algorithm-based global structural search accelerated by machine learning in combination with a local cluster sampling strategy in the active learning scheme, we reveal the structure/composition evolution of ZnxCryOz structures and uncover that the catalytic activities of these catalysts strongly depend on the Zn/Cr ratios under the syngas conversion conditions. The possible active phase at the thermodynamically stable condition is identified and the critical active site influencing the catalytic property is unraveled. We show that the catalyst Zn2Cr2O5, which consists of a thin ZnO layer and the ZnCr2O4 structures, achieves a high catalytic activity for syngas conversion and its X-ray diffraction patterns are in agreement with the experimental result. Importantly, the presence of a hexahedral configuration ([ZnCrO2]hex) is found to affect the catalyst activity significantly, and this result is further supported by the analysis based on the structure-activity relationship. | Jiawei Wu; Yulan Han; Menglei Jia; Jiayan Xu; Peijun Hu | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660f96ac21291e5d1d1c83d7/original/identifying-the-active-site-on-znx-cry-oz-for-hc-o-bond-cleavage-in-syn-gas-conversion.pdf |
62561ee2103388db39ea7291 | 10.26434/chemrxiv-2022-w9k29-v2 | A Paper-Based Cytometer for the Detection and Enumeration of White Blood Cells According to their Immunophenotype
| Total and differential white blood cell (WBC) counts are vital metrics used routinely by clinicians to aid in the identification of diseases. However, the equipment necessary to perform WBC counts restricts their operation to centralized laboratories, greatly limiting their accessibility. Established solutions for the development of point-of-care assays, namely lateral flow tests and paper-based microfluidic devices, are inherently limited in their ability to support the detection of WBCs—the pore sizes of materials used to fabricate these devices (e.g., membranes or chromatography papers) do not permit passive WBC transport via wicking. Herein, we identify a material capable of the unimpeded transport of WBCs in both lateral and vertical directions: a coffee filter. Through in situ labeling with an enzyme-labeled affinity reagent, our paper-based cytometer detects WBCs according to their immunophenotype. Using two cultured leukocyte lines (Jurkat D1.1 T cells and MAVER-1 B cells), we demonstrate the specific, colorimetric enumeration of each target cell population across the expected physiological range for total lymphocytes, 1000–4000 cells µL-1. Additionally, we highlight a potential application of this type of device as a screening tool for detecting abnormal cell counts outside the normal physiological range and in sub-classes of cell types, which could aid in the identification of certain diseases (e.g., CD4+ T lymphocytes, an important biomarker for HIV disease/AIDS). These results pave the way for a new class of paper-based devices—those capable of controlled white blood cell transport, labeling, capture, and detection—thus expanding the opportunities for low-cost, point-of-care cytometers. | Lara P. Murray; Charles R. Mace | Materials Science; Analytical Chemistry; Multilayers; Analytical Chemistry - General; Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62561ee2103388db39ea7291/original/a-paper-based-cytometer-for-the-detection-and-enumeration-of-white-blood-cells-according-to-their-immunophenotype.pdf |
60c743b5842e650a90db2306 | 10.26434/chemrxiv.9587933.v1 | Decoupling Gas Evolution from Water-Splitting Electrodes | <div><div><div><p>Bubbles are known to hinder electrochemical processes in water-splitting electrodes. In this study, we present a novel method to promote gas evolution away from the electrode surface. We consider a ring microelectrode encircling a hydrophobic microcavity from which a succession of bubbles grows. The ring microelectrode, tested under alkaline water electrolysis conditions, does not suffer from bubble coverage. Consequently, the chronopotentiometric fluctuations of the cell are weaker than those associated with conventional microelectrodes. Herein, we provide fundamental understanding of the mass transfer processes governing the transient behaviour of the cell potential. With the help of numerical transport models, we demonstrate that bubbles forming at the cavity reduce the concentration overpotential by lowering the surrounding concentration of dissolved gas, but may also aggravate the ohmic overpotential by blocking ion-conduction pathways. The theoretical and experimental insight gained have relevant implications in the design of efficient gas-evolving electrodes.</p></div></div></div> | Pablo Peñas; Peter van der Linde; Wouter Vijselaar; Devaraj van der Meer; Detlef Lohse; Jurriaan Huskens; Han Gardeniers; Miguel Modestino; David Fernandez Rivas | Transport Phenomena (Chem. Eng.); Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743b5842e650a90db2306/original/decoupling-gas-evolution-from-water-splitting-electrodes.pdf |
64feef2bb6ab98a41c3f41ce | 10.26434/chemrxiv-2023-22kh4-v2 | Raman Spectroscopy of the Iron Oxides in the Form of Minerals, Particles and Nanoparticles | Magnetic iron oxides, such as Fe3O4, α-Fe2O3, γ-Fe2O3, have unique magnetic, catalytic and biochemical features, rendering them suitable for several specific technological and biomedical applications. In a previous study, for instance, we considered the magnetite Fe3O4 nanoparticles dispersed in supporting materials to obtain composites that can better respond to electromagnetic interferences with an increased EMI shielding effectiveness. Here we investigate how to distinguish the iron oxide nanoparticles by means of their Raman spectra. We will stress that literature is evidencing a challenge. This challenge is due to the fast transformations of iron oxides when laser power is applied. Therefore, the Raman spectroscopy needs to be considered carefully for determining the nature of the iron oxide present in the investigated samples. The role of oxidation of magnetite will be addressed in detail. In the review, the reader can find the Raman “fingerprints” of some oxides such as Magnetite, Maghemite, Hematite, Goethite, Lepidocrocite, Akaganeite and Siderite, when considered as minerals or nanoparticles. Moreover, we will also discuss some Raman spectra of iron oxides in composites and other materials (encapsulated iron oxides, biochar decoration, red mud). The fitting of some Raman spectra obtained by means of the q-Gaussian Tsallis functions is also shown. | Amelia Carolina Sparavigna | Materials Science | CC BY 4.0 | CHEMRXIV | 2023-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64feef2bb6ab98a41c3f41ce/original/raman-spectroscopy-of-the-iron-oxides-in-the-form-of-minerals-particles-and-nanoparticles.pdf |
60c74740567dfe3b50ec47ad | 10.26434/chemrxiv.11577816.v1 | Ester Transfer Reaction of Aromatic Esters with Haloarenes and Arenols by a Nickel Catalyst | A catalytic ester transfer reaction of aromatic esters with aryl halides/arenols was developed. The present reaction can transfer an ester functional group from certain aromatic esters to haloarenes. This ester transfer reaction involves two oxidative additions— one from the C–C bond of the aromatic ester and one from the C–halogen bond of haloarenes— onto a nickel catalyst. The utilization of a Ni/dcypt catalyst capable of cleaving both chemical bonds was a key for the reaction progress. Furthermore, naphthol-based aryl electrophiles were also applicable to the catalytic system via C–O bond activation. | Ryota Isshiki; Naomi Inayama; Kei Muto; Junichiro Yamaguchi | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74740567dfe3b50ec47ad/original/ester-transfer-reaction-of-aromatic-esters-with-haloarenes-and-arenols-by-a-nickel-catalyst.pdf |
64c338c1658ec5f7e54c395e | 10.26434/chemrxiv-2023-qq7t7-v2 | Diastereoselective synthesis of alpha-aryl substituted LnDOTA chelates from achiral starting materials by deracemization under mild conditions | Substituted derivatives of the DOTA framework are of general interest to alter chelate properties and facilitate conjugation of chelates to other molecular structures. However, the scope of substituents that can be introduced into the alpha-position has traditionally been limited by the availability of a suitable enantiopure starting materials to facilitate a stereoselective synthesis. Tetra-substituted DOTA derivatives with phenyl and benzoate substituents in the alpha-position were prepared. Initial syntheses used enantiopure starting materials but did not afford enantiopure products. This indicates that integrity of the stereocentres was not preserved during synthesis, despite the homo-chiral diastereoisomer being the major reaction product. The homochiral diastereoisomer could be produced as the major or sole reaction product when starting from racemic or even achiral materials. Deracemization was found to occur during chelation through formation of an enolate stabilized by the aryl substituent. This general ability of aryl groups to enable deracemization greatly increases the range of substituents that can be introduced into DOTA-type ligands with diastereochemical selectivity. | Karley Maier; Lauren Rust; Charlene Kupara; Mark Woods | Organic Chemistry; Inorganic Chemistry; Stereochemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c338c1658ec5f7e54c395e/original/diastereoselective-synthesis-of-alpha-aryl-substituted-ln-dota-chelates-from-achiral-starting-materials-by-deracemization-under-mild-conditions.pdf |
6161d6b3fb86190a01f2d967 | 10.26434/chemrxiv-2021-dlczq | Synthesis of (–)-Kopsifoline A and (+)-Kopsifoline E | We report the first total synthesis of (–)-kopsifoline A and (+)-kopsifoline E. Our synthetic strategy features a biogenetically inspired regioselective C17-functionalization of a versatile intermediate containing the pentacyclic core of aspidosperma alkaloids. While this advance intermediate provides (–)-kopsifoline D via C3–C21 bond formation, regioselective C17-boronation of its indoline substructure prior to introduction of the F-ring enables access to (–)-kopsifoline A and (+)-kopsifoline E. The vinylogous urethane substructure of the key intermediate was critical in C17-boronation over a competing C7-boronation in related indole derived substrates. After oxidation of the C17–B bond to introduce the C17-ether, the C3–C21 bond of the targets is secured under the Mitsunobu reaction conditions with the vinylogous urethane as the nucleophilic component. | In-Soo Myeong; Nadide Hazal Avci; Mohammad Movassaghi | Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6161d6b3fb86190a01f2d967/original/synthesis-of-kopsifoline-a-and-kopsifoline-e.pdf |
660bc13de9ebbb4db92c99b9 | 10.26434/chemrxiv-2024-77p4z | Azaacene Diradicals Based on Non-Kekulé Meta- Quinodimethane | Non-Kekulé quinoidal azaacences m-A (1a,b) were synthesized and compared to their para- and ortho-quinodimethane analogues. m-A display high diradical characters (1b: y0 = 0.88) due to their meta-quinodimethane (m-QDM) topology. Electron paramagnetic (EPR), nuclear magnetic resonance (NMR) spectroscopies and supraquantum interference device (SQUID) measurements in combination with quantum-chemical calculations revealed singlet ground states for m-A with singlet-triplet gaps ΔEST (0.13-0.25 kcal mol-1) and thermally populated triplet states. These non-Kekulé structures are void of zwitterionic character and possess record high two-photon absorption cross sections over a broad spectral range in the near-infrared. | Kathleen Fuchs; Nils Oberhof; Gabriel Sauter; Audrey Pollien; Kerstin Brödner; Frank Rominger; Jan Freudenberg; Andreas Dreuw; Petra Tegeder; Uwe H. F. Bunz | Organic Chemistry; Materials Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660bc13de9ebbb4db92c99b9/original/azaacene-diradicals-based-on-non-kekule-meta-quinodimethane.pdf |
61826074ef38c0573e65443f | 10.26434/chemrxiv-2021-h1kw2-v2 | Site correlations, capacitance, and polarizability from protein protonisation fluctuations | We generalize the Kirkwood-Shumaker theory of protonisation fluctuation for an anisotropic distribution of dissociable charges on a globular protein. The fluctuations of the total charge and the total dipole moment, in contrast to their average values, depend on the same proton occupancy correlator, thus exhibiting a similar dependence also on the solution pH. This has important consequences for the Kirkwood-Shumaker interaction and its dependence on the bathing solution conditions. | Anže Božič; Rudolf Podgornik | Physical Chemistry; Biophysical Chemistry | CC BY 4.0 | CHEMRXIV | 2021-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61826074ef38c0573e65443f/original/site-correlations-capacitance-and-polarizability-from-protein-protonisation-fluctuations.pdf |
67c008336dde43c908ac81a9 | 10.26434/chemrxiv-2025-5733v | Amino-substituted 1,3-diazaazulenes: Synthesis, structural studies, reactivity, and photophysical properties | We report a facile method for the functionalization of 1,3-diazaazulene core at C4, C6 and C8 positions via regioselective bromination and subsequent substitution with amine nucleophiles. Both steps can be controlled to enable selective mono-, di- or trisubstitution at C4, C6 or C8. Crystallographic studies revealed significant distortion from planarity in the aromatic core of the highly substituted 2,4,6,8-tetra-amino-1,3-diazaazulenes, further confirmed by DFT. The tetra-aminosubstituted diazaazulenes displayed unusual hydrolytic reactivity in acidic media, a reaction that is rare with aminobenzenes and appears to be promoted in this case by structural distortion. The combinatorial functionalization of 1,3-diazaazulene resulted in soft-tunable optical properties observed in both solution and PMMA films. Strong low-energy absorptions (ε = 11800–38500 M⁻¹·cm⁻¹), arise from π→π* transitions, as supported by our CC2 calculations. Consequently, the fluorescence relaxation mechanism involves a π*→π transition mixed with charge transfer, producing emission spanning from deep blue to yellow (λem_max = 428–535), with a quantum yield reaching 38%. We anticipate that the modular synthesis, tunable substitution patterns, and consequent modulation of both reactivity as well as photophysical properties, renders the 1,3-diazaazulene core an intriguing molecular platform for a variety of applications. | Teppo Leino; Anton Bannykh; Toni Eskelinen; Andrey Belyaev; Petri Pihko | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c008336dde43c908ac81a9/original/amino-substituted-1-3-diazaazulenes-synthesis-structural-studies-reactivity-and-photophysical-properties.pdf |
61c43de57f367eae915d2d43 | 10.26434/chemrxiv-2022-15r0h-v2 | Synthetic Studies with the Brevicidine and Laterocidine Lipopeptide Antibiotics Including Analogues with Enhanced Properties and in vivo Efficacy | Brevicidine and laterocidine are two recently discovered lipopeptide antibiotics with promising antibacterial activity. Possessing a macrocyclic core, multiple positive charges, and a lipidated N-terminus, these lipopeptides exhibit potent and selective activity against Gram-negative pathogens, including polymyxin-resistant isolates. Given the low amounts of brevicidine and laterocidine accessible by fermentation of the producing microorganisms, synthetic routes to these lipopeptides present an attractive alternative. We here report the convenient solid-phase syntheses of both brevicidine and laterocidine and confirm their potent anti-Gram-negative activities. The synthetic routes developed also provide convenient access to novel structural analogues of both brevicidine and laterocidine that display improved hydrolytic stability while maintaining potent antibacterial activity in both in vitro assay and in vivo infection models. | Karol Al-Ayed; Ross D. Ballantine; Michael Hoekstra; Samantha Bann; Charlotte Wesseling; Alexander Bakker; Zheng Zhong; Yongxin Li; Mario van der Stelt; Stephen Cochrane; Nathaniel Martin | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Natural Products | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c43de57f367eae915d2d43/original/synthetic-studies-with-the-brevicidine-and-laterocidine-lipopeptide-antibiotics-including-analogues-with-enhanced-properties-and-in-vivo-efficacy.pdf |
60c745f3ee301c241ac793fd | 10.26434/chemrxiv.10294826.v1 | Synthesis of Vitisin A & D: Thermal Isomerization Enabled by a Persistent Radical Equilibrium | The total synthesis of oligomer natural products derived from resveratrol has been achieved through a putative biogenetic bond migration from a presumed common intermediate in a divergent biosynthetic pathway. | Kevin Romero; Mitchell Keylor; Markus Griesser; Xu Zhu; Ethan Strobel; Derek Pratt; Corey Stephenson | Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745f3ee301c241ac793fd/original/synthesis-of-vitisin-a-d-thermal-isomerization-enabled-by-a-persistent-radical-equilibrium.pdf |
60c73fdbbb8c1a7d1a3d9c1b | 10.26434/chemrxiv.7399271.v2 | Computational and Synthetic Investigation of Cationic Rearrangement in the Putative Biosynthesis of Justicane Triterpenoids | <div>
<div>
<div>
<p>A biomimetic cationic structural rearrangement of the
oleanolic acid framework is reported for the gram-scale synthesis
and structural reassignment of justicioside E aglycone. The
mechanism of the putative biosynthetic rearrangement is
investigated with kinetic, computational, and synthetic approaches.
The precursor to rearrangement was accessed through two strategic
advancements: (1) synthesis of a 1,3-diketone via oxidation of a β-silyl enone, and (2) diastereoselective 1,3-diketone reduction to form
a syn-1,3-diol using SmI2 with PhSH as a key additive.
</p>
</div>
</div>
</div> | Masha Elkin; Anthony Scruse; Aneta Turlik; Timothy Newhouse | Natural Products; Organic Synthesis and Reactions; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fdbbb8c1a7d1a3d9c1b/original/computational-and-synthetic-investigation-of-cationic-rearrangement-in-the-putative-biosynthesis-of-justicane-triterpenoids.pdf |
60c744b3337d6c8327e26e46 | 10.26434/chemrxiv.9879947.v1 | Water-Soluble Polymeric Carbon Nitride Colloidal Nanoparticles for Highly Selective Quasi-Homogeneous Photocatalysis | Heptazine-based
polymeric carbon nitrides (PCN) are well established as promising
photocatalysts for light-driven redox transformations. However, the activity of
these materials is hampered by their low surface area translating into low
concentration of active sites accessible for reactants. Herein, we report, for
the first time, a bottom-up preparation of PCN nanoparticles with a narrow size
distribution (~10±3 nm), which are fully soluble in water showing no gelation
or precipitation over several months, and allow carrying out photocatalysis
under <i>quasi</i>-homogeneous conditions.
The rate of selective (up to 100%) photooxidation of 4-methoxybenzyl alcohol to
4-methoxybenzaldehyde was enhanced by the factor of 6.5 as compared to
conventional solid PCN and was accompanied by simultaneous H<sub>2</sub>O<sub>2</sub>
production <i>via</i> reduction of oxygen.
The dissolved photocatalyst can be easily recovered and re-dissolved by simple
modulation of the ionic strength of the medium, without any loss of activity
and selectivity. This work thus establishes a new paradigm of easily operable <i>quasi-</i>homogeneous photocatalysis with PCN,
and opens up a route for other applications in which liquid aqueous operation
or processing of PCN is required. | Igor Krivtsov; Dariusz Mitoraj; Marina Ilkaeva; Mariana Sardo; Luís Mafra; Christof Neumann; Andrey Turchanin; Chunyu Li; Benjamin Dietzek; Robert Leiter; Johannes Biskupek; Ute Kaiser; Changbin Im; Björn Kirchhoff; Timo Jacob; Radim Beranek | Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744b3337d6c8327e26e46/original/water-soluble-polymeric-carbon-nitride-colloidal-nanoparticles-for-highly-selective-quasi-homogeneous-photocatalysis.pdf |
60c7476ebb8c1a68153daa78 | 10.26434/chemrxiv.11635929.v1 | Discovery of Novel Chemical Reactions by Deep Generative Recurrent Neural Network | Here, we report an application of Artificial Intelligence techniques to generate novel chemical reactions of the given type. A sequence-to-sequence autoencoder was trained on the USPTO reaction database. Each reaction was converted into a single Condensed Graph of Reaction (CGR), followed by their translation into on-purpose developed SMILES/GGR text strings. The autoencoder latent space was visualized on the two-dimensional generative topographic map, from which some zones populated by Suzuki coupling reactions were targeted. These served for the generation of novel reactions by sampling the latent space points and decoding them to SMILES/CGR.<br /> | William Bort; Igor I. Baskin; Pavel Sidorov; Gilles Marcou; Dragos Horvath; Timur Madzhidov; Alexandre Varnek; Timur Gimadiev; Ramil Nugmanov; Artem Mukanov | Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7476ebb8c1a68153daa78/original/discovery-of-novel-chemical-reactions-by-deep-generative-recurrent-neural-network.pdf |
67b5d3746dde43c908923343 | 10.26434/chemrxiv-2025-8kfrc | Divergent Organomagnesium Reactivity of Rigid, Dinucleating Naphthyridine Ligands: Subtle Changes with Big Impact | We report the synthesis and characterisation of the naphthyridine-based dippDAMN and dippNDC ligands, bearing pendant secondary amine and amide donors, respectively. We additionally report their deprotonation chemistry and reactivity with dialkylmagnesium and Grignard reagents. The Grignard reactions yield structurally distinct LMg2Cl2·(THF)n complexes, with the dippNDC-based complex exhibiting reduced steric strain from the ligand around the Mg2Cl2 core. Comparison of the steric profiles of the LMg2Cl2·(THF)n complexes reveals that this reduced steric strain stems from the difference in binding modes of the ligands, which in the dippNDC case points the bulk of sterically demanding substituents away from the Mg2Cl2 core. Reactivity of the ligands with Mg(n-Bu)2 shows divergent outcomes: dippDAMN forms the LMg2(n-Bu)2·(THF)2 complex cleanly, whereas dippNDC produces paramagnetic species via Mg–C homolysis, triggering radical reactivity which results in ligand butylation and dimerisation. These findings underscore the unique steric and electronic features of dimagnesium complexes supported by rigid, dinucleating naphthyridine ligands, highlighting how seemingly subtle variations in ligand architecture can profoundly influence coordination chemistry and reactivity. | Errikos Kounalis; Marieke M. Broekman; Puck Uyttewaal; Martin Lutz; Daniel L. J. Broere | Organometallic Chemistry; Coordination Chemistry (Organomet.); Ligand Design; Main Group Chemistry (Organomet.) | CC BY 4.0 | CHEMRXIV | 2025-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b5d3746dde43c908923343/original/divergent-organomagnesium-reactivity-of-rigid-dinucleating-naphthyridine-ligands-subtle-changes-with-big-impact.pdf |
643f3d4283fa35f8f6dfadaa | 10.26434/chemrxiv-2023-pxb4v-v2 | Sequential bond dissociation energies of (Th(CO)x)+,x = 1-6: Quantum computational studies alternative approach. The capabilities of mass-spectrometry in the determination of molecule geometry | The calculation problem of bond-dissociation energy BDE((CO)x-1Th+-CO), x = 1-6 was solved using the fundamental law of nature determining the dependence of chemical bond dissociation energy on its length. The recommended experimental values from literature are as follows bond dissociation energies BDE(Th+-CO)= 0.940.06 eV, BDE((CO)Th+-CO)=1.050.09 eV, BDE((CO)2Th+-CO)=1.090.05 eV, BDE((CO)3Th+-CO)=0.820.07 eV, BDE((CO)4Th+-CO)=0.630.05 eV, BDE((CO)5Th+-CO)=0.700.05 eV. The theoretical data calculated in this article are 0.934 eV, 1.056 eV, 1.082 eV, 0.82 eV, 0.634 eV, 0.708 eV correspondingly which is in good agreement with the literature. For the first time it was shown that experimental values of bond-dissociation energies, obtained with mass-spectrometry, can be successfully utilized in the calculations of the geometrical properties of molecules. The carried out calculations for thorium hexacarbonyl cation Th(CO)6+ determine its structure as tetragonal bipyramid. The found bond length values r((CO)x-1 Th+-CO) are 2.414 A and 2.444 A for equatorial and axial bonds correspondingly. | Adel iakubov | Theoretical and Computational Chemistry; Physical Chemistry; Quantum Computing; Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643f3d4283fa35f8f6dfadaa/original/sequential-bond-dissociation-energies-of-th-co-x-x-1-6-quantum-computational-studies-alternative-approach-the-capabilities-of-mass-spectrometry-in-the-determination-of-molecule-geometry.pdf |
6182da0af9f05b33d5eb7fc5 | 10.26434/chemrxiv-2021-zlxxf | Tetra(hetero)arylated Cyclopentadienone Iron Tricarbonyl Complexes for Noble Metal-free Photocatalytic Hydrogen Generation | A versatile method for the straightforward synthesis of rarely known tetra(hetero)arylated cyclopentadienone iron tricarbonyl complexes 3a-3j is presented. In a [2+2+1]-cycloaddition reaction, a series of di(hetero)arylated ethynylenes 1a-1j are reacted with iron pentacarbonyl to yield the corresponding “Knölker-type” complexes, which bear substituents of different electronic nature. This type of iron complexes is active in photocatalytic hydrogen evolution reaction and the influence of the substituents on the catalytic activity was investigated. | Peter Baeuerle; Saskia Riediger; Wolfgang Weigand; Philipp Buday | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Photocatalysis; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6182da0af9f05b33d5eb7fc5/original/tetra-hetero-arylated-cyclopentadienone-iron-tricarbonyl-complexes-for-noble-metal-free-photocatalytic-hydrogen-generation.pdf |
670d493451558a15ef0e3e9f | 10.26434/chemrxiv-2024-rgcw6-v2 | Pharmacological Evaluation of Enantiomers of AZ11645373 against the P2X7 Receptor | The P2X purinergic receptor 7 (P2X7) has an essential role in inflammation, innate immunity, tumor progression, neurodegenerative diseases, and several other diseases, leading subsequently to the development of P2X7 modulators. AZ11645373 is a frequently studied P2X7 antagonist tool com-pound, but always as a racemic mixture. Racemic AZ11645373 can be separated, into its respective enantiomers by chiral chromatography, albeit in small batches, and these were stereochemically in-tact over a year later, by chiral HPLC analysis. On a higher scale, significant decomposition is ob-served. One of the enantiomers was crystallised as a palladium complex and its (R)-configuration was determined by single crystal X-ray diffraction, further confirmed, in solution, by vibrational circular dichroism. Biological studies demonstrated that both (S)- and (R)-forms were able to fully inhibit human P2X7, but (R)-AZ11645373 was more potent, with an IC50 of 32.9 nM. Contrary to its effect on human P2X7, (S)-AZ11645373 was ineffective on mouse P2X7, while the (R)-AZ11645373 enantiomer was a full antagonist. These results demonstrated that the antagonistic effects of racemic AZ11645373 are mainly due to its (R)-enantiomer. Site-directed mutagenesis and molecular dynam-ics simulations indicated that the (R)-enantiomer may form specific interactions with Phe95 and the antagonists bound to the other P2X7 monomers. Phe95 is situated at the channel pore and appears to be the pivotal molecular gateway between AZ11645373 allosteric binding and locking of the closed state of the P2X7 channel. All together, these structure-function relationships should be helpful for drug design of P2X7 modulators. | Andrew Mcgown; Nicolas Renault; Amélie Barczyk; Jordan Nafie; Luciano Barluzzi; Daniel Guest; Graham Tizzard; Simon Coles; David Leach; Daniel von Emloh; Lea Sutton; Kiera Bailey; Lewis Edmunds; Barnaby Greenland; Régis Millet; John Spencer; Xavier Dezitter | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Cell and Molecular Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670d493451558a15ef0e3e9f/original/pharmacological-evaluation-of-enantiomers-of-az11645373-against-the-p2x7-receptor.pdf |
64f58dd6dd1a73847f26196d | 10.26434/chemrxiv-2023-h0k1s | Metal-Free Photocatalysis at Charged Aqueous Interface: Boosting the Photocatalytic Oxidative Coupling of Arylamines to Azoaromatics under Ambient Conditions | Azoaromatics are an important class of functional organic molecules. Herein, we formulated a sustainable metal-free photocatalytic oxidative coupling of arylamines to azoaromatics at the charged aqueous interfaces (CAIs) of micelles with excellent yields (up to 100%) and selectivity (100%) under ambient air atmosphere. The micellar surface acts as an efficient scaffold to host both Eosin Y (EY) as photocatalyst (PC) and arylamines as substrates for a non-diffusive photoinduced electron transfer (PET) with a time constant of 0.3 ps. The present approach shows fast kinetics (4 h) and a broad substrate scope with only 0.6 mole% of PC. Our present approach outperforms all the previously reported catalytic methodologies. This remarkable boosting of the catalytic efficacy arises mainly due to the non-diffusive PET and modulation of redox potentials at the CAI. Being the most sustainable and first report on the aqueous phase synthesis of azo compounds, this work opens newer opportunities in the synthesis of azoaromatics. | Shivendra Singh; Vidhi Agarwal; Tridib K. Sarma; Tushar Kanti Mukherjee | Catalysis; Homogeneous Catalysis; Photocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f58dd6dd1a73847f26196d/original/metal-free-photocatalysis-at-charged-aqueous-interface-boosting-the-photocatalytic-oxidative-coupling-of-arylamines-to-azoaromatics-under-ambient-conditions.pdf |
60c750f80f50db7fa33976b1 | 10.26434/chemrxiv.13105571.v1 | Base-Mediated Generation of Ketenimines from Ynamides: [3+2] Annulation with Azaallyl Anions. | Under basic conditions and heat, ynamides can serve as precursor to ketenimines, whose synthetic potential is often hampered by their difficulty of acces. Herein, we report that they can undergo a [3+2] cycloaddition with 2-azaallyl anions, obtained from benzylimines under the same reaction conditions. This reaction between two highly reactive intermediates, both generated in situ from bench stable starting materials, gives access to various nitrogen-rich heterocycles. The reaction usually proceeds with excellent diastereoselectivity, in favor of the cis adduct. Deuteration experiments and DFT calculation helped rationalize the regio and stereo-selectivity of the process as well as the formation of side-products.<br /> | Agathe C. A. D’Hollander; Eugénie Romero; Kamsana Vijayakumar; Camille le Houérou; Pascal Retailleau; Robert H. Dodd; Bogdan I. Iorga; Kevin Cariou | Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750f80f50db7fa33976b1/original/base-mediated-generation-of-ketenimines-from-ynamides-3-2-annulation-with-azaallyl-anions.pdf |
6537ecacc3693ca99305be1c | 10.26434/chemrxiv-2023-qb4cx | Size Matters: Computational Insights into the Crowning of Noble Gas Trioxides | In pursuit of enhancing the stability of the highly explosive and shock-sensitive compound XeO3, we performed quantum chemical calculations to investigate its possible complexation with electron-rich crown ethers, including 9-Crown-3, 12-Crown-4, 15-Crown-5, 18-Crown-6, and 21-Crown-7, as well as their thio analogues. Furthermore, we expanded our study to other noble gas trioxides (NgO3), namely KrO3 and ArO3. The basis set superposition error (BSSE) corrected binding energies for these adducts range from -13.0 kcal/mol to -48.2 kcal/mol, which is notably high for σ-hole mediated non-covalent interactions. The formation of these adducts was observed to be more favorable with the increase in the ring size of the crowns and less favorable while going from XeO3 to ArO¬3. A comprehensive analysis by various computational tools such as the mapping of the electrostatic potential (ESP), Wiberg bond indices (WBIs), Bader’s theory of atoms-in-molecules (AIM), natural bond orbital (NBO) analysis, non-covalent interaction (NCI) plots, and the energy decomposition analysis (EDA) analysis revealed that the C-H….O interactions, as well as dispersion interactions play a pivotal role in stabilizing adducts involving larger crowns. A noteworthy outcome of our study is the revelation of a coordination number of 9 for xenon in the complex formed between XeO3 and the thio analogue of 18-Crown-6, which is higher than the largest number reported to date. | Soumya Ranjan Dash; Himanshu Sharma; Mrityunjay K Tiwari; Lutz Greb; Kumar Vanka | Theoretical and Computational Chemistry; Inorganic Chemistry; Bonding; Main Group Chemistry (Inorg.); Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6537ecacc3693ca99305be1c/original/size-matters-computational-insights-into-the-crowning-of-noble-gas-trioxides.pdf |
6718ef8212ff75c3a14c4735 | 10.26434/chemrxiv-2024-ntd50 | Density functional theory investigation of Stability and Reactivity in Au-Cu nanoclusters of type AumCun (m+n=13) | Pure and doped gold clusters have been of immense use in catalyzing reactions and assembling nano functional materials for various applications. In this work, we focus on stepwise doping of copper atoms in pure 13 atom gold clusters, thereby the cluster composition investigated is Aum Cun (m+n = 13). We employ the genetic algorithm ABCluster which uses the artificial bee colony (ABC) algorithm to model the various isomers of each cluster composition. We applied DFT functional PBE and LANL2DZ basis functions to model the potential energy surface of the clusters. The minimum energy isomer of each composition was then used to study various molecular properties like binding energy, second order difference in energy, vertical ionization energy, vertical electron affinity, HOMO-LUMO gap, second order difference in energy. Odd-even oscillations in the molecular properties reveal the competing shell closing stabilization between Cu and Au atoms. To compare the activity of the clusters in catalysis, adsorption studies of small molecules O2 and C2H2 were done. This work aims to study the entire range of Cu doped 13 atom Au cluster compositions. | PRADEEP KUMAR PAL; U Deva Priyakumar | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6718ef8212ff75c3a14c4735/original/density-functional-theory-investigation-of-stability-and-reactivity-in-au-cu-nanoclusters-of-type-aum-cun-m-n-13.pdf |
Subsets and Splits
No saved queries yet
Save your SQL queries to embed, download, and access them later. Queries will appear here once saved.