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60c7547f337d6c3366e28a5a | 10.26434/chemrxiv.11860824.v2 | Synthesis of Carboxamides Tranylcypromine Analogues as LSD1 (KDM1A) Inhibitors for AML | <p>Lysine-specific demethylase 1 (LSD1/KDM1A) oxidatively removes methyl groups from histone proteins and its aberrant activity has been correlated with cancers including acute myeloid leukemia (AML). We report a novel series of tranylcypromine analogues with a carboxamide at the 4-position of the aryl ring. These compounds, such as <b>5a</b> and <b>5b</b>, had potent submicromolar IC<sub>50</sub> values for the inhibition of LSD1 as well as cell proliferation in a panel of AML cell lines. The dose-dependent increase in cellular expression levels of H3K4me2, CD86, CD11b and CD14 supported a mechanism involving LSD1 inhibition. The <i>t</i>-butyl and ethyl carbamate derivatives of these tranylcypromines, although inactive in LSD1 inhibition, were of similar potency in cell-based assays with a more rapid onset of action. This suggests carbamates can act as metabolically labile tranylcypromine prodrugs with superior pharmacokinetics.</p> | Teresa Borrello; Chak Hin Tam; Manar Shafat; Stuart Rushworth; Kristian Bowles; Sarah Bailey; Simon Crabb; Graham Packham; Patrick J. Duriez; Pr. Ganesan; Hanae Benelkebir; Leonard Douglas | Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7547f337d6c3366e28a5a/original/synthesis-of-carboxamides-tranylcypromine-analogues-as-lsd1-kdm1a-inhibitors-for-aml.pdf |
66de59aa51558a15ef756feb | 10.26434/chemrxiv-2024-0z1gn | Physics-based Modeling in the New Era of Enzyme Engineering | Enzyme engineering techniques optimize enzymes to synthesize value-added chemicals, degrade environmental pollutants, and improve therapeutics. The field is entering a new era characterized by the increasing integration of computational strategies. While bioinformatics and artificial intelligence (AI) have been extensively applied to accelerate the screening of function-enhancing mutants, physics-based modeling methods, such as molecular mechanics and quantum mechanics, serve as essential complements in engineering objectives where setting up high-throughput screening is difficult or where a deep understanding of unknown physical principles is crucial. In this perspective, we discuss the enormous, untapped potential of physics-based modeling in guiding the next step of computational enzyme engineering. We first explore the paradigm of physics-based design principles wherein insights from natural, efficient enzymes are applied to recommend beneficial mutations in silico. We examine current development of high-throughput molecular modeling workflows that aid enzyme engineering campaigns through large-scale virtual applications of design principles. We then emphasize how physics-based modeling empowers AI techniques through enriching data expressiveness and interpretability. Finally, we proposed unmet challenges for the next step advancement of computational tools for enzyme engineering. | Christopher Jurich; Qianzhen Shao; Xinchun Ran; Zhongyue Yang | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Biocatalysis; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66de59aa51558a15ef756feb/original/physics-based-modeling-in-the-new-era-of-enzyme-engineering.pdf |
60c743ae337d6c9cede26c2e | 10.26434/chemrxiv.9413573.v1 | Ligand Assisted Volatilization and Thermal Stability of [(t-BuN=)2MoCl2]2 | Volatile molybdenum containing compounds have successfully been utilized for the atomic layer deposition of MoN<i><sub>x</sub></i>, MoO<sub>3</sub>, MoS<sub>2</sub>, and MoC<i><sub>x</sub></i>N<i><sub>y</sub></i>. Most of the reported volatile molybdenum containing compounds have been prepared via salt metathesis reactions of <i>bis</i>(<i>tert</i>-butylimido)-dichloromolybdenum(VI), with anionic nitrogen based ligands. Herein we describe the preparation of several adducts of [(<i>t</i>-BuN=)<sub>2</sub>MoCl<sub>2</sub>]<sub>2</sub> (<b>2</b>) <i>via</i> ligand exchange reactions with various neutral ligands, including both mono- and bidentate ethers, amines, and phosphines, as well as an <i>N</i>-heterocyclic carbene (NHC). These compounds have been characterized using NMR spectroscopy, elemental analysis, and the solid-state structures have been determined using single crystal X-ray crystallography. The volatility and thermal stability of all compounds have been assessed using TGA and DSC, showing that the coordinated ligands can improve the volatility, but in many cases the gas phase species reverts to <b>2</b>. This highlights a strategy for using coordinative ligands that are easily thermolyzed during evaporation and delivery yet improve the volatility of a key precursor. | Michael Land; Katherine Roberston; Sean Barry | Ligands (Inorg.); Reaction (Inorg.); Transition Metal Complexes (Inorg.); Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743ae337d6c9cede26c2e/original/ligand-assisted-volatilization-and-thermal-stability-of-t-bu-n-2mo-cl2-2.pdf |
6639d77291aefa6ce15c281a | 10.26434/chemrxiv-2024-ghf2g | Cloning instruments, model maintenance and calibration transfer | Most literature on the application of Non-Destructive Spectral Sensors (NDSS) reports proofs of concept limited to model calculation (calibration) and its application on a so-called independent data set (validation, or test). However, developing NDSS also requires proving that the performance obtained during this first validation remains valid when conditions change. This generic problem is referred to as robustness in chemometrics. When the measurement conditions change, the measured spectrum is subject to a deviation. The reproducibility of the model, and thus of the sensor, with respect to this deviation, defines its robustness. The application of NDSS involves a large number of processes, and thus deviation sources. Instrument cloning, between laboratory instruments or from a benchtop to an online device, is certainly the most concerning issue for deploying NDSS-based applications. This problem has been studied for many years in chemometrics, under the paradigm of calibration transfer, through geometric corrections of spectra, spectral spaces, or calibration model corrections. The same problem has been addressed in the machine learning community under the domain adaptation paradigm. Although all these issues have been addressed separately over the last twenty years, they all fall under the same topic, i.e., model maintenance under dataset shift. This paper aims to provide a vocabulary of concepts for formalizing the calibration model maintenance problem, reviewing recent developments on the subject, and categorizing prior work according to the proposed concepts. | Jean-Michel Roger; Valeria Fonseca-Diaz; Ramin Nikzad-Langerodi | Analytical Chemistry; Agriculture and Food Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6639d77291aefa6ce15c281a/original/cloning-instruments-model-maintenance-and-calibration-transfer.pdf |
67a4b571fa469535b941cb73 | 10.26434/chemrxiv-2025-sxgk7 | Revisiting Boron Cluster Dihydrogen Bonding: Improved Reference Energies and Benchmark of Localized Coupled Cluster and DFT Methods | Dihydrogen bonds involving boron clusters have gained significant attention in chemistry, biology, and medicine. The reference interaction energies of diH-norm and diH-linear datasets (J. Fanfrlík et al., ChemPhysChem 2020, 21, 2599), which include such bonds both in bent and linear configurations, have been re-evaluated at the gold level. This re-evaluation utilizes explicitly correlated MP2-F12 near the complete basis set limit, CCSD(F12*)/cc-pVQZ-F12, and a (T) correction from conventional CCSD(T)/haV{T,Q}Z calculations. Relative to the updated reference data, Fanfrlík's original reference shows very small root mean square deviations, resulting from significant error compensation between the [CCSD-MP2] and (T) high-level corrections. Furthermore, the revised reference is employed to assess the performance of various localized-orbital coupled-cluster approaches, such as PNO-LCCSD(T), DLPNO-CCSD(T1), and LNO-CCSD(T), at their respective “Normal”, “Tight”, “vTight”, and “vvTight” accuracy settings. For these methods, gradually increasing the basis set size and tightening the accuracy cutoffs improves their performance. For the dihydrogen bonds in diH-norm set, two cost-effective methods with no noticeable loss in accuracy are PNO-LCCSD(T)/Tight/haV{T,Q}Z and DLPNO-CCSD(T1)/TightPNO/CPS(6,7)/haV{T,Q}Z. On the other hand, for the diH-linear set, LNO-CCSD(T)/vTight/haV{T,Q}Z and DLPNO-CCSD(T1)/TightPNO/CPS(6,7)/haV{T,Q}Z are the recommended low-cost methods. Among the more economical density functional methods, r2SCAN-3c demonstrates remarkably good accuracy at a very cheap cost. Additionally, for hybrid and double-hybrid functionals, the incorporation of range separation significantly enhances performance. | Golokesh Santra | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a4b571fa469535b941cb73/original/revisiting-boron-cluster-dihydrogen-bonding-improved-reference-energies-and-benchmark-of-localized-coupled-cluster-and-dft-methods.pdf |
60c73d4b9abda26370f8b695 | 10.26434/chemrxiv.5487172.v1 | Mesoscopic gelation of chitosan and genipin at below critical concentrations | Genipin is increasingly used as a crosslinking agent for chitosans due to its low cytotoxicity as a naturally occurring extract of the plant <i>Gardenia jasminoides</i>. Genipin reacts with the primary amino groups of chitosan to form blue hydrogels. We studied the gelation kinetics of different chitosans varying in their properties (molar mass 34 000-213 000 g mol<sup>-1</sup>, degree of acetylation 9-20%) and genipin in detail. We found that critical sol-gel transition times obtained from dynamic light scattering were in good agreement with the results obtained by small deformation oscillatory rheometry and microviscosimetry at high concentrations of chitosan. However, at below critical concentrations, we found a second regime of gelation that followed the same Ross-Murphy's gelation kinetics. The macroscopic appearance of these samples was a suspension of weak gel-like particles that were sensitive to mechanical forces. We believe that the material is a mesoscopic gel, as described for other polymers. To the best of our knowledge, this is the first time that this phenomenon has been described for the gelling system of chitosan and genipin. | Christoph Engwer; Ronja Loy; Ioannis S. Chronakis; Ana C. Mendes; Francisco M. Goycoolea | Aggregates and Assemblies; Biological Materials; Elastic Materials; Polyelectrolytes - Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2017-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d4b9abda26370f8b695/original/mesoscopic-gelation-of-chitosan-and-genipin-at-below-critical-concentrations.pdf |
60c757a5702a9b67d918cb29 | 10.26434/chemrxiv.14442767.v1 | Snapshots of Ce70 Toroid Assembly from Solids and Solution | Crystallization at the solid-liquid interface is difficult to spectroscopically observe and therefore
challenging to understand and ultimately control at the molecular level. The Ce70-torroid
formulated [CeIV70(OH)36(O)64(SO4)60(H2O)10]
4-
, part of a larger emerging family of MIV70-
materials (M=Zr, U, Ce), presents such an opportunity. We have elucidated assembly mechanisms
by X-ray scattering (small-angle scattering and total scattering) of solutions and solids, as well as
crystallizing and identifying fragments of Ce70 by single-crystal X-ray diffraction. Fragments
show evidence for templated growth (Ce5, [Ce5(O)3(SO4)12]
10-
) and modular assembly from
hexamer (Ce6) building units (Ce13, [Ce13(OH)6(O)12(SO4)14(Η2Ο)14]
6- and Ce62,
[Ce62(OH)30(O)58(SO4)58]
14-
). Ce62, an almost complete ring, precipitates instantaneously in the
presence of ammonium cations as two torqued arcs that interlock by hydrogen boding through
NH4
+, which can also be replaced by other cations, demonstrated with CeIII. Room temperature
rapid assembly of both Ce70 and Ce62, respectively, by addition of Li+ and NH4
+, along with ion?exchange and redox behavior, invite exploitation of this emerging material family in
environmental and energy applications. | Ian Colliard; Jessica C. Brown; Dylan B. Fast; Ashleigh Sockwell; Amy Hixon; May Nyman | Lanthanides and Actinides; Supramolecular Chemistry (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757a5702a9b67d918cb29/original/snapshots-of-ce70-toroid-assembly-from-solids-and-solution.pdf |
612c53de42198e8065678641 | 10.26434/chemrxiv-2021-rfd1m | Visible light switching of metallosupramolecular assemblies | A photoswitchable ligand and palladium(II) ions form a dynamic mixture of self-assembled metallosupramolecular structures. The photoswitching ligand is an ortho-fluoroazobenzene with appended pyridyl groups. The E-isomer is combined with palladium(II) salts affords a double-walled triangle with composition [Pd3L6]6+ and a distorted tetrahedron [Pd4L8]8+(1:2 ratio at 298 K). Irradiation with 410 nm light generates a photostationary state with ~80% of the E-isomer of the ligand which results in the selective disassembly of the tetrahedron, the more thermodynamically stable structure, and the formation of the triangle, the kinetic product. The triangle is then slowly transformed back into the tetrahedron over 2 days at 333 K. The Z-isomer of the ligand does not form any well-defined structures and has a thermal half-life of 25 days at 298K. This approach shows how a thermodynamically preferred self-assembled structure can be reversibly pumped to a kinetic trap by small perturbations of the isomer distribution using non-destructive visible light. | Aaron Kennedy; Ray DiNardi; Lucy Fillbrook; William Donald; Jonathon Beves | Physical Chemistry; Organic Chemistry; Inorganic Chemistry; Photochemistry (Org.); Supramolecular Chemistry (Inorg.); Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612c53de42198e8065678641/original/visible-light-switching-of-metallosupramolecular-assemblies.pdf |
6719cde083f22e4214f7e067 | 10.26434/chemrxiv-2024-s2w98 | Self-assembly of a Triblock Copolymer in the Presence of a Rigid Conjugated Polyelectrolyte | The properties of conducting polymers are strongly influenced by structural changes induced by long-range order, which can be achieved using block copolymers that self-assemble into crystalline structures. These blends result in unique mesophases distinct from the pure components, with self-assembly behavior modulated by solution conditions and polymer architectures. High-throughput small angle x-ray scattering data of aqueous Pluronic P123 (PEO20- PPO70-PEO20) and conjugated polyelectrolyte poly[3-(potassium-4-butanoate) thiophene-2,5-diyl] (PPBT) blends at various concentrations and temperatures were automatically classified into phase maps by autophasemap, an unsupervised statistical analysis algorithm. The outlined phase boundaries revealed that adding PPBT to high P123 concentrations induced a transition from cubic-ordered spherical micelles to hexagonally packed cylindrical micelles. Shear alignment via rheological small angle neutron scattering of the blends produced monolithic oriented cubic and hexagonal crystal gels. These insights into the self-assembly of conductive polymer blends will aid in the design of soft materials with tunable structural and electronic properties. | Karen Li; Kiran Vaddi; Soenke Seifert; Jitendra Mata; Lilo D Pozzo | Materials Science; Polymer Science; Nanostructured Materials - Materials; Conducting polymers | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6719cde083f22e4214f7e067/original/self-assembly-of-a-triblock-copolymer-in-the-presence-of-a-rigid-conjugated-polyelectrolyte.pdf |
60c74354ee301c2d3cc78f92 | 10.26434/chemrxiv.8259011.v2 | Tracking the Metal-Centered Triplet in Photoinduced Spin Crossover of Fe(phen)32+ with Tabletop Femtosecond M-edge XANES | <p>Fe(II) coordination complexes are
promising alternatives to Ru(II) and Ir(III) chromophores for photoredox
chemistry and solar energy conversion, but rapid deactivation of the initial
metal-to-ligand charge transfer (MLCT) state to low-lying (d,d) states limits
their performance. Relaxation to a <sup>5</sup>T<sub>2g</sub>
state is postulated to occur via a metal-centered triplet state, but this
mechanism remains controversial. We use
femtosecond extreme ultraviolet (XUV) transient absorption spectroscopy to
measure the excited-state relaxation of Fe(phen)<sub>3</sub><sup>2+</sup> and conclusively
identify a <sup>3</sup>T intermediate that forms in 170 fs and decays to a
vibrationally hot <sup>5</sup>T<sub>2g</sub> state in 40 fs. A coherent vibrational wavepacket with a period of 250 fs and damping time of 0.66 ps is observed on the <sup>5</sup>T<sub>2g</sub> surface, and the spectrum of this oscillation serves as a fingerprint for the Fe-N symmetric stretch. The results show that the shape of the M<sub>2,3</sub>-edge X-ray absorption near edge structure (XANES) spectrum is sensitive to the electronic structure of the metal center, and the high spin sensitivity, fast time resolution, and tabletop convenience of XUV transient absorption make it a powerful tool for studying the complex photophysics of transition metal complexes.<br /></p> | Kaili Zhang; Ryan Ash; Gregory S Girolami; Josh Vura-Weis | Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.); Theory - Computational; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74354ee301c2d3cc78f92/original/tracking-the-metal-centered-triplet-in-photoinduced-spin-crossover-of-fe-phen-32-with-tabletop-femtosecond-m-edge-xanes.pdf |
6752c530085116a1338f2297 | 10.26434/chemrxiv-2024-w6kxl-v2 | Molecular simulation study of all-silica zeolites for the adsorptive removal of airborne chloroethenes | Chloroethenes are produced and consumed in various industrial processes. As the release of these compounds into air, water, and soils can pose significant risks to human health and the environment, different techniques have been exploited to prevent or remediate chloroethene pollution. Although several previous experimental and computational studies investigated the removal of chloroethenes using zeolite adsorbents, their structural diversity in terms of pore size and pore topology has hardly been explored so far. In this work, molecular simulations using validated empirical force field parameters were used to study the gas-phase adsorption of chloroethenes in 16 structurally distinct zeolite frameworks. As all these frameworks are synthetically accessible in high-silica form, the simulations used purely siliceous zeolite models. In the most relevant concentration range (0.1 to 10 ppm by volume), substantial uptakes of tri- and tetrachloroethene were computed for several zeolite frameworks, prominently EUO, IFR, MTW, MOR, and BEA. In contrast, vinyl chloride uptakes were always too low to be of practical relevance for adsorptive removal. For selected frameworks, simulation snapshots were analyzed to investigate the impact of pore shape and, at higher uptakes, guest-guest interactions on the adsorption behavior. Hence, this study not only identifies zeolites that should be prioritized in future investigations, but also contributes to the microscopic understanding of chloroethene adsorption in crystalline microporous materials. | Michael Fischer | Theoretical and Computational Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6752c530085116a1338f2297/original/molecular-simulation-study-of-all-silica-zeolites-for-the-adsorptive-removal-of-airborne-chloroethenes.pdf |
640bf914b5d5dbe9e811d15d | 10.26434/chemrxiv-2023-7ckb1 | Charge Inversion Ion/Ion Reactions for Separations of Isomers by Ion Mobility/Mass Spectrometry: Oligosaccharides | Various ion mobility-based separation techniques and instruments have been recently developed to increase the operational resolution of ion mobility separations, especially of isomers and isobars. In addition to developments in instrumentation, different covalent and noncovalent derivatization techniques have helped achieve effective separations by magnifying minor differences in collision cross section. Among these methodologies is host-guest complex formation and, a new development presented herein, charge inversion ion-ion reactions coupled to ion mobility separations. We used these methods to enable formation of complexes between isomeric deprotonated oligosaccharides and alkaline earth metals (in solution) and alkaline earth metal-tris-phenanthroline complexes (in vacuo), observing shifts in ion mobility arrival times for the charge inversion reaction products as well as unique mobility fingerprints indicative of high resolution separations of anomers of disaccharides. For example, we have demonstrated separations between reducing disaccharides such as lactose and lactulose and nonreducing disaccharides. We also observed separations based on the hexose/pentose configurations of the isomers. These results suggest the potential for ion/ion reactions to enable isomer separation of biomolecules from various compound classes using IM-MS. | Ankita Gurav; Ian Webb | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640bf914b5d5dbe9e811d15d/original/charge-inversion-ion-ion-reactions-for-separations-of-isomers-by-ion-mobility-mass-spectrometry-oligosaccharides.pdf |
6685434a5101a2ffa846343d | 10.26434/chemrxiv-2024-z1mm2 | Methylated Arene Products Establish Ground State Electron Transfer from KOtBu in the Reductive Activation of Aryl Halides | In the presence of appropriate aryl halides, electron transfer occurs from KOtBu to form tert-butoxyl radicals that can fragment into methyl radicals. In support of electron transfer, we report the first observation of methylated arene products, arising from attack by these methyl radicals. When KOtBu is replaced by KOC(Et)3, ethyl radicals are correspondingly trapped. The conversion of KOtBu to methyl radicals happens in the presence of haloarene substrates. The reactions are not light-dependent. We illustrate the scope of the KOtBu-promoted aryl radical formation with a range of substrates that includes haloanthracenes, dihaloanthracenes, a dihalonaphthalene, and a dihalobenzene. | Kenneth Clark; Alexander Stewart; Seb Tyerman; Krystian Kolodziejczak; Laura Evans; Craig M Robertson; Alan R Kennedy; Tell Tuttle; John Murphy | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6685434a5101a2ffa846343d/original/methylated-arene-products-establish-ground-state-electron-transfer-from-k-ot-bu-in-the-reductive-activation-of-aryl-halides.pdf |
6245d293739db165481f77f2 | 10.26434/chemrxiv-2022-bj42g | Ring-Opening Fluorination of Isoxazoles | A ring-opening fluorination of isoxazoles has been developed. By treating isoxazoles with an electrophilic fluorinating agent (Selectfluor®), fluorination followed by deprotonation leads to tertiary fluorinated carbonyl compounds. The present method features mild reaction conditions, good functional group tolerance, and simple experimental procedure. Diverse transformations of the resulting α-fluorocyanoketones were also demonstrated, furnishing a variety of fluorinated compounds. | Masaaki Komatsuda; Hugo Ohki; Hiroki Kondo Jr.; Ayane Suto; Junichiro Yamaguchi | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2022-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6245d293739db165481f77f2/original/ring-opening-fluorination-of-isoxazoles.pdf |
60e46971338e926b7e086d0f | 10.26434/chemrxiv-2021-cvl69 | One-pot synthesis of benzo[c]chromene-6-ones via domino Suzuki-Miyaura cross-coupling followed by oxidative lactonization catalyzed by in situ generated palladium nanoparticles under aqueous-aerobic condition | Benzo[c]chromene-6-ones are the very significant class of lactones which constitute core structural subunits of various biologically and pharmaceutically active molecules and some important natural products.Importance of 6H-benzo[c]chromene-6-ones for its potential therapeutic and pharmaceutical properties, has attracted researchers over the decades towards the development of more convenient and straight forward route for the synthesis of these molecules.
We have efficiently constructed a novel method for the one-pot synthesis of benzo[c]chromenones and their derivatives by palladium catalyzed domino Suzuki-Miyaura cross coupling and oxidative lactonization under aqueous-aerobic condition. We started our investigation by optimizing the reaction condition.
| Jayanta Kumar Ray; Yasin Nuree | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Supramolecular Chemistry (Org.); Drug Discovery and Drug Delivery Systems; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e46971338e926b7e086d0f/original/one-pot-synthesis-of-benzo-c-chromene-6-ones-via-domino-suzuki-miyaura-cross-coupling-followed-by-oxidative-lactonization-catalyzed-by-in-situ-generated-palladium-nanoparticles-under-aqueous-aerobic-condition.pdf |
60c74a954c8919a95cad3278 | 10.26434/chemrxiv.12145413.v2 | Decoding the Chemical Bond—On the Connection between Probability Density Analysis, QTAIM, and VB Theory | Classification of bonds is essential for understanding and predicting the reactivity of chemical compounds. This classification mainly manifests in the bond order and the contribution of different Lewis resonance structures. Here, we outline a first principles approach to obtain these orders and contributions for arbitrary wave functions in a manner that is both, related to the quantum theory of atoms in molecules and consistent with valence bond theory insight: the Lewis structures arise naturally as attractors of the all-electron probability density |Ψ|². Doing so, we introduce a valence bond weight definition that does not collapse in the basis set limit. | Leonard Reuter; Arne Lüchow | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a954c8919a95cad3278/original/decoding-the-chemical-bond-on-the-connection-between-probability-density-analysis-qtaim-and-vb-theory.pdf |
64626bfafb40f6b3eea41480 | 10.26434/chemrxiv-2023-frwx6 | Nitrilium Ion Trapping as a Strategy to Access Structurally Diverse Heterobiaryl-containing Peptide Macrocycles | Biaryl and heterobiaryl-containing cyclic peptides represent promising scaffolds in the development of bioactive molecules. The incorporation of heterobiaryl motifs continues to pose synthetic challenges, which is partially due to the difficulties in effecting late-stage metal-catalyzed cross-couplings. We report a new strategy to form heterobiaryls that is based on trapping nitrilium ions. The sequence is exemplified using oxadiazole- and oxazole-containing biaryl linkages. NMR analysis and molecular dynamics simulations reveal structural control elements common to each member of the heterobiaryl containing peptide family in this study. Strategic substitutions on the C-terminal aminobenzoic acid moiety paired with installation of oxadiazole or oxazole heterobiaryl backbone linkages allow for the modulation of peptide backbone conformation, which should assist efforts to optimize the biophysical properties of peptide macrocycles. | Andrei Yudin; Matthew Diamandas; Nicholas Heller | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2023-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64626bfafb40f6b3eea41480/original/nitrilium-ion-trapping-as-a-strategy-to-access-structurally-diverse-heterobiaryl-containing-peptide-macrocycles.pdf |
60c756a9702a9b04f918c941 | 10.26434/chemrxiv.14292311.v1 | Direct Conversion of Alcohols to Long-Chain Hydrocarbons via Tandem Dehydrogenation-Decarbonylative Olefination | <p>Design of active and selective supported catalysts is
critical for developing new tandem processes for upgrading biomass-derived
alcohols. Hydrogen-free upgrading alcohols to liquid hydrocarbons is desirable
for producing drop-in fuel
substitutes, but direct and atom-economical processes are yet to be
reported. Here we report a novel alcohol upgrading and<b> </b>deoxygenation cascade that
meets these criteria. This hydrogen-free cascade is catalyzed by
multifunctional Pd catalysts, whose supports feature a range of acid-base
properties: primarily basic MgO, acidic Al<sub>2</sub>O<sub>3</sub> and Mg-Al
hydrotalcite (HT) with a combination of Lewis acidic and basic sites. The
impact of support selection on selectivity offers insights into
the design principles for next-generation catalysts for this process and related
transformations.</p> | Diana Ainembabazi; Jonathan Horlyck; Darren Dolan; Adam Lee; Karen Wilson; Adelina Voutchkova-Kostal | Base Catalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756a9702a9b04f918c941/original/direct-conversion-of-alcohols-to-long-chain-hydrocarbons-via-tandem-dehydrogenation-decarbonylative-olefination.pdf |
6630430d21291e5d1d0ce133 | 10.26434/chemrxiv-2024-7cbk2 | Acoustic Loudness Factor: An Experimental Parameter for Benchmarking Small Molecule Photoacoustic Probes | Photoacoustic imaging (PAI) is an emerging biomedical imaging modality with promise as a point-of-care diagnostic. This imaging modality relies on optical excitation of an absorber followed by production of ultrasound through the photoacoustic effect, resulting in high spatial resolution with imaging depths in the cm range. Although fluorescence brightness has guided the design and optimization of improved fluorophores for fluorescence imaging, no such benchmarking parameter exists for PAI. Consequently, there is no consensus on rational design strategies to improve photoacoustic signal from small molecule dyes. Herein, we disclose the discovery of the first benchmarking parameter for small molecule dye performance in PAI, which we term the acoustic loudness factor (ALF). Importantly, ALF can predict PAI performance without the need for access to photoacoustic instrumentation. ALF enables the prediction of PAI performance for common dye classes and can be used to guide the systematic evaluation of design strategies to enhance PAI performance. Lastly, we demonstrate that enhancements in ALF are directly translatable to in vivo PAI. Akin to the use of fluorescence brightness in fluorophore design and evaluation for fluorescence imaging, we anticipate that ALF will guide the design and evaluation of improved probes for PAI. | Frederik Brøndsted; Harry Shield; Jerimiah Moore; Xinqi Zhou; Yuan Fang; Cliff Stains | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6630430d21291e5d1d0ce133/original/acoustic-loudness-factor-an-experimental-parameter-for-benchmarking-small-molecule-photoacoustic-probes.pdf |
63d9b65629feaa447500c493 | 10.26434/chemrxiv-2023-k4z34 | Lithium-mediated mechanochemical cyclodehydrogenation | Cyclodehydrogenation is an essential synthetic method for the preparation of polycyclic aromatic hydrocarbons, polycyclic heteroaromatic compounds, and nanographenes. Among the many examples, anionic cyclodehydrogenation using potassium(0) has attracted synthetic chemists because of its irreplaceable reactivity and utility in obtaining rylene structures from binaphthyl derivatives. However, existing methods are difficult to use in terms of practicality, pyrophoricity, and lack of scalability and applicability. Herein, we report the development of a lithium(0)-mediated mechanochemical anionic cyclodehydrogenation reaction for the first time. This reaction could be easily performed using a conventional and easy-to-handle lithium(0) wire at room temperature, even under air, and the reaction of 1,1-binaphthyl is complete within 30 min to afford perylene in 94% yield. Using this novel and user-friendly protocol, we investigated substrate scope, reaction mechanism, and gram-scale synthesis. As a result, remarkable applicability and practicality over previous methods, as well as limitations, were comprehensively studied by computational studies and NMR analysis. Furthermore, we demonstrated two-, three-, and five-fold cyclodehydrogenations for the synthesis of novel nanographenes. In particular, quinterrylene ([5]rylene or pentarylene), the longest non-substituted molecular rylene, was synthesized for the first time. | Kanna Fujishiro; Yuta Morinaka; Yohei Ono; Tsuyoshi Tanaka; Lawrence Scott; Hideto Ito; Kenichiro Itami | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d9b65629feaa447500c493/original/lithium-mediated-mechanochemical-cyclodehydrogenation.pdf |
62edf640fad485af03637440 | 10.26434/chemrxiv-2022-7wk0b | Environmental health, racial/ethnic health-disparity, and climate impacts of freight transport in the United States | Atmospheric emissions from freight transportation contribute to human health and climate damage. Here, we quantify and compare three environmental impacts from inter-regional freight transportation in the contiguous United States: mortality attributable to PM2.5 air pollution, racial-ethnic disparities in mortality from PM2.5, and CO2 emissions. We compare all major transportation modes (truck, rail, barge, aircraft) and all major inter-regional routes (~30,000 routes). Our study is the first to comprehensively compare each route separately, and the first to explore racial-ethnic exposure disparities by route and mode, nationally. Impacts (health, health-disparity, climate) per tonne of freight are largest for aircraft. Among non-aircraft modes, per tonne, rail has the largest health and health-disparity impacts and the lowest climate impacts, whereas truck transport has the lowest health impacts and greatest climate impacts – an important reminder that health and climate impacts are often but not always aligned. For aircraft and truck, average monetized damages per tonne are larger for climate impacts than for PM2.5 air pollution; for rail and barge, the reverse holds. We find that average exposures for inter-regional truck and rail are the highest for White non-Hispanic people, from barge is highest for Black people, and from aircraft is highest for people who are mixed/other race. Level of exposure and disparity among racial-ethnic groups vary in urban and rural areas. This research can be used to inform, for a given inter-regional origin and destination, which freight mode offers the lowest environmental health, health-disparity, and climate impacts. | Maninder P. S. Thind; Christopher W. Tessum; Julian D. Marshall | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62edf640fad485af03637440/original/environmental-health-racial-ethnic-health-disparity-and-climate-impacts-of-freight-transport-in-the-united-states.pdf |
67147626b91c6e99718af13c | 10.26434/chemrxiv-2024-xlxgg | EEEV interferes with synaptic guidance and transmission via the SRCR/Ephrin RBD/Granulins/Sema and potassium channel-like systems | Researching the EEEV virus is challenging due to the virus's high lethality and significant risk. This study employed bioinformatics methods for domain search to investigate the pathogenesis and infection process of the EEEV virus P protein. The results demonstrated that the EEEV virus P protein contains domains that bind cholesterol/very low density lipoprotein, such as SRCR and lipid-binding serum glycoprotein. It also contains domains that interfere with synaptic guidance and transmission, such as ARF7 effector protein C-terminal, BAR, Ephrin RBD, Granulins, MHD1, Sema, TLC, transient receptor ion channel, ionotropic glutamate receptor, and voltage-dependent calcium channel alpha-2. Lastly, it contains domains that bind potassium ions, such as neurotransmitter-gated ion channel ligand-binding and neurotransmitter-gated ion channel transmembrane. This study reveals that the P protein of the EEEV virus binds to the synaptic membrane through the cholesterol/very low density lipoprotein domain. Then, it controls the activity of Ca2+ channels to make synaptic depolarization potentials or hyperpolarization potentials. These change how easily postsynaptic nerves can fire and mess up synaptic guidance. Then, similar to a potassium-ion transmembrane nerve channel, it inserts into the synaptic membrane. Its potassium ion channel function activates when bound to neurotransmitter ligands, directing the synaptic membrane to produce vesicles that encapsulate the EEEV virus and internalize it into the synapse. | wenzhong liu; hualan li | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Cell and Molecular Biology; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2024-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67147626b91c6e99718af13c/original/eeev-interferes-with-synaptic-guidance-and-transmission-via-the-srcr-ephrin-rbd-granulins-sema-and-potassium-channel-like-systems.pdf |
6585bfd966c1381729cd74e5 | 10.26434/chemrxiv-2023-d4q7n | Integrating Mobile and Fixed-Site Black Carbon Measurements to Bridge Spatiotemporal Gaps in Urban Air Quality | Urban air pollution can vary sharply in space and time. However, few monitoring strategies can concurrently resolve spatial and temporal variation at fine scales. Here, we present a new measurement-driven spatiotemporal modeling approach that transcends the individual limitations of two complementary sampling paradigms: mobile monitoring and fixed-site sensor network. We develop, validate, and apply this model using data from an intensive, 100-day field study of black carbon in West Oakland, CA. The model performs well in reconstructing patterns at fine spatial and temporal resolution (30 m, 15 minutes), demonstrating strong out-of-sample correlations for both mobile (Pearson’s R ~ 0.77) and fixed-site measurements (R ~ 0.95) while revealing features that are not effectively captured by a single monitoring approach in isolation. The model reveals sharp concentration gradients near major emission sources while capturing their temporal variability, offering valuable insights into pollution sources and dynamics. This integrated approach, offering spatiotemporal completeness, can contribute to targeted interventions and informed policy decisions while addressing the limitations of individual monitoring strategies in urban air quality research. | Chirag Manchanda; Robert Harley; Julian Marshall; Alexander Turner; Joshua Apte | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6585bfd966c1381729cd74e5/original/integrating-mobile-and-fixed-site-black-carbon-measurements-to-bridge-spatiotemporal-gaps-in-urban-air-quality.pdf |
60c7541a702a9b841718c49a | 10.26434/chemrxiv.13553837.v2 | Pyrolysis of Complexes of Metallosulphophthalocyanines with Chitosan for Obtaining Graphite-like structures | <p>Highlights:</p>
<p> </p>
<p>Polymer
complexes of chitosan with copper and cobalt phthalocyanines were obtained</p>
<p> </p>
<p>Decomposition
products of chitosan and polymer complexes with metal phthalocyanines were
determined</p>
<p> </p>
<p>Pyrolysis
of chitosan and its polymer complexes with metallosulphophthalocyanines leads
to the formation of carbonizates</p>
<p> </p>
<p>The introduction
of copper phthalocyanine into the composition of the polymer complex with
chitosan leads to an increase in the content of aliphatic structures in
carbonizates, and cobalt phthalocyanine in aromatic compounds</p> | Natalia Lebedeva; Sabir Guseinov; Elena Yurina; Yury Gubarev; Anatoly V'yugin | Physical and Chemical Processes; Solution Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7541a702a9b841718c49a/original/pyrolysis-of-complexes-of-metallosulphophthalocyanines-with-chitosan-for-obtaining-graphite-like-structures.pdf |
62cc4afd244ce0e0f244d8f9 | 10.26434/chemrxiv-2022-17nkf | Non-covalent interactions drive the Young modulus of oligolignols-cellulose complexes. | Oligolignols composition in an efficient adhesive formulation, were studied to identify the interactions that drive their contact and Young’s modulus with a cellulose surface. Oligolignols’ molecular structures were modeled to elucidate the formation of complexes over a crystallite model of cellulose Iβ. Hybrid quantum mechanics/molecular mechanics (QM/MM) computations were carried out for the coupled molecular geometries of the oligolignol-cellulose complexes. The achieved conformations were used to obtain wavefunctions at the interaction region to develop a non-covalent interactions (NCI) study from the atoms in molecules (AIM) theory, implemented through graphics processing units (GPUs) calculations. It was found that non-covalent interactions command the forces associated to adhesive-cellulose contacts, mainly by C-H···O hydrogen bonds, driving the long-range interactions that promote the adhesion of oligolignols on cellulose Iβ. Furthermore, the results of interaction energy suggest that the strongest Young’s modulus is obtained from oligolignols with two and three monolignols on our cellulose Iβ crystallite model. We propose a QM/MM study considering NCI and AIM analysis, as a significant new framework to design adhesive formulations. Besides, the present work can contribute to the description of interactions between lignin components and cellulose.
| Pablo Lopez-Albarran; Antonio Pizzi; Rafael Herrera-Bucio; Joel Sánchez-Badillo; Marco Gallo; Raymundo Hernández-Esparza; Jorge Garza | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Quantum Computing; Biophysical Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62cc4afd244ce0e0f244d8f9/original/non-covalent-interactions-drive-the-young-modulus-of-oligolignols-cellulose-complexes.pdf |
60c742ef0f50db9c28395de5 | 10.26434/chemrxiv.8852246.v1 | Analysis of Glutamine Deamidation: Products, Pathways, and Kinetics | This manuscript examines glutamine deamidation, which
is a spontaneous chemical modification similar to the much more thoroughly
characterized asparagine deamidation. Although both processes share
similarities and are known to occur in long-lived proteins, here we establish
that important differences exist as well. For example, the distribution of
isomers generated following glutamine deamidation contains far fewer
D-residues. Furthermore, with the exception of QG motifs, glutamine deamidation
occurs primarily by direct hydrolysis and produces less isoglutamic acid as a
result. In addition, we demonstrate that radical-directed dissociation
generates abundant, characteristic, fragment ions that can be used to easily
distinguish glutamic acid from isoglutamic acid. | Dylan L. Riggs; Jacob W. Silzel; Yana A. Lyon; Amrik S. Kang; Ryan Julian | Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742ef0f50db9c28395de5/original/analysis-of-glutamine-deamidation-products-pathways-and-kinetics.pdf |
63ea72c19da0bc6b33dea92d | 10.26434/chemrxiv-2023-hs7vk | Square wave voltammetry enables measurement of light-activated oxidations and reductions on n-type semiconductor/metal junction light-addressable electrochemical sensors | Light-addressable electrochemical sensing (LAES) is a photoelectrochemical technique that enables high-density, individually addressed electrochemical measurements using light to activate an electrochemical reaction at the surface of a semiconducting photoelectrode. However, one major challenge is that only one electrochemical reaction (oxidation or reduction) will be activated by light. Here, we use square wave voltammetry (SWV) to enable measurements of both types of electrochemical reactions using n-Si/Au NP LAE sensors. We demonstrated this approach for the oxidation of ferrocene methanol and the reductions of ruthenium hexamine and methylene blue. We found that for all molecules, SWV showed dramatic improvements in current under illumination in comparison with dark samples. We also demonstrate that this approach works for both fully illuminated and partially illuminated samples. Altogether, we hope these results open up new applications for LAE sensors, especially those based on semiconductor/metal junctions. | Enock Arthur; Hana Ali; Armeen Hussain; Glen O'Neil | Analytical Chemistry; Electrochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ea72c19da0bc6b33dea92d/original/square-wave-voltammetry-enables-measurement-of-light-activated-oxidations-and-reductions-on-n-type-semiconductor-metal-junction-light-addressable-electrochemical-sensors.pdf |
66224c5691aefa6ce1e32b6e | 10.26434/chemrxiv-2024-xz6sg-v2 | Energetic landscape and terminal emitters of phycobilisome cores from quantum chemical modeling | Phycobilisomes (PBs) are giant antenna supercomplexes of cyanobacteria that use phycobilin pigments to capture sunlight and transfer the collected energy to membrane-bound photosystems. In the PB core, phycobilins are bound to particular allophycocyanin (APC) proteins. Some phycobilins are thought to be terminal emitters (TEs) with red-shifted fluorescence. However, the precise identification of TEs is still under debate. In this work, we employ multiscale quantum-mechanical calculations to disentangle the excitation energy landscape of PB cores. Using the recent atomistic PB structures from Synechoccoccus PCC 7002 and Synechocystis PCC 6803, we compute the spectral properties of different APC trimers and assign the low-energy pigments. We show that the excitation energy of APC phycobilins is determined by geometric and electrostatic factors, and is tuned by the specific protein-protein interactions within the core. Our findings challenge the simple picture of a few red-shifted bilins in the PB core and instead suggest that the red-shifts are established by the entire TE-containing APC trimers. Our work provides a theoretical microscopic basis for the interpretation of energy migration and time-resolved spectroscopy in phycobilisomes. | Lorenzo Cupellini; Michal Gwizdala; Tjaart Kruger | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Biophysics; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66224c5691aefa6ce1e32b6e/original/energetic-landscape-and-terminal-emitters-of-phycobilisome-cores-from-quantum-chemical-modeling.pdf |
61c072071e13eb7336ff89ea | 10.26434/chemrxiv-2021-jx18v | Computational study of the rovibrational spectrum of H2O-HF | In this paper we report rovibrational energy levels, transition frequencies, and intensities computed
for H2O-HF using a new ab initio potential energy surface and compare with available
experimental data. We use the rigid monomer approximation. A G4 symmetry-adapted Lanczos algorithm
and an uncoupled product basis are employed. The rovibrational levels are computed up to
J = 4. The new analytic 9-D potential is t to 39771 counterpoise corrected CCSD(T)(F12*)/augcc-
pVTZ energies and reduces to the sum of uncoupled H2O and HF potentials in the dissociation
limit. On the new potential better agreement with experiment is obtained by re-assigning the R(1)
transitions of two vibrational states. | Dominika VIGLASKA; Xiao-Gang Wang; Tucker CARRINGTON; David Tew | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c072071e13eb7336ff89ea/original/computational-study-of-the-rovibrational-spectrum-of-h2o-hf.pdf |
64185e7a2bfb3dc25110d894 | 10.26434/chemrxiv-2023-d0fxs | Effects of Senna alata Extract on the Hematological and Biochemical Alterations in Rats Exposed to Carcinogen | ABSTRACT: A total of 35 female albino rats were divided into 7 groups: control, rats exposed to carcinogen, treated with varying concentrations of Senna alata plant aqueous extracts, treated with standard drug, and untreated for total 28 days of treatment.. Freshly prepared 3 fractionated doses of 50mg/kg N-Nitroso-N-ethyl urea (carcinogen) dissolved in 1/15M Phosphate buffer was given intraperitoneally at average ages 50, 65 and 80 days. At the end of the test period, hematological and biochemical parameters were determined in blood and serum samples with determination of body weights. The body weights were significantly affected in carcinogen exposed rats as compared to control rats. Compared to the control group, the carcinogen exposed rats treated group showed significances in several hematological parameters, including decreases in White blood cell (WBC), Red blood cell (RBC), and Platelet (PLT) counts. Furthermore, in comparison to the control group, the carcinogen exposed rats showed significantly increased blood glucose, serum total cholesterol, Low density lipoprotein (LDL-cholesterol), triacylglycerols levels and High density lipoprotein (HDL-cholesterol) level. The hematological and biochemical parameters in the carcinogen exposed rats treated group were approximately similar to control group. The S.alata extract significantly restored the hematological and biochemical parameters in N-Nitroso-N-ethyl urea carcinogen exposed rats | Olufunke Olugbenga; Joy Okpuzor | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2023-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64185e7a2bfb3dc25110d894/original/effects-of-senna-alata-extract-on-the-hematological-and-biochemical-alterations-in-rats-exposed-to-carcinogen.pdf |
60c7577a702a9b623b18cae0 | 10.26434/chemrxiv.14405804.v1 | Fluorescent Nanodiamonds Encapsulated by Cowpea Chlorotic Mottle Virus (CCMV) Proteins for Intracellular 3D-Trajectory Analysis | Long-term tracking of nanoparticles to resolve intracellular structures and motions is essential to elucidate fundamental parameters as well as transport processes within living cells. Fluorescent nanodiamond (ND) emitters provide cell compatibility and very high photostability. However, high stability, biocompatibility, and cellular uptake of these fluorescent NDs under physiological conditions are required for intracellular applications. Herein, highly stable NDs encapsulated with Cowpea chlorotic mottle virus capsid proteins (ND-CP) are prepared. A thin capsid protein layer is obtained around the NDs, which imparts reactive groups and high colloidal stability, while retaining the opto-magnetic properties of the coated NDs as well as the secondary structure of CPs adsorbed on the surface of NDs. In addition, the ND-CP shows excellent biocompatibility both in vitro and in vivo. Long-term 3D trajectories of the ND-CP with fine spatiotemporal resolutions are recorded; their intracellular motions are analyzed by different models, and the diffusion coefficient are calculated. The ND-CP with its brilliant optical properties and stability under physiological conditions provides us with a new tool to advance the understanding of cell biology, e.g., endocytosis, exocytosis, and active transport processes in living cells as well as intracellular dynamic parameters. <br /> | Yingke Wu; Shuqin Cao; Md Noor A Alam; Marco Raabe; Sandra Michel-Souzy; Zuyuan Wang; Manfred Wagner; Anna Ermakova; Jeroen J. L. M. Cornelissen; Tanja Weil | Carbon-based Materials; Coating Materials; Imaging; Microscopy; Nanofabrication; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7577a702a9b623b18cae0/original/fluorescent-nanodiamonds-encapsulated-by-cowpea-chlorotic-mottle-virus-ccmv-proteins-for-intracellular-3d-trajectory-analysis.pdf |
60c751cbbb8c1a2d8e3dbd6c | 10.26434/chemrxiv.13207313.v1 | Feshbach-Fano Approach for Calculation of Auger Decay Rates Using Equation-of-Motion Coupled-Cluster Wave Functions: Numerical Examples and Benchmarks | <p>This manuscript is concerned with numerical illustration of the theoretical framework for computing Auger decay rates based on the Feshbach-Fano approach and the equation-of-motion coupled-cluster ansatz, augmented with core-valence separation scheme. We consider two analytical approximations to the continuum orbital describing the Auger electron: a plane wave and a Coulomb wave with an effective charge. Theoretical Auger electron spectra are presented for benchmark systems (Ne, H<sub>2</sub>O, CH<sub>4</sub> and CO<sub>2</sub>) and compared with available experimental spectra. Results of the presented benchmark tests show that the proposed computational scheme provides reliable <i>ab initio</i> preditions of the Auger spectra. The reliability, cost-efficiency, and robust computational setup of this methodology offer advantages in applications to a large variety of systems. </p> | Wojciech Skomorowski; Anna Krylov | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751cbbb8c1a2d8e3dbd6c/original/feshbach-fano-approach-for-calculation-of-auger-decay-rates-using-equation-of-motion-coupled-cluster-wave-functions-numerical-examples-and-benchmarks.pdf |
60c74b26f96a0012ac287588 | 10.26434/chemrxiv.12292865.v1 | Fluorogenic Protein Probes with Red or Near-Infrared Emission for Genetically Targeted Live-Cell Imaging | A series of red-emitting and near-infrared fluorogenic protein probes based on push-pull molecular rotor structures was developed. After characterization of their optical properties using Bovine Serum Albumin as a model protein, they were conjugated to a halogenoalkane ligand in order to target the protein self-labeling tag HaloTag. The interaction with HaloTag was investigated in vitro and then the most promising probes were applied to live-cell imaging in wash-free conditions using fluorogenic and chemogenetic targeting of HaloTag fusion proteins.<br /> | Sylvestre
P. J. T. Bachollet; Cyril Addi; Jean-Maurice Mallet; Blaise Dumat | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b26f96a0012ac287588/original/fluorogenic-protein-probes-with-red-or-near-infrared-emission-for-genetically-targeted-live-cell-imaging.pdf |
60c74271469df48502f42fc8 | 10.26434/chemrxiv.8299301.v1 | A Robust and General Approach to Quantitatively Conjugate Enzymes to Plasmonic Nanoparticles | <div>Bioconjugates of plasmonic nanoparticles have received considerable attention due to their potential biomedical applications. Succesfull bioconjugation requires control over the number and activity of the conjugated proteins, and the colloidal stability of the particles. In practice, this requires re-optimization of the conjugation protocol for each combination of protein and nanoparticle. Here we report a robust and general protocol that allows for the conjugation of a range of proteins to different types of nanoparticles using very short polyethylene-glycol(PEG) linkers, while simultaneously preserving protein activity and colloidal stability. The use of short linkers ensures that the protein is located close to the particle surface, where their refractive index sensitivity and near-field enhancement is maximal. We demonstrate that the use a Tween20 containing stabilizing buffer is critical in maintaining colloidal stability and protein function throughout the protocol. We obtain quantitative control over the average number of enzymes per particle by either varying the number of functional groups on the particle, or the enzyme concentration during incubation. This new route of preparing quantitative protein-nanoparticle bioconjugates paves the way to develop rational and quantitative strategies to functionalize nanoparticles for applications in sensing, medical diagnostics and drug delivery.</div> | Yuyang Wang; Karsten van Asdonk; Peter Zijlstra | Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74271469df48502f42fc8/original/a-robust-and-general-approach-to-quantitatively-conjugate-enzymes-to-plasmonic-nanoparticles.pdf |
64ee2ab1dd1a73847fc8ace7 | 10.26434/chemrxiv-2023-5w98m | Thermoelectric CO2RR electrolysis | We report here a fully contained electrolyzer that drives the CO2 reduction reaction (CO2RR) with thermoelectric generators instead of a potentiostat. The thermoelectric generators generate the electricity required to drive electrolysis when the temperature difference between the two faces is at least 40 oC. We show that the temperature gradients that could exist at a geothermal plant are sufficient to drive the reduction of gaseous CO2 into CO in an electrochemical flow cell, creating an opportunity to use waste heat to help decarbonization and clean fuels production. We also show how the electrolyzer system may be relevant to the future colonization of Mars, where there are large temperature differentials and an atmosphere rich in CO2. | Curtis Berlinguette; Abhishek Soni; Xin Lu; Chris Zhou; Sneha Singh | Catalysis; Energy; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ee2ab1dd1a73847fc8ace7/original/thermoelectric-co2rr-electrolysis.pdf |
60f7b6e48f6bf695256fe97d | 10.26434/chemrxiv-2021-75t5k | V-dock: fast generation of novel drug-like molecules
using machine-learning-based docking score and
molecular optimization | In this work, we propose a novel drug-like molecular design workflow by combining an efficient global molecular property optimization, protein-ligand molecular docking, and machine learning. Computational drug design algorithms aim to find novel molecules satisfying various drug-like
properties and have a strong binding affinity between a protein and a ligand. To accomplish this goal, various computational molecular generation methods have been developed with recent advances in deep learning and the increase of biological data. However, most existing methods heavily depend on experimental activity data, which are not available for many targets. Thus, when the number of available activity data is limited, protein-ligand docking calculations should be used. However, performing a docking calculation during molecular generation on the fly
requires considerable computational resources. To address this problem, we used machine-learning models predicting docking energy to accelerate the molecular generation process. We combined this ML-assisted docking score prediction model with the efficient global molecular property optimization approach, MolFinder. We call this design approach V-dock. Using the V-dock approach, we quickly generated many molecules with high docking scores for a target protein and desirable drug-like and bespoke properties, such as similarity to a reference molecule. | Jieun Choi; Juyong Lee | Physical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f7b6e48f6bf695256fe97d/original/v-dock-fast-generation-of-novel-drug-like-molecules-using-machine-learning-based-docking-score-and-molecular-optimization.pdf |
62d757337aab586d1ec73492 | 10.26434/chemrxiv-2022-k20zm | Cement clinker production in an electrolyser | The manufacture of cement from limestone is the single largest industrial source of CO2(g) emissions into the atmosphere. We report here an electrochemical flow reactor (electrolyser) that continuously converts limestone (CaCO3(s)) into Ca(OH)2(s) at a high rate of product formation (486 mg h-1 at 100 mA cm-2). The Ca(OH)2(s) product (slaked lime) is a chemical precursor to cement clinker, the main component of Portland cement, and other cement varieties. This three-compartment electrolyser operates with ~100% current efficiency at a cell voltage of 2.9 V and generates pure O2(g), H2(g), and CO2(g) streams that can be utilized downstream without purification. To demonstrate this feature, we feed the CO2(g) released from limestone directly to a second electrolyser that valorizes CO2(g) into higher value carbon-containing products (e.g., CO). A life-cycle analysis indicates that the proposed electrochemical process can decrease CO2 emissions per tonne of cement by 75% and achieve cost-parity with incumbent cement manufacturing processes with a carbon tax of $50/tonne CO2. | Zishuai Zhang; Benjamin A.W. Mowbray; Colin Parkyn; Chris Waizenegger; Aubry S. R. Williams; Eric W. Lees; Shaoxuan Ren; Ryan P. Jansonius; Curtis P. Berlinguette | Physical Chemistry; Energy; Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d757337aab586d1ec73492/original/cement-clinker-production-in-an-electrolyser.pdf |
60c750b6702a9b158b18be26 | 10.26434/chemrxiv.13075745.v1 | Evidence for a Solid-Electrolyte Inductive Effect in Superionic Conductors | <p>Identifying and optimizing highly-conducting lithium-ion solid electrolytes is a critical step towards the realization of commercial all–solid-state lithium-ion batteries. Strategies to enhance ionic conductivities in solid electrolytes typically focus on the effects of modifying their crystal structures or of tuning mobile-ion stoichiometries. A less-explored approach is to modulate the chemical-bonding interactions within a material to promote fast lithium-ion diffusion. Recently, the idea of a solid-electrolyte inductive effect was proposed, whereby changes in bonding within the solid-electrolyte host-framework modify the potential-energy landscape for the mobile ions, resulting in an enhanced ionic conductivity. This concept has since been invoked to explain anomalous conductivity trends in a number of solid electrolytes. Direct evidence for a solid-electrolyte inductive effect, however, is lacking—in part because of the challenge of quantifying changes in local bonding interactions within a solid-electrolyte host-framework. <a></a><a>Here, we consider the evidence for a solid-electrolyte inductive effect in the archetypal superionic lithium-ion conductor Li<sub>10</sub>Ge<sub>1−<i>x</i></sub>Sn<i><sub>x</sub></i>P<sub>2</sub>S<sub>12</sub>, using Rietveld refinements against high-resolution temperature-dependent neutron-diffraction data, Raman spectroscopy, and density functional theory calculations.</a> Substituting Ge for Sn weakens the {Ge,Sn}–S bonding interactions and increases the charge-density associated with the S<sup>2-</sup> ions. This charge redistribution modifies the Li<sup>+</sup> substructure causing Li<sup>+</sup> ions to bind more strongly to the host-framework S anions; which in turn modulates the Li-ion potential-energy surface, increasing local barriers for Li-ion diffusion. Each of these effects is consistent with the predictions of the solid-electrolyte inductive effect model. Density functional theory calculations further predict that this inductive effect occurs even in the absence of changes to the host-framework geometry due to Ge → Sn substitution. These results provide direct evidence in support of a measurable solid-electrolyte inductive effect and demonstrate its application as a practical strategy for tuning ionic conductivities in superionic lithium-ion conductors.</p> | Sean Culver; Alex Squires; Nicolo Minafra; Callum Armstrong; Thorben Krauskopf; Felix Boecher; Cheng Li; Benjamin Morgan; Wolfgang Zeier | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750b6702a9b158b18be26/original/evidence-for-a-solid-electrolyte-inductive-effect-in-superionic-conductors.pdf |
60c74d15bb8c1a31d73db503 | 10.26434/chemrxiv.12587438.v1 | Ideal Current-voltage Characteristics and Rectification Performance of Molecular Rectifier under Single Level based Tunneling and Hopping Transport | In this work, we systematically studied the rectifying properties of molecular junction based on asymmetric tunneling and hopping charge transport in a single electronic state model using Landauer formula and Marcus theory. We first analyzed the asymmetric I-V characteristics and revealed distinct physical origins of the rectification under the two types of transports. We found significant difference in I-V characteristics of the two and the hopping transport can afford a much higher rectification ratio than tunneling. Next, the effect of key physical parameters on rectification performance under tunneling and hopping, like asymmetric factor, energy barrier, temperature and molecule-electrode coupling et al, were extensively evaluated, which provided a theoretical baseline for molecular diode design and performance modulation. At last, we further analyzed representative experimental results using the two models. We successfully reproduced the experimental results by adjusting the model parameters and revealed the coexistence of the tunneling and hopping processes in the ferrocene based molecular diode. The model method thus can work as powerful tool in mechanism analysis for the molecular rectification study. | Xianneng Song; Xi Yu; Wenping Hu | Quantum Mechanics; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d15bb8c1a31d73db503/original/ideal-current-voltage-characteristics-and-rectification-performance-of-molecular-rectifier-under-single-level-based-tunneling-and-hopping-transport.pdf |
6645961b91aefa6ce12000ec | 10.26434/chemrxiv-2024-4gl8d-v2 | Key role of density functional approximation in predicting M-N-C catalyst activities for oxygen reduction | Metal-Nitrogen-Carbon motifs present intriguing structural and electronic properties for a number of applications, including as oxygen reduction catalysts. However, computational investigations of M-N-C-catalyzed reactions have must grapple with their complex electronic structures. In the present study, we evaluate the impact of the density functional approximation on calculated M-N-C catalyst activities for oxygen reduction. Using metalloporphyrins as model catalysts, we find a significant split between pure (GGA) and hybrid functionals, with hybrid functionals, in particular B3LYP, showing greater agreement with DLPNO-CCSD(T) reaction energies. Notably, double-hybrids offered no noticeable improvement over the much more computationally efficient B3LYP and PBE0. Other discrepancies between functionals, including ground state spin and geometry, are also considered in this work. Finally, both hybrid and double-hybrid functionals greatly reduced the gas phase errors associated with the main group molecules in the oxygen reduction reaction relative to GGA calculations, leading us to question the application of widely used empirical corrections to O$_2$. | Brett Henderson; Sofia Donnecke; Scott N. Genin; Ilya G. Ryabinkin; Irina Paci | Theoretical and Computational Chemistry; Catalysis; Energy; Computational Chemistry and Modeling; Electrocatalysis; Fuel Cells | CC BY 4.0 | CHEMRXIV | 2024-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6645961b91aefa6ce12000ec/original/key-role-of-density-functional-approximation-in-predicting-m-n-c-catalyst-activities-for-oxygen-reduction.pdf |
60c756519abda20b06f8e4e0 | 10.26434/chemrxiv.13728109.v2 | Assessing the Accuracy of the SCAN Functional for Water Through a Many-Body Analysis of the Adiabatic Connection Formula | <div>
<div>
<div>
<p>We present a systematic analysis of the accuracy of a series of SCANα functionals for
water, with varying fractions (α) of exact exchange, which are constructed through the adiabatic connection formula. Our results indicate that that all SCANα functionals exhibit substantial errors in the representation of the water 2-body energies. Importantly, the inclusion
of exact exchange is found to have opposite effects on the ability of the SCANα functionals
to describe the interaction energies of water clusters with 2-dimensional and 3-dimensional
hydrogen-bonding arrangements. These errors are found to directly affect the ability of the
SCANα functionals to describe the structure of liquid water at ambient conditions, which is
investigated using explicit many-body models (MB-SCANα) derived from the corresponding
SCANα data. In particular, it is found that all MB-SCANα models predict a more compact first hydration shell, which results in a denser liquid with a more ice-like structure. These ap-
parent opposite trends can be explained by the inability of all SCANα functionals to provide
a balanced description of the water 2B and 3B energies at the fundamental level. The analyses
presented in this study provide new insights that can guide future developments of improved
exchange-correlation functionals for water.</p>
</div>
</div>
</div> | Eleftherios Lambros; Jie Hu; Francesco Paesani; Paesani Lab | Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Properties; Solution Chemistry; Statistical Mechanics; Structure; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756519abda20b06f8e4e0/original/assessing-the-accuracy-of-the-scan-functional-for-water-through-a-many-body-analysis-of-the-adiabatic-connection-formula.pdf |
60c74438337d6c758be26d5c | 10.26434/chemrxiv.8327162.v2 | Selective Nucleobase Pairing Extends Plausibly Prebiotic Conditions to the Solid State | Despite its immense relevance in the context of the emergence of life, the pairing of nucleobases has only been observed for regioselectively methylated adenine and thymine. This is surprising as it raises the question why would nucleobases be incorporated into DNA if they were unable to self-assemble beforehand. Here, we have discovered that elusive pairing of methylated guanine and cytosine is readily available in the solid state by heating, where the two nucleobases self-assemble via Watson-Crick hydrogen-bonding. Dry heating preserves DNA-specificity as a four-component mixture of nucleobases provides self-assembly only of complementary pairs. We thus emphasize the importance of the solid state as the reaction medium, even for the supramolecular chemistry of life, which was thus far underexplored in the prebiotic context.<br /> | Tomislav Stolar; Stipe Lukin; Maša Rajić Linarić; Martin Etter; Krunoslav Užarević; Ivan Halasz; Ernest Meštrović | Supramolecular Chemistry (Org.); Aggregates and Assemblies; Solid State Chemistry; Physical and Chemical Processes; Self-Assembly; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74438337d6c758be26d5c/original/selective-nucleobase-pairing-extends-plausibly-prebiotic-conditions-to-the-solid-state.pdf |
662a7c0e418a5379b0b54354 | 10.26434/chemrxiv-2024-dc48x-v3 | FragHub: A mass spectral libraries data integration workflow | Open mass spectral libraries (OMSL) are critical for metabolite annotation and machine learning, especially given the rising volume of untargeted metabolomic studies and the development of annotation pipelines. Despite their importance, the practical application of OMSLs is hampered by the lack of standardized file formats, metadata fields, and supporting ontology. Current libraries, often restricted to specific topics or matrices such as natural products, lipids, or the human metabolome, may limit the discovery potential of untargeted studies. FragHub addresses these challenges by integrating multiple OMSLs into a single comprehensive database, supporting various data formats and harmonizing metadata. It also proposes some generic filters for mass spectrum using a graphical user interface. Additionally, a workflow to generate in-house libraries compatible with FragHub is proposed. FragHub dynamically segregates libraries based on ionization modes and chromatography techniques, thereby enhancing data utility in metabolomic research. The FragHub Python code is publicly available under a MIT license, at the following repository: https://github.com/eMetaboHUB/FragHub. Generated data can be accessed at https://doi.org/10.5281/zenodo.11057687. | Axel Dablanc; Solweig Hennechart; Amélie Perez; Guillaume Cabanac; Yann Guitton; Emilien Jamin; Bernard Lyan; Nils Paulhe; Franck Giacomoni; Guillaume Marti | Analytical Chemistry; Chemoinformatics; Mass Spectrometry | CC BY NC 4.0 | CHEMRXIV | 2024-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662a7c0e418a5379b0b54354/original/frag-hub-a-mass-spectral-libraries-data-integration-workflow.pdf |
60c741a90f50db3a5b395b9e | 10.26434/chemrxiv.8100164.v1 | Observation of High-Temperature Macromolecular Confinement in Lyophilised Protein Formulations Using Terahertz Spectroscopy | Characterising the structural dynamics of proteins and the effects of excipients are critical for optimising the design of formulations. In this work we investigated four lyophilised formulations containing bovine serum albumin (BSA) and three formulations containing a monoclonal antibody (mAb, here mAb1), and explore the role of the excipients polysorbate 80, sucrose, trehalose, and arginine on stabilising proteins. By performing temperature variable terahertz time-domain spectroscopy (THz-TDS) experiments it is possible to study the vibrational dynamics of these formulations. The THz-TDS measurements reveal two distinct glass transition processes in all tested formulations. The lower temperature transition, <i>T</i><sub>gβ</sub>, is associated with the onset of local motion due to the secondary relaxation whilst the higher temperature transition, <i>T</i><sub>gα</sub>, marks the onset of the α relaxation. For some of the formulations, the globular BSA as well as mAb1, the absorption at terahertz frequencies does not increase further at temperatures above <i>T</i><sub>gα</sub>. Such behaviour is in contrast to our previous observations for small organic molecules as well as linear polymers where absorption is always observed to steadily increase with temperature due to the stronger absorption of terahertz radiation by more mobile dipoles. The absence of such further increase in absorption with higher temperatures therefore suggests a localised confinement of the protein/excipient matrix at high temperatures that hinders any further increase in mobility. Additionally, we used Fourier-transform infrared spectroscopy (FTIR), circular dichroism (CD), and solid-state nuclear magnetic resonance (ssNMR) experimental data to further investigate the structural changes associated with our terahertz spectroscopy measurements. None of these techniques were able to resolve the subtle changes associated with vibrational confinement observed by terahertz spectroscopy. No evidence was found for any conformational changes in the protein structure upon reconstitution. We found that subtle changes in excipient composition had an effect on the transition temperatures <i>T</i><sub>gα </sub>and <i>T</i><sub>gβ</sub> as well as the vibrational confinement in the solid state. Further work is required to establish the potential significance of the vibrational confinement in the solid state on formulation stability and chemical degradation as well as what role the excipients play in achieving such confinement. | Talia Shmool; Philippa J. Hooper; Markus Leutzsch; Amberley
D. Stephens; Mario Gaimann; Michael Mantle; Gabi Kaminski; Christopher F. van der Walle; J. Axel Zeitler | Bioengineering and Biotechnology; Biophysics; Drug Discovery and Drug Delivery Systems; Biophysical Chemistry; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2019-05-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741a90f50db3a5b395b9e/original/observation-of-high-temperature-macromolecular-confinement-in-lyophilised-protein-formulations-using-terahertz-spectroscopy.pdf |
6582ad6d66c1381729a0e9c3 | 10.26434/chemrxiv-2023-40cx0 | Pull-down assay coupled to non-target mass spectrometry analysis as a tool to identify unknown endocrine disruptive transthyretin ligands in waste and surface water | Surface and treated wastewaters are contaminated with highly complex mixtures of micropollutants, which may cause adverse effects on aquatic biota or humans, often mediated by endocrine disruption. However, there is very limited knowledge regarding some important modes of action, such as interference with thyroid hormone (TH) regulation and the compounds driving these effects. The effects of environmental samples observed in bioassays addressing various endpoints in the endocrine, namely thyroid hormone pathways, remain largely unexplained with known active chemicals. Transthyretin (TTR) is a serum transport protein distributing thyroid hormones to target tissues in vertebrates; its binding inhibition by xenobiotics may lead to adverse effects such as impaired (neuro)development. In this study, we describe a novel approach for the identification of compounds with the potential to bind to TTR, based on the specific separation of these compounds in a pull-down assay followed by non-target analysis (NTA). The pull-down assay using purified TTR protein was established and optimized with known TTR ligands. The method was applied to separate and identify compounds responsible for TH displacing activity in highly complex wastewater and surface water samples. The samples after the pull-down assay elicited TH displacing activity and the specific separation of TTR ligands provided a substantial reduction of chromatographic features from the original complex water extract. The applied non-target screening workflow resulted in the identification of 34 structures. Thirteen identified compounds with available analytical standards were quantified in the original water extracts and their TH-displacement potency was confirmed. Twelve compounds were discovered as TTR binders for the first time and linear alkylbenzene sulfonates (LAS) were highlighted as contaminants of concern regarding the TH-displacement activity. Pull-down assay combined with NTA proved to be a well-functioning approach for the identification of bioactive compounds in complex environmental mixtures with great application potential across various biological target endpoints and environmental compartments. | Petra Mikusova; Zuzana Tousova; Ludek Sehnal; Jan Kuta; Katerina Grabicova; Ganna Fedorova; Martin Marek; Roman Grabic; Klara Hilscherova | Earth, Space, and Environmental Chemistry; Environmental Science; Hydrology and Water Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6582ad6d66c1381729a0e9c3/original/pull-down-assay-coupled-to-non-target-mass-spectrometry-analysis-as-a-tool-to-identify-unknown-endocrine-disruptive-transthyretin-ligands-in-waste-and-surface-water.pdf |
60c75041842e65b17cdb39ac | 10.26434/chemrxiv.13013297.v1 | Non-Destructive Analysis of Mummification Balms in Ancient Egypt, Based on EPR of Vanadyl and Organic Radical Markers of Bitumen | The black matter employed in funeral context by ancient Egyptian is a complex mixture of plant-based compounds with variable amounts of bitumen. Asphaltene, the most resistant component of bitumen, contain Vanadyl porphyrins and carbonaceous radicals which can be used as paramagnetic probes to investigate embalming materials without sample preparation. Electron Paramagnetic Resonance (EPR) at X-band, combining in-phase and out-of-phase detection schemes, provides new information in a non-destructive way about the presence, the origin, and the evolution of bitumen in these complex materials. It is found that the relative EPR intensity of radicals and vanadyl porphyrins is sensitive to the origin of the bitumen. The presence of non-porphyrinic vanadyl complexes in historical samples is likely due to the complexation of VO2+ ions by carboxylic functions at the interface between bitumen and other biological components of the embalming matter. The absence of such oxygenated vanadyl complex in natural bitumen and in one case of historical human mummy acquired by a museum in the 19th century reveals a possible, non-documented, ancient restoration of this mummy by pure bitumen. The linear correlation between in-phase and out-of phase EPR intensities of radicals and vanadyl porphyrins in balms and in natural bitumen, reveals a nanostructuration of radicals and vanadyl porphyrin complexes, which was not affected by the preparation of the balm. This points to the remarkable chemical stability of paramagnetic probes in historical bitumen in ancient Egypt. | Charles-Emmanuel Dutoit; Laurent Binet; Hitomi Fujii; Agnes Lattuati-Derieux; Didier Gourier | Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75041842e65b17cdb39ac/original/non-destructive-analysis-of-mummification-balms-in-ancient-egypt-based-on-epr-of-vanadyl-and-organic-radical-markers-of-bitumen.pdf |
60c74caaf96a00a590287806 | 10.26434/chemrxiv.12116175.v2 | Conjugation of Carboxylated Graphene Quantum Dots with Cecropin P1 for Bacterial Biosensing Applications | <p>Quantum
dots have proven to be strong candidates for biosensing applications in recent
years, due to their strong light emission properties and their ability to be
modified with a variety of functional groups for the detection of different
analytes. Here, we investigate the use
of conjugated carboxylated graphene quantum dots (CGQDs) for the detection of <i>E. coli</i>, using a biosensing procedure
that focuses on measuring changes in fluorescence quenching. We have also further developed this biosensing assay into a compact, field-deployable test kit focused on rapidly measuring changes in absorbance to determine bacterial concentration. Our CGQDs were conjugated with cecropin P1, a
naturally-produced antibacterial peptide that facilitates the attachment of CGQDs
to <i>E. coli</i> cells. We also confirm the structural modification
of these conjugated CGQDs in addition to analyzing their optical
characteristics. Our findings have the
potential to be used in situations where rapid, reliable detection of bacteria
in liquids, such as drinking water, is required, especially given our biosensor’s
relatively low observed limit of detection (LOD).</p><br /> | Jonathan Bruce; Jude Clapper | Carbon-based Materials; Nanostructured Materials - Materials; Optical Materials; Nanostructured Materials - Nanoscience; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74caaf96a00a590287806/original/conjugation-of-carboxylated-graphene-quantum-dots-with-cecropin-p1-for-bacterial-biosensing-applications.pdf |
6389dc2b0a8127ba5ccffad9 | 10.26434/chemrxiv-2022-7kxlh | Fast Dynamic Synthesis of MIL-68(In) Thin Films in High Optical Quality for Optical Cavity Sensing | Fabrication of metal-organic framework (MOF) thin films rigidly anchored on suitable substrates is a crucial prerequisite for the integration of these porous hybrid materials into electronic and optical devices. Thus far, the structural variety for MOF thin films available through layer-by-layer deposition was limited, as the preparation of those surface-anchored metal-organic frameworks (SURMOFs) has several requirements: Mild conditions, low temperatures, day-long reaction times, and non-aggressive solvents. We herein present a fast method for the preparation of the first MIL SURMOF on Au-surfaces under rather harsh conditions: Using a dynamic layer-by-layer synthesis for MIL-68(In), thin films of adjustable thickness between 50-2000 nm could be deposited within only 60 min. The MIL-68(In) thin film growth was monitored in-situ using a quartz crystal microbalance. In-plane X-ray diffraction revealed oriented MIL-68(In) growth with the pore-channels of this interesting MOF aligned parallel to the support. SEM data demonstrated an extraordinarily low roughness of the MIL-68(In) thin films. Mechanical properties and lateral homogeneity of the layer were probed through nanoindentation. These thin films showed extremely high optical quality. By applying a PMMA layer and further depositing an Au-mirror to the top, a MOF optical cavity was fabricated that can be used as Fabry-Perot interferometer. The MIL-68(In)-based cavity showed a series of sharp resonances in the UV-Vis regime. Changes in the refractive index of MIL-68(In) caused by exposure to volatile compounds, led to pronounced position shifts of the resonances. Thus, these cavities are well suited to be used as optical read-out sensors. | Bahram Hosseini Monjezi; Salih Okur; René Limbach; Abhinav Chandresh; Kaushik Sen; Tawheed Hashem; Matthias Schwotzer; Lothar Wondraczek; Christof Wöll; Alexander Knebel | Physical Chemistry; Materials Science; Hybrid Organic-Inorganic Materials; Optical Materials; Thin Films; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6389dc2b0a8127ba5ccffad9/original/fast-dynamic-synthesis-of-mil-68-in-thin-films-in-high-optical-quality-for-optical-cavity-sensing.pdf |
60c754ff9abda2432ff8e284 | 10.26434/chemrxiv.13809527.v1 | Progress Towards a Large-Scale Synthesis of Molnupiravir (MK-4482, EIDD-2801) from Cytidine | <div>
<div>
<div>
<p>Molnupiravir (MK-4482, EIDD-2801) is a promising orally bioavailable drug candidate for
treatment of COVID-19. Herein we describe a supply-centered and chromatography-free synthesis
of molnupiravir from cytidine, consisting of two steps: a selective enzymatic acylation followed
by transamination to yield the final drug product. Both steps have been successfully performed on
decagram scale: the first step at 200 g, and the second step at 80 g. Overall, molnupiravir has been
obtained in a 41% overall isolated yield compared to a maximum 17% isolated yield in the patented
route. This route provides many advantages to the initial route described in the patent literature and would decrease the cost of this pharmaceutical should it prove safe and efficacious in ongoing
clinical trials.</p>
</div>
</div>
</div> | Grace P. Ahlqvist; Catherine P. McGeough; Chris Senanayake; Joseph D. Armstrong; Ajay Yadaw; Sarabindu Roy; Saeed Ahmad; David R. Snead; Tim Jamison | Organic Synthesis and Reactions; Process Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754ff9abda2432ff8e284/original/progress-towards-a-large-scale-synthesis-of-molnupiravir-mk-4482-eidd-2801-from-cytidine.pdf |
60c749ce4c89194182ad3127 | 10.26434/chemrxiv.12108618.v1 | Helical Graphene Nanostructures Embedded with an Azulene Cluster | An azulene cluster is a structural defect of graphenes,
and it alters the electronic, magnetic, and structural properties of graphenes
and graphene nanoribbons. However, detailed experimental investigations of
graphenes or graphene nanostructures embedded with an azulene cluster are
limited because they are difficult to synthesise. Herein, azulene-embedded
graphene nanostructures <b>(</b>AGNs<b>)</b>
were synthesised by following a newly developed synthetic protocol. The nanostructures
comprising pentagons, hexagons, and heptagons<b> </b>has three characteristic
edges, viz., zigzag-, armchair-, and cove-type edges. Experimental and
theoretical investigations of the properties of AGN<b> </b>revealed that the cove edge has stable helical
chirality with a racemisation barrier of 29.2 kcal/mol, in contrast to normal
cove-type edges that undergo rapid racemisation. The in-solution
self-association behaviour and the structural, electronic, and electrochemical properties
of AGN are also described in detail. | Yousuke Yamaoka; Naoki Ogawa; Hiroshi Takikawa; Ken-ichi Yamada; Kiyosei Takasu | Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749ce4c89194182ad3127/original/helical-graphene-nanostructures-embedded-with-an-azulene-cluster.pdf |
66176d4391aefa6ce150c0d6 | 10.26434/chemrxiv-2024-cdm8w | Top 20 Influential AI-Based Technologies in Chemistry | The beginning and ripening of digital chemistry is analyzed focusing on the role of artificial intelligence (AI) in an expected leap in chemical sciences to bring this area to the next evolutionary level. The analytic description selects and highlights the top 20 AI-based technologies and 7 broader themes that are reshaping the field. It underscores the integration of digital tools such as machine learning, big data, digital twins, the Internet of Things (IoT), robotic platforms, smart control of chemical processes, virtual reality and blockchain, among many others, in enhancing research methods, educational approaches, and industrial practices in chemistry. The significance of this study lies in its focused overview of how these digital innovations foster a more efficient, sustainable, and innovative future in chemical sciences. This article not only illustrates the transformative impact of these technologies but also draws new pathways in chemistry, offering a broad appeal to researchers, educators, and industry professionals to embrace these advancements for addressing contemporary challenges in the field. | Valentine Ananikov | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Machine Learning; Artificial Intelligence; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66176d4391aefa6ce150c0d6/original/top-20-influential-ai-based-technologies-in-chemistry.pdf |
60c7551c0f50db15e9397e3d | 10.26434/chemrxiv.14043503.v1 | Improved Prediction of Solvation Free Energies by Machine-Learning Polarizable Continuum Solvation Model | In the present study, we develop and introduce the Machine-Learning Polarizable Continuum solvation Model (ML-PCM) for a substantial improvement of the predictability of solvation free energy. The performance and reliability of the developed models are validated through a rigorous and demanding validation procedure. The ML-PCM models developed in the present study improve the accuracy of widely accepted continuum solvation models by almost one order of magnitude with almost no additional computational costs. A freely available software is developed and provided for a straightforward implementation of the new approach.<br /> | Amin Alibakhshi; Bernd Hartke | Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Artificial Intelligence; Quantum Computing; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7551c0f50db15e9397e3d/original/improved-prediction-of-solvation-free-energies-by-machine-learning-polarizable-continuum-solvation-model.pdf |
64c925ba658ec5f7e58fff6c | 10.26434/chemrxiv-2023-76q3g | Continuous Wave Photon Upconversion from a
Copper Selenide Nanocrystal Film | Photon upconversion is of great interest for improving the efficiency of silicon photovoltaic cells, for biological imaging, and for thermal management strategies. Currently, the vast majority of materials being developed for solar upconversion are composed of rare and expensive elemental compounds. Moving forward, the development of earth abundant, non-toxic materials that efficiently convert near infrared light into visible light would be ideal. Copper selenide-based materials meet these criteria, and are of great interest due to their unique thermoelectric and plasmonic properties. In particular, doped copper selenides (Cu2−xSe) have tunable near infrared localized surface plasmon resonances, large Seebeck coefficients, and low thermal conductivity, with a range of chemical and thermoelectric applications. Here, we observe another interesting application of this material in the upconversion of near infrared light from a silica xerogel film containing degenerately doped Cu2−xSe nanocrystals, with an onset flux of ∼ 1.96 ± 0.29 kW/cm^2 and at least 1% quantum yield. Our investigations suggest a plasmon-driven thermal mechanism likely plays a role in this upconversion process. | Christopher Warkentin; Riti Sen; Jill Millstone; Renee Frontiera | Materials Science; Nanoscience; Nanostructured Materials - Materials; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c925ba658ec5f7e58fff6c/original/continuous-wave-photon-upconversion-from-a-copper-selenide-nanocrystal-film.pdf |
672bd061f9980725cf58f626 | 10.26434/chemrxiv-2024-52hq3 | Diethylzinc-Amylates – Selective Halogen-Zinc Exchange Reagents at Room-Temperature | The cheapest available organozinc species (diethylzinc) – yet rarely employed in halogen-Zn exchanges – is used in a combination with amylate salts to generate new overtime stable reagents that allow smooth iodide-zinc exchange at room temperature, preventing therefore the need for fastidious and time-consuming preparation of complex mixtures. The scope of the reaction has been explored on polyfunctionalized alkenes (including sensitive cyclobutenes, steroids and glycals), aryls and heteroaryls. | Florian Trauner; Bilel Boutet; Flavie Rambaud; Van Nhi Ngo; dorian didier | Organic Chemistry; Organometallic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Small Molecule Activation (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672bd061f9980725cf58f626/original/diethylzinc-amylates-selective-halogen-zinc-exchange-reagents-at-room-temperature.pdf |
60c756b0f96a00b78b288b35 | 10.26434/chemrxiv.13603325.v2 | Large Scale Membrane Movement Induced by a Cation Switch | <p></p><p>A biomembrane sample system where millimolar changes of cations induce reversible large scale (≥ 200 Å) changes in the membrane-to-surface distance is described. The system composes of a free-floating bilayer (FFB), formed adjacent to a self-assembled monolayer (SAM). To examine the membrane movements, differently charged FFBs in the presence and absence of Ca2+ and Na+, respectively, were examined using neutron reflectivity (NR) and quartz crystal microbalance (QCM) measurements, alongside molecular dynamics (MD) simulations. In NR the variation of Ca2+ and Na+ concentration enabled precision manipulation of the FFB-to-surface distance. Simulations suggest that Ca2+ ions bridge between SAM and bilayer whereas the more diffuse binding of Na+, especially to bilayers, is unable to fully overcome the repulsion between anionic FFB and anionic SAM. Reproduced NR results with QCM demonstrate the potential of this easily producible sample system to become a standard analysis tool for e.g. investigating membrane binding effects, endocytosis and cell signalling.<br /></p><p></p> | Laura. H. John; Gail. M. Preston; Mark S. P. Sansom; Luke Clifton | Biocompatible Materials; Thin Films; Nanodevices; Bioengineering and Biotechnology; Bioinformatics and Computational Biology; Biophysics; Computational Chemistry and Modeling; Biophysical Chemistry; Interfaces; Self-Assembly; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756b0f96a00b78b288b35/original/large-scale-membrane-movement-induced-by-a-cation-switch.pdf |
613268f0d5f0803706ba0c79 | 10.26434/chemrxiv-2021-4qkg8-v2 | Model agnostic generation of counterfactual explanations for molecules | An outstanding challenge in deep learning in chemistry is its lack of interpretability. The inability of explaining why a neural network makes a prediction is a major barrier to deployment of AI models. This not only dissuades chemists from using deep learning predictions, but also has led to neural networks learning spurious correlations that are difficult to notice. Counterfactuals are a category of explanations that provide a rationale behind a model prediction with satisfying properties like providing chemical structure insights. Yet, counterfactuals are have been previously limited to specific model architectures or required reinforcement learning as a separate process. In this work, we show a universal model-agnostic approach that can explain any black-box model prediction. We demonstrate this method on random forest models, sequence models, and graph neural networks in both classification and regression. | Geemi P Wellawatte; Aditi Seshadri; Andrew D White | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence | CC BY NC 4.0 | CHEMRXIV | 2021-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613268f0d5f0803706ba0c79/original/model-agnostic-generation-of-counterfactual-explanations-for-molecules.pdf |
60c746a8bb8c1a4fd23da8e4 | 10.26434/chemrxiv.11312567.v1 | Membrane-Tethered Mucin-like Polypeptides Sterically Inhibit Binding and Slow Fusion Kinetics of Influenza A Virus | <div>
<div>
<div>
<p>The mechanism(s) by which cell-tethered mucins modulate infection by Influenza A viruses (IAVs) remains an open question. Mucins form both a protective barrier that can block virus binding and recruit IAVs to bind cells via the sialic acids of cell-tethered mucins. To elucidate the molecular role of mucins in flu pathogenesis, we constructed a synthetic glycocalyx to investigate membrane-tethered mucins in the context of IAV binding and fusion. We designed and synthesized lipid-tethered glycopolypeptide mimics of mucins and added them to lipid bilayers, allowing chemical control of length, glycosylation, and surface density of a model glycocalyx. We observed that the mucin mimics undergo a conformational change at high surface densities from a compact to an extended architecture. At high surface densities asialo mucin mimics inhibited IAV binding to underlying glycolipid receptors and this density correlated to the mucin mimic’s conformational transition. Using a single virus fusion assay, we observed that while fusion of virions bound to vesicles coated with sialylated mucin mimics was possible, the kinetics of fusion were slowed in a mucin density-dependent manner. These data provide a molecular model for a protective mechanism by mucins in IAV infection, and therefore this synthetic glycocalyx provides a useful reductionist model for studying the complex interface of host-pathogen interactions.
</p>
</div>
</div>
</div> | Corleone Delaveris; Elizabeth Webster; Steven Banik; Steven Boxer; Carolyn Bertozzi | Biophysics; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746a8bb8c1a4fd23da8e4/original/membrane-tethered-mucin-like-polypeptides-sterically-inhibit-binding-and-slow-fusion-kinetics-of-influenza-a-virus.pdf |
60c74c95469df454c3f440f0 | 10.26434/chemrxiv.12469853.v1 | Electrolyte Oxidation Pathways in Lithium-Ion Batteries | <p>The
mitigation of decomposition reactions of lithium-ion battery electrolyte
solutions is of critical importance in controlling device lifetime and
performance. However, due to the
complexity of the system, exacerbated by the diverse set of electrolyte
compositions, electrode materials, and operating parameters, a clear
understanding of the key chemical mechanisms remains elusive. In this work, operando
pressure measurements, solution NMR, and electrochemical methods were combined
to study electrolyte oxidation and reduction at multiple cell voltages. Two-compartment
LiCoO<sub>2</sub>/Li cells were cycled with a lithium-ion conducting glass-ceramic
separator so that the species formed at each electrode could be
identified separately and further reactions of these species at the opposite
electrode prevented. One principal finding is that chemical oxidation (with an
onset voltage of ~4.7 V vs Li/Li<sup>+</sup> for LiCoO<sub>2</sub>), rather
than electrochemical reaction, is the dominant decomposition process at the
positive electrode surface in this system. This is ascribed to the well-known
release of reactive oxygen at higher states-of-charge, indicating that reactions
of the electrolyte at the positive electrode are intrinsically linked to
surface reactivity of the active material. Soluble electrolyte decomposition products formed
at both electrodes are characterised, and a detailed reaction scheme is
constructed to rationalise the formation of the observed species. The insights
on electrolyte decomposition through reactions with reactive oxygen species identified
through this work have direct impact on understanding and mitigating
degradation in high voltage/higher energy density LiCoO<sub>2</sub>-based
cells,<sub> </sub>and more generally for cells containing nickel-containing
cathode materials (e.g. LiNi<sub>x</sub>Mn<sub>y</sub>Co<sub>z</sub>O<sub>2</sub>;
NMCs), as they lose oxygen at lower operating voltages.</p> | Bernardine L. D. Rinkel; David S. Hall; Israel Temprano; Clare P. Grey | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c95469df454c3f440f0/original/electrolyte-oxidation-pathways-in-lithium-ion-batteries.pdf |
6426a6a0647e3dca99cdbcad | 10.26434/chemrxiv-2023-fhmvj | Dumbbells, chains, and ribbons: anisotropic self-assembly of isotropic nanoparticles | Functionalizing the surface of metal nanoparticles can assure their stability in solution or mediate their self-assembly into aggregates with controlled shapes. Here we present a computational study of the colloidal aggregation of gold nanoparticles (Au NPs) isotropically functionalized by a mixture of charged and hydrophobic ligands. We show that, by varying the relative proportion of the two ligands, the NPs form anisotropic aggregates with markedly different topologies: dumbbells, chains, or ribbons. In all cases, two kinds of connections keep the aggregates together: hydrophobic bonds and ion bridges. We show that the anisotropy of the aggregates derives from the NP shell reshaping due to the formation of the hydrophobic links, while ion bridges are accountable for the “secondary structure” of the aggregates. Our findings provide a general physical principle that can also be exploited in different self-assembled systems: anisotropic/directional aggregation can be achieved starting from isotropic objects through a soft moldable surface. | Enrico Lavagna; Sebastian Salassi; Davide Bochicchio; GIULIA ROSSI | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Computational Chemistry and Modeling; Physical and Chemical Properties; Self-Assembly | CC BY 4.0 | CHEMRXIV | 2023-03-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6426a6a0647e3dca99cdbcad/original/dumbbells-chains-and-ribbons-anisotropic-self-assembly-of-isotropic-nanoparticles.pdf |
60c744beee301c3465c791cf | 10.26434/chemrxiv.9911783.v1 | Superelectrophilic Aluminum(III)-Ion Pairs Promote a Distinct Reaction Path for Carbonyl-Olefin Metathesis of Medium-Sized Rings | We describe the development of a new catalyst system for carbonyl-olefin ring-closing metathesis reactions that relies on Lewis acidic superelectrophiles and significantly expands the current scope of this transformation to medium-sized rings. <div>Importantly, these superelectrophiles are shown to promote carbonyl-olefin metathesis via a distinct and unprecedented mechanism. </div> | Rebecca Watson; Ashlee J. Davis; Jessica L. Gomez-Lopez; Daniel Nasrallah; Corinna Schindler | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744beee301c3465c791cf/original/superelectrophilic-aluminum-iii-ion-pairs-promote-a-distinct-reaction-path-for-carbonyl-olefin-metathesis-of-medium-sized-rings.pdf |
669ba8c301103d79c5a9e6c7 | 10.26434/chemrxiv-2024-xntct | Description of ion properties using molecular orbital energy levels | The study reveals correlations between the parameters of ions and their HOMO and LUMO orbital energy level values. In particular, it demonstrates a clear correlation for the ion adsorption parameters on model electrodes: the aluminum oxide (0001) surface, graphene and Au (111) surface. Correlations are also ob-served for the parameters of ion binding to water and dimethyl carbonate molecules, which are often used as solvents. In addition, the dipole moment, polarizability and solvation energy of ions are well correlated with the values of the molecular orbital energies, and for anions a dependence on the oxidation potential is observed. The obtained descriptors make it possible to select ions with desired values for a specific problem. As an illustrative example, in this work we consider the problem of displacement of water molecules from the inner electric double layer by ions, which is one of the factors increasing the potential window in electrolytes of aqueous batteries. This approach can be applied in the rapidly developing field of aqueous electrolytes for battery or supercapacitor design, catalysis control through surface composition variations, as well as in studies of heavy metal ion binding to sorption materials. | Sergey V. Doronin | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Electrochemistry - Mechanisms, Theory & Study; Physical and Chemical Properties; Solution Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669ba8c301103d79c5a9e6c7/original/description-of-ion-properties-using-molecular-orbital-energy-levels.pdf |
621f579497f21026a7fa5e24 | 10.26434/chemrxiv-2022-g64jp | Steering the Mechanism of the Furan-Maleimide Retro-Diels-Alder Reaction to a Sequential Pathway with an External Mechanical Force | Mechanical forces are known to control rates of chemical reactions and govern reaction pathways, possibly inducing a change of mechanism with respect to the zero force one. We report on a switching of mechanism of the retro Diels-Alder bond breaking from concerted at zero force to sequential under tension for four furan–maleimide adducts, mechanophores widely used in polymer mechanochemistry because they can undergo reversible breakage under tension. The four different adducts differ by their regio- and stereochemistry. The reaction paths on the force modified potential energy surfaces were characterized by isometric and isotensional approaches and determining stationary points (equilibrium geometries and transition states) as a function of the applied force, as well as by analyzing the redistribution of strain energy over the internal degrees of freedom. We evidence different bond breaking pathways and rate constants for the four isomers, the proximal configurations being favored over the distal ones. The switch from a concerted pathway at zero force to a sequential one occurs for a threshold force that is significantly higher (≈ 2.4 nN) for the distal-exo adduct than for the other three (≈ 1 nN), explaining its larger resistance to breaking and its almost inert character under tension. The switch is accompanied by the rupture of one of the two scissile bonds which leads to a twice smaller imaginary frequency of the transition state and an increase of the activation barrier, which then decreases for higher force strengths (> 3nN) to become barrierless at a critical force value. | Manuel Cardosa-Gutierrez; Guillaume De BO; Anne-Sophie Duwez; Francoise Remacle | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621f579497f21026a7fa5e24/original/steering-the-mechanism-of-the-furan-maleimide-retro-diels-alder-reaction-to-a-sequential-pathway-with-an-external-mechanical-force.pdf |
667255475101a2ffa8eb0ae7 | 10.26434/chemrxiv-2024-8kw51-v2 | Non-fertilizer uses of phosphorus | Phosphorus is a non-substitutable element required for the storage of genetic information, energy transfer and the structural integrity of biological systems. Agricultural use of phosphorus fertilizers and supplements aims to balance the biological phosphorus stoichiometry, for optimal growth and yield of crops and animals. Most of the commercial phosphorus industry aims to produce phosphates and polyphosphates for fertilizers. However, about 10% of the mineral resources are allocated for non-fertilizer uses via purification of phosphoric acid, or thermal processing of phosphate rock to elemental phosphorus to white phosphorus (P4), which serves as the parent compound for hundreds of phosphorus-containing derivatives with diverse chemistry and practical uses. True P4 derivatives are made only from P4 and include intermediates such as phosphorus pentoxide (P2O5), phosphorus trichloride (PCl3), phosphorus oxychloride (POCl3), phosphorus pentachloride (PCl5), phosphorus pentasulphide (P2S5), phosphines (containing PH3), red P (amorphous elemental P), hypophosphites (H2PO2-) and phosphides (P3-). This review explains the synthesis and applications of these non-fertilizer phosphorus compounds as flame retardants and plastic stabilizers, for metal sequestration and extraction, in catalyst ligands, as electrolytes in batteries, as crop protection agents and as anti-wear substances. | Willem Schipper | Chemical Engineering and Industrial Chemistry; Industrial Manufacturing | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667255475101a2ffa8eb0ae7/original/non-fertilizer-uses-of-phosphorus.pdf |
670c553912ff75c3a153da31 | 10.26434/chemrxiv-2024-fxq2s-v2 | COCONUT 2.0: A comprehensive overhaul and curation of the collection of open natural products database | The COCONUT (COlleCtion of Open Natural prodUcTs) database was launched in 2021 as an aggregation of openly available natural product datasets and has been one of the biggest open natural product databases since. Apart from the chemical structures of natural products, COCONUT contains information about names and synonyms, species, and organism parts in which the natural product has been found, geographic information about where the respective sample has been collected, and literature references, where available. COCONUT is openly accessible at https://coconut.naturalproducts.net. Users can search textual information and perform structure, substructure, and similarity searches. The data in COCONUT is available for bulk download as SDF, CSV, and a database dump. The web application for accessing the data is open-source. Here, we describe COCONUT 2.0, for which the web application has been completely rewritten, and the data has been newly assembled and extensively curated. New features include data submissions by users and community curation facilitated in various ways. | Venkata Chandrasekhar Nainala; Kohulan Rajan; Sri Ram Sagar Kanakam; Nisha Sharma; Viktor Weißenborn; Jonas Schaub; Christoph Steinbeck | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Chemoinformatics; Drug Discovery and Drug Delivery Systems; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670c553912ff75c3a153da31/original/coconut-2-0-a-comprehensive-overhaul-and-curation-of-the-collection-of-open-natural-products-database.pdf |
60c75538f96a001e9b2887f4 | 10.26434/chemrxiv.13151069.v1 | Intrinsically Polar Piezoelectric Self-Assembled Oligopeptide Monolayers | <div><div><div><p>Flexible, bio-compatible piezoelectric materials are of considerable research interest for a variety of applications, but many suffer from low response or high cost to manufacture. Herein, novel piezoelectric force and touch sensors based on self-assembled monolayers of oligopeptides are presented which produce large piezoelectric voltage response and are easily manufactured without the need for electrical poling. While the devices generate modest piezoelectric charge constants (d33) of up to 9.8 pC N−1, they exhibit immense piezoelectric voltage constants (g33) up to 2 V m N−1. Furthermore, a flexible device prototype is demonstrated that produces open-circuit voltages of nearly 6 V under gentle bending motion. Improvements in peptide selection and device construction promise to further improve the already outstanding voltage response and open the door to numerous practical applications.</p></div></div></div> | Christopher Petroff; Giuseppe Cassone; Jiří Šponer; Geoffrey Hutchison | Biocompatible Materials; Piezoelectricity and Thermoelectricity; Interfaces; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75538f96a001e9b2887f4/original/intrinsically-polar-piezoelectric-self-assembled-oligopeptide-monolayers.pdf |
66ed4b0d12ff75c3a1e8aaa0 | 10.26434/chemrxiv-2024-dwwm6 | High Charge Carrier Mobility in Porphyrin Nanoribbons | Polydisperse edge-fused nickel(II) porphyrin nanoribbons have been synthesized by Yamamoto coupling followed by gold(III)-mediated fusion, with average degrees of polymerization of up to 37 repeat units (length 31 nm). Time-resolved optical-pump terahertz spectroscopy measurements indicate that photo-generated charge carriers have dc mobilities of up to 205 cm2 V–1 s–1 in these nanoribbons, exceeding the values previously reported for most other types of nanoribbon or π-conjugated polymer. | He Zhu; Guanzhao Wen; Wenhao Zheng; Nicholas Rees; Wojciech Stawski; Hai Wang; Mischa Bonn; Harry Anderson | Organic Chemistry; Polymer Science; Physical Organic Chemistry; Conducting polymers; Organic Polymers; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ed4b0d12ff75c3a1e8aaa0/original/high-charge-carrier-mobility-in-porphyrin-nanoribbons.pdf |
67d15003fa469535b9f5cd35 | 10.26434/chemrxiv-2025-k7dtx | Structural Revisions of Macrocyclic Ellagitannin Dimers Bridged by Two Hexahydroxydiphenoyl Groups | Ellagitannin dimers, 1,1′;2,2′-diHHDP-diglucose and 3,3′;4,4′-diHHDP-6,6′-digalloyl-diglucose, were recently isolated from the wood of the sweet chestnut (Castanea sativa Mill.). These compounds were originally reported to possess unprecedented macrocyclic dimeric structures bridged by two hexahydroxydiphenoyl (HHDP) groups. However, reinvestigation of their spectroscopic data revealed that these compounds correspond to known ellagitannin monomers, namely 2,3-O-(Sa)-HHDP-D-glucopyranose and gemin D (3-O-galloyl-4,6-O-(Sa)-HHDP-D-glucopyranose), respectively. A comparison of the originally reported NMR data for 1,1′;2,2′-diHHDP-diglucose and 3,3′;4,4′-diHHDP-6,6′-digalloyl-diglucose with those of authentic 2,3-O-(Sa)-HHDP-D-glucopyranose and gemin D, in combination with DFT-based NMR chemical shift calculations, unequivocally confirmed these structural revisions. | Ryo Ohtsuka; Yosuke Matsuo; Yoshinori Saito; Koji Yamada; Takashi Tanaka; Fumika Yakushiji | Theoretical and Computational Chemistry; Organic Chemistry; Agriculture and Food Chemistry; Bioorganic Chemistry; Natural Products; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2025-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d15003fa469535b9f5cd35/original/structural-revisions-of-macrocyclic-ellagitannin-dimers-bridged-by-two-hexahydroxydiphenoyl-groups.pdf |
618d8cbbe0ea84f61e93ca16 | 10.26434/chemrxiv-2021-89q05 | Supramolecular Reinforcement of a Large Pore 2D Covalent Organic Framework | Two dimensional covalent organic frameworks
(2D-COFs) are a class of crystalline porous organic polymers that consist of covalently linked, two dimensional sheets that can stack together through non-covalent interactions. Here we report the synthesis of a novel COF, called PyCOFamide, which has an experimentally observed pore size that is greater than 6 nm in diameter. This is among the largest pore size reported to date for a 2D-COF. PyCOFamide exhibits permanent porosity and high crystallinity as evidenced by the nitrogen adsorption, powder X-ray diffraction, and high-resolution transmission electron microscopy. We show that the pore size of PyCOFamide is large enough to accommodate fluorescent proteins such as Superfolder green fluorescent protein and mNeonGreen. This work demonstrates the utility of non-covalent structural reinforcement in 2D-COFs to produce larger, persistent pore sizes than previously possible. | Shashini Diwakara; Whitney Ong; Yalini Wijesundara; Robert Gearhart; Fabian Herbert; Sarah Fisher; Gregory McCandless; Sampath Alahakoon; Jeremiah Gassensmith; Sheel Dodani; Ronald Smaldone | Organic Chemistry; Supramolecular Chemistry (Org.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618d8cbbe0ea84f61e93ca16/original/supramolecular-reinforcement-of-a-large-pore-2d-covalent-organic-framework.pdf |
678f83c181d2151a02172269 | 10.26434/chemrxiv-2024-53jpl-v2 | First Principles Assessment of Solvent Induced Cage Effects on Intramolecular Hydrogen Transfer in the Free Radical Polymerization of Acrylates | We investigate the rate constant of poly-butyl acrylate backbiting between 310 and 510 K using semi-empirical metadynamics in the gas phase, bulk and solution. The simulations in condensed phase are performed through a hybrid quantum mechanics/molecular mechanics approach. The free energy landscape associated to the reactive events in vacuum and in condesed phase are used to correct harmonic transition state theory (TST) rate constants. The Arrhenius parameters so determined are introduced in a semi-detailed mechanistic kinetic mechanism of butyl acrylate polymerization in bulk and in solution, allowing to test how butyl acrylate polymerization rate is affected by solvent-induced cage effects on backbiting. The results show that the backbiting rate constant is higher in the condensed phase than in the gas phase. In addition, a twofold increase is observed in xylene compared to bulk. These results differ significantly from previous theoretical calculations, especially at high temperatures, aligning better with experimental rate measurements. The semi-detailed model, incorporating our calculated rate coefficients, is validated against monomer concentration profiles from bulk and solution polymerizations in various reactor configurations, demonstrating good agreement with experimental data. This study paves the way for developing detailed kinetic models in the condensed phase using a priori kinetic parameters derived from molecular simulations, thus widening their range of applicability beyond the one experimentally accessible. | Francesco Serse; Matteo Salvalaglio; Matteo Pelucchi | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Reaction Engineering; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678f83c181d2151a02172269/original/first-principles-assessment-of-solvent-induced-cage-effects-on-intramolecular-hydrogen-transfer-in-the-free-radical-polymerization-of-acrylates.pdf |
664bb48a418a5379b0d3c257 | 10.26434/chemrxiv-2024-zfbs2 | Unlocking Delocalization: How Much Coupling Strength can Overcome Energy Disorder in Molecular Polaritons? | We investigated the criteria to ensure delocalization exists in molecular polaritons – quasiparticles formed from the collective strong coupling of light and matter that have shown capabilities to modify chemical reactions. Importantly, delocalization, i.e., polaritons possess delocalized wavefunctions, is one of the hallmarks of polaritons which enables energy transport and chemical dynamics. Delocalization in polariton systems has been long assumed to be robust against energy disorder that is ubiquitous in real molecular systems. However, this study reveals that disorder destroys delocalization in polaritons. In order to mitigate the impact of disorder, a collective coupling strength exceeding 3 times the inhomogeneous linewidth is necessary. When the coupling strength is smaller, the delocalization properties of polaritons are significantly compromised both in a static picture and from a dynamic point of view. This observation indicates a more stringent criterion for preserving the unique characteristics of polaritons compared to the conventionally adopted standard (collective coupling strengths larger than photonic and molecular spectral linewidths). This work sheds lights on previous works to explain why the onset of modified dynamics is larger than the strong coupling criteria, and also serves as an important consideration for existing and future polariton studies involving high levels of energy disorder. | Tianlin Liu; Guoxin Yin; Wei Xiong | Physical Chemistry; Quasiparticles and Excitations | CC BY NC 4.0 | CHEMRXIV | 2024-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664bb48a418a5379b0d3c257/original/unlocking-delocalization-how-much-coupling-strength-can-overcome-energy-disorder-in-molecular-polaritons.pdf |
60c745c1f96a003c34286c3d | 10.26434/chemrxiv.10148684.v1 | Radiolysis Generates a Complex Organosynthetic Chemical Network | <p><a></a><a>Origins of life chemistry has
progressed from seeking out the production of specific molecules to seeking out
conditions in which macromolecular precursors may interact with one another in
ways that lead to biological organization. Reported precursor synthesis networks
generally lack biological organizational attributes. </a>Radical species are highly
reactive, but do their chemical reaction networks resemble living systems? Here we report the results of radiolysis reaction experiments that
connect abundant geochemical reservoirs to the production of carboxylic acids,
amino acids, and ribonucleotide precursors and study the topological properties
of the resulting network. The network exhibits attributes associated with
biological systems: it is hierarchically organized, there are families of
closed loop cycles, and the species and cycle histograms exhibit heterogeneous
(heavy-tailed) distributions. The core cycles of the network are made possible
by the high reactivity of radical species such as H and OH. Radiolysis is
implicated as a unique prerequisite for driving abiotic organosynthetic
self-organization. </p> | Zachary Adam; Albert C. Fahrenbach; Sofia Marie Jacobson; Betul Kacar; Dmitry
Yu. Zubarev | Geochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745c1f96a003c34286c3d/original/radiolysis-generates-a-complex-organosynthetic-chemical-network.pdf |
62cdc62381efd03336a6c5c4 | 10.26434/chemrxiv-2022-61gmn | Chloride-Mediated Alkene Activation Drives Enantioselective Thiourea and Hydrogen Chloride Co-Catalyzed Prins Cyclizations | The mechanism of chiral hydrogen-bond donor (HBD) and hydrogen chloride (HCl) co-catalyzed Prins cyclizations was analyzed through a combination of experimental and computational methods and revealed to involve an unexpected and previously unrecognized mode of alkene activation. Kinetic and spectroscopic studies support the participation of a HCl•HBD complex that displays reduced Brønsted acidity relative to HCl alone. Nevertheless, rate acceleration relative to the HCl-catalyzed background reaction as well as high levels of enantioselectivity are achieved. This inverse Brønsted correlation is ascribed to chloride-mediated substrate activation in the rate-limiting and enantiodetermining cyclization transition state. Density-functional theory (DFT) calculations, distortion–interaction analysis, and quasiclassical dynamics simulations support a stepwise mechanism in which rate acceleration and enantioselectivity are achieved through precise positioning of the chloride anion within the active site of the chiral thiourea to enhance the nucleophilicity of the alkene and provide transition state stabilization through local electric field effects. This mode of selective catalysis through anion positioning likely has general implications for the design of enantioselective Brønsted acid catalyzed reactions involving π-nucleophiles. | Dennis Kutateladze; Corin Wagen; Eric Jacobsen | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Acid Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62cdc62381efd03336a6c5c4/original/chloride-mediated-alkene-activation-drives-enantioselective-thiourea-and-hydrogen-chloride-co-catalyzed-prins-cyclizations.pdf |
67b8a0876dde43c908e00666 | 10.26434/chemrxiv-2025-rfc48-v2 | Spontaneous or Stimulated? Investigating Raman’s Detection Limits in Aqueous Environments | Raman spectroscopy is a powerful method for analyzing chemical compositions across diverse samples. Spontaneous Raman scattering (spRS) provides complete Raman spectra but typically yields low signal levels, requiring long signal integration times. In contrast, stimulat-ed Raman scattering (SRS) produces much stronger signals, allowing for rapid spectral acquisition, and has been widely used to accelerate chemical imaging. Despite advances in both techniques, it remains unclear which method offers superior limits of detection (LODs) for molecules in biological samples. While theoretical comparisons under ideal conditions suggest that performance depends on photon flux and integration time, no experimental studies have directly compared the LOD of spRS and SRS spectroscopy. In this study, we systemati-cally compare the LOD of frequency-domain spRS and SRS for water-soluble analytes in aqueous solutions, a common environment for biological specimens. We first introduce a simplified LOD estimation methodology by taking only three measurements to derive the dilu-tion maximum (DM). This methodology achieved LOD estimates closely aligned with those obtained through serial dilution. Using this approach, we assessed the impact of various parameters, including Stokes laser power, the presence of beam scanning, number of pixels, and pixel dwell time, on the LOD of SRS spectroscopy and determined optimal conditions for SRS. Our results demonstrate that at short inte-gration times, SRS exhibits shot-noise-limited performance, with LOD inversely proportional to the square root of the acquisition time. At longer integration times, photothermal effects can cause deviations from ideal LOD scenarios. Under optimized experimental conditions, spectral-domain SRS confidently detects ~700 μM dimethyl sulfoxide in water and 1 g/L glucose and bovine serum albumin in aqueous solutions without spectral averaging. This performance can surpass that of spRS spectroscopy, even with equal or longer integration times. | Karsten Mohn; Bin Dong; Shivam Mahapatra; Ishaan K. Singh; Justin P. Lomont; Boyong Wan; Chi Zhang | Analytical Chemistry; Analytical Chemistry - General; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b8a0876dde43c908e00666/original/spontaneous-or-stimulated-investigating-raman-s-detection-limits-in-aqueous-environments.pdf |
60c746c54c89190da8ad2bc9 | 10.26434/chemrxiv.11369628.v1 | Direct Measurement of the Visible to UV Photodissociation Processes for the PhotoCORM TryptoCORM | We apply laser photodissociation spectroscopy in the
gas phase to
TryptoCORM, a known photoCORM that has been shown to destroy <i>Escherichia coli</i> upon visible-light
activation. Our experiments allow us to fully map TryptoCORM’s photochemistry across a
wide wavelength range by using novel laser-interfaced mass
spectrometry (LIMS). We complement these measurements with Cryogenic
Ion Vibrational Spectroscopy (CIVS), to structurally characterise gaseous
TryptoCORM. | Rosaria Cercola; Kaitlyn Fischer; Summer Scherman; etienne garand; Natalie Wong; Anders Hammarback; Jason Lynam; Ian Fairlamb; Caroline E. H. Dessent | Bioinorganic Chemistry; Spectroscopy (Inorg.); Theory - Inorganic; Transition Metal Complexes (Inorg.); Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Physical and Chemical Processes; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746c54c89190da8ad2bc9/original/direct-measurement-of-the-visible-to-uv-photodissociation-processes-for-the-photo-corm-trypto-corm.pdf |
663bc49b418a5379b0cc98ff | 10.26434/chemrxiv-2024-gr0ll | Illuminating Disorder: Optical Properties of Complex Plasmonic Assemblies | The optical properties of disordered plasmonic nanoparticle assemblies can be continuously tuned through the structural organization and composition of their colloidal building blocks. However, progress in the design and experimental realization of these materials has been limited by challenges associated with controlling and characterizing disordered assemblies and predicting their optical properties. This perspective discusses integrated studies of experimental assembly of disordered optical materials, such as doped metal oxide nanocrystal gels and metasurfaces, with electromagnetic computations on large-scale simulated structures. The simulations prove vital for connecting experimental parameters to disordered structural motifs and optical properties, revealing structure-property relations that inform design choices. Opportunities are identified for optimizing optical property designs for disordered materials using computational inverse methods and tools from machine learning. | Zachary M. Sherman; Jiho Kang; Delia J. Milliron; Thomas M. Truskett | Theoretical and Computational Chemistry; Materials Science; Nanostructured Materials - Materials; Optical Materials; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2024-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663bc49b418a5379b0cc98ff/original/illuminating-disorder-optical-properties-of-complex-plasmonic-assemblies.pdf |
60c74ec5702a9b73e118ba6e | 10.26434/chemrxiv.12800168.v1 | Isomerization Reactions in Anionic Mesoionic Carbene-Borates and Control of Properties and Reactivities in the resulting CoII Complexes through Agostic Interactions | A unique rearrangement reaction is presented for borate containing mesoionic carbenes. The corresponding Co<sup>II</sup> complexes display spin states, coordination geeometries and reactivities that are controlled through aogstic interactions on the secondary coordination sphere. A comprehensive NMR spectroscopic, crystallographic, EPR spectroscopic and theoretical study is presented on the ligands and the metal complexes.<br /> | Biprajit Sarkar; Jessica Stubbe; Nicolás I. Neuman; Ross McLellan; Michael G. Sommer; Maite Nößler; Julia Beerhues; Robert Mulvey | Bond Activation; Coordination Chemistry (Organomet.); Ligand Design; Spectroscopy (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ec5702a9b73e118ba6e/original/isomerization-reactions-in-anionic-mesoionic-carbene-borates-and-control-of-properties-and-reactivities-in-the-resulting-co-ii-complexes-through-agostic-interactions.pdf |
67d03e6181d2151a02ff6f7b | 10.26434/chemrxiv-2025-8k236 | A combined density functional and coupled-cluster theory study on correlation-bound anions of perfluorinated compounds | Perfluorinated cage molecules are hypothesized to have excellent electron-capture abilities, since they have the capacity to host an electron inside the carbon framework. The formed anions have been characterized as correlation-bound, meaning that they are unbound at the Hartree-Fock level. In this paper, we assess the performance of Hartree-Fock theory, density functional and coupled-cluster methods for the calculation of electron affinities of perfluorotetrahedrane, perfluorocubane, perfluoroadamantane and perfluorobenzene. We also characterize the anionic states using the electronic Fukui function and the electron localization function, and investigate geometry changes upon electron attachment. To this end, use is made of the charge stabilization method for describing metastable anionic states whenever they occur. Hartree-Fock theory indeed fails to describe attachment and detachment energies correctly and leads to inaccuracies in the obtained electron densities. For valence anions, density functional theory turns out to perform at a similar level as spin-scaled versions of the second-order approximate coupled cluster singles and doubles theory with the resolution-of-the-identity, but is not as accurate for describing correlation-bound anions. Only for the largest considered cage molecule, perfluoroadamantane, we found evidence for electron capture inside the cage, and this only before the molecular geometry was allowed to relax. For anions that are described as metastable, the localization inside the cage became less pronounced. | Charlotte Titeca; Garrette Pauley Paran; Frank De Proft; Thomas-Christian Jagau | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d03e6181d2151a02ff6f7b/original/a-combined-density-functional-and-coupled-cluster-theory-study-on-correlation-bound-anions-of-perfluorinated-compounds.pdf |
62430dbe7ffcd43620e21742 | 10.26434/chemrxiv-2022-2xrx4 | Concise Syntheses of ent-Aquilanol A and Aquilanol B via Retro-cycloisomerization of (-)-Caryophyllene Oxide. Access to Medium-sized Oxygenated Carbocyclic Scaffolds | The first concise synthesis of naturally occurring aquilanols A and B, two unprecedented 7/10 bicyclic sesquiterpenoids, is present-ed. Key features of the synthesis are a retrocycloisomerization event on (-)-caryophyllene oxide to form the eleven-membered car-bocyclic frame and an intramolecular epoxide opening to construct the bicyclic skeleton. The latter provides evidence to plausible biosynthesis of natural compounds, rendering our synthesis biomimetic. Our plan provides selectively access to other medium-sized carbocyclic oxygenated compounds, thus enhancing the structural diversity of final products. | Anastasia Maliori; Theodora Athanasiadou; Venetia Psomiadou; Christos Stathakis | Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-03-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62430dbe7ffcd43620e21742/original/concise-syntheses-of-ent-aquilanol-a-and-aquilanol-b-via-retro-cycloisomerization-of-caryophyllene-oxide-access-to-medium-sized-oxygenated-carbocyclic-scaffolds.pdf |
60c756a0702a9bb5cc18c92b | 10.26434/chemrxiv.14282021.v1 | Superconcentrated Electrolytes Widens Insertion Electrochemistry to Soluble Layered Halides | Insertion compounds provide the fundamental
basis of today’s commercialized Li-ion batteries. Throughout history, intense
research has focus on the design of stellar electrodes mainly relying on
layered oxides or sulfides, and leaving aside the corresponding halides because
of solubility issues. This is no longer true. In this work, we show for the
first time the feasibility to reversibly intercalate electrochemically Li<sup>+</sup>
into VX<sub>3</sub> compounds (X = Cl, Br, I) via the use of superconcentrated
electrolytes, (5 M LiFSI in dimethyl carbonate), hence opening access to a
novel family of Li<sub>x</sub>VX<sub>3</sub> phases. Moreover, through an
electrolyte engineering approach we unambiguously prove that the positive attribute
of superconcentrated electrolytes against solubility of inorganic compounds is
rooted in a thermodynamic rather than a kinetic effect. The mechanism and
corresponding impact of our findings enrich the fundamental understanding of
superconcentrated electrolytes and constitute a crucial step in the design of
novel insertion compounds with tunable properties for a wide range of
applications beyond Li-ion batteries. | Nicolas Dubouis; Thomas Marchandier; Gwenaëlle Rousse; Florencia Marchini; François Fauth; Maxim Avdeev; Antonella Iadecola; Benjamin Porcheron; Michael Deschamps; Jean-Marie Tarascon; Alexis Grimaud | Solid State Chemistry; Energy Storage; Solution Chemistry; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756a0702a9bb5cc18c92b/original/superconcentrated-electrolytes-widens-insertion-electrochemistry-to-soluble-layered-halides.pdf |
6478eff1e64f843f412a9b0f | 10.26434/chemrxiv-2022-f90tv-v4 | Assessing the validity of NMR relaxation rates obtained from coarse-grained simulations of PEG-water mixtures | NMR relaxometry is a powerful and well-established experimental approach to characterize dynamic processes in soft matter systems. All-atom (AA) resolved simulations are typically employed to gain further microscopic insights while reproducing the relaxation rates R1. However, such approaches are limited to time and length-scales that hinder modeling of systems like long polymer chains or hydrogels. Coarse-graining (CG) can overcome this barrier at the cost of loosing atomistic details that impede the calculation of NMR relaxation rates. Here, we address this issue by systematic characterization of dipolar relaxation rates R1 while performing systematic measurements on a PEG-H2O mixture at two different levels of details: AA and CG. Remarkably, we show that NMR relaxation rates R1 obtained at the CG level obey the same trends when compared to AA calculations, but with a systematic offset. This offset is due to, on the one hand, the lack of an intra-monomer component and, on the other hand, the inexact positioning of the spin carriers. We show that the offset can be corrected for quantitatively by reconstructing a posteriori the atomistic details for the CG trajectories. | Simon Gravelle; David Beyer; Mariano Brito; Alexander Schlaich; Christian Holm | Physical Chemistry; Polymer Science; Statistical Mechanics; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6478eff1e64f843f412a9b0f/original/assessing-the-validity-of-nmr-relaxation-rates-obtained-from-coarse-grained-simulations-of-peg-water-mixtures.pdf |
60c75908bdbb89019da3aea9 | 10.26434/chemrxiv.12762269.v2 | Magnetic control over the fractal dimension of supramolecular rod networks | <p>Controlling supramolecular polymerization is of fundamental importance to create advanced materials and devices. Here we show that the thermodynamic equilibrium of Gd<sup>3+</sup>-bearing supramolecular rod networks is shifted reversibly at room temperature in a static magnetic field of up to 2 T. Our approach opens opportunities to control the structure formation of other supramolecular or coordination polymers that contain paramagnetic ions.</p> | Vincent Marichez; Akihiro Sato; Peter Dunne; Jorge Leira-Iglesias; Georges Formon; Michaela Schicho; Isja de Feijter; Pascal Hébraud; Matthieu Bailleul; Pol Besenius; M. Venkatesan; J.M.D. Coey; E.W. (Bert) Meijer; Thomas Hermans | Supramolecular Chemistry (Org.); Magnetic Materials; Magnetism; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75908bdbb89019da3aea9/original/magnetic-control-over-the-fractal-dimension-of-supramolecular-rod-networks.pdf |
65ba415ee9ebbb4db959b8b9 | 10.26434/chemrxiv-2024-qfd6s | Dye adsorption studies using a novel bio-derived calcite material | As the global population increases, food production including aquaculture is increasing to provide for this. At the same time, this means more waste is produced. Waste from farming blue mussels (Mytilus edulis) is dominated by shells rich in calcite. A ‘soft’ calcite material prepared from waste mussels was investigated for its adsorptive properties and its possible use in wastewater remediation. The adsorption of two cationic dyes, methylene blue and safranin-O, on this material were evaluated through isothermal and kinetic modelling. The adsorption systems for both methylene blue and safranin-O can be described using Langmuir isotherms and the respective adsorption capacities were 1.81 mg/g and 1.51 mg/g. The adsorption process was dominated by pseudo-second order rate kinetics. | Sachel Christian-Robinson; Francesca Kerton | Analytical Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ba415ee9ebbb4db959b8b9/original/dye-adsorption-studies-using-a-novel-bio-derived-calcite-material.pdf |
6798d17bfa469535b92c1752 | 10.26434/chemrxiv-2024-4f99b-v2 | Zirconium Fluoride-Supported High-Entropy Fluoride: A
Catalyst for Enhanced Oxygen Evolution Reaction | Extended hydrogen initiatives promote the urgency of research on water splitting technologies and therein oxygen evolution reaction catalysts being developed. A route to access a ZrF4 supported high-entropy fluoride catalyst using a facile sol-gel route is presented. The high-entropy character of the catalyst was confirmed by scanning transmission electron microscopy and energy dispersive X-ray spectroscopy (STEM-EDX) as well as inductively coupled plasma-mass spectrometry (ICP-MS). Additional investigations on the local structure were performed using extended X-ray absorption fine structure spectroscopy (EXAFS) and pair distribution function (PDF) analysis. The catalyst shows significant potential for oxygen evolution reaction (OER) in alkaline media with a current density of 100 mA cm-2 at approximately 1.60 V, thus outperforming benchmark materials such as IrO2, despite a significant reduction in electrochemical mass loading. A potential mechanism is suggested based on free energy calculation using DFT calulations. | Christian Heinekamp; Arkendu Roy; Stephanos Karafiludis; Sourabh Kumar; Ana Guilherme Buzanich; Tomasz M. Stawski; Aistė Miliūtė; Marcus von der Au; Mike Ahrens; Thomas Braun; Franziska Emmerling | Catalysis; Energy; Electrocatalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6798d17bfa469535b92c1752/original/zirconium-fluoride-supported-high-entropy-fluoride-a-catalyst-for-enhanced-oxygen-evolution-reaction.pdf |
65c314419138d2316196dced | 10.26434/chemrxiv-2024-jk7p3 | Computing accurate bond dissociation energies of emerging per- and polyfluoroalkyl substances: Achieving chemical accuracy using connectivity-based hierarchy schemes | Understanding the bond dissociation energies (BDEs) of per- and polyfluoroalkyl substances (PFAS) bonds helps in devising their efficient degradation pathways. However, there is only limited experimental data on the PFAS BDEs, and there are uncertainties associated with the BDEs computed using density functional theory. Although quantum chemical methods like the G4 composite method can provide highly accurate BDEs (< 1 kcal mol-1), they are limited to small system sizes. To address DFT's accuracy limitations and G4's system size constraints, we examined the connectivity-based hierarchy (CBH) scheme and found that it can provide BDEs that are reasonably close to the G4 accuracy while retaining the computational efficiency of DFT. To further improve the accuracy, we modified the CBH scheme and demonstrated that BDEs calculated using it have a mean-absolute deviation of 0.7 kcal mol-1 from G4 BDEs. To validate the reliability of this new scheme, we computed the ground state free energies of seven PFAS compounds and BDEs for 44 C–C and C–F bonds at the G4 level of theory. Our results suggest that the modified CBH scheme can accurately compute the BDEs of both small and large PFAS at near G4 level accuracy, offering promise for more effective PFAS degradation strategies. | Samir Kumar Nayak; Sharma S. R. K. C. Yamijala | Earth, Space, and Environmental Chemistry; Environmental Science; Hydrology and Water Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c314419138d2316196dced/original/computing-accurate-bond-dissociation-energies-of-emerging-per-and-polyfluoroalkyl-substances-achieving-chemical-accuracy-using-connectivity-based-hierarchy-schemes.pdf |
654d39b3dbd7c8b54bf817cf | 10.26434/chemrxiv-2023-bqnt6 | Quantum Dynamical Averaging Over an Ensemble of Molecular Orientations by a Singular Value Decomposition of the Density Matrix | We report a robust and compact methodology for averaging quantum photoexcitation dynamics over the initial orientations of the molecules with respect to an ultrashort light pulse. We use singular value decomposition of the density matrix of the excited molecules which allows identifying the few dominant principal molecular orientations with respect to the polarization direction of the electric field. The massive compaction of the density matrix of the ensemble of randomly oriented pumped molecules enables a most efficient fully quantum mechanical time propagation scheme. Two examples are discussed for the quantum dynamics of the LiH molecule in the manifolds of its electronically excited Sigma and Pi states. | Manuel Cardosa-Gutierrez; Raphael D. Levine; Francoise Remacle | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654d39b3dbd7c8b54bf817cf/original/quantum-dynamical-averaging-over-an-ensemble-of-molecular-orientations-by-a-singular-value-decomposition-of-the-density-matrix.pdf |
65e092d19138d2316153500a | 10.26434/chemrxiv-2024-7jn0d | Life cycle assessment of a process for paracetamol flow synthesis from bio-waste derived β-pinene | The synthesis of functional molecules from bio-waste feedstocks with retention of key structural molecular motifs is a potentially effective strategy to replace conventional fossil-based synthesis routes. In this work we are focusing on the synthesis of functional molecules from terpenes, a class of underutilised bio-waste molecules generated, for instance, as a by-product of Kraft paper pulping. Recent literature studies demonstrated a possible pathway for a continuous flow synthesis of paracetamol from β-pinene. While this process is currently not of commercial interest, the available literature synthesis demonstrates the technical feasibility of such chemical conversion as well as several new chemical transformations. However, the environmental efficiency of the proposed flow synthesis was not determined. Here, we perform a life cycle assessment to quantify the environmental impacts of a potential industrial-scale paracetamol manufacture from bio-waste β-pinene. For this purpose, scaled-up process models of continuous paracetamol manufacture were developed in Aspen Plus and a complete life cycle inventory was estimated. A GWP of 58 kg CO2-eq./kg product was predicted, and key impact contributing aspects of the designed process were identified through a hotspot analysis. A comparative feedstock analysis showed that β-pinene derived from Kraft pulping waste can be a cleaner feedstock than the benchmark feedstock benzene. The obtained LCA results represent highly conservative estimates, given the early design stage, and thus promise to surpass standard industry practises, once optimised. The results presented in this study can serve as a basis for comparison against conventional paracetamol production LCA datasets. | Sabine Hallamasek; Veera Ubbenjans; Alexei Lapkin | Chemical Engineering and Industrial Chemistry; Industrial Manufacturing | CC BY 4.0 | CHEMRXIV | 2024-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e092d19138d2316153500a/original/life-cycle-assessment-of-a-process-for-paracetamol-flow-synthesis-from-bio-waste-derived-pinene.pdf |
6328d0b8ba8a6d04fc551df7 | 10.26434/chemrxiv-2022-gx9gb | Unbiasing Retrosynthesis Language Models with Disconnection Prompts | Data-driven approaches to retrosynthesis have thus far been limited in user interaction, in the diversity of their predictions, and the recommendation of unintuitive disconnection strategies. Herein, we extend the notions of prompt- based inference in natural language processing to the task of chemical language modeling. We show that by using a prompt describing the disconnection site in a molecule, we can steer the model to propose a wider set of precursors, overcoming training data biases in retrosynthetic recommendations and achiev- ing a 39 % performance improvement over the baseline. For the first time, the use of a disconnection prompt empowers chemists by giving them back greater control over the disconnection predictions, resulting in more diverse and creative recommendations. In addition, in place of a human-in-the-loop strategy, we propose a schema for automatic identification of disconnection sites, followed by prediction of reactant sets, achieving a 100 % improvement in class diversity as compared to the baseline. The approach is effective in mitigating prediction biases deriving from training data. In turn, this provides a larger variety of usable building blocks, which improves the end-user digital experience. We demonstrate its application to different chemistry domains, from traditional to enzymatic reactions, in which substrate specificity is key. | Amol Thakkar; Alain Vaucher; Andrea Byekwaso; Philippe Schwaller; Alessandra Toniato; Teodoro Laino | Theoretical and Computational Chemistry; Organic Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6328d0b8ba8a6d04fc551df7/original/unbiasing-retrosynthesis-language-models-with-disconnection-prompts.pdf |
66e077c712ff75c3a1f5d0e3 | 10.26434/chemrxiv-2024-l2q53 | Universal Workflow Language and Software Enables Geometric Learning and FAIR Scientific Protocol Reporting | The modern technological landscape has trended towards increased precision and greater digitization of information. However, the methods used to record and communicate scientific procedures have remained largely unchanged over the last century. Written text as the primary means for communicating scientific protocols poses notable limitations in human and machine information transfer. Therefore, successful replication and analysis of experimental protocols necessitates a new approach for high-fidelity communication. In this work, we present the Universal Workflow Language (UWL) and the open-source Universal Workflow Language interface (UWLi). UWL is a graph-based data architecture that can capture arbitrary scientific procedures through workflow representation of protocol steps and embedded procedure metadata. It is machine readable, discipline agnostic, and compatible with Findable, Accessible, Interoperable, and Reusable reporting standards. UWLi is an accompanying software package for building and manipulating UWL files into tabular and plain text representations in a controlled, detailed, and multilingual environment. UWL transcription of protocols from three high-impact publications resulted in the identification of substantial deficiencies in the detail of the reported procedures. UWL transcription of these publications identified seventeen procedural ambiguities and thirty missing parameters for every one hundred words in published procedures. In addition to preventing and identifying procedural omission, UWL files were found to be compatible with geometric learning techniques for representing scientific protocols. In a surrogate function designed to represent an arbitrary multi-step experimental process, graph transformer networks were able to predict outcomes in approximately 6,000 fewer experiments than equivalent linear models. Implementation of UWL and UWLi into the scientific reporting process will result in higher reproducibility between both experimentalists and machines, thus proving an avenue to more effective modeling and control of complex systems. | Robert Epps; Amanda Volk; Robert White; Robert Tirawat; Rosemary Bramante; Joseph Berry | Materials Science; Energy; Chemical Engineering and Industrial Chemistry; Quality Control | CC BY NC 4.0 | CHEMRXIV | 2024-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e077c712ff75c3a1f5d0e3/original/universal-workflow-language-and-software-enables-geometric-learning-and-fair-scientific-protocol-reporting.pdf |
668f52c3c9c6a5c07aed7941 | 10.26434/chemrxiv-2024-x939w | Controlling Solvent Effects on in situ Pd Nanoparticle Synthesis Allows ß-Selective Heck Reactions of Unprotected Cinnamylamines | The control of regioselectivity for insertion reactions of allylamines is almost exclusively biased towards γ-functionalization for internal alkenes. Until recently these reactions also required protecting groups to prevent amine oxidation and other side reactions. To expand the synthetic toolbox to access unique new allylamine structures, we’ve found that by using the free amine, we have discovered a general method to synthesize complex allylamines through β-arylation with superior β-selectivity compared to traditional directing/protecting group-modified allylamine substrates which give preferentially γ-arylation or poor selectivity, demonstrating the orthogonality of free amine-directed methods. A comprehensive examina-tion of both the catalyst structure and role of the amine group is presented, with the proposed selectivity deriving from the amount of surface charge of the in situ-formed catalyst. | Kendra K. Shrestha; Olutayo N. Farinde; Abigail M. Gohmann; Radha Kondapalli; Vanaparthi Satheesh; Justin M. Maxwell; Vinod G. Landge; Allison V. Gottshall; G. Brant Hunt; Michael C. Young | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668f52c3c9c6a5c07aed7941/original/controlling-solvent-effects-on-in-situ-pd-nanoparticle-synthesis-allows-selective-heck-reactions-of-unprotected-cinnamylamines.pdf |
60c750bf4c8919572fad3e1a | 10.26434/chemrxiv.13078067.v1 | Formaldehyde-Doxorubicin Dual Polymeric Drug Delivery System for Higher Efficacy and Limited Cardiotoxicity of Anthracyclines | <p>We report the synthesis of a dual delivery
system composed of a chemically bound pH-responsive formaldehyde polymer
prodrug and pH-responsive doxorubicin loaded nanoparticles to increase the
therapeutic index of anthracyclines by limiting the cardiotoxicity of
doxocrubicin by working in synergy with formaldehyde to enable the formation of
DOX-DNA adducts. Polyacrylates bearing 1,2- and 1,3- pendant diols were
synthesized via reversible addition fragmentation chain transfer (RAFT)
polymerization to conjugate formaldehyde, forming 5- or 6-membered acetal rings
with tunable conjugation percentages (1.5 – 10 wt%) for controlled release in
acidic environments of the tumor extracellular matrix. The
formaldehyde-conjugated prodrugs are then combined with polyester nanoparticles
formed by intermolecular crosslinking via oxime click chemistry of less than
200 nm in size containing 14 wt% encapsulated Doxorubicin (DOX). Release
kinetics show a sustained release of both DOX and formaldehyde at pH 5.0,
mimicking the low pH of the tumor environment whereas insignificant release was
recorded at physiological pH. The cell viability of the dual delivery system
combination was evaluated in 4 T1 breast cancer cells resulting in a
considerably increase of cell death of about 4-fold compared to free DOX alone.
The resulting polymeric delivery system is the first example reported of a DOX
and formaldehyde co-administration, demonstrating the potential significant
effect of formaldehyde for an improved anti-cancer efficacy of DOX and towards
a reduced cardiotoxicity of DOX.</p> | Estela Ordonez; Laken Kendrick-Williams; EVA HARTH | Drug delivery systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750bf4c8919572fad3e1a/original/formaldehyde-doxorubicin-dual-polymeric-drug-delivery-system-for-higher-efficacy-and-limited-cardiotoxicity-of-anthracyclines.pdf |
65527f272c3c11ed7153014c | 10.26434/chemrxiv-2023-0lb60-v3 | Vibrational spectra of highly anharmonic water clusters:
Molecular dynamics and harmonic analyses revisited with
constrained nuclear-electronic orbital methods | Vibrational spectroscopy is widely used to gain insights into structural and dynamic properties of chemical, biological and material systems. Thus, an efficient and accurate method to simulate vibrational spectra is desired. In this paper, we justify and employ a microcanonical molecular simulation scheme to calculate the vibrational spectra of
three challenging water clusters: the neutral water dimer (H4O2), the protonated water trimer (H7O3+), and the protonated water tetramer (H9O4+). We find that with the accurate description of quantum nuclear delocalization effects through the constrained nuclear-electronic orbital framework, including vibrational mode coupling effects through molecular dynamics simulations can additionally improve the vibrational spectrum calculations. In contrast, without the quantum nuclear delocalization picture, conventional ab initio molecular dynamics may even lead to less accurate results than harmonic analysis. | Yuzhe Zhang; Yiwen Wang; Xi Xu; Zehua Chen; Yang Yang | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65527f272c3c11ed7153014c/original/vibrational-spectra-of-highly-anharmonic-water-clusters-molecular-dynamics-and-harmonic-analyses-revisited-with-constrained-nuclear-electronic-orbital-methods.pdf |
679c9fd9fa469535b98be180 | 10.26434/chemrxiv-2025-0p0zz | Molecular determinants of solvent nanoseparation by nanoporous carbon materials | The manifold tunable properties of nanoporous carbon materials, including high surface area, mechanical and chemical stability, electrical and thermal conductivity, rich surface chemistry, and biocompatibility render them a perfect platform for energy storage and conversion, catalysis, nanoseparation, water purification, and drug delivery. Here, we construct molecular models of nanoporous carbon materials and unveil the molecular determinants of solvent nanoseparation and self-diffusion by coarse-grained molecular dynamics simulations. Best nanoseparation is achieved at pore diameters just above size exclusion and surface oxidation is the major selective modifier of self-diffusion of polar molecules in solvent mixtures. The shape of the solvents, and to a lesser extent, the geometry of the pore network also influence nanoseparation. To quantify the impact of pore-network geometry, we derived a Markov state model, which estimates the probability of a molecule following a certain path. Our simulation framework for material construction, simulation, and analysis provides a robust foundation for future investigations on how solvent nanoseparation in amorphous nanoporous materials is governed by the interplay of surface chemistry, pore geometry, and molecular properties. | Sofia Kolin; Moritz Marquardt; Gotthold Fläschner; Stefan Naumann; Kristyna Pluhackova | Theoretical and Computational Chemistry; Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679c9fd9fa469535b98be180/original/molecular-determinants-of-solvent-nanoseparation-by-nanoporous-carbon-materials.pdf |
64e76bc53fdae147fabbf1bb | 10.26434/chemrxiv-2023-tvmr0 | Relaxation and ligand hyperfine effects in an isostructural early lanthanide series [Ln(Cptt)3] (Ln = Ce, Nd, Sm; Cptt = C5H3tBu2-1,3) by pulsed EPR spectroscopy | We examine lanthanide (Ln)-ligand bonding in a family of early Ln3+ complexes [Ln(Cptt)3] (1-Ln, Ln = La, Ce, Nd, Sm; Cptt = C5H3tBu2-1,3) by pulsed electron paramagnetic resonance (EPR) methods, and provide the first characterization of 1-La and 1-Nd by single crystal XRD, multinuclear NMR, IR and UV/Vis/NIR spectroscopy. We measure electron spin T1 and Tm relaxation times of 12 and 0.2 μs (1-Nd), 89 and 1 μs (1-Ce) and 150 and 1.7 μs (1-Sm), respectively, at 5 K: the T1 relaxation of 1-Nd is more than 102 times faster than its valence isolelectronic uranium analogue. 13C and 1H hyperfine sublevel correlation (HYSCORE) spectroscopy reveals that the extent of covalency is negligible in these Ln compounds, with much smaller hyperfine interactions than observed for equivalent actinide (Th and U) complexes. This is corroborated by ab initio calculations, confirming the predominant electrostatic nature of the metal-ligand bonding in these complexes. | Lydia Nodaraki; Jingjing Liu; Ana-Maria Ariciu; Fabrizio Ortu; Meagan Oakley; Letitia Birnoschi; Gemma Gransbury; Philip Cobb; Nicholas Chilton; David Mills; Eric McInnes; Floriana Tuna | Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e76bc53fdae147fabbf1bb/original/relaxation-and-ligand-hyperfine-effects-in-an-isostructural-early-lanthanide-series-ln-cptt-3-ln-ce-nd-sm-cptt-c5h3t-bu2-1-3-by-pulsed-epr-spectroscopy.pdf |
65434717c573f893f1a590e3 | 10.26434/chemrxiv-2023-66xp5 | Rapid and Self-Administrable Capillary Blood Microsampling Demonstrates Statistical Equivalence with Standard Venous Collections in NMR-Based Lipoprotein Analysis | We investigated plasma and serum blood derivatives from capillary blood microsamples (500 μL, MiniCollect® tubes) and corresponding venous blood (10 mL vacutainers). Samples from twenty healthy participants were analysed by 1H-NMR and 112 lipoprotein subfraction parameters; 3 supramolecular phospholipid composite (SPC) parameters from SPC1, SPC2, and SPC3 subfractions; 2 N-acetyl signals from α-1-acid glycoprotein (Glyc), GlycA and GlycB; and 3 calculated parameters, SPC (total), SPC3/SPC2, Glyc (total)—were assessed. Using linear regression between capillary and venous collection sites, explained variance (Adj. R2 ≥ 0.8, p < 0.001) was witnessed for 86% of plasma parameters (103/120), and 88% of serum parameters (106/120), indicating capillary lipoprotein, SPC, and Glyc concentration follows changes in venous concentra-tions. These results indicate capillary blood microsamples are suitable for sampling in remote areas and for high-frequency longitudinal sampling of the majority of lipoproteins, SPCs, and Glycs. | Jayden Lee Roberts; Luke Whiley; Nicola Gray; Melvin Gay; Philipp Nitschke; Reika Masuda; Elaine Holmes; Jeremy Kirk Nicholson; Julien Wist; Nathan Lawler | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65434717c573f893f1a590e3/original/rapid-and-self-administrable-capillary-blood-microsampling-demonstrates-statistical-equivalence-with-standard-venous-collections-in-nmr-based-lipoprotein-analysis.pdf |
60c753c7337d6c09dbe288ea | 10.26434/chemrxiv.13547813.v1 | Electrochemical Characterisations to Elucidate the Pseudocapacitance Mechanisms of a CdS/WOx Nanocomposite Photoanode in Acidic Aqueous Electrolytes | <p>The electrochemical
properties of a cadmium sulphide/tungsten(VI) sub-oxide (CdS/WO<sub>x</sub>) nanocomposite
have been explored using aqueous solutions of acetic acid (pH 2.2) and acidified
sodium acetate (pH 5.0), for the purpose of evaluating the origin of
pseudocapacitance within the material. Through transient photocurrent response,
galvanostatic charge/discharge and electrochemical impedance measurements, it
was established that cation-intercalation phenomena were principally responsible
for charge-accumulation in the composite and that the incorporation of ionic
species into interstitial surface sites was more energetically favourable for protons
than for sodium ions. The composite displayed promising capacitive performance
in the tested electrolytes, exhibiting Coulombic efficiencies of up to 88% under
galvanostatic cycling at 1.0 mA cm<sup>-2</sup> alongside a peak differential
capacitance value of 560 mF cm<sup>-2</sup> during the discharge phase. From
electrochemical impedance spectroscopy data it was further determined that whilst
illumination by white light acted to decrease the series resistance of the photoanode,
all other resistive and capacitive components of the impedance characteristics were
affected negligibly by the irradiation. In combination, the investigations detailed
herein provide an instructive resource for the development of CdS/WO<sub>x</sub>
composites and the optimisation of electrolytes to improve the performance and
chemical stability of such materials. Furthermore, the study serves as a potential
foundation from which to advance the concept of integrating the conversion and
storage of solar energy into a single dual-functional electrode, in turn
facilitating a new generation of photo-supercapacitor devices.</p> | Daniel Jones; Charles W. Dunnill | Composites; Core-Shell Materials; Nanostructured Materials - Materials; Electrochemical Analysis; Nanostructured Materials - Nanoscience; Electrochemistry; Energy Storage; Photovoltaics; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753c7337d6c09dbe288ea/original/electrochemical-characterisations-to-elucidate-the-pseudocapacitance-mechanisms-of-a-cd-s-w-ox-nanocomposite-photoanode-in-acidic-aqueous-electrolytes.pdf |
6763b42581d2151a022fa90c | 10.26434/chemrxiv-2024-xbsdb | Accounting for the Vibrational Contribution to the Configurational Entropy in Disordered Solids with Machine Learned Forcefields: A Case Study of Garnet Electrolyte Li7La3Zr2O12 | Accounting for lattice vibrations to accurately determine the phase stabilities of site-disordered solids is a long-standing challenge in computational material designs, due to the high computational cost associated with sampling the vast configurational space to obtain the converged thermodynamic quantities. One example is the garnet electrolyte Li7La3Zr2O12, the high-temperature and high-ion-mobility cubic phase of which is disordered in its Li+ site occupations, such that both the vibrational and configurational entropic contributions to its phase stability cannot be ignored. Understanding the subtle interplay between vibrational and configurational entropies in this material will therefore play a critical role in the rational manipulation of dopants and defects to stabilise cubic Li7La3Zr2O12 at room temperature for practical applications. Here, by developing machine learned forcefields based on an equivariant message-passing neural network SO3krates, we follow a strict statistical thermodynamic protocol to quantify the phase stability of cubic Li7La3Zr2O12 through structural optimisations, as well as molecular dynamic simulations at 300 and 1500 K, for a total of 70,120 configurations of cubic Li7La3Zr2O12. Although this only covers a tiny fraction of the configurational space (7x10^34 configurations in total), we are able to deterministically show the vibrational contributions to the total configurational free energy at 1500 K are significant (on the order of 1 eV/atom) in correctly ordering the stability of the cubic Li7La3Zr2O12 over its tetragonal counterpart, thanks to the high data efficiency, accuracy, stability and good transferability of the transformer-based equivariant network architecture behind SO3krates. Therefore, our work opens up new avenue to accelerate the accurate computational designs of disordered solids, such as solid electrolytes, for technologically important applications. | Jack Yang; Ziqi Yin; Sean Li | Theoretical and Computational Chemistry; Materials Science; Ceramics; Computational Chemistry and Modeling; Artificial Intelligence; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6763b42581d2151a022fa90c/original/accounting-for-the-vibrational-contribution-to-the-configurational-entropy-in-disordered-solids-with-machine-learned-forcefields-a-case-study-of-garnet-electrolyte-li7la3zr2o12.pdf |
6404ccb39789de3dd9f7fe6b | 10.26434/chemrxiv-2023-xdc31 | Excited State Electronic Structure and Dynamics in Diblock pi-Conjugated Oligomers | The excited state electronic structure and ultrafast energy transfer in two diblock oligomers F3-TBT and F3-mP-TBT was explored (F3 = tri-(9,9-dioctylfluorene), TBT = 4,7-di(thiophen-2-yl)benzo[c][1,2,5]thiadiazole, mP = meta-phenylene). These diblock oligomers feature strongly coupled, pi-conjugated F3 and TBT segments that have different bandgaps. In F3-TBT, the two conjugated chromophores are directly linked whereas in F3-mP-TBT the chromophores are spaced by a meta-linked phenylene unit. The oligomers excited state dynamics were probed by steady-state UV-visible absorption, fluorescence and excitation wavelength dependent ultrafast time resolved transient absorption (TA) spectroscopy. Density functional theory (DFT) calculations were applied to provide insight concerning the electronic structure of the oligomers. The diblock oligomers feature distinct absorption bands due to transitions mainly localized on the F3 (high energy) and TBT (low energy) segments. Time-dependent DFT calculations support the assignments of the electronic transitions. Ultrafast TA spectroscopy with excitation corresponding to the low energy TBT unit reveals that the initial excitation is localized on TBT and does not vary with time. By contrast, excitation corresponding to high energy F3 produces an excited state that evolves rapidly (200 300 fs) into the lower energy state that is localized on the TBT chromophore. The ultrafast process is attributed to relaxation of an excited state that is predominantly localized on F3 into a lower energy state that is localized on TBT. The extent of delocalization of the initial state and the rate of relaxation depends on the extent of electronic coupling between the F3 and TBT segments. | Kirk Schanze; Habtom Gobeze; Daniel Martinez | Physical Chemistry; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6404ccb39789de3dd9f7fe6b/original/excited-state-electronic-structure-and-dynamics-in-diblock-pi-conjugated-oligomers.pdf |
60c756a0ee301c7fe8c7b3b7 | 10.26434/chemrxiv.14275652.v1 | Transforming Growth Factor-β1 Is Resilient to Heat-Induced Conformational Change | TGF-beta1 is an essential signaling protein in numerous important biological pathways. Traditionally, TGF-beta1 is considered a sensitive protein so that this protein was handled with extreme care for production and storage. TGF-beta1 also exists in foods from animal sources, such as milk, and has been proven to be absorbed through ingestion. The food sourced TGF-beta1 was also not considered active after normal food processing, such as heating. Our research calls into question these concepts and encourages the research community to reconsider the activity of heated TGF-beta1 for both biomedical and nutrition applications.<br /> | Rui Tang; Kaelyn Gasvoda; Jacob Rabin; Eben Alsberg | Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756a0ee301c7fe8c7b3b7/original/transforming-growth-factor-1-is-resilient-to-heat-induced-conformational-change.pdf |
674c119f7be152b1d08ebb86 | 10.26434/chemrxiv-2024-3gh15 | Suspended water at/near room temperature and new physical state of systematically isolated ions and molecular clusters with high electrical mobility | The macroscopic levitation and zero-resistance characteristics exhibited by superconductivity are truly impressive. However, achieving and manipulating levitation at the microscopic level poses significant challenges, including the non-ideal behavior of microscopic particles, maintaining long-term stability, and precise control of particle motion. This paper introduces an innovative strategy that utilizes the spontaneous electrostatic equilibrium established between ionic charges and polar molecules in solution within confined spaces to create a stable microscopic levitation state over a broad temperature range. This novel state of matter transcends traditional classifications of solid, liquid, and gas, with a density between that of a solid and a gas, and exhibits unique structural features. Through the combination of molecular dynamics simulations and first-principles calculations, we have discovered, for the first time, a levitated water form with a density nearly a thousand times that of water vapor, existing in a suspended state with charged ions at room or near-room temperatures. In this unique state of matter, chloride ions achieve an electrical mobility equivalent to that of hydrogen ions and higher than that of hydroxyl ions due to the unique structure of levitated water. As the temperature further decreases, water molecules arrange orderly into chain-like networks, forming porous, atomically precise charged ice structures. We have also identified levitated clusters with a density over a hundred times that of water vapor and about one-ninth that of a solid. Compared to the aforementioned levitated water, these clusters have a lower density and an increased ion ratio, transforming levitated water into a system composed of isolated ions and molecular clusters. These clusters, in the form of several water molecules combined with charged ions or individual ions, levitate independently in space, filling the confined space with a spacing much larger than that of a solid lattice. Even at temperatures below the freezing point of water, this new state of matter remains unfrozen and retains high electrical mobility similar to hydrogen ions. Furthermore, this paper elucidates the principles of preparing charged solutions and pure single-ion charged solutions, as well as the design of related instrumental systems. Finally, we discuss the observability of microscopic levitation states and their potential applications. In summary, microscopic levitation states offer a promising yet challenging research frontier. By developing novel levitation mechanisms and control techniques, this paper achieves more precise and stable levitation of microscopic particles, explores new physical phenomena and laws, and provides fresh insights and methodologies for scientific research and technological innovation, potentially revealing more mysteries of the material world. | Miao Zhongzheng | Physical Chemistry; Materials Science; Nanoscience; Nanostructured Materials - Materials; Nanodevices; Clusters | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674c119f7be152b1d08ebb86/original/suspended-water-at-near-room-temperature-and-new-physical-state-of-systematically-isolated-ions-and-molecular-clusters-with-high-electrical-mobility.pdf |
64e4521801042bc1cc780764 | 10.26434/chemrxiv-2023-dt8kb | Bowl-Direction Control of Monofluorosumanene in the Solid State | A new curved π-conjugated molecule-1-fluorosumanene (1) was designed and synthesized which possesses one fluorine atom on the benzylic carbon of sumanene. This compound is able to exhibit bowl inversion in solution, leading to the formation of two diastere-omers 1endo and 1exo with different dipole moment. Experimental and theoretical investigation revealed energetical relationship among 1exo, 1endo and solvent to realize the control of exo:endo ratio in the single crystals of 1 by the correct choice of the crystalliza-tion solvent. Significantly, the molecular dynamics (MD) simulations revealed that 1exo positively worked for elongation of the stacking structure and the final exo:endo ratio was affected by the relative stability difference between 1endo and 1exo derived by solv-ation. Such controllable exo:endo ratio of 1 realized the preparation of unique materials showing totally different dielectric response from the same molecule 1 just by changing crystallization solvent. | Yumi Yakiyama; Minghong Li; Dongyi Zhou; Tsuyoshi Abe; Chisato Sato; Kohei Sambe; Tomoyuki Akutagawa; Teppei Matsumura; Nobuyuki Matubayashi; Hidehiro Sakurai | Organic Chemistry; Physical Organic Chemistry; Materials Chemistry; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e4521801042bc1cc780764/original/bowl-direction-control-of-monofluorosumanene-in-the-solid-state.pdf |
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