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655243b8dbd7c8b54b2f1fa5
|
10.26434/chemrxiv-2023-xt3rv-v2
|
Conformational dynamics of the most efficient carboxylase contributes to efficient CO2 fixation
|
Crotonyl-CoA carboxylase/reductase (Ccr) is one of the fastest CO2 fixing enzymes and has become part of efficient artificial CO2-fixation pathways in vitro, paving the way for future applications. The underlying mechanism of its efficiency, however, is not completely understood. X-ray structures of different intermediates in the catalytic cycle reveal tetramers in a dimer of dimers configuration with two open and two closed active sites. Upon binding a substrate, this active site changes its conformation from the open to the closed state. It is challenging to predict how these coupled conformational changes will alter the CO2 binding affinity to the reaction's active site. To determine whether the open or closed conformations of Ccr affect CO2 binding to the active site, we performed all-atom molecular simulations of the various conformations of Ccr. The open conformation without a substrate showed the highest binding affinity. The CO2 binding sites are located near the catalytic relevant Asn81 and His365 residues and in an optimal position for CO2 fixation. Furthermore, they are unaffected by substrate binding, and CO2 molecules stay in these binding sites for a longer time. Longer times in these reactive binding sites facilitate CO2 fixation through the nucleophilic attack of the reactive enolate in the closed conformation. We have previously demonstrated that the Asn81Leu variant cannot fix CO2. Simulations of the Asn81Leu variant explain the loss of activity through the removal of the Asn81 and His365 binding sites. Overall, our findings show that the conformational dynamics of the enzyme control CO2 binding. Conformational changes in Ccr increase CO2 in the open subunit before the substrate is bound, the active site closes, and the reaction starts. The full catalytic Ccr cycle alternates between CO2 addition, conformational change, and chemical reaction in the four subunits of the tetramer coordinated by communication between the two dimers.
|
Aharon Gomez; Tobias J Erb; Helmut Grubmüller; Esteban Vöhringer-Martinez
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Computational Chemistry and Modeling; Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-11-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655243b8dbd7c8b54b2f1fa5/original/conformational-dynamics-of-the-most-efficient-carboxylase-contributes-to-efficient-co2-fixation.pdf
|
633bfb3cf764e649ed0d9b04
|
10.26434/chemrxiv-2022-l66wp
|
Ions Salting Out Ions at the Water-Air Interface
|
In common aqueous systems, including naturally occurring sweet and salt water, as well as tap water, multiple ion species are co-solvated. At the water-air interface, these ions are known to affect chemical reactivity, aerosol formation, climate, and water odor. Yet, the composition of ions at the water interface has remained enigmatic. Here, using surface-specific vibrational spectroscopy, we quantify the relative surface activity of two co-solvated ions in solution. We find that more hydrophobic ions are salted out to the interface in the presence of the hydrophilic ions. This tendency of the salting-out follows the Hofmeister series. Simulations show that the solvation free energy difference between the ions and the intrinsic surface propensity of ions determine the extent of salting-out of ions by other ions. This mechanism provides a unified view of the salting-out of monatomic and polyatomic ions at interfaces of electrolyte solutions with air.
|
Takakazu Seki; Chun-Chieh Yu; Kuo-Yang Chiang; Xiaoqing Yu; Mischa Bonn; Yuki Nagata
|
Physical Chemistry; Interfaces; Spectroscopy (Physical Chem.); Surface
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633bfb3cf764e649ed0d9b04/original/ions-salting-out-ions-at-the-water-air-interface.pdf
|
66ec2d5812ff75c3a1d3a0a0
|
10.26434/chemrxiv-2024-qcgfd-v2
|
Exascale Quantum Mechanical Simulations: Navigating the Shifting Sands of Hardware and Software
|
The era of exascale computing presents both exciting opportunities and unique challenges for quantum mechanical simulations. While the transition from petaflops to exascale computing has been marked by a steady increase in computational power, the shift towards heterogeneous architectures, particularly the dominant role of graphical processing units (GPUs), demands a fundamental shift in software development strategies. This review examines the changing landscape of hardware and software for exascale computing, highlighting the limitations of traditional algorithms and software implementations in light of the increasing use of heterogeneous architectures in high-end systems. We discuss the challenges of adapting quantum chemistry software to these new architectures, including the fragmentation of the software stack, the need for more efficient algorithms (including reduced precision versions) tailored for GPUs, and the importance of developing standardized libraries and programming models.
|
Ravindra Shinde; Claudia Filippi; Anthony Scemama; William Jalby
|
Theoretical and Computational Chemistry; Materials Science; Computational Chemistry and Modeling; Machine Learning
|
CC BY 4.0
|
CHEMRXIV
|
2024-09-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ec2d5812ff75c3a1d3a0a0/original/exascale-quantum-mechanical-simulations-navigating-the-shifting-sands-of-hardware-and-software.pdf
|
60c74afd0f50db258e396b50
|
10.26434/chemrxiv.12277889.v1
|
A Unified Model to Explain the Large Chiroptical Effects in Polymer Systems Through Natural Optical Activity
|
<div><div><div><p>Polymer thin films that emit and absorb circularly polarised light have been demonstrated with the promise of achieving important technological advances; from efficient, high-performance displays, to 3D imaging and all-organic spintronic devices. However, the origin of the large chiroptical effects in such films has, until now, remained elusive. We investigate the emergence of such phenomena in achiral polymers blended with a chiral small-molecule additive (1-aza[6]helicene) and intrinsically chiral-sidechain polymers using a combination of spectroscopic methods and structural probes. We show that – under conditions relevant for device fabrication – the large chiroptical effects are caused by coupling of electric and magnetic transition dipole moments (natural optical activity), not structural chirality as previously assumed, and may occur because of local order in a cylinder blue phase-type organisation. This disruptive mechanistic insight into chiral polymer thin films will offer new approaches towards chiroptical materials development after almost three decades of research in this area.</p></div></div></div>
|
Jess Wade; James Hilfiker; Jochen R. Brandt; Letizia Liirò-Peluso; Li Wan; Xingyuan Shi; Francesco Salerno; Seán Ryan; Stefan Schöche; Oriol Arteaga; Tamás Jávorfi; Giuliano Siligardi; Cheng Wang; David B. Amabilino; Peter Beton; Alasdair Campbell; Matthew Fuchter
|
Stereochemistry; Carbon-based Materials; Optical Materials; Thin Films; Conducting polymers; Organic Polymers; Polymer morphology; Plasmonic and Photonic Structures and Devices; Self-Assembly; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74afd0f50db258e396b50/original/a-unified-model-to-explain-the-large-chiroptical-effects-in-polymer-systems-through-natural-optical-activity.pdf
|
66220456418a5379b0297f8d
|
10.26434/chemrxiv-2024-1p82f
|
Large Language Models Open New Way of AI-Assisted Molecule Design for Chemists
|
Recent advancements in artificial intelligence (AI)-based molecular design methodologies have offered synthetic chemists new ways to design functional molecules with their desired properties. While various AI-based molecule generators have significantly advanced toward practical applications, their effective use still requires specialized knowledge and skills concerning AI techniques. Here, we develop a large language model (LLM)-powered chatbot, ChatChemTS, that enables chemists to design new molecules using an AI-based molecule generator through only chat interactions, including automated construction of reward functions for the specified properties. Our study showcases the utility of ChatChemTS through de novo design cases involving chromophores and anticancer drugs (epidermal growth factor receptor inhibitors), exemplifying single- and multiobjective molecule optimization scenarios, respectively. ChatChemTS is provided as an open-source package on GitHub at https://github.com/molecule-generator-collection/ChatChemTS.
|
Shoichi Ishida; Tomohiro Sato; Teruki Honma; Kei Terayama
|
Theoretical and Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-04-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66220456418a5379b0297f8d/original/large-language-models-open-new-way-of-ai-assisted-molecule-design-for-chemists.pdf
|
635fbe52ca86b804fbcaa412
|
10.26434/chemrxiv-2022-g1trc-v2
|
Atomistic insights into the pre-nucleation phase of
Zeolitic Imidazolate Frameworks growth
|
We have studied the clusters involved in the initial stages of nucleation of Zeolitic Imidazolate Frameworks, employing a
wide range of computational techniques. In the pre-nucleating solution, the prevalent cluster is the ZnIm4 cluster (formed by a zinc cation, Zn2+ , and four imidazolate anions, Im−), although clusters such as ZnIm3, Zn2Im5, Zn2Im7, Zn3Im9, Zn3Im10, or Zn4Im12 have energies that are not much higher, so they would also be present in solution at appreciable quantities. All these species, except ZnIm3, have a tetrahedrally coordinated Zn2+ cation. Small Znx Imy clusters are less stable than the ZnIm4 cluster. The first cluster that is found to be more stable than ZnIm4 is the Zn41Im88 cluster, which is a disordered cluster with glassy structure. Bulk-like clusters do not begin to be more stable than glassy clusters until much larger sizes,
since the larger cluster we have studied (Zn144Im288) is still less stable than the glassy Zn41Im88 cluster, suggesting that Ostwald’s rule (the less stable polymorph crystallizes first) could be fulfilled, not for kinetic, but for thermodynamic reasons. Our results suggest that the first clusters formed in the nucleation process would be glassy clusters, which then undergo transformation to any of the various crystal structures possible, depending on the kinetic routes provided by the synthesis conditions. Our study helps elucidate the way in which the various species present in solution interact, leading to nucleation
and crystal growth.
|
Salvador R G Balestra; Bruno Martínez-Haya; Norge Cruz-Hernández; Dewi W. Lewis; Scott M. Woodley; Rocío Semino; Guillaume Maurin; A. Rabdel Ruiz-Salvador; Said Hamad
|
Physical Chemistry; Materials Science; Nanoscience; Hybrid Organic-Inorganic Materials; Self-Assembly
|
CC BY 4.0
|
CHEMRXIV
|
2022-11-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635fbe52ca86b804fbcaa412/original/atomistic-insights-into-the-pre-nucleation-phase-of-zeolitic-imidazolate-frameworks-growth.pdf
|
60c74c2e9abda26a94f8d226
|
10.26434/chemrxiv.12442736.v1
|
Virtual Drug Repurposing Study Against SARS-CoV-2 TMPRSS2 Target
|
<p>Currently, the world suffers from a new coronavirus SARS-CoV-2 that causes COVID-19. Therefore, there is a need for the urgent development of novel drugs and vaccines for COVID-19. Since it can take years to develop new drugs against this disease, here we used a hybrid combined molecular modeling approach in virtual drug screening repurposing study to identify new compounds against this disease. One of the important SARS-CoV-2 targets namely type 2 transmembrane serine protease (TMPRSS2) was screened with NPC’s NIH small molecule library which includes approved drugs by FDA and compounds in clinical investigation. We used 6654 small molecules in molecular docking and top-50 docking scored compounds were initially used in short (10-ns) molecular dynamics (MD) simulations. Based on average MM/GBSA binding free energy results, long (100-ns) MD simulations were employed for the identified hits. Both binding energy results as well as crucial residues in ligand binding were also compared with a positive control TMPRSS2 inhibitor, Camostat mesylate. Based on these numerical calculations we proposed a compound (benzquercin) as strong TMPRSS2 inhibitor. If these results can be validated by in vitro and in vivo studies, benzquercin can be considered to be used as inhibitor of TMPRSS2 at the clinical studies.</p>
|
Serdar Durdagi
|
Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c2e9abda26a94f8d226/original/virtual-drug-repurposing-study-against-sars-co-v-2-tmprss2-target.pdf
|
62b46b5358b3d6f8175bba3e
|
10.26434/chemrxiv-2022-vxl2s
|
Interaction of imidazolium-based ionic liquids with supported phospholipid bilayers as model biomembranes
|
The cytotoxicity of Ionic Liquids (ILs) has been raising attention in the context of the biological and environmental impact of their vast field of applications. It is ascertained that the cell membrane is the main target of ILs when they interact with microorganisms, cells and bacteria; nevertheless, studies on the micro- and nanoscale aimed at better understanding the fundamental mechanisms of toxicity of ILs are lacking. In this work, we used atomic force microscopy (AFM) to investigate the impact of room-temperature ILs on the mechanical, morphological and electrostatic properties of solid-supported DOPC phospholipid bilayers, taken as models of biomembranes. In particular, we have characterized the concentration-dependent and time-dependent evolution of the morphological, structural and mechanical properties of DOPC lipid membranes in the presence of imidazolium-based ILs with different alkyl chain length and hydrophilic/hydrophobic character.
The majority of ILs investigated were found to possess the ability of restructuring the lipid bilayer, through the formation of new ILs/lipid complexes, showing distinctive morphological features (increase of area and roughness). The nanomechanical analysis of the lipid membrane exposed to ILs revealed a progressive, concentration-dependent perturbation of the structural ordering and rigidity of the membrane, evidenced by a decrease in the breakthrough force, Young’s modulus and area stretching modulus. AFM detected a modification of the electrostatic double-layer at the membrane surface, in terms of a reduction of the original negative surface charge density, suggesting a progressive stratification of cations on the exposed leaflet of the lipid membrane. Our findings may be helpful in designing novel ILs with tailored interaction with biological membranes.
|
Massimiliano Galluzzi; Lorenzo Marfori; Stefania Asperti; Alessandro De Vita; Matteo Giannangeli; Alessandro Caselli; Paolo Milani; Alessandro Podestà
|
Physical Chemistry; Nanoscience; Biophysical Chemistry; Interfaces; Physical and Chemical Properties
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-07-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b46b5358b3d6f8175bba3e/original/interaction-of-imidazolium-based-ionic-liquids-with-supported-phospholipid-bilayers-as-model-biomembranes.pdf
|
6155bf419f1b447d1adabe14
|
10.26434/chemrxiv-2021-kk41s
|
Visualization of spatial electrochemical activity via a combined thermal-electric potentiostat
|
The electrolysis of water, CO2 and N2 provide options for producing fossil-free fuels and feedstocks at global scales. Technological advancements are challenged by the complexity of phenomena spanning broad physical scales (angstroms to meters) and scientific domains. Further, activity is presently quantified indirectly, hindering disambiguation of catalytic and system effects. Here, we present a spatial thermal-electric potentiostat (STEP) which links local electrochemical activity to an associated operando heat signature. The STEP then directly maps catalytic activity with fine resolutions in temperature (10 mK), time (0.2 s) and space (0.1 mm), capturing operational phenomena as they occur. We demonstrate STEP’s potential for catalyst screening, degradation measurements and spatial mapping through water and CO2 electrolysis experiments up to 0.2 A cm-2. We identify rapid catalytic temperature spikes with activity (>10 K at 0.2 A cm-2) and localized activity fluctuations in operation, both which challenge many perceptions of the electrocatalyst and reaction environment during operation.
|
Hugo-Pieter Iglesias van Montfort; Thomas Burdyny
|
Energy; Chemical Engineering and Industrial Chemistry; Energy Storage; Fuels - Energy Science; Fuel Cells
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-10-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6155bf419f1b447d1adabe14/original/visualization-of-spatial-electrochemical-activity-via-a-combined-thermal-electric-potentiostat.pdf
|
60d50843461f5647cc48a867
|
10.26434/chemrxiv-2021-t404r
|
High Spin Cobalt Complexes Supported by a Trigonal Tris(Phosphinimide) Ligand
|
Terminal, π-basic moieties occupy a prominent position in the stabilization of unusual or reactive inorganic species. The electron-releasing, π-basic properties of phosphinimides have been employed to stabilize electron deficient early transition metals and lanthanides. In principle, a ligand field comprised of terminal PN groups should enable access to high-valent states of late first row transition metals. Herein, we report a new class of multidentate phosphinimide ligands to logically explore this hypothesis. Access to such ligands is made possible by a new procedure for the electrophilic amination of rigid, sterically-encumbering, multidentate phosphines. Such frameworks facilitate terminal PN coordination to Cobalt as demonstrated by the synthesis of a three-coordinate CoIII complex, which exhibits an exceedingly rare S = 2 ground state. Combined XRD, magnetic susceptibility, and DFT studies highlight that terminally-bound PNs engage in strong dπ-pπ interactions that present a weak ligand field appropriate to stabilize high-spin states of late transition metals.
|
Heui Beom Lee; Nicholas Ciolkowski; Charles Winslow; Jonathan Rittle
|
Inorganic Chemistry; Coordination Chemistry (Inorg.); Ligands (Inorg.); Transition Metal Complexes (Inorg.)
|
CC BY 4.0
|
CHEMRXIV
|
2021-06-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d50843461f5647cc48a867/original/high-spin-cobalt-complexes-supported-by-a-trigonal-tris-phosphinimide-ligand.pdf
|
621028cfc86ae2d6bb2688f3
|
10.26434/chemrxiv-2022-dhxvv
|
What is the Smallest Zeolite that Could be Synthesized?
|
Zeolites with a few unit cells are promising as catalyst and adsorbents. The quest to synthesize the smallest zeolites has recently resulted in 4 to 8 nm nanozeolites, about 2 to 4 unit cells, obtained with a smart choice of structure directing agent. These findings pose the question of what is the smallest zeolite that could be obtained by hydrothermal synthesis. Here we address this question using molecular simulations and thermodynamic analysis. The simulations predict that amorphous precursors as small as 4 nm can crystallize zeolites, in agreement with the experiments. We find that interfacial forces dominate the structure of smaller particles, resulting in size-dependent compact isomers that have ring and pore distributions different from open framework zeolites. The instability of zeolites smaller than 4 nm precludes a classical mechanism of nucleation from solution or through assembly of small nanoslabs.
|
Debdas Dhabal; Andressa Bertolazzo; Valeria Molinero
|
Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Physical and Chemical Processes; Self-Assembly; Thermodynamics (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-02-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621028cfc86ae2d6bb2688f3/original/what-is-the-smallest-zeolite-that-could-be-synthesized.pdf
|
61682024b564b6e01c7713f7
|
10.26434/chemrxiv-2021-w8lml-v2
|
Photoinduced Collective Motion of Oil Droplets and Concurrent Pattern Formation in Surfactant Solution
|
Collective motion is ubiquitous in living systems. Although various biomimetic artificial systems have been constructed, there have been few studies reported on collective motion induced by the coupling of chemical reactions, diffusion and convection in a far-from-equilibrium state. In this study, we report an artificial system of oil droplets in a surfactant solution wherein the collective motion of multiple droplets and pattern formation occurred concurrently. Using photo-responsive surfactants with an azobenzene moiety, the assembly of droplets and the formation of circular patterns around the formed droplet clusters occurred under UV illumination, whereas the disassembly of droplets and disappearance of the patterns occurred under subsequent visible light illumination. The observed dynamics were induced by Marangoni flows based on the reversible photoisomerisation of azobenzene-containing surfactants. The phenomena were considered analogous to the bioconvection of microorganisms. These findings could be useful for understanding the mechanism of motion of life in terms of physicochemical aspects.
|
Tomoya Kojima; Hiroyuki Kitahata; Kouichi Asakura; Taisuke Banno
|
Physical Chemistry; Interfaces
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-10-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61682024b564b6e01c7713f7/original/photoinduced-collective-motion-of-oil-droplets-and-concurrent-pattern-formation-in-surfactant-solution.pdf
|
60c74f93567dfe5fbfec56f4
|
10.26434/chemrxiv.12922136.v1
|
Fast Response Organic Supramolecular Transistors Utilizing In-situ π-ion Gels
|
<p>Despite their remarkable charge carrier mobility when forming well-ordered fibers, supramolecular transistors often suffer from poor processability that hinders device integration, resulting in disappointing transconductance and output currents. Here, a new class of supramolecular transistors, π-ion gel transistors (PIGTs), is presented. An <i>in situ</i> π-ion gel, which is an unprecedented composite of semiconducting nanofibers and an enclosed ionic liquid, is directly employed as an active material and internal capacitor. In comparison to other superamolecular transistors, PIGT displays a high transconductance (133 µS) and output current (139 µA at -6 V), while retaining a high charge-carrier mobility (0.16 cm<sup>2</sup> V<sup>-1</sup> s<sup>-1</sup>) and on/off ratio (3.7*10<sup>4</sup>). Importantly, the unique device configuration and the high ionic conductivity associated with the distinct nanosegregation enable the fastest response among accumulation-mode electrochemical-based transistors (< 20 µs). Considering the advantages of the absence of dielectric layers and the facile fabrication process, PIGT has great potential to be utilized in printed flexible devices. The device platform is widely applicable to various supramolecular assemblies, shedding light on the interdisciplinary research of supramolecular chemistry and organic electronics.</p>
|
Soh Kushida; Emanuel Smarsly; Irene Wacker; Yohei Yamamoto; Rasmus R. Schröder; Uwe Bunz
|
Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-09-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f93567dfe5fbfec56f4/original/fast-response-organic-supramolecular-transistors-utilizing-in-situ-ion-gels.pdf
|
614c0dff1df4a11aea792637
|
10.26434/chemrxiv-2021-zfrcn
|
Lowering the C-H Bond Activation Barrier of
Methane Using SAC@Cu(111): A Periodic
DFT Investigations
|
Methane has long captured the world's spotlight for being the simplest and yet one of the most notorious hydrocarbon. Exploring its potential to be converted into value added products has raised a compelling interest. In the present work, we have studied the efficiency of Single-Atom Catalysts (SACs) for methane activation employing Density Functional Theory (DFT). The Climbing Image-Nudged Elastic Bond (CI-NEB) method is used in tandem with the Improved Dimer (ID) method to determine the
minimum energy pathway for the first C-H bond dissociation of methane. Our study reported that the transition-metal doped Cu(111) surfaces enhance adsorption, activate
C-H bond, and reduce activation barrier for first C-H bond cleavage of methane. The results suggest Ru/Co/Rh doped Cu(111) as promising candidates for methane activation with minimal activation barrier and less endothermic reaction. For these SACs, the calculated activation barriers for first C-H bond cleavage are 0.17 eV, 0.24 eV, and 0.26 eV respectively, which is substantially lower than 1.13 eV, the activation barrier for Cu(111).
|
Meema Bhati; Jignesh Dhumal; Kavita Joshi
|
Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2021-09-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614c0dff1df4a11aea792637/original/lowering-the-c-h-bond-activation-barrier-of-methane-using-sac-cu-111-a-periodic-dft-investigations.pdf
|
677a1f5581d2151a02ec6ba5
|
10.26434/chemrxiv-2024-rr0c3-v2
|
Cation-controlled diffusion of chloride ions during electrochemical chlorine evolution in acidic media
|
Impurity ions pose a major challenge towards diversifying water usage for electrolysis. In particular, millimolar-level chloride impurities remaining in reverse osmosis filtrates significantly diminish the selectivity and longevity of water electrolyzers. Here, we show that alkali metal cations can modulate the diffusion coefficient of chloride ions, enabling suppression of chlorine evolution during water electrolysis at diffusion-limiting conditions. Evidence for the cation-dependent diffusion coefficient is provided by non-zero intercepts in both Levich and modified Koutecký−Levich plots using a rotating ring disk electrode, indicating the presence of an additional, cation-dependent diffusion layer that suppresses chloride diffusion. Numerical simulations based on the double diffusion model quantify this effect, resulting in a linear correlation between the cation-dependent diffusion barrier and the structural entropy of cation hydration. These findings suggest that the cation-dependent structuring of water significantly influences mass transport, which is particularly important at practical current densities where impurity ions are diffusion-limited.
|
Taejung Lim; Hideshi Ooka; Ryuhei Nakamura
|
Physical Chemistry; Catalysis; Electrocatalysis; Transport phenomena (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677a1f5581d2151a02ec6ba5/original/cation-controlled-diffusion-of-chloride-ions-during-electrochemical-chlorine-evolution-in-acidic-media.pdf
|
63db60e401ecc690f91e2915
|
10.26434/chemrxiv-2023-wxk36-v2
|
Intermolecular pi-pi-packing-induced thermally activated delayed fluorescence: a novel pathway toward luminescence efficiency of nearly 100%
|
Efficient utilization of triplet excitons is vital in organic optoelectronics. One important strategy for harvesting triplets is thermally activated delayed fluorescence (TADF). In most TADF materials, the first singlet (S1) and triplet (T1) excited states both show strong charge-transfer (CT) character to reduce their energetic gap (EST); however, the negative consequence is small spin-orbit coupling and broad fluorescence emission width. To overcome this trade-off, our present work developed a novel strategy, i.e., intermolecular pi-pi-packing-induced (pi3) TADF, named pi3TADF. Distinct from the previously reported TADF systems, the excited states of our intermolecular pi3TADF systems show weak CT-excitation character. Our designed coplanar molecules based on a 1,5,9-trioxo-13-azatriangulene core show low photoluminescent quantum yields (PLQYs) in dilute solutions while their PLQYs in solid films reach ~ 100%. Their face-to-face pipi packings lead to the hybridization of intermolecular CT and localized pi-pi* excitations as well as electronic delocalization in the S1 states, while their T1 states show little changes. Consequently, with a dense manifold of the triplet states, the EST is significantly reduced while the large spin-orbit couplings are induced, thus leading to efficient TADF and significantly enhanced PLQYs in films. Organic light-emitting diodes exploiting the intermolecular pi3TADF systems as emitters show simultaneously high maximum external quantum efficiencies (e.g., over 30%) and narrow emission spectral widths (e.g., 44 nm). Our present work not only develops a new strategy, i.e., pi3TADF, for efficient TADF but also provides an in-depth understanding of its photophysical mechanism, thus opening a new approach for designing novel and efficient TADF materials.
|
Kai Wang; Xiao-Chun Fan; Dandan Zhang; Youichi Tsuchiya; Le Mei; Yi-Zhong Shi; Masaki Tanaka; Zesen Lin; Yi-Ting Lee; Yue Xie; Yuanyuan Pan; Xiang Zhang; Wei Liu; Gao-Le Dai; Jia-Xiong Chen; Bing Wu; Jun Zhong; Jian-Yu Yuan; Cai-Jun Zheng; Jia Yu; Alex K. Y. Jen; Xian-Kai Chen; Chun-Sing Lee; Chihaya Adachi; Xiaohong Zhang
|
Organic Chemistry; Materials Science; Organic Compounds and Functional Groups
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-02-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63db60e401ecc690f91e2915/original/intermolecular-pi-pi-packing-induced-thermally-activated-delayed-fluorescence-a-novel-pathway-toward-luminescence-efficiency-of-nearly-100.pdf
|
66b033285101a2ffa81c2743
|
10.26434/chemrxiv-2023-891j3-v2
|
Structural and kinetic insights into the stereospecific oxidation of R-2,3-dihydroxypropanesulfonate by DHPS-3-dehydrogenase from Cupriavidus pinatubonensis
|
2,3-Dihydroxypropanesulfonate (DHPS) and sulfolactate (SL) are environmentally important organosulfur compounds that play key roles as metabolic currencies in the sulfur cycle. Despite their prevalence, the pathways governing DHPS and SL production remain poorly understood. Here, we study DHPS-3-dehydrogenase CpHpsN from Cupriavidus pinatubonensis, a bacterium capable of utilizing DHPS as a sole carbon source. Kinetic analysis of CpHpsN reveals a strict preference for R-DHPS, catalyzing its 4-electron oxidation to R-SL, with high specificity for NAD+ over NADP+. The 3D structure of CpHpsN in complex with Zn2+, NADH and R-SL, elucidated through X-ray crystallography, reveals a fold akin to bacterial and plant histidinol dehydrogenases, and identical coordination geometry around the octahedral Zn2+ centre and involving the sulfonate group as a ligand. A key residue, His126, distinguishes DHPS dehydrogenases from histidinol dehydrogenases, by structural recognition of the sulfonate substrate of the former. Site-directed mutagenesis pinpoints Glu318, His319, and Asp352 as active-site residues important for the catalytic activity of CpHpsN. Taxonomic and pathway distribution analysis reveals the prevalence of HpsN homologues within different pathways of DHPS catabolism and across bacterial classes including Alpha-, Beta-, Gamma-, and Deltaproteobacteria and Desulfobacteria, emphasizing its importance in the biogeochemical sulfur cycle.
|
Laura Burchill; Arashdeep Kaur; Artur Nastasovici; Mihwa Lee; Spencer Williams
|
Biological and Medicinal Chemistry; Catalysis; Biochemistry; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b033285101a2ffa81c2743/original/structural-and-kinetic-insights-into-the-stereospecific-oxidation-of-r-2-3-dihydroxypropanesulfonate-by-dhps-3-dehydrogenase-from-cupriavidus-pinatubonensis.pdf
|
65e1ec9e9138d231616d5b8c
|
10.26434/chemrxiv-2024-7kqg1
|
Mixing enthalpies of fluorinated precursors for textile industry in ionic liquids
|
Per- and polyfluoroalkyl substances (PFAS) are widely used for technical purposes in textile finishing, giving water or oil repellence to the fibres. During their production, textile manufacturing or consumer-use, these additives can be degraded into their precursors and released in the environment. These substances are volatile, bio accumulative and persistent, and their release in the environment is more and more regulated in the EU . For a textile recycling purpose, it is necessary to find ways to safely remove them from the fibres. Among other alternative solvents, ionic liquids showed solvation properties that are promising for recycling textile waste. We have used the COSMO-SAC modelling approach to screen a large number of ionic liquids and, by the calculation of infinite dilution activity coefficients, find the most appropriate solvents for two representative fluorinated precursors likely to be found in textile products. We could determine which ionic liquids were able to interact favourably with perfluorobutyric acid (PFBA) and 6:2 fluorotelomer alcohol (6:2 FTOH). These information could be quantified using isothermal titration calorimetry (ITC) for PFBA in 1-butyl-3-metylimidazolium bis(trifluoromethylsulfonyl)imide, [C4C1Im][NTf2], predicted by COSMO-SAC as a weak solvent, as well as in 1-ethyl-3 methylimidazolium methylsulfonate, [C2C1Im][MeSO3] and 1-butyl-3-methylimidazolium acetate, [C4C1Im][OAc], expected to have strong interactions with the textile additive. Mixing enthalpies of 6:2 FTOH were measured in selected ionic liquids, namely triethylammonium methylsulfonate, [N222H][MeSO3], 1-ethyl-3 methylimidazolium methylsulfonate, [C2C1Im][MeSO3] and acetate, [C2C1Im][OAc]. A proton transfer from PFBA to AcO– (and to a lesser extent from 6:2 FTOH to AcO–) was investigated and described with DFT calculations, 1H NMR analysis and FT-IR spectroscopy.
|
Guillaume Simon; Jocasta Avila; Agilio Padua; Margarida Costa Gomes
|
Chemical Engineering and Industrial Chemistry; Thermodynamics (Chem. Eng.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e1ec9e9138d231616d5b8c/original/mixing-enthalpies-of-fluorinated-precursors-for-textile-industry-in-ionic-liquids.pdf
|
60c740a3bdbb89aa60a381c7
|
10.26434/chemrxiv.7791683.v1
|
Biological Relevance of Charge Transfer Branching Pathways in Photolyases
|
In PhrA, a class III CPD photolyase, two branching tryptophan charge transfer pathways have been characterized in the mechanism of FAD photoreduction. To provide a molecular explanation of the charge transfer abilities of both pathways, we performed simulations where the protein motion and the positive charge are simultaneously propagated. Our computational approach reveals that one pathway drives a very fast charge transfer whereas the other pathway provides a very good thermodynamic stabilization of the positive charge. During the simulations, the positive charge firstly moves on the fast triad, allowing the stabilization of reduced FAD. After one nanosecond, we observe a nearly equal probability to find the charge at ending tryptophan of either pathway. Our results highlight the role of the protein environment, which manages the association of a kinetic and a thermodynamic pathways to trigger a fast and efficient FAD photoreduction.
|
Daniel Holub; Tilman Lamparter; Marcus Elstner; Natacha Gillet
|
Biochemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740a3bdbb89aa60a381c7/original/biological-relevance-of-charge-transfer-branching-pathways-in-photolyases.pdf
|
664dfb0691aefa6ce1b138c8
|
10.26434/chemrxiv-2024-bd942
|
Unlocking the Potential of Organopalladium Complexes for High-Grade Serous Ovarian Cancer Therapy
|
High-Grade Serous Ovarian Cancer (HGSOC) is the most common and lethal subtype of ovarian cancer, known for its high aggressiveness and extensive genomic alterations. Typically diagnosed at an advanced stage, HGSOC presents formidable challenges in drug therapy. The limited efficacy of standard treatments, development of chemoresistance, scarcity of targeted therapies, and significant tumor heterogeneity render this disease incurable with current treatment options, highlighting the urgent need for novel therapeutic approaches to improve patient outcomes.
In this study we report a straightforward and stereoselective synthetic route to novel Pd(II)-vinyl and -butadienyl complexes bearing a wide range of monodentate and bidentate ligands. Most of the synthesized complexes exhibited good to excellent in vitro anticancer activity against ovarian cancer cells. Particularly promising is the water-soluble complex bearing two PTA (PTA = 1,3,5-triaza-7-phosphaadamantane) ligands and the Pd(II)-butadienyl fragment. This compound combines excellent cytotoxicity towards cancer cells with substantial inactivity towards non-cancerous ones. This derivative was selected for further studies on ex vivo tumor organoids and in vivo mouse models, which demonstrate its remarkable efficacy with surprisingly low collateral toxicity even at high dosages. Moreover, this class of compounds appears to operate through a ferroptotic mechanism, thus representing the first such example for an organopalladium compound.
|
Thomas Scattolin; Enrico Cavarzerani; Dario Alessi; Matteo Mauceri; Eleonora Botter; Giovanni Tonon; Isabella Caligiuri; Ombretta Repetto; Urska Kamensek; Simona Kranjc Brezar; Maria Dalla Pozza; Stefano Palazzolo; Maja Cemazar; Vincenzo Canzonieri; Nicola Demitri; Steven Patrick Nolan; Gilles Gasser; Fabiano Visentin; Flavio Rizzolio
|
Organometallic Chemistry; Bioorganometallic Chemistry; Transition Metal Complexes (Organomet.)
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-05-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664dfb0691aefa6ce1b138c8/original/unlocking-the-potential-of-organopalladium-complexes-for-high-grade-serous-ovarian-cancer-therapy.pdf
|
60c74472567dfe3220ec4292
|
10.26434/chemrxiv.9791162.v1
|
Directed Evolution of P450 Fatty Acid Decarboxylases via High-Throughput Screening Towards Improved Catalytic Activity
|
P450 fatty acid
decarboxylases (FADCs) have recently been attracting considerable attention owing
to their one-step direct production of industrially important 1-alkenes from biologically abundant
feedstock free fatty acids under mild conditions. However, attempts to improve
the catalytic activity of FADCs have met with little success. Protein
engineering has been limited to selected residues and small mutant libraries
due to lack of an effective high-throughput screening (HTS) method. Here, we
devise a catalase-deficient <i>Escherichia
coli</i> host strain and report an HTS approach based on colorimetric detection
of H<sub>2</sub>O<sub>2</sub>-consumption activity of FADCs. Directed evolution
enabled by this method has led to effective identification for the first time
of improved FADC variants for medium-chain 1-alkene production from both DNA
shuffling and random mutagenesis libraries. Advantageously, this screening
method can be extended to other enzymes that stoichiometrically utilize H<sub>2</sub>O<sub>2</sub>
as co-substrate.
|
Huifang Xu; Weinan Liang; Linlin Ning; Yuanyuan Jiang; Wenxia Yang; Cong Wang; Feifei Qi; Li Ma; Lei Du; Laurent Fourage; Yongjin J. Zhou; Shengying Li
|
Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-09-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74472567dfe3220ec4292/original/directed-evolution-of-p450-fatty-acid-decarboxylases-via-high-throughput-screening-towards-improved-catalytic-activity.pdf
|
64d1619569bfb8925a8ae3c6
|
10.26434/chemrxiv-2023-v0xj4-v3
|
Expanded Coverage of Phytocompounds by Mass Spectrometry Imaging Using On-Tissue Chemical Derivatization by 4-APEBA
|
Probing the entirety of any species metabolome is an analytical grand challenge, especially at a cellular scale. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a common spatial metabolomics assay, but this technique has limited molecular coverage for several reasons. To expand the application space of spatial metabolomics, we developed an on-tissue chemical derivatization (OTCD) workflow using 4-APEBA for confident identification of several dozen elusive phytocompounds. Overall, this new OTCD method enabled the annotation of roughly 280 metabolites, with only 10% overlap in metabolic coverage when compared to analog negative ion mode MALDI-MSI on serial sections. We demonstrate that 4-APEBA outperforms other derivatization agents providing: (1) broad specificity towards carbonyls, (2) low background, and (3) introduction of bromine isotopes. Notably, the latter two attributes also facilitate more confidence in our bioinformatics for data processing. The workflow detailed here trailblazes a path towards spatial hormonomics within plant samples, enhancing detection of carboxylates, aldehydes, and plausibly other carbonyls. As such, several phytohormones, which have various roles within stress responses and cellular communication can now be spatially profiled, as demonstrated in poplar root and soybean root nodule.
|
Kevin Zemaitis; Vivian Lin; Amir Ahkami; Tanya Winkler; Christopher Anderton; Dušan Veličković
|
Analytical Chemistry; Earth, Space, and Environmental Chemistry; Analytical Chemistry - General; Imaging; Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d1619569bfb8925a8ae3c6/original/expanded-coverage-of-phytocompounds-by-mass-spectrometry-imaging-using-on-tissue-chemical-derivatization-by-4-apeba.pdf
|
64cd2bfe4a3f7d0c0d9936b8
|
10.26434/chemrxiv-2023-tmvpb
|
Quantum Spin Coherence and Electron Spin Distribution Channels in Vanadyl-containing Lantern Complexes
|
We herein investigate the heterobimetallic lantern complexes [PtVO(SOCR)4] as electrically neutral electronic qubits based on vanadyl complexes (S = 1/2) with nuclear spin-free donor atoms. The derivatives with R = Me (1) and Ph (2) give highly resolved X-band EPR spectra in frozen CH2Cl2/toluene solution, which evidence the usual hyperfine coupling to the 51V nucleus (I = 7/2) and an additional superhyperfine interaction with the I = 1/2 nucleus of the 195Pt isotope (natural abundance ca. 34%). DFT calculations ascribe the spin-density delocalization on the Pt2+ ion to a combination of π and δ pathways, with the former representing the predominant channel. Spin relaxation measurements in frozen CD2Cl2/toluene-d8 solution between 90 and 10 K yield Tm values (1-6 μs in 1 and 2-11 μs in 2) which match or even outperform those of known vanadyl-based qubits in similar matrices. Coherent spin manipulations indeed prove possible at 70 K, as shown by the observation of Rabi oscillations in nutation experiments. The results indicate that the heavy Group 10 metal is not detrimental to the coherence properties of the vanadyl moiety and that Pt-VO lanterns can be used as robust spin-coherent building blocks in materials science and quantum technologies.
|
Manuel Imperato; Alessio Nicolini; Marco Borsari; Matteo Briganti; Mario Chiesa; Yu-Kai Liao; Antonio Ranieri; Arsen Raza; Enrico Salvadori; Lorenzo Sorace; Andrea Cornia
|
Physical Chemistry; Inorganic Chemistry; Magnetism; Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64cd2bfe4a3f7d0c0d9936b8/original/quantum-spin-coherence-and-electron-spin-distribution-channels-in-vanadyl-containing-lantern-complexes.pdf
|
644be9630d87b493e3717c9b
|
10.26434/chemrxiv-2023-zms3n
|
Automated Multiscale Universal Simulation Environment
|
Multiscale techniques should allow for the integration of detailed atomistic information on materials and reactions to predict the catalytic performance of full-scale reactors. Although many attempts have been presented in the literature, difficulties still appear. These challenges are grouped into two main groups: catalytic complexity and differences between time and length scales of chemical and transport phenomena. Here, we introduce AMUSE (Automated Multiscale Universal Simulation Environment), which allows for building a seamless Multiscale modeling workflow. Starting from Density Functional Theory (DFT) data and automated analysis of the reaction networks through graph theory, microkinetic modeling is integrated into a standard open-source Computational Fluid Dynamics (CFD) code. We present technologically relevant case studies to demonstrate the capabilities of AMUSE by applying it to the CO2 hydrogenation on In2O3-based catalysts and isopropanol dehydrogenation on two Co facets.
|
Albert Sabadell-Rendón; Kamila Kaźmierczak; Santiago Morandi; Florian Euzenat; Daniel Curulla-Ferré; Núria López
|
Theoretical and Computational Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Reaction Engineering; Heterogeneous Catalysis
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-05-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644be9630d87b493e3717c9b/original/automated-multiscale-universal-simulation-environment.pdf
|
60c74f5d9abda2ceccf8d838
|
10.26434/chemrxiv.11876505.v3
|
Compaction of RNA Hairpins and Their Kissing Complexes in Native Electrospray Mass Spectrometry
|
When electrosprayed from typical native MS solution conditions, RNA hairpins and kissing complexes acquire charge states at which they get significantly more compact in the gas phase than their initial structure in solution. Here we show the limits of using force field molecular dynamics to interpret the gas-phase structures of nucleic acid complexes in the gas phase, and we suggest that higher-level calculation levels should be used in the future.<br />
|
Joséphine Abi-Ghanem; Clémence Rabin; Massimiliano Porrini; Frédéric Rosu; Valerie Gabelica
|
Mass Spectrometry; Biophysics; Biophysical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f5d9abda2ceccf8d838/original/compaction-of-rna-hairpins-and-their-kissing-complexes-in-native-electrospray-mass-spectrometry.pdf
|
66708e2e5101a2ffa8cbd354
|
10.26434/chemrxiv-2024-rj946-v2
|
Self-Driving Laboratories for Chemistry and Materials Science
|
Self-driving laboratories (SDLs) promise an accelerated application of the scientific method. Through the automation of experimental workflows, along with the autonomization of experiment planning, SDLs hold the potential to greatly accelerate research in chemistry and materials discovery. This review article provides an in-depth analysis of the state-of-the-art in SDL technology, its applications across various scientific disciplines, and the potential implications for research, and industry. This review additionally provides an overview of the enabling technologies for SDLs, including their hardware, software, and integration with laboratory infrastructure. Most importantly, this review explores the diverse range of scientific domains where SDLs have made significant contributions, from drug discovery and materials science to genomics and chemistry. We provide a comprehensive review of existing real-world examples of SDLs, their different levels of automation, and the challenges and limitations associated with each domain.
|
Gary Tom; Stefan P. Schmid; Sterling G. Baird; Yang Cao; Kourosh Darvish; Han Hao; Stanley Lo; Sergio Pablo-García; Ella M. Rajaonson; Marta Skreta; Naruki Yoshikawa; Samantha Corapi; Gun Deniz Akkoc; Felix Strieth-Kalthoff; Martin Seifrid; Alán Aspuru-Guzik
|
Biological and Medicinal Chemistry; Organic Chemistry; Materials Science; Organic Synthesis and Reactions; Biological Materials; Hybrid Organic-Inorganic Materials
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-06-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66708e2e5101a2ffa8cbd354/original/self-driving-laboratories-for-chemistry-and-materials-science.pdf
|
61720bb9ff3ba933bb9bfcb4
|
10.26434/chemrxiv-2021-wmmbt
|
Low cost and open source purification apparatus for GMP [13N]ammonia production
|
Nitrogen-13 labeled ammonia ([13N]NH3) has been used for myocardial perfusion imaging with Positron Emission Tomography for decades. Recent increases to regulatory oversight have led to stricter adherence Good Manufacturing Practice (GMP) to produce this short half-life (9.97 min) radiopharmaceutical. This has increased production costs. Our cyclotron facility initially developed a
manual GMP production method, but it was prone to human error. With increased costs in mind, we developed and validation an Arduino-based device to purifying [13N]NH3 for clinical use. Construction, programming, and GMP validation results are discussed. The automated method was found to produce equivalent quality radiopharmaceutical but was more reproducible and robust.
|
Farah Kamar; Michael S. Kovacs; Justin W. Hicks
|
Biological and Medicinal Chemistry; Biophysics; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-10-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61720bb9ff3ba933bb9bfcb4/original/low-cost-and-open-source-purification-apparatus-for-gmp-13n-ammonia-production.pdf
|
6731a1337be152b1d0af9183
|
10.26434/chemrxiv-2024-nb8wl
|
Reference Electrode-Free Electrochemical Detection Using a Bare Interdigitated Array Electrode and Initial Counterbalancing O2 Reduction
|
In this study, we introduce a reference electrode-free two-electrode system that utilizes the electrochemical reduction of naturally dissolved O2 in aqueous solutions to counterbalance the oxidation of 4-aminophenol (AP) at an Au interdigitated array electrode. This system minimizes the potential variation at the working electrode and eliminates the need for a large potential difference between the two electrodes. The oxidation of AP produces 4-quinoneimine, inducing electrochemical-electrochemical (EE) redox cycling. Operating in phosphate-buffered saline (pH 7.4) ensures a low anodic background current within a potential range where AP (formal potential = 0.07 V vs Ag/AgCl) undergoes oxidation. Concurrently, the reduction of O2 occurs effectively near 0.0 V. This setup enables the application of a small potential difference (0.3 V) to simultaneously achieve AP oxidation and O₂ reduction, followed by efficient EE redox cycling. Unwanted side reactions involving O₂ and H₂O₂ are minimal and do not interfere with the redox cycling. We applied this system to detect proteases (3CL protease from coronavirus SARS-CoV-2 and aminopeptidase N) that catalyze the release of AP from electro-inactive AP-conjugated peptides. Our approach demonstrates the potential for efficient EE re-dox cycling without requiring a reference electrode and added redox species.
|
Jihyeon Kim; Seonhwa Park; Haesik Yang
|
Analytical Chemistry; Electrochemical Analysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6731a1337be152b1d0af9183/original/reference-electrode-free-electrochemical-detection-using-a-bare-interdigitated-array-electrode-and-initial-counterbalancing-o2-reduction.pdf
|
60c7488f9abda23b28f8cacd
|
10.26434/chemrxiv.11931633.v1
|
Overcoming Selectivity Issues in Reversible Catalysis – A Transfer Hydrocyanation Exhibiting High Kinetic Control
|
<p><i>Typically, reversible
catalytic reactions operate under thermodynamic control and thus establishing a
selective catalytic system poses a considerable challenge. In this manuscript,
we report a reversible yet kinetically selective transfer hydrocyanation
protocol. Selectivity is achieved by exploiting the lower barrier for C–CN oxidative
addition and reductive elimination at benzylic positions in the absence of
co-catalytic Lewis acid. The design of a novel type of HCN donor was crucial to
realizing this practical, branched-selective, HCN-free transfer hydrocyanation.
The synthetically useful resolution of a mixture of branched and linear nitrile
isomers was also demonstrated to underline the value of reversible and
selective transfer reactions. In a broader context, this work demonstrates that
high kinetic selectivity can be achieved in reversible transfer reactions, thus
opening new horizons for their synthetic applications.</i></p>
|
Benjamin N. Bhawal; Julia C. Reisenbauer; Christian Ehinger; Bill Morandi
|
Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-03-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7488f9abda23b28f8cacd/original/overcoming-selectivity-issues-in-reversible-catalysis-a-transfer-hydrocyanation-exhibiting-high-kinetic-control.pdf
|
61dfff3ddeeafa46d61b46c8
|
10.26434/chemrxiv-2021-fm09s-v2
|
Micellar photocatalysis enables divergent C-H arylation and N dealkylation of benzamides via N-acyliminium cations
|
Micellar photocatalysis has recently opened new avenues to activate strong carbon halide bonds. So far, however, it has mainly explored strongly reducing conditions restricting the available chemical space to radical or anionic reactivity. Here, we demonstrate a radical-polar crossover process involving cationic intermediates, which enables chemodivergent modification of chlorinated benzamide derivatives via either C H arylation or N dealkylation. The catalytic system operates under mild conditions employing methylene blue as a photocatalyst and blue LEDs as the light source. Factors determining the reactivity of substrates and preliminary mechanistic studies are presented.
|
Martyna Cybularczyk-Cecotka; Jędrzej Predygier; Stefano Crespi; Joanna Szczepanik; Maciej Giedyk
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Supramolecular Chemistry (Org.); Photocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-01-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61dfff3ddeeafa46d61b46c8/original/micellar-photocatalysis-enables-divergent-c-h-arylation-and-n-dealkylation-of-benzamides-via-n-acyliminium-cations.pdf
|
60c748a2ee301cf9cbc79904
|
10.26434/chemrxiv.11950647.v1
|
Profiling Substrate Promiscuity of Wild-Type Sugar Kinases for Multi-Fluorinated Monosaccharides
|
Manuscript and SI
|
Tessa Keenan; Fabio Parmeggiani; Julien Malassis; Clement Fontenelle; Jean-Baptiste Vendeville; Wendy Offen; Peter Both; kun huang; Andrea Marchesi; Alex Heyam; Carl Young; Simon J. Charnock; Gideon J. Davies; Bruno Linclau; Sabine Flitsch; Martin Fascione
|
Biochemistry; Chemical Biology; Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-03-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748a2ee301cf9cbc79904/original/profiling-substrate-promiscuity-of-wild-type-sugar-kinases-for-multi-fluorinated-monosaccharides.pdf
|
6650d94921291e5d1d2f0897
|
10.26434/chemrxiv-2024-q5klh
|
Water Induced Reversible Switching of Optical Transparency of an Elastomer-Hydrogel based Two-phase Composite
|
We have examined reversible switching of optical transparency of a two-phase material consisting of hydrogel micro-spheres dispersed inside a continuous medium of crosslinked poly(dimethylsiloxane) (PDMS). Here, aqueous solution of gelatin is dispersed as drops in PDMS oligomers mixed with the crosslinker. Both phases get crosslinked to form an elastomeric material. Films of this material remain optically opaque in the unswelled state of the embedded hydrogel, but, when placed inside water for prolonged period, water diffuses through the silicone phase and gets absorbed by gelatin. At this, gelatin swells with consequent change in transparency with time. We show that the size of dispersed microspheres and the extent of crosslinking of the PDMS, both affect the kinetics of this process. In fact, for some range of parameter values, the rate of change in transparency turns more pronounced than would have been expected for simple Fickian diffusion of water through the film. We show also that selective swelling of the dispersed phase is necessary for the film to get transparent. Furthermore, it is possible to dye the dispersed phase with a water-soluble dye implying that the dye molecules can co-diffuse with water through the network. We highlight also few potential applications of this material.
|
Kuldeep Kuhar; Animangsu Ghatak
|
Materials Science; Chemical Engineering and Industrial Chemistry; Composites; Optical Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6650d94921291e5d1d2f0897/original/water-induced-reversible-switching-of-optical-transparency-of-an-elastomer-hydrogel-based-two-phase-composite.pdf
|
6142416e90051e3ed9f49ef2
|
10.26434/chemrxiv-2021-hb4dq
|
A General Method for Synthesis of Isomaleimide Derivatives
|
A mild and efficient method for the synthesis of isoimide by a simple reaction of 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (EDC) with various kinds of maleimicacid, succimicacid, pthaleimicacid in dichloromethane at room temperature is described.
|
SUDERSHAN GONDI
|
Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions
|
CC BY 4.0
|
CHEMRXIV
|
2021-09-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6142416e90051e3ed9f49ef2/original/a-general-method-for-synthesis-of-isomaleimide-derivatives.pdf
|
6710e27012ff75c3a1af5b25
|
10.26434/chemrxiv-2024-078mj
|
Closing the Loop for Benzylic Polyacylhydrazone(PAcHy) Soft Materials
|
The earth faces a pressing environmental challenge with the annual pollution of millions of tons of plastic waste. This issue is exacerbated by the inherent characteristics of plastics, including their high thermal stability and low biodegradability. In response, the scientific community has dedicated significant efforts to combat plastic pollution and develop environmentally sustainable soft materials. A promising approach is the creation of soft materials that can be efficiently recycled within a closed-loop system, thereby minimizing their chemical impact on the environment. This study introduces polyacylhydrazones as a novel class of soft materials with the potential for closed-loop recycling. Closed-loop polymers are sought after as sustainable materials of the future. Dynamic covalent polymers have the potential to act as closed-loop materials because of their reversible linkages. However, very few materials currently exist. Polyacylhydrazones have been explored as dynamic covalent polymers with multiple uses. Herein we demonstrate the first study that shows their potential as closed-loop materials. We show novel synthetic techniques that produce hydrophobic polyacylhydrazones with unique length and morphology under kinetic control. We demonstrate preliminary potential applications. Finally, we show the facile decom-position of a benzylic hydrazone bond down to monomeric units and extraction-based separation, without the need for chromatography. This work advances our understanding of these innovative materials and validates benzylic polyacylhydrazones as “closed-loop” materials for a more sustainable future.
|
Matthew Minus; Chukwuzubelu Ufodike; Al Mazedur Rahman; Evan McHenry; Marco Giles; Gaius Nzebuka
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Polymer Science; Organic Polymers; Polymer chains; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2024-11-04
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6710e27012ff75c3a1af5b25/original/closing-the-loop-for-benzylic-polyacylhydrazone-p-ac-hy-soft-materials.pdf
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60c754ce4c89198243ad45ab
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10.26434/chemrxiv.13728373.v1
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Outstanding Enhancement in the Axial Coordination Ability of the Highly Rigid Cofacial Cyclic Metalloporphyrin Dimer
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<div>Copper- and nickel-porphyrin complexes show extremely weak axial coordination ability without any electron-withdrawing groups. Herein, we report axial ligation on Cu<sup>II</sup>- and Ni<sup>II</sup>-porphyrins in a highly rigid cofacial porphyrin dimer with a bidentate ligand, 1,4-diazabicyclo[2.2.2]octane (DABCO). To the best of our knowledge, this is the first report on the use of Cu<sup>II</sup>- and Ni<sup>II</sup>-porphyrins for coordination-induced guest binding of porphyrin-based host molecules without the help of other metal ions. The high rigidity of the dimer induces guest binding through the cooperative effect of weak axial ligation. The results showed that Cu<sup>II</sup>- and Zn<sup>II</sup>-complexes bind one DABCO molecule inside their cavities, whereas the Ni<sup>II</sup>-complex binds two additional DABCO molecules outside to form a stable 6-coordinate paramagnetic Ni<sup>II</sup>-complexes. <br /></div>
|
Ken-ichi Yamashita; Kazuhiro Furutani; Takuji Ogawa
|
Physical Organic Chemistry; Supramolecular Chemistry (Org.); Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Crystallography – Inorganic; Crystallography – Organic
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-02-09
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754ce4c89198243ad45ab/original/outstanding-enhancement-in-the-axial-coordination-ability-of-the-highly-rigid-cofacial-cyclic-metalloporphyrin-dimer.pdf
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670639cacec5d6c142aa53a2
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10.26434/chemrxiv-2024-nsp7n-v2
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Data-efficient modeling of catalytic reactions via enhanced sampling and on-the-fly learning of machine learning potentials
|
Simulating catalytic reactivity under operative conditions poses a significant challenge due to the dynamic nature of the catalysts and the high computational cost of electronic structure calculations. Machine learning potentials offer a promising avenue to simulate dynamics at a fraction of the cost, but they require datasets containing all relevant configurations, particularly reactive ones. Here we present a scheme to construct reactive potentials in a data-efficient manner. This is achieved by combining enhanced sampling methods first with Gaussian processes to discover transition paths and then with graph neural networks to obtain a uniformly accurate description. The necessary configurations are extracted via a Data-Efficient Active Learning (DEAL) procedure based on local environment uncertainty. We validated our approach by studying several reactions related to the decomposition of ammonia on iron-cobalt alloy catalysts. Our scheme proved efficient, requiring only ~1,000 DFT calculations per reaction, and robust, sampling reactive configurations from the different accessible pathways. Using this potential, we calculated free energy profiles and characterized reaction mechanisms, showing the ability to provide microscopic insights into complex processes under dynamic conditions.
|
Simone Perego; Luigi Bonati
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Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Machine Learning
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-10-09
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670639cacec5d6c142aa53a2/original/data-efficient-modeling-of-catalytic-reactions-via-enhanced-sampling-and-on-the-fly-learning-of-machine-learning-potentials.pdf
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60c7401c0f50db1ec33958c4
|
10.26434/chemrxiv.7594988.v1
|
Assessment of Heavy Metals in the Dust Fall from Three Universities' Motor Parks in Nigeria
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<div>Dust fall samples in University of Ilorin, University of Ibadan and Kwara State University motor parks were collected using open bucket sampler based on ASTM D1739 of 1998 (2010) for five months from November, 2014 to March, 2015. 0.1g of dust sample was digested with 20 ml of HNO3, HClO4 and HF in ratio of (3:2:1) respectively and the heavy metals (Mn, Cu, Zn, Cd, Pb, and Ni) were analysed using atomic absorption spectrophotometer. </div><div>Generally, decrease in the following order; 1479.75, 1255.675, 241.498, 128.00, 85.25, and 9.625 mg/kg for Mn, Zn, Pb, Ni, Cu and Cd respectively were found at University of Ibadan. The decreased in average mass of heavy metals obtained in University of Ilorin were found to be 1145.75, 797.75, 219.625, 133.51, 58.25 and 23.125 mg/kg for Mn, Zn, Pb, Ni, Cu and Cd respectively. For Kwara State University, decrease in the following order; 778.5, 323.875, 259.375, 101.375, 34.375, and 4.625 mg/kg for Mn, Zn, Pb, Ni, Cu and Cd respectively were found. Generally, the heavy metal concentrations decreases in the following order Mn>Zn>Pb>Ni>Cu>Cd for all the three sites.</div>
|
Zaccheus Shehu
|
Atmospheric Chemistry; Analytical Chemistry - General; Environmental Analysis
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CC BY NC ND 4.0
|
CHEMRXIV
|
2019-01-21
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7401c0f50db1ec33958c4/original/assessment-of-heavy-metals-in-the-dust-fall-from-three-universities-motor-parks-in-nigeria.pdf
|
660458d79138d23161760460
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10.26434/chemrxiv-2024-q7k8v
|
FROG : exploiting all-atom Molecular Dynamics trajectories to calculate linear and non-linear optical responses of molecular liquids within Dalton’s QM/MM polarizable embedding scheme
|
Quantum mechanical/molecular mechanics (QM/MM) methods are interesting to model the impact of a complex environment on the spectroscopic properties of a molecule. In this context, FROG code is a tool to exploit molecular dynamics trajectories to perform QM/MM calculations of molecular optical properties. FROG stands for 'FROm molecular dynamics to second harmonic Generation' since it was developed for the calculations of hyperpolarizabilities. These are relevant to model non-linear optical intensities, and compare them with those obtained from second harmonic scattering or second harmonic generation experiments. FROG's specificity is that it is designed to study simple molecular liquids, including solvents or mixtures, from the bulk to the surface. For the QM/MM calculations, FROG relies on the Dalton package: its electronic-structure models, response theory and polarizable embedding (PE) schemes. FROG helps with the global workflow needed to deal with numerous QM/MM calculations: it permits the user to separate the system into QM and MM fragments, to write \Dalton’s inputs, to manage the submission of QM/MM calculations, to check whether \Dalton’s calculation finished successfully, and finally to perform averages on relevant QM observables. All molecules within the simulation box and several time steps are tackled within the same workflow. The platform is written in Python and installed as a package. Intermediate data such as local electric fields or individual molecular properties are accessible to the users in the form of Python object arrays. The resulting data are easily extracted, analyzed, and visualized using Python scripts that are provided in tutorials.
|
Le Breton Guillaume; Bonhomme Oriane; Benichou Emmanuel; Claire Loison
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-03-29
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660458d79138d23161760460/original/frog-exploiting-all-atom-molecular-dynamics-trajectories-to-calculate-linear-and-non-linear-optical-responses-of-molecular-liquids-within-dalton-s-qm-mm-polarizable-embedding-scheme.pdf
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60c743b04c8919d1f6ad268f
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10.26434/chemrxiv.9209180.v1
|
Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires
|
<p>We report a mechanism of adenosine triphosphate (ATP)
to cyclic adenosine monophosphate (cAMP) conversion by the mammalian type V
adenylyl cyclase revealed in molecular dynamics (MD) and quantum
mechanics/molecular mechanics (QM/MM) simulations. We characterize a set of
computationally derived enzyme-substrate (ES) structures showing an important role
of coordination shells of magnesium ions in the solvent accessible active site.
Several stable six-fold coordination shells of Mg<sub>A</sub><sup>2+ </sup>are observed
in MD simulations of ES complexes. In the lowest energy ES conformation, the
coordination shell of Mg<sub>A</sub><sup>2+ </sup>does not include the O<sub>δ1</sub>
atom of the conserved Asp440 residue. Starting from this conformation, a
one-step reaction mechanism is characterized which includes proton transfer
from the ribose O<sup>3'</sup>H<sup>3' </sup>group in ATP to Asp440 via a
shuttling water molecule and P<sup>A</sup>-O<sup>3A</sup> bond cleavage and O<sup>3'</sup>-P<sup>A</sup>
bond formation. The energy profile of
this route is consistent with the observed reaction kinetics. In a higher
energy ES conformation, Mg<sub>A</sub><sup>2+</sup> is bound to the O<sub>δ1</sub>(Asp440)
atom as suggested in the relevant crystal structure of the protein with a
substrate analog. The computed energy profile initiated by this ES is
characterized by higher energy expenses to complete the reaction. Consistently
with experimental data, we show that the Asp440Ala mutant of the enzyme should
exhibit a reduced but retained activity. All considered reaction pathways
include proton wires from the O<sup>3'</sup>H<sup>3' </sup>group via shuttling
water molecules. </p>
|
Bella Grigorenko; Igor Polyakov; Alexander Nemukhin
|
Biochemistry; Computational Chemistry and Modeling; Biophysical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-08-12
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743b04c8919d1f6ad268f/original/mechanisms-of-atp-to-c-amp-conversion-catalyzed-by-the-mammalian-adenylyl-cyclase-a-role-of-magnesium-coordination-shells-and-proton-wires.pdf
|
62ced58a4e76bf853d8bc23a
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10.26434/chemrxiv-2022-x73nn
|
P-terminated InP(001) surfaces: Surface band bending and reactivity to water
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Stable InP(001) surfaces are characterized by fully occupied and empty surface states close to the bulk valence and conduction band edges, respectively. The present photoemission data show, however, a surface Fermi level pinning only slightly below the mid-gap energy that gives rise to an appreciable surface band bending. By means of density-functional theory calculations, it is shown that this apparent discrepancy is due to surface defects that form at finite temperature. In particular, the desorption of hydrogen from metalorganic vapor phase epitaxy grown P-rich InP(001) surfaces exposes partially filled P dangling bonds that give rise to band gap states. These defects are investigated with respect to surface reactivity in contact with molecular water by low-temperature water adsorption experiments using photoemission spectroscopy and are compared to our computational results. Interestingly, these hydrogen related gap-states are robust with respect to water adsorption, provided that water does not dissociate, due to missing adsorption sites in close neighborhood.
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Dominik Christian Moritz; Isaac Azahel Ruiz Alvarado; Mohammad Amin Zare Pour; Agnieszka Paszuk; Tilo Frieß; Erich Runge; Jan Philipp Hofmann; Thomas Hannappel; Wolf Gero Schmidt; Wolfram Jaegermann
|
Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Optical Materials; Interfaces; Surface
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CC BY 4.0
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CHEMRXIV
|
2022-07-18
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ced58a4e76bf853d8bc23a/original/p-terminated-in-p-001-surfaces-surface-band-bending-and-reactivity-to-water.pdf
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60c7420d337d6c2e6de269b7
|
10.26434/chemrxiv.8206634.v1
|
Light-Driven Deracemization Enabled by Excited-State Electron Transfer
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A new strategy for catalytic deracemization is presented, wherein amine derivatives undergo spontaneous optical enrichment upon exposure to visible light in the presence of three distinct molecular catalysts. Initiated by an excited-state iridium chromophore, this reaction proceeds <i>via </i>a sequence of favorable electron, proton, and hydrogen atom transfer steps that serve to break and reform a stereogenic C–H bond. The enantioselectivity in these reactions is jointly determined by two independent stereoselective steps that occur in sequence within the catalytic cycle, giving rise to a composite selectivity that is higher than that of either step individually. These reactions represent a distinct and potentially general approach to creating out-of-equilibrium product distributions between substrate enantiomers using excited-state redox events.
|
Nick Shin; Jonathan Ryss; Xin Zhang; Scott Miller; Robert Knowles
|
Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry; Stereochemistry; Photocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-05-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7420d337d6c2e6de269b7/original/light-driven-deracemization-enabled-by-excited-state-electron-transfer.pdf
|
6765dba1fa469535b94b9577
|
10.26434/chemrxiv-2024-41hkj
|
Enabling stability at a high working voltage of a
P2-Na0.85Li0.17Ni0.21Mn0.64O2 sodium-ion battery cathode via utilization of succinic anhydride as an electrolyte additive
|
The practical implementation of P2-Na0.85Li0.17Ni0.21Mn0.64O2 as sodium-ion battery cathode has been hampered by problems of self-discharge and poor cycling stability caused by electrolyte oxidation. Here, we developed an electrolyte formulation that makes use of succinic anhydride as a key additive to alleviate these drawbacks. The composition of the electrolyte was optimized and the so-optimized electrolyte enables a safe performance of the cathode in a 2-4.2 V vs. Na+/Na electrochemical window. Electrochemical studies including electrochemical impedance spectroscopy and microscopy studies showed that succinic anhydride favours the formation of a cathode electrolyte interface that protects the cathode against electrolyte oxidation. As compared
to the electrodes tested in the succinic anhydride-free electrolyte, self-discharge processes were substantially reduced and cycling stability (up to 100 cycles, 2-fold improvement) and Coulombic efficiency were improved. More remarkable was the improvement on power density performance. The cathode tested in the optimized electrolyte performed up to the high current density of 5.78C delivering a high power of 1.88 kW kg−1, whereas the cathode tested in the SA-free electrolyte faded readily at 1.77C. Equally, the cathode showed a much more stable average voltage of 3.17-2.89 V vs. Na+/Na, over such a wider range of operating current rates. The cathode delivered a maximum energy density of 377 Wh kg−1. Importantly, SA also aided in preventing corrosion of
aluminum current collectors in the electrochemical window of interest.
|
Beatriz Mendoza-Sánchez; Vicente José Esteve-Cano; Cécile Autret; Benedicte Montigny; Jesús Santos-Peña
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Energy; Energy Storage
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CC BY NC 4.0
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CHEMRXIV
|
2024-12-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6765dba1fa469535b94b9577/original/enabling-stability-at-a-high-working-voltage-of-a-p2-na0-85li0-17ni0-21mn0-64o2-sodium-ion-battery-cathode-via-utilization-of-succinic-anhydride-as-an-electrolyte-additive.pdf
|
644c1b786ee8e6b5ed445527
|
10.26434/chemrxiv-2023-pjf8t
|
Colloidal Interactions in Ionic Liquids– the electrical double layer inferred from ion layering and aggregation
|
Ionic liquids (ILs) are organic salts that remain liquid in absence of a solvent over a wide range of temperatures, often at room temperature. This chapter summarizes the progress in understanding colloidal interactions mediated by ILs and their electrical double layer (EDL) based on experimental observations and theory. It is well known that short-range oscillatory forces in ILs originate from the overscreening provided by ion layers that accumulate close to the charged surface. In contrast, the origin of the more surprising long-range decaying force is not well understood yet. There is experimental and theoretical evidence opposing the originally proposed dilute behavior of ILs, arising from either ion pair formation or solvent/voids/alkyl tails being the effective charge carrier. Here, we overview experiments and theory that supports an alternative explanation of this long-range force based on ion aggregation.
|
Rosa M. Espinosa-Marzal; Zachary A. H. Goodwin; Xuhui Zhang; Qianlu Zheng
|
Theoretical and Computational Chemistry; Physical Chemistry; Materials Science
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-05-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644c1b786ee8e6b5ed445527/original/colloidal-interactions-in-ionic-liquids-the-electrical-double-layer-inferred-from-ion-layering-and-aggregation.pdf
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6468b4f3fb40f6b3eee522f8
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10.26434/chemrxiv-2023-xvwp0
|
Theoretical Insights into Dynamics of Gas-Phase Bimolecular Reactions with Submerged Barriers
|
Much attention has been paid to dynamics of both activated gas-phase bimolecular reactions, which feature monotonically increasing integral cross sections and Arrhenius kinetics, and their barrierless capture counterparts, which manifest monotonically decreasing integral cross sections and negative temperature dependence of the rate coefficients. In this Perspective, we focus on dynamics of gas-phase bimolecular reactions with submerged barriers, which often involve radicals or ions and are prevalent in combustion, atmospheric chemistry, astrochemistry, and plasma chemistry. The temperature dependence of rate coefficients for such reactions is often non-Arrhenius and complex, and the corresponding dynamics may also be quite different from those with significant barriers or those completely dominated by capture. Recent experimental and theoretical studies of such reactions, particularly at relatively low temperatures or collision energies, have revealed interesting dynamical behaviors, which are discussed here. The new knowledge enriches our understanding of dynamics of these unusual reactions.
|
Hongwei Song; Hua Guo
|
Physical Chemistry
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CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6468b4f3fb40f6b3eee522f8/original/theoretical-insights-into-dynamics-of-gas-phase-bimolecular-reactions-with-submerged-barriers.pdf
|
6287e55df053df420a230e5d
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10.26434/chemrxiv-2022-z72gt
|
Efficient crystal structure prediction for structurally related molecules with accurate and transferable tailor-made force fields
|
Crystal structure prediction (CSP) has been historically used to complement experimental solid form screening and applied to individual molecules in drug development. The fast development of algorithms and computing resources offers the opportunity to use CSP earlier and for a broader range of applications in the drug design cycle. This study presents a novel paradigm of CSP specifically designed for structurally related molecules, referred to as Quick-CSP. The approach prioritizes more accurate physics through robust and transferable tailor-made force fields (TMFFs), such that significant efficiency gains are achieved through the reduction of expensive ab initio calculations. The accuracy of the TMFF is increased by the introduction of electrostatic multipoles and the fragment-based force field parameterization scheme is demonstrated to be transferable for a family of chemically related molecules. The protocol is benchmarked with structurally related compounds from the Bromodomain and Extraterminal (BET) domain inhibitors series. A new convergence criterion is introduced that aims at performing only as many ab initio optimizations of crystal structures as required to locate the bottom of the crystal energy landscape within a user-defined accuracy. The overall approach provides significant cost savings ranging from three to eight-fold less than the Full-CSP workflow. The reported advancements expand the scope and utility of the underlying CSP building blocks as well as their novel reassembly to other applications earlier in the drug design cycle to guide molecule design and selection.
|
Alessandra Mattei; Richard S. Hong; Hanno Dietrich; Dzmitry Firaha; Julian Helfferich; Yifei Michelle Liu; Kiran Sasikumar; Nathan S. Abraham; Rajni Miglani Bhardwaj; Marcus A. Neumann; Ahmad Y. Sheikh
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-05-23
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6287e55df053df420a230e5d/original/efficient-crystal-structure-prediction-for-structurally-related-molecules-with-accurate-and-transferable-tailor-made-force-fields.pdf
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62348e88d6d3edc4ae960358
|
10.26434/chemrxiv-2022-d8bfz
|
Unexpected Emission of Poly[(methylenelactide)-co-(2-vinylpyridine)] from Single-chain Luminogen
|
Non-conjugated luminescent polymers (NCLPs) have attracted great interest due to their novel emission mechanism and potential for applications in a variety of areas. Copolymerization is a facile and effective approach to develop NCLPs from two or more types of non-luminescent comonomers by integrating critical elements that are necessary for inducing intrinsic emissions. In the present work, we report unexpected photoluminescence (PL) of poly[(methylenelactide)-co-(2-vinylpyridine)] random copolymers (PLVPs), which possess intense blue emissions in dilute solution with quantum yield higher than 20 %. The intrinsic PL of PLVPs is attributed to the intra-chain interactions of chains, namely, ‘single-chain luminogen’. As a result, the PL of PLVPs exhibits aggregation-caused quenching (ACQ) feature, which is different from conventional NCLPs based on clustering-triggered emission (CTE). The dependence of emissions on the molecular weights and monomer ratios of PLVPs, as well as excitation wavelength, in both solution and solid states were investigated. This work provides new insight into the design and preparation of NCLPs.
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Xinyu Li; Mengmeng Xu; Rongchun Zhang; Youqing Yu; Yuanyuan Pei; Qianqian Yu; Kunkun Liu; Yiliu Liu; Linge Wang; Tao Wen
|
Polymer Science; Materials Chemistry
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CC BY 4.0
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CHEMRXIV
|
2022-03-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62348e88d6d3edc4ae960358/original/unexpected-emission-of-poly-methylenelactide-co-2-vinylpyridine-from-single-chain-luminogen.pdf
|
60c74d7bbdbb89e4b8a399d6
|
10.26434/chemrxiv.12624965.v1
|
Terphenyl(bisamino)phosphines: Electron-rich Ligands for Gold-Catalysis
|
Terphenyl(bisamino)phosphines
have been identified as effective ligands in cationic gold(I) complexes for the
hydroamination of acetylenes. These systems are related to Buchwald phosphines
and their steric properties have been evaluated. Effective hydroamination was
noted even at low catalyst loadings and a series of cationic gold(I) complexes
has been structurally characterized clearly indicating stabilizing effects
through gold-arene interactions.
|
Jan-Erik Siewert; André Schumann; Malte Fischer; Christoph Schmidt; Christian Hering-Junghans
|
Coordination Chemistry (Inorg.); Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d7bbdbb89e4b8a399d6/original/terphenyl-bisamino-phosphines-electron-rich-ligands-for-gold-catalysis.pdf
|
60c74bba469df4598df43f7b
|
10.26434/chemrxiv.12375215.v1
|
Chemoselectivity Switching through Coupled Equilibria
|
Complex mixtures are found in biological and petrochemical feedstocks, and in the primordial soup implicated in the origins of life. Reacting individual compounds within these mixtures is challenging because of the difficulty in controlling the chemoselectivity of such reactions. We show that the selectivity of imine oxidation can be controlled within doubly dynamic combinatorial libraries, wherein two coupled equilibria determine whether the most oxidizable aldehyde precursor is made available to the oxidant or sequestered away from it. Under the slow oxidation conditions, the most electron-rich precursor can traverse the shallow energy landscape and its oxidation product dominates the final mixture. Faster oxidation captures the imine mixture composition, favoring the products derived from electron poorer push-pull imines. <br />
|
Ognjen Miljanic; Thamon Puangsamlee
|
Physical Organic Chemistry; Supramolecular Chemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bba469df4598df43f7b/original/chemoselectivity-switching-through-coupled-equilibria.pdf
|
65765f3629a13c4d47248166
|
10.26434/chemrxiv-2023-bgvbj
|
Structural Order and Plasmonic Response of Nanoparticle Monolayers
|
Collective plasmon resonances in superlattice assemblies of metallic nanoparticles are influenced by nanoparticle attributes and assembly structure. Although grain boundaries and other structural defects are inherent to superlattices assembled in the lab, their impact on near- and far-field optical properties remains poorly understood. Here, we study variations in structural and optical properties of model 2D superlattices of spherical metallic nanoparticles, focusing on large-scale monolayers of approximately constant area fraction formed by different assembly rates. Our modeling addresses how disorder generates distributions of hot spot intensities and nanoparticle-level resonant frequencies. The highest intensities occur in narrow gaps between particle pairs aligned parallel to the field polarization. Despite the structural diversity of the monolayers investigated, we find the highest hot-spot intensity adjacent to a nanoparticle strongly correlates with the particle’s resonant frequency, though the introduction of realistic variability in nanoparticle dielectric parameters weakens the link. These trends hold for different nanoparticle compositions, and predictions are compared to experimentally prepared monolayers of tin-doped indium oxide nanocrystals. Though defectivity only modestly influences ensemble extinction peak frequency and surface-enhanced infrared absorption, increasing structural disorder broadens spectral lineshapes and boosts surface-enhanced Raman scattering enhancement factors. The magnitude of spectroscopic enhancement and the sensitivity of optical properties to local structural order depends primarily on dipole polarizability contrast. These results can help inform tolerances and tradeoffs relevant to designing materials and assembly protocols to achieve desired optical properties for applications, including sensitive molecular detection.
|
Allison M. Green; Woo Je Chang; Zachary M. Sherman; Zarko Sakotic; Kihoon Kim; Daniel Wasserman; Delia J. Milliron; Thomas M. Truskett
|
Nanoscience; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65765f3629a13c4d47248166/original/structural-order-and-plasmonic-response-of-nanoparticle-monolayers.pdf
|
62922c06d504186779c66b84
|
10.26434/chemrxiv-2022-16cj5
|
Bypassing Backmapping: Coarse-Grained Electronic Property Distributions Using Heteroscedastic Gaussian Processes
|
We employ deep kernel learning electronic coarse-graining (DKL-ECG) with approximate Gaussian Processes as a flexible and scalable framework for learning heteroscedastic electronic property distributions as a smooth function of coarse-grained (CG) configuration. The appropriateness of the Gaussian prior on the predictive CG property distributions is justified as a function of CG model resolution by examining the statistics of the target distributions. The certainties of the predictive CG distributions are shown to be limited by CG model resolution, with DKL-ECG predictive noise converging to the intrinsic physical noise induced by the CG mapping operator for multiple chemistries. Further analysis of the resolution dependence of the learned CG property distributions allows for the identification of CG mapping operators that capture CG degrees of freedom with strong electron-phonon coupling. We further demonstrate the ability to construct the exact quantum chemical valence electronic density of states (EDOS), including behavior in the tails of the EDOS, from an entirely CG model by combining iterative boltzmann inversion and DKL-ECG. DKL-ECG provides a means of learning CG distributions of all-atom properties that are traditionally ``lost" in CG model development, introducing a robust methodological alternative to backmapping algorithms commonly employed to recover all-atom property distributions from CG simulations.
|
Charlie Maier; Nicholas Jackson
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-05-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62922c06d504186779c66b84/original/bypassing-backmapping-coarse-grained-electronic-property-distributions-using-heteroscedastic-gaussian-processes.pdf
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63cf3b47fa87eb7c18521e2b
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10.26434/chemrxiv-2023-936js
|
Ambient Photovoltaics for Self-Powered and Self-Aware IoT
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As the number of Internet of Things devices is rapidly increasing, there is an urgent need for
sustainable and efficient energy sources and management practices in ambient environments. In
response, we developed a high-efficiency ambient photovoltaic based on sustainable non-toxic
materials and present a full implementation of a long short-term memory (LSTM) based energy
management using on-device prediction on IoT sensors solely powered by ambient light harvesters.
The power is supplied by dye-sensitised photovoltaic cells based on a copper(II/I) electrolyte with
an unprecedented power conversion efficiency at 38% and 1.0V open-circuit voltage at 1 000 lux
(fluorescent lamp). The on-device LSTM predicts changing deployment environments and adapts
its computational load accordingly to perpetually operate the energy-harvesting circuit and avoid
power losses or brownouts. Harvesting ambient light combined with artificial intelligence gives
the opportunity to make fully autonomous self-powered sensor devices for industry, healthcare,
homes and smart cities.
|
Hannes Michaels; Michael Rinderle; Richard Freitag; Iacopo Benesperi; Alessio Gagliardi; Marina Freitag
|
Energy; Photovoltaics
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CC BY NC ND 4.0
|
CHEMRXIV
|
2023-01-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63cf3b47fa87eb7c18521e2b/original/ambient-photovoltaics-for-self-powered-and-self-aware-io-t.pdf
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6795c20981d2151a0200d40c
|
10.26434/chemrxiv-2024-f1nsj-v2
|
Glycan Mixture Analysis by Kernel Component Composition for Matrix Factorization
|
A major challenge in structural glycomics is the presence of isomeric glycan structures, which may not be fully resolved by separation techniques such as liquid chromatography (LC) and ion mobility spectrometry (IMS). Tandem mass spectrometry (MS/MS) can be employed following on-line separation to distinguish unresolved features, as the temporal profiles of various fragment ions reflect different combinations of those from their respective precursor ions. However, traditional principal component analysis can produce negative signals that are unrealistic for real data, and classic non-negative matrix factorization (NMF) methods may result in factors that include contributions from multiple components.
This paper introduces a new variation of NMF, termed kernel component composition (KCC), which enables users to impose domain-specific prior knowledge about the components as parametric kernels. These kernel parameters are then learned directly from the data. We developed a theoretically guaranteed algorithm based on proximal gradient descent to solve the optimization problem posed by KCC and derived detailed parameter update rules when using Gaussian kernels. The effectiveness of the KCC algorithm is demonstrated through simulation tests and its application to deconvoluting chemical datasets, including LC- and IM-MS/MS analysis of isomeric glycan mixtures.
|
Pengyu Hong; Chaoshuang Xia; Yang Tang; Juan Wei; Cheng Lin
|
Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry
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CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6795c20981d2151a0200d40c/original/glycan-mixture-analysis-by-kernel-component-composition-for-matrix-factorization.pdf
|
665801e3418a5379b09a65f3
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10.26434/chemrxiv-2024-zlsw1
|
4-Vinylbenzenesulfonyl fluoride (VBSF): a highly reactive monomer for RAFT polymerization and exhaustive SuFEx postpolymerization sulfonamidation
|
We designed and synthesized a 4-fluorosulfonyl styrene monomer, 4-vinylbenzenesulfonyl fluoride (VBSF), for the evaluation of the efficiency of our catalytic sulfonamidation of sulfonyl fluorides in post-polymerization modification. Our preliminary studies indicated that this monomer was compatible with “living”/controlled free radical polymerizations such as RAFT and ATRP. Using the slightly modified protocols of catalytic amidation of sulfonyl fluorides established in our laboratory previously, we have achieved the exhaustive sulfonamidation of poly(4-vinylbenzenesulfonyl fluoride)s. Nucleophiles such as aliphatic amines, aromatic amines and phenols were all viable, and six novel polystyrene-analogous sulfonamide (or sulfonate) polymers were prepared. In addition, the exhaustive amidation of poly(VBSF-co-St) was also investigated.
|
Yongqi Zhang; le Li; Pengfei Ma; Wu Bin; Christopher M. Plummer; Yi Zhang
|
Polymer Science; Polymerization (Polymers)
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CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665801e3418a5379b09a65f3/original/4-vinylbenzenesulfonyl-fluoride-vbsf-a-highly-reactive-monomer-for-raft-polymerization-and-exhaustive-su-f-ex-postpolymerization-sulfonamidation.pdf
|
63ea781b9da0bc6b33ded43e
|
10.26434/chemrxiv-2023-9f4zq
|
A photoswitchable solvatochromic dye for probing membrane ordering by RESOLFT super-resolution microscopy
|
A switchable solvatochromic fluorescent dyad can be used to map ordering of lipids in vesicle membranes at a resolution better than the diffraction limit. Combining a Nile Red fluorophore with a photochromic spironaphthoxazine quencher allows the fluorescence to be controlled using visible light, via photoswitching and FRET quenching. Synthetic lipid vesicles of varying composition were imaged with an average 2.5-fold resolution enhancement, compared to the confocal images. Ratiometric detection was used to probe the membrane polarity, and domains of different lipid ordering were distinguished within the same membrane.
|
Andrew Frawley; Kathryn Leslie; Virginia Wycisk; Silvia Galiani; Dilip Shrestha; Christian Eggeling; Harry Anderson
|
Physical Chemistry; Organic Chemistry; Photochemistry (Org.); Biophysical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-02-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ea781b9da0bc6b33ded43e/original/a-photoswitchable-solvatochromic-dye-for-probing-membrane-ordering-by-resolft-super-resolution-microscopy.pdf
|
60c753febb8c1a1d303dc162
|
10.26434/chemrxiv.13602869.v1
|
Following Electroenzymatic Hydrogen Production by Rotating Ring Disk Electrochemistry and Mass Spectrometry
|
<p>We report on two new approaches to study H<sub>2</sub>-producing metalloenzymes using electrochemistry and mass spectrometry, where H<sup>+</sup> reduction is driven by hydrogenase within an electrochemically active polymer (redox polymer). Researchers have established electrochemical approaches to utilize the H<sub>2</sub>-processing metalloenzyme hydrogenase at electrode surfaces. However, it is more-than-often the case that hydrogenase electrodes are employed for H<sub>2</sub> oxidation. There is significant interest in using renewable electrical energy to drive low-potential reductive reactions such as H<sub>2</sub> evolution and N<sub>2</sub> fixation, particularly with metalloenzymes. However, much work is required to understand metalloenzymes.</p><p>The use of rotating ring disk electrochemistry with hydrogenase is innovative in that it provides a live method to quantify the H<sub>2</sub> being produced by the enzyme. This method will be valuable in determining product distributions for such enzymes in real-time, at electrode surfaces.</p>There is also significant interest in utilizing isotopes of enzymatic substrates when performing electrochemistry, since the rate of the reaction corresponds to the current at the electrode. However, researchers of electroenzymatic H<sup>+</sup> reduction have yet to utilize online mass spectrometry to analyze the products of hydron reduction. We report on the ability to follow and differentiate the formation of H<sub>2</sub>, HD and D<sub>2</sub> in real-time, permitting the calculation of apparent kinetic isotope effects. This approach will be valuable to characterizing rate-limiting steps involving H<sup>+</sup>, as well as for other gas-processing metalloenzymes.
|
Jaloliddin Khushvakov; Robin Nussbaum; Cécile Cadoux; Jifu Duan; Sven T. Stripp; Ross Milton
|
Bioinorganic Chemistry; Electrochemistry; Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-01-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753febb8c1a1d303dc162/original/following-electroenzymatic-hydrogen-production-by-rotating-ring-disk-electrochemistry-and-mass-spectrometry.pdf
|
60c73ed6567dfe7e5fec388d
|
10.26434/chemrxiv.7097960.v1
|
DeepSMILES: An Adaptation of SMILES for Use in Machine-Learning of Chemical Structures
|
<div>Background</div><div><br /></div><div>There has been increasing interest in the use of deep neural networks for de novo design of molecules with desired properties. A common approach is to train a generative model on SMILES strings and then use this to generate SMILES strings for molecules with a desired property. Unfortunately, these SMILES strings are often not syntactically valid due to elements of SMILES syntax that must occur in pairs.</div><div><br /></div><div>Results</div><div><br /></div><div>We describe a SMILES-like syntax called DeepSMILES that addresses two of the main reasons for invalid syntax when using a probabilistic model to generate SMILES strings. The DeepSMILES syntax avoids the problem of unbalanced parentheses by only using close parentheses, where the number of parentheses indicates the branch length. In addition, DeepSMILES avoids the problem of pairing ring closure symbols by using only a single symbol at the ring closing location, where the symbol indicates the ring size. We show that this syntax can be interconverted to/from SMILES with string processing without any loss of information, including stereo configuration.</div><div><br /></div><div>Conclusion</div><div><br /></div><div>We believe that DeepSMILES will be useful, not just for those using SMILES in deep neural networks, but also for other computational methods that use SMILES as the basis for generating molecular structures such as genetic algorithms.</div>
|
Noel O'Boyle; Andrew Dalke
|
Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2018-09-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ed6567dfe7e5fec388d/original/deep-smiles-an-adaptation-of-smiles-for-use-in-machine-learning-of-chemical-structures.pdf
|
62ff4f1211986c3a6e3df827
|
10.26434/chemrxiv-2022-21brb-v2
|
Evidence for multiple binding modes in the initial contact between SARS-CoV-2 spike S1 protein and cell surface glycans
|
Infection of host cells by SARS-CoV-2 begins with recognition by the virus S (spike) protein of cell surface heparan sulfate (HS), tethering the virus to the extracellular matrix environment, and causing the subunit S1-RBD to undergo a conformational change into the ‘open’ conformation. These two events promote the binding of S1-RBD to the angiotensin converting enzyme 2 (ACE2) receptor, a preliminary step toward viral-cell membrane fusion. Combining ligand-based NMR spectroscopy with molecular dynamics, oligosaccharide analogues were used to explore the interactions between S1-RBD of SARS CoV-2 and HS, revealing several low-specificity binding modes and previously unidentified potential sites for the binding of extended HS polysaccharide chains. The evidence for multiple binding modes also suggest that highly specific inhibitors will not be optimal against protein S but, rather, diverse HS-based structures, characterized by high affinity and including multi-valent compounds, may be required.
|
Michela Parafioriti; Minghong Ni; Maurice Petitou; Courtney J. Mycroft-West; Timothy R. Rudd; Neha S. Gandhi; Vito Ferro; Jeremy E. Turnbull; Marcelo A. Lima; Mark A. Skidmore; David G. Fernig; Edwin A. Yates; Antonella Bisio; Marco Guerrini; Stefano Elli
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Polymer Science; Biopolymers; Biochemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-08-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ff4f1211986c3a6e3df827/original/evidence-for-multiple-binding-modes-in-the-initial-contact-between-sars-co-v-2-spike-s1-protein-and-cell-surface-glycans.pdf
|
60c754f1bdbb895404a3a729
|
10.26434/chemrxiv.13606055.v1
|
Amyloid β-binding Bifunctional Chelators with Favorable Lipophilicity for 64Cu PET Imaging in Alzheimer’s Disease
|
Herein we report a
new series of bifunctional chelators (BFCs) with high affinity for amyloid
aggregates, strong binding affinity towards Cu(II) and favorable lipophilicity
for potential blood-brain barrier (BBB) penetration. The alkyl carboxylate
pendant arms offer up to three orders of magnitude higher binding affinity
towards Cu(II) vs. the parent chelating fragment, and can generate fairly
stable Cu complexes, including <sup>64</sup>Cu-radiolabeled compounds. Among
the five compounds tested, the <sup>64</sup>Cu-YW-7 and <sup>64</sup>Cu-YW-10
complexes exhibit strong and specific staining of amyloid plaques in <i>ex vivo</i>
autoradiography studies. Importantly, these compounds have promising partition
coefficient (Log D) values of 0.91-1.26 and show moderate brain uptake in
biodistribution studies using CD-1 mice. Overall, these BFCs could serve as
lead compounds for the development of positron emission tomography (PET)
imaging agents for AD diagnosis.
|
Yujue Wang; Truc T. Huynh; Hong-Jun Cho; Wang Yung-Ching; Buck E. Rogers; Liviu M. Mirica
|
Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-02-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754f1bdbb895404a3a729/original/amyloid-binding-bifunctional-chelators-with-favorable-lipophilicity-for-64cu-pet-imaging-in-alzheimer-s-disease.pdf
|
62b480667da6ceed361d06e0
|
10.26434/chemrxiv-2022-8qv90-v2
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5D Total Scattering Computed Tomography Reveals the Full Reaction Mechanism of a bismuth vanadate lithium ion battery anode
|
We have used operando 5D synchrotron total scattering computed tomography (TSCT) to understand the cycling and possible long term deactivation mechanisms of the lithium-ion battery anode bismuth vanadate. This anode material functions via a combined conversion/alloying mechanism in which nanocrystals of lithium-bismuth alloy are protected by an amorphous matrix of lithium vanadate. This composite is formed in situ during the first lithiation of the anode. The operando TSCT data were analyzed and mapped using both pair distribution function and Rietveld methods. We can follow the lithium-bismuth alloying reaction at all stages, gaining real structural insight including variations in nanoparticle sizes, lattice parameters and bond lengths, even when the material is completely amorphous. We also observe for the first time structural changes related to the cycling of lithium ions in the lithium vanadate matrix which displays no order beyond the first shell of V-O bonds. The first 3D operando mapping of the distribution of different materials in an amorphous anode reveals a decline in coverage caused by either agglomeration or partial dissolution of the active material, hinting at the mechanism of long-term deactivation. The numerous observations from the operando experiment are backed up by post mortem HRTEM studies and theoretical calculations to provide a complete picture of an exceptionally complex cycling mechanism.
|
Jonas Sottmann; Amund Ruud; Øystein Fjellvåg; Gavin Vaughan; Helmer Fjellvåg; Oleg Lebedev; Marco Di Michiel; Pooniah Vajeeston ; David Wragg
|
Inorganic Chemistry; Energy; Electrochemistry; Power; Materials Chemistry; Crystallography – Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-06-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b480667da6ceed361d06e0/original/5d-total-scattering-computed-tomography-reveals-the-full-reaction-mechanism-of-a-bismuth-vanadate-lithium-ion-battery-anode.pdf
|
60c752debdbb8979aaa3a375
|
10.26434/chemrxiv.13359440.v1
|
From Starphenes to Non-Benzenoid Linear Conjugated Polymers by Substrate Templating
|
Combining on-surface synthetic methods with the power of scanning tunneling microscopy to characterize novel materials at the single molecule level, we show how to steer the reactivity of one anthracene-based precursor towards different product nanostructures. Whereas using a two-dimensional Au(111) surface results in the dominant formation of a starphene derivative, the templating effect of a reconstructed Au(110) surface allows the selective growth of non-benzenoid linear conjugated polymers. We further assess the electronic properties of each of the observed product structures via tunneling spectroscopy and DFT calculations, altogether advancing in the synthesis and characterization of molecular structures of notable scientific interest that have been only scarcely investigated to date, as applied to both starphenes and to non-benzenoid conjugated polymers. <br />
|
Mohammed S. G. Mohammed; James Lawrence; Fátima García; Pedro Brandimarte; Alejandro Berdonces-Layunta; Dolores Pérez; Daniel Sánchez-Portal; Diego Peña; Dimas de Oteyza
|
Carbon-based Materials
|
CC BY 4.0
|
CHEMRXIV
|
2020-12-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752debdbb8979aaa3a375/original/from-starphenes-to-non-benzenoid-linear-conjugated-polymers-by-substrate-templating.pdf
|
65ddc928e9ebbb4db96136c3
|
10.26434/chemrxiv-2023-wfx5d-v3
|
Photoresponsive Arylazopyrazole Surfactant/PDADMAC Mixtures: Reversible Control of Bulk and Interfacial Properties
|
In many applications of polyelectrolyte/surfactant (P/S) mixtures, it is difficult to fine-tune them after mixing the components without changing the sample composition, e.g. pH or the ionic strength. Here we report on a new approach where we use photoswitchable surfactants to enable drastic changes in both the bulk and interfacial properties. Poly(diallyldimethylammonium chloride) (PDADMAC) mixtures with three alkyl-arylazopyrazole butyl sulfonates (CnAAP) with -H, -butyl and -octyl tails are applied and E/Z photoisomerization of the surfactants is used to cause substantially different hydrophobic interactions between the surfactants and PDADMAC. This affects significantly the P/S binding and allows for tuning both the bulk and interfacial properties of PDADMAC/CnAAP mixtures through light irradiation. For that, we have fixed the surfactant concentrations at values where they exhibit pronounced surface tension changes upon E/Z photoisomerization with 365 nm UV light (Z) and 520 nm green (E) light and have varied the PDADMAC concentration. The electrophoretic mobility can be largely tuned by photoisomerisation of CnAAP surfactants and P/S aggregates, which can even exhibit a charge reversal from negative to positive values or vice versa. In addition, low colloidal stability at equimolar concentrations of PDADMAC with CnAAP surfactants in the E configuration lead to the formation of large aggregates in the bulk which can be redissolved by irradiation with UV light when the surfactant‘s alkyl chain is short enough (C0AAP). Vibrational sum-frequency generation (SFG) reveals changes at the interface similar to the bulk, where the charging state at air-water interfaces can be modified with light irradiation. Using SFG spectroscopy, we interrogated the O-H stretching modes of interfacial H2O and provide qualitative information on surface charging that is complemented by neutron reflectometry, from which we resolved the surface excess of PDADMAC and CnAAP at the air-water interface, independently.
|
Michael Hardt; Christian Honnigfort; Javier Carrascosa-Tejedor; Marius Braun; Samuel Winnall; Dana Glikman; Philipp Gutfreund; Richard A. Campbell; Bjoern Braunschweig
|
Physical Chemistry; Interfaces
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-02-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ddc928e9ebbb4db96136c3/original/photoresponsive-arylazopyrazole-surfactant-pdadmac-mixtures-reversible-control-of-bulk-and-interfacial-properties.pdf
|
60c74638ee301c0febc79486
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10.26434/chemrxiv.10315502.v1
|
Activity-Dependent Probes Containing Epsilon-N-Thioacyllysine and -Epsilon-N-Acyl-(Delta-Aza)lysine Residues
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Posttranslational modifications (PTMs) are important in the regulation of protein function, trafficking, localization, and marking for degradation. Here, we describe development of peptide activity-based probes for the discovery of proteins that recognize novel acyl-based PTMs on lysine residues in the proteome. The probes contain surrogates of epsilon-<i>N</i>-acyllysine by introduction of either hydrazide or thioamide functionalities to circumvent hydrolysis of the modification during the experiments. In addition to the modified PTMs, the developed chemotypes were analyzed with respect to effect of peptide sequence. The photo cross-linking conditions and subsequent functionalization of the covalent adducts were systematically optimized by applying fluorophore labeling and gel electrophoresis (in-gel fluorescence measurements). Finally, selected probes, containing the epsilon-<i>N</i>-glutaryllysine and epsilon<i>-N</i>-myristoyllysine analogues, were successfully applied to enrichment of native, endogenous proteins from cell lysate, recapitulating the expected interactions of SIRT5 and SIRT2, respectively. Interestingly, the latter mentioned was able to pull down two different splice variants of SIRT2, which has not been achieved with a covalent probe before. Based on this elaborate proof-of-concept study, we expect that the technology will have broad future applications for pairing of novel PTMs with the proteins that target them in the cell.
|
Michael Bæk,; Pablo Martín-Gago; Jonas S. Laursen; Julie L. H. Madsen; Saswati Chakladar; Christian Adam Olsen
|
Bioorganic Chemistry; Organic Compounds and Functional Groups; Biochemistry; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-11-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74638ee301c0febc79486/original/activity-dependent-probes-containing-epsilon-n-thioacyllysine-and-epsilon-n-acyl-delta-aza-lysine-residues.pdf
|
66c60c72a4e53c487620a21e
|
10.26434/chemrxiv-2024-tdsl7
|
Self-assembly of monodisperse graphene nanoribbons into submicron architectures with long-range order and uniform orientation
|
Fabricating organic semi-conducting materials into large-scale well-organized architectures is critical for building high performance molecular electronics. While graphene nanoribbons (GNRs) hold enormous promise for various device applications, their assembly into a well-structured monolayer or multilayer architecture poses a substantial challenge. Here we report the preparation of length-defined monodisperse GNRs and their self-assembly into submicron-architectures with long-range order, uniform orientation as well as regular layers. The use of short alkyl side chains benefits forming stable multi-layers through interlocking structures. By changing the length and backbone shapes of these monodisperse GNRs, various three-dimensional assemblies including multilayer stripes, monolayer stripes, and nanowires, can be achieved, leading to different photophysical properties and band gaps. The discovery of these intriguing self-assembly behaviors of length-defined GNRs is expected to open the door for various future applications.
|
Jiangliang Yin; Daniel Pyle; Shinyoung Choi; Jeffrey Guest; Guangbin Dong
|
Organic Chemistry; Polymer Science; Supramolecular Chemistry (Org.); Conducting polymers; Organic Polymers; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c60c72a4e53c487620a21e/original/self-assembly-of-monodisperse-graphene-nanoribbons-into-submicron-architectures-with-long-range-order-and-uniform-orientation.pdf
|
60c74253bdbb89d1d3a3849f
|
10.26434/chemrxiv.8256047.v1
|
Considerations on the Derivative of the Titration Curve of a Weak Diacid
|
We show that the derivative of the titration curve of a diacid can be used to assess the first equivalent as well as the second equivalent point, but also the value for which pH=pKa. This is controlled by the difference between both pKa's of the diacid. A bifurcation is observed for the values of volume of titrant for which the first derivative cancels.<br />
|
Marc Blétry
|
Chemical Education - General
|
CC BY NC ND 4.0
|
CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74253bdbb89d1d3a3849f/original/considerations-on-the-derivative-of-the-titration-curve-of-a-weak-diacid.pdf
|
64b50f99b053dad33a65d7f8
|
10.26434/chemrxiv-2023-gzs6g
|
Deciphering the Mitochondrial Viscosity and Interplay Between Mitochondria and Plasma Membrane Using Far Red-emitting Molecular Rotor
|
The dysfunctions in the mitochondria are associated with various pathological conditions like neurodegeneration, metabolic disorder, and cancer, leading to dysregulated cell death. Here, we have designed and synthesized a julolidine-based molecular rotor (JMT) to target mitochondria with far-red emission accounting for mitochondrial dysfunction. JMT showed an excellent viscosity sensitivity with 160-fold and 4-times enhancement in fluorescence intensity and lifetime, respectively. The origin of the dark state in a lower viscous environment was investigated through density functional calculations. JMT has monitored mitochondrial dysfunction under stressed and inflammatory conditions. Moreover, we reported tracking small fluorescent molecules switching from mitochondria to the plasma membrane. On treating the mitochondria potential uncoupler, JMT relocates to the cell membrane and can be utilized for understanding the interplay between mitochondria and cell membranes.
|
Akshay Silswal; Anup Pramanik; Apurba Lal Koner
|
Biological and Medicinal Chemistry; Analytical Chemistry; Chemical Biology; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-07-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b50f99b053dad33a65d7f8/original/deciphering-the-mitochondrial-viscosity-and-interplay-between-mitochondria-and-plasma-membrane-using-far-red-emitting-molecular-rotor.pdf
|
640f1e25b5d5dbe9e8318ca4
|
10.26434/chemrxiv-2023-lvdcn
|
Guidelines for reliable urea detection in electrocatalysis
|
Electrochemical urea synthesis offers a promising green alternative to fossil fuel-based approaches to support the increasing global demand for nitrogen fertilizers. Unfortunately, the conventional urea detection methods produce inconsistent and unreliable results, hindering progress in this field. Both false positives and negatives can be observed depending on environmental factors and interfering chemicals. In this regard, we propose new rigorous 13C NMR and LC-MS protocols for accurate urea detection to analyze catalyst activity in an accessible and reproducible manner.
|
Tiange Yuan; Oleksandr Voznyy
|
Catalysis; Energy; Electrocatalysis; Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640f1e25b5d5dbe9e8318ca4/original/guidelines-for-reliable-urea-detection-in-electrocatalysis.pdf
|
66d7653dcec5d6c1420823b6
|
10.26434/chemrxiv-2024-71qrl
|
Memory Kernel Minimization Based Neural Networks for Discovering Slow Collective Variables of Biomolecular Dynamics
|
Identifying collective variables (CVs) that accurately capture the slowest timescales of protein conformational changes is crucial to comprehend numerous biological processes. In this work, we develop a novel algorithm, the Memory kErnel Minimization based Neural Networks (MEMnets), that accurately identifies the slow CVs of biomolecular dynamics. MEMnets is distinct from popular deep-learning approaches (such as VAMPnets or SRVs) that assume Markovian dynamics. Instead, MEMnets is built on the integrative generalized master equation (IGME) theory, which incorporates non-Markovian dynamics by encoding them in a memory kernel for continuous CVs. The key innovation of MEMnets is to identify optimal CVs by minimizing time-integrated memory kernels. To accomplish this, MEMnets process time sequences of molecular dynamics (MD) conformations by using parallel encoder neural networks that project high-dimensional MD data into a low-dimensional latent space. The time-integrated memory kernels, derived from IGME theory, are then computed in the latent space as the objective function. We demonstrate that our MEMnets algorithm can effectively identify the slow CVs involved in the folding of FIP35 WW-domain with high accuracy, and successfully reveal two parallel folding pathways. Furthermore, we test MEMnets’ on the clamp opening of a bacterial RNA polymerase (RNAP), a much more complex conformational change (a system containing over 540K atoms), where sampling from all-atom MD simulations is limited. Our results demonstrate that MEMnets greatly outperforms SRVs, which is based on Markovian dynamics and may result in disconnected dynamics along the identified CVs. We anticipate that MEMnets holds promise to be widely to study biomolecular conformational changes.
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Bojun Liu; Siqin Cao; Jordan G Boysen; Mingyi Xue; Xuhui Huang
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biophysics; Theory - Computational; Machine Learning
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CC BY NC 4.0
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CHEMRXIV
|
2024-09-04
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d7653dcec5d6c1420823b6/original/memory-kernel-minimization-based-neural-networks-for-discovering-slow-collective-variables-of-biomolecular-dynamics.pdf
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668db48f01103d79c5888013
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10.26434/chemrxiv-2024-dh2rw
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FeatureDock: Protein-Ligand Docking Guided by Physicochemical Feature-Based Local Environment Learning using Transformer
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Molecular docking, the task of predicting the binding structures between a protein and a small molecule ligand, plays a significant role in structural-based drug discovery. In recent years, numerous deep learning-based methods for molecular docking have emerged. State-of-the-art approaches such as DiffDock formulate the docking problem using diffusion generative models, exhibiting superior performance than traditional docking algorithms. However, despite the strong performance of these deep learning-based docking methods in predicting binding poses, they often lack a well-defined scoring function. This limitation poses challenges in effectively distinguishing between the strong and weak inhibitors during virtual screening. To address this limitation, we introduce FeatureDock, a transformer-based deep learning framework, which can accurately predict the protein-ligand binding poses as well as achieve a strong scoring power for virtual screening. FeatureDock extracts chemical features from local environments within protein structures and utilizes a Transformer encoder to predict probability density envelopes indicating where ligands are most likely to bind in the protein pocket. We also designed a scoring function, which encodes the predicted probability density envelope, to optimize and score the ligand poses. In addition, the attention mechanism in FeatureDock’s Transformer further enhances the model’s interpretability by providing the attention weights of each chemical feature from the protein structures in predicting the binding probabilities. When applied to virtual screening, we demonstrated that FeatureDock outperforms DiffDock, Smina and AutoDock Vina in distinguishing strong inhibitors from weak ones for both Cyclin-Dependent Kinase 2 (CDK2, an inactivated form) and Angiotensin-converting enzyme (ACE). The performance was assessed using Kullback–Leibler (KL) divergence and area under receiver operating characteristic (AUC) evaluation metrics. We also demonstrate that FeatureDock can accurately predict the binding poses, achieving an average RMSD of 2.4 Å when compared to CDK2-ligand co-crystal structures. We anticipate that our FeatureDock holds promise to be widely applied in virtual screening to assist in drug design. FeatureDock is available at https://github.com/xuhuihuang/featuredock.
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Mingyi Xue; Bojun Liu; Siqin Cao; Xuhui Huang
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Biological and Medicinal Chemistry
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CC BY NC 4.0
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CHEMRXIV
|
2024-07-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668db48f01103d79c5888013/original/feature-dock-protein-ligand-docking-guided-by-physicochemical-feature-based-local-environment-learning-using-transformer.pdf
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67dd5459fa469535b9195606
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10.26434/chemrxiv-2025-zgn2c
|
Electronic excitation transfer dynamics in a
3-site system using an incoherent Born-Markov
rate model
|
The role of coherence in electronic excitation transfer (EET) dynamics in multi-site systems is typically investigated by comparing results from exact quantum dynamical methods with those derived from incoherent approaches such as the Fermi’s Golden Rule (FGR) model. Recent studies [1,2] on three-site systems have highlighted a remarkable dependence of EET dynamics on intersite coupling for specific configurations. To explore the influence of coherence in such behavior, we adapt the secular Redfield theory to develop an incoherent model by systematically excluding terms that couple populations and coherences in the site basis. The dynamics predicted by this model are then compared with those obtained from the coherent Lindbladian master equation and the incoherent FGR models. This framework provides a general approach for evaluating the role of coherence in a wide range of open quantum systems operating within the weak system-bath coupling regime.
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Amit Kumar Upadhyay; Karthik Sasihithlu
|
Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Biophysical Chemistry; Physical and Chemical Processes
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CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-24
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dd5459fa469535b9195606/original/electronic-excitation-transfer-dynamics-in-a-3-site-system-using-an-incoherent-born-markov-rate-model.pdf
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6100f68e032114fa00b85bab
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10.26434/chemrxiv-2021-947db-v2
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Toward the Creation of Induced Pluripotent Small (iPS) Molecules: Establishment of a Modular Synthetic Strategy to the Heronamide C-type Polyene Macrolactams and Their Conformational and Reactivity Analysis
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A highly modular synthetic strategy to the heronamide C-type polyene macrolactams was established by synthesizing 8-deoxyheronamide C (2). The developed strategy enabled not only the total synthesis of 8-deoxyheronamide C (2) but also the unified synthesis of four heronamide-like molecules named “heronamidoids” (5–8). Conformational and reactivity analysis of the heronamidoids clarified that (1) the C19 stereochemistry mainly affected the conformation of the amide linkage, resulting in the change of alignment of two polyene units and reactivity towards photochemical [6π+6π] cycloaddition, and (2) the C8,C9-diol moiety is important for the conversion to the heronamide A-type skeleton from the heronamide C skeleton.
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Naoki Kanoh; Yuta Terajima; Suguru Tanaka; Ryusei Terashima; Hiromichi Nishiyama; Shota Nagasawa; Yusuke Sasano; Yoshiharu Iwabuchi; Shinichi Nishimura; Hideaki Kakeya
|
Organic Chemistry; Organic Synthesis and Reactions
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-07-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6100f68e032114fa00b85bab/original/toward-the-creation-of-induced-pluripotent-small-i-ps-molecules-establishment-of-a-modular-synthetic-strategy-to-the-heronamide-c-type-polyene-macrolactams-and-their-conformational-and-reactivity-analysis.pdf
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662e5e9b21291e5d1dee8bbd
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10.26434/chemrxiv-2024-35nc4
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Ion-Radical Mediated Multi-Color Ultra-Long Afterglow Materials
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Pure organic persistent room temperature phosphorescence (RTP) has shown great potential in numerous applications, ranging from information encryption and display technologies to bio-applications and beyond. In this work, a suite of multi-color long-lived RTP materials featuring distinct afterglow emissions was constructed using an ion-radical mediated approach. b[c]p/MeBPO emitted a vivid yellow afterglow centered at 560 nm with an impressively long lifetime of 860.01 ms. While compound b[a]a exhibited a near-infrared (NIR) afterglow (τ = 215.96 ms) after doping into the matrix. The transient absorption spectroscopy investigations disclosed that the observed afterglow phenomenon was fundamentally tied to the generation of radical ions rather than the exciplex. These radical ions resulted from the reduction quenching process of the triplet excited state of compound BPO by the ground state of the doping agent. A novel evaluation methodology was devised, rooted in Marcus theory, to gauge the potential of a specific dopant-matrix combination towards generating pronounced afterglow. According to this framework, the enhancement of the afterglow is directly proportional to the decrease in the activation energy (ΔG≠) associated with the electron transfer reaction occurring between the dopant and the matrix. Notably, when the ΔG≠ surpasses 30 kcal/mol, no observable afterglow occurs, as higher ΔG≠ values significantly impede the electron transfer reaction between the two components. Furthermore, the system exhibits exceptional sensitivity, with the dopant as low as 0.02‰ molar ratio between the dopant and the host material. This remarkable dependence of afterglow intensity on the dopant concentration renders the bi-component RTP system highly promising for applications requiring ultra-high sensitivity and broad-spectrum detection capabilities.
|
Liangwei Ma; Yiwei Liu; Tao Jiang; Lei Zhou; Qiaochun Wang; He Tian; Xiang Ma
|
Organic Chemistry; Photochemistry (Org.)
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CC BY NC 4.0
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CHEMRXIV
|
2024-04-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662e5e9b21291e5d1dee8bbd/original/ion-radical-mediated-multi-color-ultra-long-afterglow-materials.pdf
|
60c73dd2ee301c3822c7861e
|
10.26434/chemrxiv.6108467.v1
|
Bottom-up Evolution from Disks to High-Genus Polymersomes
|
<div><div><div><p>We report the design of polymersomes using a bottom-up approach where the self-assembly of amphiphilic copolymers poly(2-(methacryloyloxy) ethyl phosphorylcholine)–poly(2-(diisopropylamino) ethyl methacrylate) (PMPC-PDPA) into membranes is tuned using pH and temperature. We study this process in detail using transmission electron microscopy (TEM), nuclear magnetic resonance (NMR) spectroscopy, dynamic light scattering (DLS), and stop-flow ab- sorbance disclosing the molecular and supramolecular anatomy of each structure observed. We report a clear evolution from disk micelles to vesicle to high-genus vesicles where each passage is controlled by pH switch or temperature. We show that the process can be rationalised adapting membrane physics theories disclosing important scaling principles that allow the estimation of the vesiculation minimal radius as well as chain entanglement and coupling. This allows us to propose a new approach to generate nanoscale vesicles with genus from 0 to 70 which have been very elusive and difficult to control so far.</p></div></div></div>
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Claudia Contini; Russell Pearson; Linge Wang; Lea Messager; Jens Gaitzsch; Loris Rizzello; Lorena Ruiz-Pérez; Giuseppe Battaglia
|
Polymer chains; Polymer morphology; Self-Assembly
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CC BY NC ND 4.0
|
CHEMRXIV
|
2018-04-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd2ee301c3822c7861e/original/bottom-up-evolution-from-disks-to-high-genus-polymersomes.pdf
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62575b815b9009f6750d41bd
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10.26434/chemrxiv-2022-5nm8t
|
Automated design of Li+-conducting polymer by quantum-inspired annealing
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Automated molecule design by computers has been an essential topic in materials informatics. Still, generating practical structures is not easy because of the difficulty in treating material stability, synthetic difficulty, mechanical properties, and other miscellaneous parameters, often leading to the generation of junk molecules. We tackle the problem by introducing supervised/unsupervised machine learning and quantum-inspired annealing. Our autonomous molecular design system can help experimental researchers discover practical materials more efficiently. Like the human design process, new molecules are explored based on knowledge of existing compounds. A new solid-state polymer electrolyte for lithium-ion batteries is designed and synthesized, giving a promising room temperature conductivity of 10^-5 S/cm with reasonable thermal, chemical, and mechanical properties.
|
Kan Hatakeyama-Sato; Hiroki Adachi; Momoka Umeki ; Takahiro Kashikawa; Koichi Kimura; Kenichi Oyaizu
|
Theoretical and Computational Chemistry; Polymer Science; Polyelectrolytes - Polymers; Machine Learning; Quantum Computing; Materials Chemistry
|
CC BY NC ND 4.0
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CHEMRXIV
|
2022-04-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62575b815b9009f6750d41bd/original/automated-design-of-li-conducting-polymer-by-quantum-inspired-annealing.pdf
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65605eab29a13c4d47e04529
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10.26434/chemrxiv-2023-lwnwj
|
Copper-Catalyzed Sulfimidation in Aqueous Media: a Fast, Chemoselective and Biomolecule-Compatible Reaction
|
Performing transition metal-catalyzed reactions in cells and living systems has equipped scientists with a toolbox to study biological processes and release drugs on demand. Thus far, an impressive scope of reactions has been performed in these settings, but many are yet to be introduced. Nitrene transfer presents a rather unexplored new-to-nature reaction. The reaction products are frequently encountered motifs in pharmaceuticals, presenting opportunities for the controlled, intracellular synthesis of drugs. Hence, we explored the transition metal-catalyzed sulfimidation reaction in water for future in vivo application. Two Cu(I) complexes containing trispyrazolylborate ligands (Tpx) were selected, and the catalytic system was evaluated with the aid of three fitness factors. The excellent nitrene transfer reactivity and high chemoselectivity of the catalysts, coupled with good biomolecule compatibility, successfully enabled the sulfimidation of thioethers in aqueous media. We envision that this copper-catalyzed sulfimidation reaction could be an interesting starting point to unlock the potential of nitrene transfer catalysis in vivo.
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Eva Meeus; María Álvarez; Emma Koelman; Pedro J. Pérez; Joost N. H. Reek; Bas de Bruin
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Catalysis; Homogeneous Catalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-11-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65605eab29a13c4d47e04529/original/copper-catalyzed-sulfimidation-in-aqueous-media-a-fast-chemoselective-and-biomolecule-compatible-reaction.pdf
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60c74bffbdbb893445a396d1
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10.26434/chemrxiv.12408548.v1
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Peptidyl Acyloxymethyl Ketones as Activity-Based Probes for the Main Protease of SARS-CoV-2
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<div>The global pandemic caused by SARS-CoV-2 calls for a fast development of antiviral drugs </div><div>against this particular coronavirus. Chemical tools to facilitate inhibitor discovery as well as </div><div>detection of target engagement by hit or lead compounds from high throughput screens are </div><div>therefore in urgent need. We here report novel, selective activity-based probes that enable </div><div>detection of the SARS-CoV-2 main protease. The probes are based on acyloxymethyl ketone </div><div>reactive electrophiles combined with a peptide sequence including non-natural amino acids </div><div>that targets the non-primed site of the main protease substrate binding cleft. They are the first </div><div>activity-based probes for the main protease of coronaviruses and display target labeling within </div><div>in a human proteome without background. We expect that these reagents will be useful in the </div><div>drug development pipeline, not only for the current SARS-CoV-2, but also for other </div><div>coronaviruses. </div>
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Merel Van de Plassche; Marta Barniol-Xicota; Steven Verhelst
|
Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bffbdbb893445a396d1/original/peptidyl-acyloxymethyl-ketones-as-activity-based-probes-for-the-main-protease-of-sars-co-v-2.pdf
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666301b2409abc0345dd3188
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10.26434/chemrxiv-2024-64jxb
|
Purification of Au/Au Core/Satellite Supraparticles by Asymmetric Flow Field Flow Fractionation for SERS Nanotag-based Applications
|
Over the last decades, nanoparticles have been increasingly used in biomedical applications, such as immunolabelling, requiring high control over size and shape. Nanoparticle synthesis often lacks the required reaction control which necessitates additional purification steps. For this purpose, asymmetric flow field flow fractionation (AFFF) is a powerful tool to purify particles and characterize them online. Here, we systematically studied the usability of AFFF for the purification of a colloid primarily containing self-assembled Au/Au core/satellite particles (C/S particles). In this case, purification of C/S particles from unbound monomeric AuNP satellites, which were added in excess during synthesis, is needed. We successfully demonstrated the effective separation of monomeric SERS-inactive AuNP satellites from the highly SERS-active C/S particles. While centrifugation is a commonly used and easy bench-top method, separation with AFFF offers an improved resolution and recovery. A linearly decreasing crossflow profile enabled us to achieve a separation with sufficient resolution and good recovery. Purified C/S colloids exhibit an increase in SERS activity of 25%, improving their usability for SERS-based applications by avoiding false-negative results.
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Louisa Waasmann; Annika Kleinschmidt; Elzbieta Stepula; Carolin Sanders; Bernd Walkenfort; Sebastian Schlücker
|
Analytical Chemistry; Nanoscience; Separation Science; Spectroscopy (Anal. Chem.); Plasmonic and Photonic Structures and Devices
|
CC BY 4.0
|
CHEMRXIV
|
2024-06-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666301b2409abc0345dd3188/original/purification-of-au-au-core-satellite-supraparticles-by-asymmetric-flow-field-flow-fractionation-for-sers-nanotag-based-applications.pdf
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65e5dcf39138d23161a4d3b3
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10.26434/chemrxiv-2024-w75d9
|
Large Local Internal Stress in an Elastically Bent Molecular Crystal Revealed by Raman Shifts
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The structural dynamics involved in the mechanical flexibility of molecular crystals are not well understood yet. Here, we report an elastically bending lipidated molecular crystal that shows systematic shifts in characteristic vibrational frequencies across the bent crystal region - revealing the nature of structural changes during bending and the local internal stress distribution. The elastic flexibility is rendered by intermolecular N-H∙∙∙O hydrogen-bonded chains along with strong yet flexible alkyl-chain hydrophobic interactions in this crystal structure. The blue shifts in the bond stretching modes (such as C=O and C-H modes) in the inner arc region and red shifts in the outer arc region of the bent crystals observed via micro-Raman mapping are counterintuitive to the bending models based on intermolecular hydrogen bonds. Correlating these shifts with the trends observed from high-pressure Raman studies on the crystal reveals the local stress difference between the inner arc and outer arc regions of the bent crystal to be ~2 GPa, more than an order of magnitude higher than the previously proposed value in elastically bending crystals. High local internal stress can have direct ramifications on the properties of molecular piezoelectric energy harvesters, actuators, semiconductors, and flexible optoelectronic materials.
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Atiqur Rahman; Srijan Mondal; Mantu Modak; Ashi Singh; Hanuman Singh; Navdeep S. Thayat; Jack K. Clegg; Himanshu K. Poswal; V. Haridas; Sajesh P. Thomas
|
Physical Chemistry; Physical and Chemical Properties; Materials Chemistry; Crystallography
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CC BY NC 4.0
|
CHEMRXIV
|
2024-03-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e5dcf39138d23161a4d3b3/original/large-local-internal-stress-in-an-elastically-bent-molecular-crystal-revealed-by-raman-shifts.pdf
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6615495921291e5d1d7600a6
|
10.26434/chemrxiv-2023-5880w-v2
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Lights on the synthesis of surfactant-free colloidal gold nanoparticles in alcohol and water mixtures
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Surfactant-free colloidal syntheses in aqueous media are attractive to develop nanomaterials relevant for various applications, e.g. catalysis or medicine. However, controlled green syntheses without surfactants of metal nanoparticles in aqueous media remain scarce. Here, room temperature syntheses of gold (Au) nanoparticles (NPs) that require only HAuCl4, alkaline water and an alcohol, i.e. relatively benign chemicals and mild reaction conditions, are developed. The findings of a comprehensive multi-parameters screening performed in small volumes (< 3 mL) over 1000+ experiments, that pave the way to greener high throughput screening of large parametric spaces and leads to scalable (100 mL) synthetic strategies, are summarized. A rational selection of the alcohol is proposed. The influence of lights with defined wavelengths (222-690 nm) is investigated. It is found that lights with lower wavelengths favor the formation of smaller 5 nm NPs. Different kinetics and formation pathways are observed for different alcohols and for lights with different wavelengths. The sensitivity to various experimental parameters increases in the order glycerol < ethylene glycol < ethanol < methanol. New strategies for a rational fine size control, and to some extend shape control, are identified. The results lead to more sustainable and reproducible surfactant-free colloidal syntheses of NPs.
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Ditte Røjkjær Rasmussen; Nina Lock; Jonathan Quinson
|
Materials Science; Nanoscience; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Materials Chemistry
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CC BY 4.0
|
CHEMRXIV
|
2024-04-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6615495921291e5d1d7600a6/original/lights-on-the-synthesis-of-surfactant-free-colloidal-gold-nanoparticles-in-alcohol-and-water-mixtures.pdf
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66e230c912ff75c3a113faee
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10.26434/chemrxiv-2024-06gf1
|
High Dimensional and Complex Spectrometric Data Analysis of an Organic Compound using Large Multimodal Models and Chained Outputs
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Large Multimodal Models (LMMs) possess the ability to analyze chemical spectra of an organic compound using state of the art conversational AI. These outputs can then be chained together and introduced as a text input for other LLMs or LMMs to predict the compound name. Here, a challenging 15 carbon molecule problem with 13 complex and high dimensional chemical spectra were analyzed as images by unmodified versions of Claude 3.5 Sonnet and OpenAI ChatGPT-4o models. ScholarGPT judged the responses across the 13 spectra with an average score of 9.01/10, and the highest response scores per individual spectra for 3.5 Sonnet or GPT-4o were used as the text-based chain. For Part B, the chain was then combined with two different prompt formats and the molecular formula to 8 different LMMs or LLMs which produced new compound predictions. 3.5 Sonnet had the highest proficiency in utilizing the formula simultaneously with complex data for three identical compound generations across two prompts, but was likely limited by the quality regarding the chain of 13, primarily with data from 6 2D NMR Spectra. 3.5 Sonnet's compound prediction was then further improved in Part C by utilizing manual chained explanations of the spectra by the author to yield what is believed to be the correct structure with stereochemistry to the unknown problem. To the author's best knowledge, this is the first LMM to generate the C15H22O2 drug compound derivative (S)-ibuprofen ethylester using high dimensional data from 13 detailed spectra. The purpose of this study was to utilize cutting edge natural language processing techniques to evaluate an advanced chemical structure consisting of IR, 1H-NMR, 13C-NMR, DEPT-NMR, GCOSY60, GTOCSY, GHMQC, GHMBC, GNOESY, and expanded views of spectra.
|
Kevin Kawchak
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Organic Chemistry; Analytical Chemistry; Organic Compounds and Functional Groups; Spectroscopy (Anal. Chem.)
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CC BY 4.0
|
CHEMRXIV
|
2024-09-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e230c912ff75c3a113faee/original/high-dimensional-and-complex-spectrometric-data-analysis-of-an-organic-compound-using-large-multimodal-models-and-chained-outputs.pdf
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6253ff7a103388a467e92d4c
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10.26434/chemrxiv-2022-2g6dl
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High Pressure Induced Formation of Carbon Nanorods from Tetracosane
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Morphology control of carbon nanostructures is essential for improving their performance in many applications. Direct pyrolysis of organic precursors, however, usually yields bulk amorphous carbon. Therefore, traditional methods for controlling the morphology of carbon nanostructures involve multistep processes and complex precursor molecules. While various methods have been developed under ambient pressure, the impact of pressure on the morphology of the resulting carbon nanostructures remains unexplored. Herein, we present the synthesis of carbon nanorods by direct pyrolysis of the low-cost aliphatic hydrocarbon tetracosane under high pressure conditions. The diameters of the carbon nanorods are adjusted by simply varying the synthetic pressures. High pressure allows controlling both the nanorod morphology as well as the degree of order, and local conductivity of the thus prepared nanorods has been confirmed by conductive AFM measurements. Our method promises a convenient strategy to synthesize carbon nanostructures with controlled morphology and high ordered chemical structure, which opens opportunities for potential electronic and electrochemical applications.
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Jiaxu Liang; Christopher P. Ender; Pascal Rohrbeck; Robert Graf; Ingo Lieberwirth; Manfred Wagner; Stefan A. L. Weber; Klaus Müllen; Tanja Weil
|
Physical Chemistry; Materials Science; Nanoscience; Carbon-based Materials; Nanostructured Materials - Nanoscience; Self-Assembly
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-04-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6253ff7a103388a467e92d4c/original/high-pressure-induced-formation-of-carbon-nanorods-from-tetracosane.pdf
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60c744d90f50db483d396178
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10.26434/chemrxiv.9917150.v1
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Exhaustive Reduction of Esters Enabled by Nickel Catalysis
|
We report a one-step procedure to directly reduce unactivated aryl esters into their corresponding tolyl-derivatives. This is achieved by the action of a Ni/NHC catalyst and an organosilane reducing agent that is activated in situ by stoichiometric KOtBu. The resulting conditions provide a direct and efficient alternative to multi-step procedures for this transformation that often require use of hazardous metal hydrides. Applications in the synthesis of –CD3 containing products, derivatization of bioactive molecules, and chemoselective reduction in the presence of other C–O bonds is demonstrated.
|
sekar prakash; Adam Cook; yan-long zheng; Stephen Newman
|
Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-10-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744d90f50db483d396178/original/exhaustive-reduction-of-esters-enabled-by-nickel-catalysis.pdf
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63fe867b897b18336f4c5709
|
10.26434/chemrxiv-2023-cbfs1
|
Amination of a Green Solvent via Immobilized Biocatalysis for the Synthesis of Nemtabrutinib
|
Enzymes are capable of unique and selective transformations that can enable sustainable chemical production. While many industrial processes have been developed using free enzymes in aqueous solutions, immobilizing enzymes on a solid support can offer considerable advantages, including improved reaction efficiency, enzyme stability, the ability to perform reactions in non-aqueous media, and simplified separation of product from enzyme. Herein, we describe the development of a biocatalytic transaminase reaction of CyreneTM (2) utilizing an immobilized, evolved transaminase enzyme in an organic solvent to provide amine intermediate 3a en route to the Brutons tyrosine kinase (BTK) inhibitor nemtabrutinib. Enzyme immobilization is critical to facile isolation of the water-soluble product. Improved reaction kinetics and diastereoselectivity were achieved by bridging directed enzyme evolution with the selection of an optimal reaction solvent and solid support for immobilization, enabling a unified solvent system and direct isolation of 3a as a crystalline salt with dr > 50:1.
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Christopher K. Prier; Karla Camacho Soto; Jacob H. Forstater; Nadine Kuhl; Jeffrey T. Kuethe; Wai Ling Cheung-Lee; Michael J. Di Maso; Claire M. Eberle; Shane T. Grosser; Hsing-I Ho; Erik Hoyt; Anne Maguire; Kevin M. Maloney; Amanda Makarewicz; Jonathan P. McMullen; Jeffrey C. Moore; Grant S. Murphy; Karthik Narsimhan; Weilan Pan; Nelo R. Rivera; Anumita Saha-Shah; David A. Thaisrivongs; Deeptak Verma; Adeya Wyatt; Daniel Zewge
|
Organic Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Process Chemistry; Pharmaceutical Industry; Biocatalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-03-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63fe867b897b18336f4c5709/original/amination-of-a-green-solvent-via-immobilized-biocatalysis-for-the-synthesis-of-nemtabrutinib.pdf
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620b59264e899e77464e4aa7
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10.26434/chemrxiv-2022-xbq1j
|
Visible Light Promoted Stereoselective C(sp3)-H Glycosylation for the Synthesis of C-Glycoamino Acids and C-Glycopeptides
|
Glycosylative modification of peptides could improve the pharmacological properties of peptide drugs and deliver them efficiently to the target sites. Compared with O-/N-glycosides, C-glycosides exhibit more metabolic stability. We here disclose the first example of visible-light promoted and Cu-catalyzed stereoselective C-glycosylations. The mild reaction conditions are compatible with various carbohydrate substrates, including a series of mono monosaccharides and disaccharide, and is amenable to the synthesis of a wild variety of C-glycoamino acids and C-glycopeptidomimetics with good yields and excellent stereoselectivities. The dual-functional photocatalyst formed in situ via coordination of glycine derivatives and chiral phosphine Cu complex could not only catalyze the photoredox process but also control the stereoselectivity of glycosylation reaction.
|
Rupeng Qi; Chao Wang; Zijian Ma; Hongying Wang; Qiao Chen; Liangyu Liu; Da Pan; Xiaoyu Ren; Rui Wang; Zhaoqing Xu
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Photocatalysis
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CC BY NC 4.0
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CHEMRXIV
|
2022-02-16
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620b59264e899e77464e4aa7/original/visible-light-promoted-stereoselective-c-sp3-h-glycosylation-for-the-synthesis-of-c-glycoamino-acids-and-c-glycopeptides.pdf
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63f7951032cd591f125fe49e
|
10.26434/chemrxiv-2023-4f6kr
|
Peptide-Directed Attachment of Hydroxylamines to Specific Lysines of IgG Antibodies for Bioconjugations with Acylboronates
|
The role of monoclonal antibodies as vehicles to deliver payloads has evolved as a powerful tool in cancer therapy in recent years. The clinical development of therapeutic antibody-conjugates with precise payloads holds great promise for targeted therapeutic interventions. The use of affinity-peptide mediated functionalization of native off-the-shelf antibodies offers an effective approach to selectively modify IgG antibodies with a drug antibody ratio (DAR) of 2. Here, we report the traceless, peptide-directed attachment of two hydroxylamines to native IgGs followed by chemoselective KAT ligation with quinolinium acyltrifluoroborates (QATs), which provide enhanced ligation rates with hydroxylamines under physiological conditions. By applying KAT ligation to the modified antibodies, conjugation of small molecules, proteins, and oligonucleotides to off-the-shelf IgGs proceeds efficiently, in good yields, and with simultaneous cleavage of the affinity peptide-directing moiety.
|
Matthias Tanriver ; Marco Müller; Daniel Richards; Sohei Majima; Andrew deMello; Jeffrey Bode
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Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-02-24
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f7951032cd591f125fe49e/original/peptide-directed-attachment-of-hydroxylamines-to-specific-lysines-of-ig-g-antibodies-for-bioconjugations-with-acylboronates.pdf
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630ce1b9d147b2e393bd1480
|
10.26434/chemrxiv-2022-c21jc
|
Green Light Photoelectrocatalysis with Sulfur-Doped Carbon Nitride: Using Triazole-Purpald for Enhanced Benzylamine Oxidation and Oxygen Evolution Reactions
|
Novel high performing materials will dictate the pace of reinventing industrial chemical processes to attain desired carbon neutrality targets. Regarding the urgency of exploiting solar irradiation long range visible-light photoelectrocatalysts from abundant resources will play a key role in the aforementioned effort. Anionic doping via co-polymerization and pre-organization of precursors results in tuneable and extrinsic semiconductors, making this a highly attractive methodology. Triazole derivative-purpald, an unexplored precursor but sulfur (S) container, combined with melamine during one solid-state polycondensation reaction with two thermal steps leads to S-doped carbon nitrides (C3N4). The series of S-doped/C3N4-based materials demonstrated enhanced optical, electronic, structural, geometric, textural, and morphological properties and exhibited higher performance in organic benzylamine photooxidation, oxygen evolution, and similar storing energy (capacitor brief investigation) than references. Among the five composites, 50M-50P exhibited the highest photooxidation conversion yield (84±3%) of benzylamine to imine at 535 nm – green light for 48h, due to an extra discrete shoulder reaching ~700 nm, an unusual high sulfur content, preservation of crystal size, new intraband energy states, rare deep structural defects by layer distortion, hydrophobic surface, low porosity, and 10-16 nm pores. An in-depth analysis of S doping was investigated coupling x-ray photoelectron spectroscopy, transmission electron microscope, and elemental analysis, providing insights on bonds, distribution, and surface/bulk content. This work contributes to the development of amorphous photocatalysts with long-visible-light range for solar energy conversion and storage.
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Maria Jerigova ; Yevheniia Markushyna; Ivo F. Teixeira ; Bolortuya Badamdorj ; Mark Isaacs; Daniel Cruz; Iver Lauermann; Miguel Ángel Muñoz-Márquez; Nadezda V. Tarakina; Nieves López-Salas; Oleksandr Savateev ; Pablo Jiménez Calvo
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Materials Science; Catalysis; Energy; Electrocatalysis; Heterogeneous Catalysis; Photocatalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-08-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630ce1b9d147b2e393bd1480/original/green-light-photoelectrocatalysis-with-sulfur-doped-carbon-nitride-using-triazole-purpald-for-enhanced-benzylamine-oxidation-and-oxygen-evolution-reactions.pdf
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60c74fc3337d6ca654e281b6
|
10.26434/chemrxiv.12931406.v1
|
A Chemical-Physical View of the Interpretation of Wavefunction
|
Here, based on different experimental setups and thought experiments it
is shown that some of the predictions of the nonlocal probabilistic
interpretation of wavefunction are not observed and that this interpretation
does not account for the real-world physical and chemical interactions.
Considering these interactions, classical and quantum mechanics are unified and
a testable, local, and probabilistic interpretation of wavefunction is proposed
in explaining the outcome of a double-slit experiment. This analysis suggests
that there is no spooky action at a distance.
|
Kourosh Ebrahimi
|
Quantum Mechanics
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CC BY NC ND 4.0
|
CHEMRXIV
|
2020-09-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fc3337d6ca654e281b6/original/a-chemical-physical-view-of-the-interpretation-of-wavefunction.pdf
|
6625a37791aefa6ce10d4b04
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10.26434/chemrxiv-2024-83h5q-v2
|
Estimating Free Energy Surfaces and their Convergence from multiple, independent static and history-dependent biased molecular-dynamics simulations with Mean Force
Integration.
|
Addressing the sampling problem is central to obtaining quantitative insight from molecular dynamics
simulations. Adaptive biased sampling methods, such as metadynamics, tackle this issue
by perturbing the Hamiltonian of a system with a history-dependent bias potential, enhancing the
exploration of the ensemble of configurations and estimating the corresponding free energy surface
(FES). Nevertheless, efficiently assessing and systematically improving their convergence remains an
open problem. Here, building on Mean Force Integration (MFI), we develop and test a metric for estimating
the convergence of free energy surfaces obtained by combining asynchronous, independent
simulations subject to diverse biasing protocols, including static biases, different variants of metadynamics,
and various combinations of static and history-dependent biases. The developed metric
and the ability to combine independent simulations granted by MFI enable us to devise strategies to
systematically improve the quality of FES estimates. We demonstrate our approach by computing
FES and assessing the convergence of a range of systems of increasing complexity, including one- and
two-dimensional analytical free energy surfaces, alanine dipeptide, a Lennard-Jones supersaturated
vapour undergoing liquid droplet nucleation, and the model of a colloidal system crystallizing via
a two-step mechanism. The methods presented here can be generally applied to biased simulations
and are implemented in pyMFI, a publicly accessible, open-source Python library.
|
Antoniu Bjola; Matteo Salvalaglio
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-04-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6625a37791aefa6ce10d4b04/original/estimating-free-energy-surfaces-and-their-convergence-from-multiple-independent-static-and-history-dependent-biased-molecular-dynamics-simulations-with-mean-force-integration.pdf
|
631aff720429d631389829b5
|
10.26434/chemrxiv-2022-4nvqq
|
Collective Total Synthesis of Mavacuran Alkaloids via an Intermo-lecular 1,4-Addition Approach
|
We report a synthetic endeavor towards the highly strained pentacyclic caged framework of the mavacuran alkaloids which culminated with the concise total synthesis of C-fluorocurine, C-profluorocurine, C-mavacurine, normavacurine, 16-epi-pleiocarpamine and taberdivarine H. We designed an original strategy which involves a late stage construction of the D ring via a Michael addition of a vinylic nucleophile to a 2-indolyl acrylate moiety. While the intramolecular Michael addition did not succeed, we were able to perform a diastereoselective unusual intermolecular 1,4-addition of a functionalized vinyl lithium reagent onto a readily accessible Michael acceptor. Final cyclization was achieved via nucleophilic substitution into an ammo-nium intermediate. The first total syntheses of C-profluorocurine and C-fluorocurine were finalized via respectively the dihy-droxylation of C-mavacurine and a pinacol rearrangement.
|
Audrey Mauger; Maxime Jarret; Aurélien Tap; Rémi Perrin; Régis Guillot; Cyrille Kouklovsky; Guillaume Vincent
|
Organic Chemistry; Natural Products; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631aff720429d631389829b5/original/collective-total-synthesis-of-mavacuran-alkaloids-via-an-intermo-lecular-1-4-addition-approach.pdf
|
62dfa092e7fc8f2b8e88ed7e
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10.26434/chemrxiv-2022-gjxkd
|
Accurate determination of interfacial thermal resistance inside particle-laden composites based on high-throughput computation and machine learning
|
Particle-laden composites are typical thermal interfacial materials (TIMs) in the electronic applications, which are widely used in the electron packaging fields. The effective thermal conductivity (effective TC) of the particle-laden composites is dominant by the particle-matrix and particle-particle interfacial thermal resistance (ITR). The reliable identification of ITR is essential for the accurate prediction of TC of the composites, which has potential in the design of TIMs. In this work, we propose an efficient strategy to identify the interfacial thermal resistance in the particle-laden composites combining the numerical simulation, high-throughput computation, machine learning algorithm and simple experimental measurement. Firstly, the high-throughput computation is conducted based on the numerical modeling of the standard samples, in which the input parameters are ITRs in the composites. Afterwards, a prototypical function-based machine learning strategy is employed on the database to describe the numerical relation between the effective TC and the input parameters.
Finally, comparing the numerical predictions from the machine learning model with the experimental measurement of the effective TC, a high-throughput screening of the ITRs is executed for the identification of their values. The reliability of the strategy is validated by an example of Al2O3-AlN/silicone composites, showing that the particle-particle ITR is higher than particle-matrix ITR.
|
XIAOXIN LU; JIABIN HUANG; NAN CHENG; LINLIN REN; JIANBIN XU; JIBAO LU; RONG SUN
|
Materials Science; Composites
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-11-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62dfa092e7fc8f2b8e88ed7e/original/accurate-determination-of-interfacial-thermal-resistance-inside-particle-laden-composites-based-on-high-throughput-computation-and-machine-learning.pdf
|
60c748d3bb8c1ac6eb3dad41
|
10.26434/chemrxiv.11982180.v1
|
Synthesis, Characterization and Antiparasitic Activity of Organometallic Derivatives of the Anthelmintic Drug Albendazole
|
Helminthiases, a group of neglected tropical diseases, affect more than one billion people mainly in tropical and subtropical regions. Albendazole (ABZ) is a broad‐spectrum anthelmintic recommended by the World Health Organisation (WHO). However, drug resistance is emerging due to its widespread use. In order to tackle this problem, taking into account the spectacular results obtained with the organometallic derivatization of the antimalarial drug chloroquine, we have prepared, in this study, a series of new ferrocenyl and ruthenocenyl derivatives of the organic drug ABZ and assessed their activity against different helminths but also protozoans, namely Trichuris muris adult, Heligmosomoides polygygrus adult, Schistosoma mansoni adult, Giardia lamblia, Haemonchus contortus xL3s and Toxoplasma gondii to determine the full potential of our new compounds. Worthy of note, the ferrocene‐containing ABZ analogue 2d exhibited over 70% activity against T. muris adult in vitro and no toxicity to mammalian cells up to 100 µM. Against T. gondii, the ferrocene‐containing ABZ analogues 1a and 2d showed better in vitro activity than ABZ and low toxicity to the host cells. However, the activity of the analogous ruthenocenyl compound 2b against S. mansoni and T. gondii in vitro could rather be attributed to its toxicity towards the host cells rather than a specific antiparasitic activity. These results demonstrate that the choice of the organometallic moieties attached to the organic drug is playing a very important role. Two of our organometallic compounds, namely 1b and 2d, were tested in T. muris infected mice. At a 400 mg/kg dose, the compounds showed moderate worm burden reductions and low worm expulsion rates. Overall, this work, which is one of the first studies reporting the potential of organometallic compounds on a very broad range of parasitic helminths and protozoan, is a clear confirmation of the potential of organometallic complexes against parasites of medical and veterinary importance.<br />
|
Yan Lin; Yih Ching Ong; Sarah Keller; Johannes Karges; Rafika Bouchene; Eric Manoury; Olivier Blacque; Joachim Müller; Nicoleta Anghel; Andrew Hemphill; Aya Taki; ROBIN GASSER; Kevin Cariou; Jennifer Keiser; Gilles Gasser
|
Bioinorganic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-03-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748d3bb8c1ac6eb3dad41/original/synthesis-characterization-and-antiparasitic-activity-of-organometallic-derivatives-of-the-anthelmintic-drug-albendazole.pdf
|
62a3951999b7836e25fbe614
|
10.26434/chemrxiv-2022-czn71
|
Transfer and Active Learning of High Dimensional Neural Network
Potentials for Transition Metal Clusters and Bulk
|
Classical molecular dynamics (MD) simulations represent a very popular and powerful tool for materials modeling
and design. The predictive power of MD hinges on the ability of the interatomic potential to capture the underlying
physics and chemistry. There have been decades of seminal work on developing interatomic potentials albeit with
a focus predominantly on capturing the properties of bulk materials. Such physics-based models, while extensively
deployed for predicting dynamics and properties of nanoscale systems over the past two decades, tend to perform poorly
in predicting nanoscale potential energy surface when compared to high-fidelity first-principles calculations. These
limitations stem from the lack of flexibility in such models, which rely on a pre-defined functional form. Machine
learning models and approaches have emerged as a viable alternative to capture the diverse size-dependent cluster
geometries, nanoscale dynamics and the complex nanoscale potential energy surfaces (PES), without sacrificing the
bulk properties. Here, we introduce an ML workflow that combines transfer and active learning strategies to develop
high-dimensional neural networks (NN) for capturing cluster and bulk properties for several different transition metals
with applications in catalysis, microelectronics, and energy storage to name a few. Our NN first learns the bulk PES
from the high-quality physics-based models in literature and subsequently augments this learning via retraining with a
higher fidelity first-principles training dataset to concurrently capture both the nanoscale and bulk PES. Our workflow
departs from status-quo in its ability to learn from a sparsely sampled dataset that nonetheless covers a diverse range
of cluster configurations from near-equilibrium to highly non-equilibrium as well as learning strategies that iteratively
improves the fingerprinting depending on model fidelity. All the developed models are rigorously tested against an
extensive first-principles dataset of energies and forces of cluster configurations as well as several properties of bulk
configurations for 10 different transition metals. Our approach is material agnostic and provides a methodology to
transfer and build upon the learnings from decades of seminal work in molecular simulations on to a new generation of
ML trained potentials to accelerate materials discovery and design.
|
Bilvin Varughese; Sukriti Manna; Troy Loeffler; Rohit Batra; Mathew Cherukara; Subramanian K.R.S. Sankaranarayanan
|
Theoretical and Computational Chemistry; Materials Science; Nanoscience; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence
|
CC BY 4.0
|
CHEMRXIV
|
2022-06-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a3951999b7836e25fbe614/original/transfer-and-active-learning-of-high-dimensional-neural-network-potentials-for-transition-metal-clusters-and-bulk.pdf
|
662a572c21291e5d1db05e9e
|
10.26434/chemrxiv-2024-pzs58
|
Investigating Interaction Dynamics of an Enantioselective Peptide Catalyzed Acylation Reaction
|
Nuclear magnetic resonance (NMR) is a key method to investigate molecular recognition in biomacromolecules and to detect molecular motions on the µs to s timescale revealing transient conformational states. Changes in kinetics of interconversions between those states can be linked to binding, folding or catalytic events. Here, we investigated whether these methods allow detection of changes in the dynamics of a small, highly selective peptide catalyst during recognition of its enantiomeric substrates. The flexible tetrapeptide Boc-L-(π-Me)-His-AGly-L-Cha-L-Phe-OMe, used for the monoacetylation of cycloalkane-diols, is probed at natural abundance using carbon relaxation dispersion in the rotating frame (13C-R1ρ) and proton chemical exchange saturation transfer (1H-CEST). Indeed, we detected differences in dynamics of the peptide upon interaction with the diol. Importantly, these differ depending on the enantiomer of the substrate used providing insights into the recognition of the substrates. These enantiospecific influences of the substrates on the dynamics of the peptide catalyst revealed are rationalized using. computational techniques. Moreover, findings obtained are supported by experimental reaction monitoring of the acetylation reaction.
|
Matthias Brauser; Katja Petzold; Christina M. Thiele
|
Organic Chemistry; Physical Organic Chemistry; Stereochemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-04-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662a572c21291e5d1db05e9e/original/investigating-interaction-dynamics-of-an-enantioselective-peptide-catalyzed-acylation-reaction.pdf
|
63dc1178068fd759791a8e75
|
10.26434/chemrxiv-2022-wbssg-v2
|
Revisiting -dicyanovinyl substituted calix[4]pyrrole : toward the chemodosimetric detection of hydrazine in solution
|
Calix[4]pyrrole derivatives are usually used to recognize charged species or polar guests through non-covalent interactions, but the chemodosimetric approach remains scarce in the literature. In this study, the selective chemodosimetric detection and quantification of hydrazine, a hazardous pollutant commonly used in industy, was performed using UV-spectroscopy with a repurposed -dicyanovinyl substituted calix[4]pyrrole sensor. The selectivity of the chemodosimeter towards hydrazine was evaluated in acetonitrile with various nucleophiles (nitrogen-containing compounds and a thiol). In addition, the influence of several parameters (time, water content, and temperature) on hydrazine detection by the sensor was evaluated. This study allows for the sensing of hydrazine with a limit of detection (LOD) of 1.3 mg/L and a linear response in the 10-1000 M range. The ability to detect hydrazine with the naked eye has also been demonstrated. This paper reports one of the first chemodosimetric approach employed with calix[4]pyrrole to detect and quantify a neutral molecule, namely hydrazine.
|
Amaury Kasprowiak; Ishfaq Ahmad Rather; Rashid Ali; Pierre-Edouard Danjou
|
Analytical Chemistry; Environmental Analysis
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-02-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63dc1178068fd759791a8e75/original/revisiting-dicyanovinyl-substituted-calix-4-pyrrole-toward-the-chemodosimetric-detection-of-hydrazine-in-solution.pdf
|
64bbdbddae3d1a7b0d278f37
|
10.26434/chemrxiv-2023-fjqs6
|
Synergistic degradation mechanism in single crystal Ni-rich NMC//graphite cells
|
Oxygen loss at high voltages in Ni-rich NMC//graphite Li-ion batteries promotes degradation but increasing evidence from full cells has shown the depth of discharge choice can further accelerate aging i.e. synergistic degradation. In this letter, we employ
cycling protocols of single crystal LiNi0.834Mn0.095Co0.071O2//graphite pouch cells
to examine the origin of the synergistic degradation in terms of material degradation mechanisms. In regimes where oxygen loss is not promoted (V < 4.3 V), discharging to a lower cutoff voltage improves capacity retention despite significant graphite expansion
occurring. In contrast, when NMC surface oxygen loss is induced (V > 4.3 V), the deeper depths of discharge lead to pronounced faster aging. Using a combination of
post-mortem analysis and density functional theory we present a mechanistic description of evolution of the surface densification as a function of voltage and its impact on lithium-ion kinetics to explain the observed cycling results.
|
Galo J. Páez Fajardo; Eleni Fiamegkou; James Gott; Heng Wang; Israel Temprano; Ieuan Seymour; Ashok Menon; Ifan E. L. Stephens; Muhammad Ans; Wesley Dose; Tien-Lin Lee; Pardeep K. Thakur; Michaël F. L. De Volder; Clare P. Grey; Louis F. J. Piper
|
Materials Science; Energy
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-07-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64bbdbddae3d1a7b0d278f37/original/synergistic-degradation-mechanism-in-single-crystal-ni-rich-nmc-graphite-cells.pdf
|
60c7546b567dfe0571ec6088
|
10.26434/chemrxiv.12531314.v3
|
Network Representation Learning-Based Drug Mechanism Discovery and Anti-Inflammatory Response Against COVID-19
|
<p>Recent studies have been demonstrated that
the excessive inflammatory response is an important factor of death in COVID-19
patients. In this study, we proposed a network representation learning-based
methodology, termed AIdrug2cov, to discover drug mechanism and
anti-inflammatory response for patients with COVID-19. This work explores the
multi-hub characteristic of a heterogeneous drug network integrating 8 unique
networks. Inspired by the multi-hub characteristic, we design three billion
special meta paths to train a deep representation model for learning
low-dimensional vectors that integrate long-range structure dependency and
complex semantic relation among network nodes. Using the representation
vectors, AIdrug2cov identifies 40 potential targets and 22 high-confidence
drugs that bind to tumor necrosis factor(TNF)-α or interleukin(IL)-6 to prevent excessive
inflammatory responses in COVID-19 patients. Finally, we analyze mechanisms of
action based on PubMed publications and ongoing clinical trials, and explore
the possible binding modes between the new predicted drugs and targets via
docking program. In addition, the results in 5 pharmacological application suggested
that AIdrug2cov significantly outperforms 5 other state-of-the-art network
representation approaches, future demonstrating the availability of AIdrug2cov
in drug development field. In summary, AIdrug2cov is practically useful for
accelerating COVID-19 therapeutic development. The source code and data can be
downloaded from https://github.com/pengsl-lab/AIdrug2cov.git.</p>
|
Wang Xiaoqi; Bin Xin; Zhijian Xu; Kenli LI; Fei Li; Wu Zhong; Weihong Tan; Shaoliang Peng
|
Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-01-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7546b567dfe0571ec6088/original/network-representation-learning-based-drug-mechanism-discovery-and-anti-inflammatory-response-against-covid-19.pdf
|
676127f26dde43c908691d3e
|
10.26434/chemrxiv-2024-rr5p5
|
Dibromocarbene Addition to Bicyclo[1.1.0]butanes: A Facile Route to Substituted Bicyclo[1.1.1]pentanes
|
Strained, multicyclic hydrocarbons are increasingly important structural motifs for drug discovery. In particular, substituted bicyclo[1.1.1]pentanes (BCPs) have risen to prominence as bioisosteres for the ubiquitous benzene ring. Despite their favorable pharmacokinetic properties, synthetic strategies towards BCPs suffer from significant drawbacks – namely an overreliance on [1.1.1]propellane – an operationally challenging starting material which complicates scale-up and hampers widespread adoption of these motifs. In this work, the synthesis of 2,2-dibromo BCPs is described, presenting a class of novel substituted BCPs and circumventing the need for [1.1.1]propellane-based precursors. Scalable access to these compounds is demonstrated in a simple and inexpensive process, and their applicability for medicinal chemistry campaigns is highlighted, including through development of an electrochemical method for BCP bridge arylation to afford direct access to valuable BCP building blocks.
|
Flynn C. Attard; Andrii Slobodianyk; Roman Bychek; Yaroslav Panasiuk; Philipp Neigenfind; Luca Massaro; Vadym V. Levterov; Phil S. Baran; Pavel K. Mykhailiuk; Lara R. Malins
|
Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-12-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676127f26dde43c908691d3e/original/dibromocarbene-addition-to-bicyclo-1-1-0-butanes-a-facile-route-to-substituted-bicyclo-1-1-1-pentanes.pdf
|
60c74ef8337d6c2706e28072
|
10.26434/chemrxiv.12824834.v1
|
Development of Triantennary N-Acetylgalactosamine Conjugates as Degraders for Extracellular Proteins
|
<br />Targeted protein degradation (TPD) technology has drawn significant attention from researchers in both academia and industry. It is rapidly evolved as a new therapeutic modality and also a useful chemical tool in selectively depleting various protein targets. As most efforts focus on cytosolic proteins using PROteolysis TArgeting Chimera (PROTAC), LYsosome TArgeting Chimera (LYTAC) recently emerged as a promising technology to deliver extracellular protein targets to lysosome for degradation through cation-independent mannose-6-phosphate receptor (CI-M6PR). In this study, we exploited the potential of asialoglycoprotein receptor (ASGPR), a lysosomal targeting receptor specifically expressed on liver cells, for the degradation of extracellular proteins. The ligand of ASGPR, triantennary N-acetylgalactosamine (tri-GalNAc), was conjugated to biotin, antibodies, or fragments of antibodies to generate a new class of degraders. We demonstrated that the extracellular protein targets could be successfully internalized and delivered into lysosome for degradation in a liver cell line specifically by these degraders. We also observed that more efficient delivery could be achieved for smaller degrader/target complexes. This work will add a new dimension to the TPD with cell type specificity.<br />
|
Yaxian Zhou; peng teng; Weiping Tang
|
Biochemistry; Bioengineering and Biotechnology; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ef8337d6c2706e28072/original/development-of-triantennary-n-acetylgalactosamine-conjugates-as-degraders-for-extracellular-proteins.pdf
|
661064e921291e5d1d2bc860
|
10.26434/chemrxiv-2024-979fz
|
Extracting Structured Data from Organic Synthesis Procedures Using a Fine-Tuned Large Language Model
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The popularity of data-driven approaches and machine learning (ML) techniques in the field of organic chemistry and its various subfields has increased the value of structured reaction data. Most data in chemistry is represented by unstructured text, and due to the vastness of the organic chemistry literature (papers, patents), manual conversion from unstructured text to structured data remains a largely manual endeavor. Software tools for this task would facilitate downstream applications such as reaction prediction and condition recommendation. In this study, we leverage the power of fine-tuned large language models (LLMs) to extract reaction information from organic synthesis procedure text into structured data following the Open Reaction Database (ORD) schema, a comprehensive data structure designed for organic reactions. The fine-tuned model produces syntactically correct ORD records with an average accuracy of 91.25% for ORD “messages” (e.g., full compound, workups, or condition definitions) and 92.25% for individual data fields (e.g., compound identifiers, mass quantities), with the ability to recognize compound-referencing tokens and to infer reaction roles. We investigate its failure modes and evaluate performance on specific subtasks such as reaction role classification.
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Qianxiang Ai; Fanwang Meng; Jiale Shi; Brenden Pelkie; Connor W. Coley
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Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Machine Learning
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CC BY 4.0
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CHEMRXIV
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2024-04-08
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661064e921291e5d1d2bc860/original/extracting-structured-data-from-organic-synthesis-procedures-using-a-fine-tuned-large-language-model.pdf
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6699224f01103d79c555738e
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10.26434/chemrxiv-2024-zz89s-v2
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Classical Density Functional Theory as a Fast and Accurate Method for Adsorption Property Prediction of Porous Materials
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Physical adsorption separation is vital for many industrial processes, prompting researchers to develop new materials for energy-efficient processes. Porous adsorbent materials are of particular interest due to their diverse design possibilities and computational screening has accelerated the search for optimal materials. Classical density functional theory (cDFT) has recently been used as a faster alternative to state-of-the-art computational methods for screening of porous materials. However, extensive validation of cDFT predictions has not been performed for many materials, in a wide range of conditions, and with guest molecules exhibiting strong Coulombic interactions. In this paper, we validate the cDFT predictions by calculating the adsorption properties for more than 500 Metal-Organic Frameworks with three adsorbate molecules (CH4, N2, and CO2) and comparing them to state-of-the-art results from Grand Canonical Monte Carlo (GCMC) simulations. For CO2, we introduce the computation of Coulombic interactions between the MOF and the molecule, which are necessary to accurately describe this system. Our results demonstrate cDFT's ability to accurately replicate GCMC adsorption isotherms and enthalpies of adsorption while needing a median time of only 6 minutes per material. These features position cDFT as a serious candidate for adsorption properties estimations of porous materials for a wide range of physical adsorption-based processes.
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Vincent Dufour-Décieux; Philipp Rehner; Johannes Schilling; Elias Moubarak; Joachim Gross; André Bardow
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Theoretical and Computational Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry; Nanostructured Materials - Materials; Computational Chemistry and Modeling; Theory - Computational
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CC BY 4.0
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CHEMRXIV
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2024-07-19
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6699224f01103d79c555738e/original/classical-density-functional-theory-as-a-fast-and-accurate-method-for-adsorption-property-prediction-of-porous-materials.pdf
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66b9cec6c9c6a5c07afc3a71
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10.26434/chemrxiv-2024-d688z
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How to Determine Glass Transition Temperature of Polymer Electrolytes from Molecular Dynamics Simulations
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Molecular dynamics (MD) simulations become increasingly important to study polymer electrolytes, which are a promising solution for solid-state batteries. Nevertheless, a less-known issue is that the effective temperature in MD simulations is different from those used in experiments partly due to the accuracy of underlying molecular force fields. This calls to use the normalized temperature in MD simulations to better connect with experiment and to report the glass transition temperature (Tg) of simulation systems. Here we show how one can determine Tg with a good consensus by delving into the practical intricacies of setting up MD simulations, choosing different methods of annealing simulations and analyzing the results.
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HARISH GUDLA; Chao Zhang
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Theoretical and Computational Chemistry; Polymer Science; Energy; Polymer chains; Computational Chemistry and Modeling
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CC BY 4.0
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CHEMRXIV
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2024-08-13
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b9cec6c9c6a5c07afc3a71/original/how-to-determine-glass-transition-temperature-of-polymer-electrolytes-from-molecular-dynamics-simulations.pdf
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