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62a76b9f8f92d915724f9f90 | 10.26434/chemrxiv-2022-tnpsv | Materials availability and supply chain considerations for vanadium in grid-scale redox flow batteries | Redox flow batteries (RFBs) are a promising electrochemical storage solution for power sector decarbonization, particularly emerging long-duration needs. While the battery architecture can host many different redox chemistries, the vanadium RFB (VRFB) represents the current state-of-the-art due to its favorable combination of performance and longevity. However, the relatively high and volatile price of vanadium has hindered VRFB financing and deployment opportunities. Here we evaluate the vanadium supply chain to understand how it enables or constrains VRFB advancement and assess opportunities for accelerated growth. We find that – while vanadium may not be scarce – its abundance is confounded by highly concentrated production coupled with the disperse nature of sources suitable for potential supply increase. These factors challenge rapid growth, limiting deployment rate and magnitude. We estimate gigawatt-hour deployment scales are feasible over the next decade, which would represent marked expansion of the RFB industry and drive down system costs substantially, though this would require growth rates above historical averages. Accordingly, we review opportunities to accelerate supply chain growth and economic strategies to stabilize the market. Finally, we posit terawatt-hour deployment scales will be challenged by vanadium market conditions and, even, resource availability, motivating the continued efforts developing next-generation RFB chemistries. | Kara Rodby; Robert Jaffe; Elsa Olivetti; Fikile Brushett | Materials Science; Energy; Chemical Engineering and Industrial Chemistry; Geological Materials; Materials Processing; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a76b9f8f92d915724f9f90/original/materials-availability-and-supply-chain-considerations-for-vanadium-in-grid-scale-redox-flow-batteries.pdf |
60c73e51469df49e32f42831 | 10.26434/chemrxiv.6790568.v1 | Zero-Field Quantum Tunneling of the Magnetization in a Series of High Energy-Barrier Dysprosium (III) Single-Molecule Magnets | <p>Energy barriers to magnetisation reversal (U<sub>eff</sub>)
in single-molecule magnets (SMMs) have vastly increased recently, but only for
the dysprosocenium SMM [Dy(Cp<sup>ttt</sup>)<sub>2</sub>][B(C<sub>6</sub>F<sub>5</sub>)<sub>4</sub>]
(Cp<sup>ttt</sup> = C<sub>5</sub>H<sub>2</sub><sup>t</sup>Bu<sub>3</sub>-1,2,4)
has this translated into a considerable increase in magnetic hysteresis
temperatures. The lack of concomitant increases in hysteresis temperatures with
U<sub>eff</sub> values is due to efficient magnetic relaxation at zero-field,
referred to as quantum tunnelling of the magnetisation (QTM); however, the
exact nature of this phenomenon is unknown. Recent hypotheses suggest that both
transverse dipolar magnetic fields and hyperfine coupling play a significant
role in this process for Dy(III) SMMs. Here, by studying the compounds [Dy(<sup>t</sup>BuO)Cl(THF)<sub>5</sub>][BPh<sub>4</sub>]
(<b>1</b>), [K(18-crown-6-ether)(THF)<sub>2</sub>][Dy(BIPM)<sub>2</sub>]
(<b>2</b>, BIPM = C{PPh<sub>2</sub>NSiMe<sub>3</sub>}<sub>2</sub>),
and [Dy(Cp<sup>ttt</sup>)<sub>2</sub>][B(C<sub>6</sub>F<sub>5</sub>)<sub>4</sub>]
(<b>3</b>), we show conclusively that
neither of these processes are the main contributor to zero-field QTM for Dy(III)
SMMs, and suggest that its origin instead owes to molecular flexibility. By
analysing the vibrational modes of the three molecules, we show that the modes
that most impact the magnetic ion occur at the lowest energies for <b>1</b>, at intermediate energies for <b>2</b> and at higher energies for <b>3</b>, in correlation with their ability to
retain magnetisation. Therefore, we conclude that SMM performance could be improved
by employing more rigid ligands with higher-energy metal-ligand vibrational
modes.</p> | Fabrizio Ortu; Daniel Reta; You-Song Ding; Conrad A. P. Goodwin; Matthew P. Gregson; Eric
J. L. McInnes; Richard E. P. Winpenny; Yan-Zhen Zheng; Stephen T. Liddle; David P. Mills; Nicholas F. Chilton | Coordination Chemistry (Inorg.); Lanthanides and Actinides; Magnetism; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2018-07-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e51469df49e32f42831/original/zero-field-quantum-tunneling-of-the-magnetization-in-a-series-of-high-energy-barrier-dysprosium-iii-single-molecule-magnets.pdf |
60c74a140f50db0a5d3969e2 | 10.26434/chemrxiv.12078582.v2 | α-Methylene-β-Lactone Probe for Measuring Live-Cell Reactions of Small Molecules | The novel use of the α-methylene-β-lactone (MeLac) moiety as a warhead of multiple electrophilic sites is reported. In this study, we demonstrate that a MeLac-alkyne is a competent covalent probe and reacts with diverse proteins in live cells. Proteomics analysis of affinity-enriched samples identifies probe-reacted proteins, resolves their modified peptides/residues, and thus characterizes probe-protein reactions. Unique methods are developed to evaluate confidence in the identification of the reacted proteins and modified peptides. Tandem mass spectra of the peptides reveal that MeLac reacts with nucleophilic cysteine, serine, lysine, threonine, and tyrosine residues, through either Michael addition or acyl addition. A peptide-centric proteomics platform, using MeLac-alkyne as the measurement probe, successfully analyzes the Orlistat selectivity in live HT-29 cells. MeLac is a versatile warhead demonstrating enormous potential to expedite the development of covalent probes and inhibitors in interrogating protein (re)activity. MeLac-empowered platforms in chemical proteomics are widely adaptable for measuring the live-cell action of reactive molecules. | Lei Wang; Louis Riel; Bekim Bajrami; Bin Deng; Amy Howell; Xudong Yao | Bioorganic Chemistry; Organic Synthesis and Reactions; Mass Spectrometry; Separation Science; Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a140f50db0a5d3969e2/original/methylene-lactone-probe-for-measuring-live-cell-reactions-of-small-molecules.pdf |
651d57c845aaa5fdbb4997d5 | 10.26434/chemrxiv-2023-v613z | A Sulfur Monoxide Surrogate Designed for the Synthesis of Sulfoxides and Sulfinamides | Sulfur monoxide (SO) is a highly reactive species that cannot be isolated in bulk. However, SO can play a pivotal role as a fundamental building block in organic synthesis. Reported herein is the design and application of a sulfinylhydrazine reagent as an easily prepared sulfur monoxide surrogate. We show facile thermal SO transfer from this reagent to dienes where a reaction using a mechanistic probe suggests the generation of singlet SO. Combined with Grignard reagents and appropriate carbon or nitrogen electrophiles, the reagent serves as an effective “SO” donor to enable the one-pot, three-component synthesis of sulfoxides and sulfinamides. | David Austrup; Fumito Saito | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651d57c845aaa5fdbb4997d5/original/a-sulfur-monoxide-surrogate-designed-for-the-synthesis-of-sulfoxides-and-sulfinamides.pdf |
60eea5c5609d0d29d4da97a6 | 10.26434/chemrxiv-2021-mdt29-v3 | Powerful Statistical Tests for Ordered Data | <p>The inference of models from one-dimensional ordered data subject to noise is a fundamental and ubiquitous task in the physical and life sciences. A prototypical example is the analysis of small- and wide-angle solution scattering experiments using x-rays (SAXS/WAXS) or neutrons (SANS). In such cases, it is common practice to check the quality of a fit by using Pearson's chi-square test, which ignores the order of the data. We usually plot the residuals and check visually for systematic deviations without quantifying them. To quantify these deviations, we developed test statistics based on the distributions of the lengths of the runs of the signs of the residuals. Specifically, we use the probability of run-length distributions, for which we provide analytical expressions, to rank them and to calculate their P-values. We introduce the Shannon information distribution as an elegant and versatile tool for calculating P-values. We find that these distributions follow shifted gamma distributions, such that they are summarized by three parameters only. We show for a set of six models that our test statistics are more powerful than Pearson's chi-square test and common sign-based tests. We provide an open source Python 3 implementation of our tests free of charge at https://github.com/bio-phys/hplusminus.</p> | Jürgen Köfinger; Gerhard Hummer | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60eea5c5609d0d29d4da97a6/original/powerful-statistical-tests-for-ordered-data.pdf |
67c0232b81d2151a024405fb | 10.26434/chemrxiv-2025-wjvld | Light-Driven Constitutional Pump Powers Far-From-Equilibrium Dynamic-Covalent Behavior | Accessing non-equilibrium states in dynamic covalent chemistry (DCC) remains fundamentally challenged by microscopic reversibility and rapid equilibration. Drawing inspiration by the kinetic asymmetry mechanisms prevalent in living organisms, we introduce a light-driven constitutional pump that establishes a unidirectional kinetic pathway beyond intrinsic equilibria, that autonomously driving a dynamic covalent C=C/C=N metathesis reaction far from equilibrium. This pump operates through a kinetic ratchet mechanism under single-wavelength photonic control: (1) photocyclization of a diarylethene-based Knoevenagel derivative generates a high-energy photoisomer (ΔG = 22.5 kcal/mol), (2) irreversible covalent metathesis (K > 10^16) releases stored chemical potential, and (3) a photon-energy-gated ring-opening reaction enforces pathway unidirectionality. The resulting strong directional bias drives the system to a non-equilibrium steady state (NESS), achieving a 28-fold amplification of the equilibrium constant while preserving closed-system reversibility. Integrated into polymer networks, this pump enables spatiotemporal control over crosslink density, producing photo-adaptamers with non-equilibrium modulus switching. Unlike catalytic approaches, this platform achieves kinetic control by elevating the energy of intermediates through photonic programming, establishing DCC as a versatile toolbox for designing life-inspired adaptive materials. | Huiping Wu; Pengyun Li Li; Ruirui GU; Chong Li; Rui Wang; Wei-Hong Zhu; He Tian; Jean-Marie Lehn; Ben L. Feringa; Da-Hui Qu | Organic Chemistry; Polymer Science; Chemical Engineering and Industrial Chemistry; Photochemistry (Org.); Supramolecular Chemistry (Org.); Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c0232b81d2151a024405fb/original/light-driven-constitutional-pump-powers-far-from-equilibrium-dynamic-covalent-behavior.pdf |
66fd348acec5d6c142e5ace1 | 10.26434/chemrxiv-2024-ch1qj | 3D Printing of Models of Carbon Nanotubes and related Nanomaterials | The structure of materials determines their properties. Visualizing molecular or nanoscale structures is crucial to understand this relationship. Carbon nanomaterials are a particularly good example. Single walled carbon nanotubes (SWCNTs) have different structures (chiralities), which translate into distinct optical colors and fluorescence properties. Nevertheless, it is difficult to comprehend why materials made only from carbon atoms have these different properties. Haptic materials can play a significant role in engaging newcomers, for public outreach as well as visualizing and explaining basic concepts of chemistry and physics for more advanced scientists. This article provides a beginner friendly workflow to create 3D models of SWCNTs, graphene (nanoribbons/nanosheets) or modifications from scratch.
All used programs for chemical modeling are free to use, and no prior experience is required to follow the instructions. Exemplarily, a model of a single walled carbon nanotube (SWCNT) is created in Avogadro. This file is then imported into Blender to customize the layout. In a next step the generated files are processed (sliced) to translate it into the language of a 3D printer. This article provides a tutorial to 3D print SWCNTs and related materials, introduces the computational tools that are necessary and discusses teaching examples.
| Juliana Gretz; Sebastian Kruss | Chemical Education; Chemical Education - General | CC BY NC 4.0 | CHEMRXIV | 2024-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fd348acec5d6c142e5ace1/original/3d-printing-of-models-of-carbon-nanotubes-and-related-nanomaterials.pdf |
61bcd18202c2142684295ef2 | 10.26434/chemrxiv-2022-7f103 | Shape-Assisted Self-Assembly | Self-assembly and molecular recognition are critical processes both in life and material sciences. They usually depend on strong, directional non-covalent interactions to gain specificity and to make long-range organization possible. Most supramolecular constructs are also at least partially governed by topography, whose role is hard to disentangle. This makes it nearly impossible to discern the potential of shape and motion in the creation of complexity. Here, we demonstrate that long-range order in supramolecular constructs can be driven by the topography of the individual units even in the absence of directional interactions. Here, molecular units of remarkable simplicity self-assemble in solution to give homogeneous single-molecule thin two-dimensional supramolecular polymers of defined boundaries. This dramatic example spotlights the critical function that topography can have in molecular assembly and paves the path to rationally designed systems of increasing sophistication. | Joseph F. Woods; Lucía Gallego; Pauline Pfister; Mounir Maaloum; Andreas Vargas Jentzsch; Michel Rickhaus | Organic Chemistry; Materials Science; Polymer Science; Supramolecular Chemistry (Org.); Aggregates and Assemblies; Carbon-based Materials | CC BY NC 4.0 | CHEMRXIV | 2022-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61bcd18202c2142684295ef2/original/shape-assisted-self-assembly.pdf |
615c30ca7d3da589d8ed8691 | 10.26434/chemrxiv-2021-1bkkg | Stable open-shell aromatic nitric acid radicals: accessing highly efficient photothermal conversion with restricted radiative decay | Most of the open-shell radicals are usually thermodynamically or kinetically unstable in air due to their incompletely satisfied valency. As phenol radical without steric hindrance group protection, aromatic nitric acid radical exhibits high electrochemical and thermal stability due to its rich resonance structures including closed-shell nitro-like and open-shell nitroxide structure with unpaired electrons delocalized in conjugated backbones. Herein, a series of star-shaped aromatic nitric acid radical materials were prepared via facile demethylation and consequent oxidation of their phenolic hydroxyl precursors in air. Interestingly, they exhibit extremely high spin concentration and highly enhanced nonradiative decay, which make them exhibit great potential for photothermal conversion. Among them, TPA-TPA-O6 exhibits high photothermal conversion efficiency and negligible photobleaching effect in seawater desalination. Under irradiation of one sunlight, the water evaporation efficiency of TPA-TPA-O6 is recorded as high as 89.41% and the water evaporation rate is 1.293 kg/m2 h, which represent as the top performance in pure organic small molecule photothermal materials. | zejun wang; Zhou Jiawen; Yiheng Zhang; Weiya Zhu; Yuan Li | Materials Science; Composites | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615c30ca7d3da589d8ed8691/original/stable-open-shell-aromatic-nitric-acid-radicals-accessing-highly-efficient-photothermal-conversion-with-restricted-radiative-decay.pdf |
60c741aa567dfe578dec3e19 | 10.26434/chemrxiv.8107751.v1 | Activity-Based Screening of Homogeneous Catalysts through the Rapid Assessment of Theoretically Derived Turnover Frequencies | In homogeneous catalysis, the turnover frequency (TOF) and turnover number (TON) are the most commonly used quantities that experimentally describe catalytic activity. Computational studies, on the other hand, generally yield the ubiquitous free energy profile, which only provides the relative heights of different intermediates and transition states for a given reaction mechanism. This information, however, can be converted into a theoretical TOF through use of the energy span model. Clearly, directly computing turnover frequencies not only allows easy comparison of the activity of different catalysts, but also provides a means of directly comparing theory and experiment. Nonetheless, obtaining detailed free energy profiles for many catalysts is computationally costly. To overcome this and accelerate the rate at which prospective catalysts can be screened, here we use linear scaling relationships in tandem with the energy span model to create volcano plots that relate an easily and quickly computed energetic descriptor variable with a catalyst’s turnover frequency. As a demonstration of their ability, we use these “TOF volcanoes” to rapidly screen prospective transition metal/pincer-ligand catalysts based on activity in facilitating the hydrogenation of CO<sub>2</sub>to formate. | Matthew Wodrich; Boodsarin Sawatlon; Ephrath Solel; sebastian kozuch; Clemence Corminboeuf | Computational Chemistry and Modeling; Homogeneous Catalysis; Catalysis; Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741aa567dfe578dec3e19/original/activity-based-screening-of-homogeneous-catalysts-through-the-rapid-assessment-of-theoretically-derived-turnover-frequencies.pdf |
630e06721945ad189bec66de | 10.26434/chemrxiv-2022-lb8b8-v2 | Reaxtica: A knowledge-guided machine learning platform for fast and accurate reaction selectivity and yield prediction | Reaction selectivity and yield prediction are important for chemical synthesis. Most existing computational methods use either computational expensive and complicated quantum mechanics-based models that are not easy for experimental chemists to use or black-box deep learning models that do not generalize well outside of the training space and lack explanation. Herein, using convenient physics-based electronic descriptors and structure-based steric descriptors, we developed an explainable machine learning platform, Reaxtica, that outperformed previous methods in four different reaction types and tasks, including regioselectivity, site-selectivity, enantioselectivity, and yield predictions. Further descriptor analysis helps understand reaction mechanisms behind the data. As a practical and robust toolbox, Reaxtica can be easily applied to different chemical reactions and extended to out-of-sample reaction. To assist chemists’ daily research, we further built an easy-to-use webserver, which only takes seconds to run and can be accessed at http://www.pkumdl.cn:8000/reaxtica/. | Kangjie Lin; Junren Li; Haoyu Lin; Jianfeng Pei; Luhua Lai | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630e06721945ad189bec66de/original/reaxtica-a-knowledge-guided-machine-learning-platform-for-fast-and-accurate-reaction-selectivity-and-yield-prediction.pdf |
64ce6f9c4a3f7d0c0da83b65 | 10.26434/chemrxiv-2023-vw184 | An Accurate and Efficient SAXS/SANS Implementation Including Solvation Layer Effects Suitable for Molecular Simulations. | Small-angle X-ray and neutron scattering (SAXS/SANS) provide valuable information on biomolecules in solution and are particularly well-suited to complement a wide range of structural techniques, including molecular dynamics simulations. As contrast-based techniques, they are sensitive not only to structural properties but also to the solvent-solute interactions. Their use in molecular dynamics simulations requires a forward model that should be as fast and accurate as possible. Here we show that it is possible to calculate SAXS and SANS using a coarse-grained representation of one bead per amino acid and three beads for nucleic acid with form factors that can be corrected on-the-fly to account for their interaction with the solvent at no additional computational cost. We use SAXS data measured for the closed state of Gelsolin and previous data for a UP1-microRNA complex to show that such approach allows to refine the structure and dynamics of proteins and nucleic acids. Our hybrid resolution small angle scattering (hySAS) implementation, being distributed in PLUMED, is ready to be coupled with atomistic and coarse-grained simulations using diverse restraining strategies. | Federico Ballabio; Cristina Paissoni; Michela Bollati; Matteo de Rosa; Riccardo Capelli; Carlo Camilloni | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Biophysics; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ce6f9c4a3f7d0c0da83b65/original/an-accurate-and-efficient-saxs-sans-implementation-including-solvation-layer-effects-suitable-for-molecular-simulations.pdf |
635766fecf6de9a9a420fa90 | 10.26434/chemrxiv-2022-b1tm1 | A scalable microstructure photonic coating fabricated by roll-to-roll “defects” for daytime sub-ambient passive radiation cooling | The deep space’s coldness (~4K) provides a ubiquitous and inexhaustible thermodynamic resource to suppress the cooling energy consumption. However, it is nontrivial to achieve sub-ambient radiative cooling during daytime under strong direct sunlight, which requires rational and delicate photonic design for simultaneous high solar reflectivity (> 94%) and thermal emissivity. A great challenge arises when trying to meet such strict photonic microstructure requirements while maintaining manufacturing scalability. Herein, we demonstrate a rapid, low-cost, template-free roll-to-roll method to fabricate spike microstructured photonic nanocomposite coatings with Al2O3 and TiO2 nanoparticles embedded that possess 97.5% of solar reflectivity and 98.6% of thermal emissivity. A novel Roll-to-roll Defects Coefficient is proposed to predict the microstructure density. When facing direct sunlight at summer noon (806 W/m2 solar intensity), the meta-coatings show a radiative cooling power of 99.2 W/m2. Combined with the coatings’ superhydrophobic and contamination resistance merits, the potential 15.1% cooling energy saving capability is numerically demonstrated across the United States. | Sipan Liu; Chenxi Sui; Myers Harbinson; Michael Pudlo; Himendra Perera; Zhenzhen Zhang; Ruguan Liu; Zahyun Ku; Md Didarul Islam; Yuxuan Liu; Yong Zhu; Jan Genzer; Saad Khan; Po-Chun Hsu; Jong Eun Ryu | Materials Science; Nanoscience; Energy; Metamaterials; Optical Materials; Nanofabrication | CC BY NC 4.0 | CHEMRXIV | 2022-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635766fecf6de9a9a420fa90/original/a-scalable-microstructure-photonic-coating-fabricated-by-roll-to-roll-defects-for-daytime-sub-ambient-passive-radiation-cooling.pdf |
61f924978d70c353ea14fcb3 | 10.26434/chemrxiv-2022-0m04m | Complex coacervation and compartmentalized conversion of prebiotically relevant metabolites | Metabolism and compartmentalization are two of life’s most central elements. Constructing synthetic assemblies based on prebiotically relevant molecules that combine these elements can provide insight into the requirements for the formation of life-like protocells from abiotic building blocks. In this work, we show that a wide variety of small anionic metabolites have strong enough interactions with oligoarginine (R10) to form coacervate protocells through liquid-liquid phase separation. The stability of the coacervates can be rationalized by the molecular structure of the metabolites, and we show that three negative charges for carboxylates or two negative charges complemented with an unsaturated functional group for phosphates and sulfates is sufficient for phase separation. We show that these metabolites remain reactive in compartmentalized systems. Protometabolic reactions that lead to an increased interaction with the oligopeptide can be exploited to induce the formation of coacervate protocells. The resulting coacervates can localize other metabolites and enhance their conversion. Finally, reactions of compartmentalized metabolites can also alter the physicochemical properties of the coacervates and ultimately lead to protocell dissolution if the reaction products decrease the coacervate stability. These results reveal the intricate interplay between (proto)metabolic reactions and coacervate compartments, and show that coacervates are excellent candidates for metabolically active protocells. | Iris B. A. Smokers; Merlijn H. I. van Haren; Tiemei Lu; Evan Spruijt | Physical Chemistry; Organic Chemistry; Catalysis; Chemical Kinetics; Physical and Chemical Properties; Self-Assembly | CC BY NC 4.0 | CHEMRXIV | 2022-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f924978d70c353ea14fcb3/original/complex-coacervation-and-compartmentalized-conversion-of-prebiotically-relevant-metabolites.pdf |
60c740ef469df477f8f42d46 | 10.26434/chemrxiv.7466789.v2 | Secondary Structural Changes in Proteins as a Result of Electroadsorption at Aqueous-Organogel Interfaces | The electroadsorption of proteins at aqueous-organic interfaces offers the possibility to examine protein structural rearrangements upon interaction with lipophilic phases, without modifying the bulk protein or relying on a solid support. The aqueous-organic interface has already provided a simple means of electrochemical protein detection, often involving adsorption and ion complexation; however, little is yet known about the protein structure at these electrified interfaces. This work focuses on the interaction between proteins and an electrified aqueous-organic interface via controlled protein electroadsorption. Four proteins known to be electroactive at such interfaces were studied: lysozyme, myoglobin, cytochrome c, and hemoglobin. Following controlled protein electroadsorption onto the interface, ex situ structural characterization of the proteins by FTIR spectroscopy was undertaken, focusing on secondary structural traits within the amide I band. The structural variations observed included unfolding to form aggregated anti-parallel β-sheets, where the rearrangement was specifically dependent on the interaction with the organic phase. This was supported by MALDI ToF MS measurement, which showed the formation of protein-anion complexes for three of these proteins, and molecular dynamic simulations, which modelled the structure of lysozyme at an aqueous-organic interface. Based on these findings, the modulation of protein secondary structure by interfacial electrochemistry opens up unique prospects to selectively modify proteins.<br /> | Samuel Booth; Bren Mark B. Felisilda; Eva Alvarez de Eulate; Ove J.
R. Gustafsson; Mahreen Arooj; Ricardo L. Mancera; Robert
A. W. Dryfe; Mark J. Hackett; Damien
W. M. Arrigan | Analytical Chemistry - General; Electrochemical Analysis; Mass Spectrometry; Spectroscopy (Anal. Chem.); Computational Chemistry and Modeling; Interfaces; Self-Assembly; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740ef469df477f8f42d46/original/secondary-structural-changes-in-proteins-as-a-result-of-electroadsorption-at-aqueous-organogel-interfaces.pdf |
66ffa3ca51558a15ef06b05e | 10.26434/chemrxiv-2024-p7159-v2 | Magnetically Responsive Enzyme and Hydrogen-bonded Organic Framework Biocomposites for Biosensing | We report the one-pot synthesis of multicomponent hydrogen-bonded organic framework (HOF) biocomposites. The coimmoblization of magnetic nanoparticles (MNPs) and enzymes into the HOF crystals yielded a nano-composite biocatalytic material (MNPs-enzyme@BioHOF-1) that posses dynamic localization properties. Using a permanent magnet, it is possible to separate the MNPs-enzyme@BioHOF-1 particles from a solution. When coimmobilized with MNPs, Catalase (CAT) and glucose oxidase (GOx) showed an increased retention of their activity when coimmobilized with MNPs. MNPs-GOx@BioHOF-1 biocomposites were used to prepare a proof-of-concept glucose microfluidic biosensor, where a magnet allowed to position and keep in place the biocomposite inside a microfluidic chip. The magnetic response of these biocatalysts can pave the way to new applications for the emerging HOF biocomposites | Francesco Carraro; Margherita Aghito; Simone Dal Zilio; Heimo Wolinski; Christian Doonan; Bernd Nidetzky; Paolo Falcaro | Materials Science; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ffa3ca51558a15ef06b05e/original/magnetically-responsive-enzyme-and-hydrogen-bonded-organic-framework-biocomposites-for-biosensing.pdf |
66e3c66151558a15efd633d2 | 10.26434/chemrxiv-2024-44vd8 | Circularly Polarized Room Temperature Red Phosphorescence from a [9]-Heterohelicene Diimide | Circularly polarized room temperature phosphorescence (CP-RTP) in the red region is fascinating, however, challenging to achieve in organic molecules. The difficulty stems from two necessary conditions required to design such molecules. Firstly, achieving circularly polarized luminescence, with higher emission quantum yield in the longer wavelength region is challeng-ing. Secondly, attaining phosphorescence from such molecules under ambient conditions is difficult. Achieving both the cri-teria together in a single molecule is ambitious. In this work, we devise a novel design strategy to realize CP-RTP from a [9]-heterohelicene diimide. The designed molecule possesses helical chirality and an extended conjugation affording chiroptical responses in the red region. Interestingly a four-fold increment in the dissymmetry factor has been achieved by switching the solvent polarity. Furthermore, the incorporation of sulphur atom in the molecular framework facilitates a prolonged emis-sion lifetime of 1.09 ms under ambient conditions, making it the only example of a rylene diimide exhibiting CP-RTP. | Shivangee Jha; Kundan Singh Mehra; Pradip Kumar Mondal; Camelia Dutta ; Jatish Kumar; Sentamizh Selven Ramalingam; Sankar Jeyaraman | Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Supramolecular Chemistry (Org.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e3c66151558a15efd633d2/original/circularly-polarized-room-temperature-red-phosphorescence-from-a-9-heterohelicene-diimide.pdf |
60c74bf1567dfe1ae4ec5074 | 10.26434/chemrxiv.11106806.v3 | Capturing the Flexibility of a Protein-Ligand Complex: Binding Free Energies from Different Enhanced Sampling Techniques | Enhanced sampling techniques are a promising approach to obtain reliable binding free energy profiles for flexible protein-ligand complexes from molecular dynamics (MD) simulations. To put four popular enhanced sampling techniques to a biologically relevant and challenging test, we studied the partial dissociation of an antigenic peptide from the Major Histocompatibility Complex I (MHC I) HLA-B*35:01 to systematically investigate the performance of Umbrella Sampling (US), Replica Exchange with Solute Tempering 2 (REST2), Bias Exchange Umbrella Sampling (BEUS, or replica-exchange umbrella sampling), and well-tempered Metadynamics (MTD). With regard to the speed of sampling and convergence, the peptide-MHC I complex (pMHC I) under study showcases intrinsic strengths and weaknesses of the four enhanced sampling techniques used. We found that BEUS can handle best the sampling challenges that arise from the coexistence of an enthalpically and an entropically stabilized free energy minimum in the pMHC I under study. These findings might be relevant also for other flexible biomolecular systems with competing enthalpically and entropically stabilized minima.<br /> | Sebastian Wingbermühle; Lars V. Schäfer | Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bf1567dfe1ae4ec5074/original/capturing-the-flexibility-of-a-protein-ligand-complex-binding-free-energies-from-different-enhanced-sampling-techniques.pdf |
65427efea8b423585abc79fc | 10.26434/chemrxiv-2023-cq1h6 | Consensus screening for a challenging target: the quest for P-glycoprotein inhibitors | ATP-binding cassette (ABC) transporters are a large family of proteins involved in membrane transport of a wide variety of substrates. Among them, ABCB1, also known as MDR-1 or P-glycoprotein (P-gp), is the most characterized. By exporting xenobiotics out of the cell, P-gp activity can affect the ADME properties of several drugs. Moreover, P-gp has been found to mediate multidrug resistance in cancer cells. Thus, the inhibition of P-gp activity may lead to increased absorption and/or intracellular accumulation of co-administered drugs, enhancing their effectiveness. Using the human cryoEM 3D structure of the P-gp in the inhibitor-bound intermediate form (PDBID: 6qee), approximately 200'000 commercially available natural compounds from the ZINC database were virtually screened. To build a model able to discriminate between substrate and inhibitors, two datasets of compounds with known activity, including P-gp inhibitors, substrates, and inactive molecules were also docked. The best docking pose of selected substrates and inhibitors were used to generate 3D common feature pharmacophoric models that were combined with the Autodock Vina binding energy values to prioritize compounds for visual inspection. With this consensus approach, 13 potential candidates were identified and then tested for their ability to inhibit P-gp, using zosuquidar, a P-gp inhibitor of clinical use, as a reference drug. Eight compounds were found to be active with 6 of them having an IC50 lower than 5 µM in a membrane-based ATPase activity assay. Moreover, the P-gp inhibitory activity was also confirmed by two different cell-based in vitro methods. These results demonstrate the ability of the combined structure-based pharmacophore modeling and docking-based virtual screening approach to predict novel hit compounds with inhibitory activity toward P-gp. The resulting chemical scaffolds could serve as inspiration for the optimization of novel and more potent P-gp inhibitors. | Paolo Governa; Marco Biagi; Fabrizio Manetti; Stefano Forli | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65427efea8b423585abc79fc/original/consensus-screening-for-a-challenging-target-the-quest-for-p-glycoprotein-inhibitors.pdf |
60c74bf5469df4ca43f43fdc | 10.26434/chemrxiv.12403940.v1 | Virtual Screening of Naturally Occurring Antiviral Molecules for SARS-CoV-2 Mitigation Using Docking Tool on Multiple Molecular Targets | <p>The coronavirus catastrophe (COVID-19)
caused by a novel strain of coronavirus (SARS-CoV-2) has turned the world
upside down at an unprecedented level and has been declared as a pandemic by
World Health Organization (WHO). It has resulted huge number of fatalities and
infections due to the severe lower respiratory tract sickness in the infected
people. Research across the world is in progress to identify inhibitors against
various molecular targets associated with this viral infection. Among these
targets, a very important one is a cysteine like protease or 3CL protease
(3CLpro) and that is required for the replication of the virus. In the present
study, initially we have investigated the potential of twenty naturally
occurring antiviral molecules to function as inhibitors against the activity of
main viral protease (3CLpro) so as to put a halt on viral replication. The
investigation has been carried out through docking of the molecules with 3CLpro.
Based on the results, three most potential molecules (bilobetin, ginkgetin and
sciadopitysin) have been screened. Further these molecules were subjected for checking
their activity on other molecular targets like a papain like protease (PLpro),
spike protein S1, RNA dependent RNA polymerase (RdRp), angiotensin converting
enzyme 2 (ACE2) receptor. In addition to 3CLpro inhibition, ginkgetin was
predicted as an inhibitor of PLpro also. But none of these three compounds was
found effective on rest other molecular targets. </p> | Shiwani Rana; Sanjay Sharma; Kalyan Sundar Ghosh | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bf5469df4ca43f43fdc/original/virtual-screening-of-naturally-occurring-antiviral-molecules-for-sars-co-v-2-mitigation-using-docking-tool-on-multiple-molecular-targets.pdf |
665de20321291e5d1dfb9de3 | 10.26434/chemrxiv-2024-wfl5b | Decoupling interlayer spacing and cation dipole on exciton binding energy in layered halide perovskites | Layered halide perovskites (LHPs) are emerging semiconductor materials due to their superior environmental stability compared to traditional halide perovskites. While LHPs have tunable optoelectronic properties, quantum and dielectric confinement effects due to organic spacer layers limit their application. Recent attempts to mitigate the high exciton binding energy (Eb) of LHPs by organic cation engineering have been demonstrated, however systematic studies to decouple the influence of interlayer spacing and molecular dipole are very limited. Here, we designed a new class of organic spacer employing a malononitrile (MN) functionality giving a calculated dipole moment of 7.9 D. Malononitrile phenethyl ammonium (MNPEA) was successfully incorporated into lead iodide-based LHPs thin films and as single crystals. Comparing the MNPEA-based LHP to phenethyl ammonium (PEA) and biphenethyl ammonium (BPEA), selected as reference cations to elucidate the influence of increased dipole moment while excluding the contribution of increased interlayer distance, clarified the effect of the large organic dipole. Binding energies, Eb, estimated by temperature-dependent photoluminescence spectroscopy for MNPEA2PbI4, PEA2PbI4 and BPEA2PbI4 were 122, 354 and 183 meV, respectively. Moreover, the similar interlayer spacing of BPEA2PbI4 and MNPEA2PbI4 (21.04 Å and 21.36 Å, respectively) confirms the importance of dipole on tuning the optoelectronic properties. Photovoltaic devices with n = 1 LHPs demonstrated a higher fill factor and open circuit voltage with MNPEA2PbI4 compared to the reference layered perovskites likely due to the favored charge dissociation and transport afforded by the malononitrile-based cation. | YeonJu Kim; Simon Nussbaum; Danxuan Chen; Nicolas Grandjean; Rosario Scopelliti; Han-Hee Cho; Jun-Ho Yum; Kevin Sivula | Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665de20321291e5d1dfb9de3/original/decoupling-interlayer-spacing-and-cation-dipole-on-exciton-binding-energy-in-layered-halide-perovskites.pdf |
60c74a21ee301cfbd5c79bd2 | 10.26434/chemrxiv.11798568.v2 | Solvent Dependence of Structural Dynamics and Spin-flip Processes in 3,4,5-tri(9H-carbazole-9-yl)benzonitrile (ortho-3CzBN) | We have investigated the solvent-dependence of structural changes along with intersystem crossing of a thermally activated delayed fluorescence (TADF) molecule, 3,4,5-tri(9H-carbazole-9-yl)benzonitrile (o-3CzBN), in toluene, tetrahydrofuran, and acetonitrile solutions using time-resolved infrared (TR-IR) spectroscopy and DFT calculations. We found that the geometries of the S1 and T1 states are very similar in all solvents though the photophysical properties mostly depend on the solvent. In addition, the time-dependent DFT calculations based on these geometries suggested that the thermally activated delayed fluorescence process of o-3CzBN is governed more by the higher-lying excited states than by the structural changes in the excited states.<br /> | Masaki Saigo; Kiyoshi Miyata; Hajime Nakanotani; Chihaya Adachi; Ken Onda | Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a21ee301cfbd5c79bd2/original/solvent-dependence-of-structural-dynamics-and-spin-flip-processes-in-3-4-5-tri-9h-carbazole-9-yl-benzonitrile-ortho-3cz-bn.pdf |
64ad56039ea64cc167d3f6ce | 10.26434/chemrxiv-2023-0vq59 | Melt electrowriting of nylon-12 microfibers with an open-source 3D printer | This study demonstrates how either a heated flat or cylindrical collector enables defect-free melt electrowriting (MEW) of complex geometries from high melting temperature polymers. The open-source "MEWron" printer uses nylon-12 filament and combined with a heated flat or cylindrical collector, produces well-defined fibers with diameters ranging from 33±4 µm to 95±3 µm. We optimize processing parameters for stable jet formation and minimal defects based on thermal modeling for hardware design. We achieve the balance of processing temperature and collector temperature to achieve auxetic patterns, while showing that annealing nylon-12 tubes significantly alters their mechanical properties. The samples exhibit varied pore sizes and wall thicknesses influenced by jet dynamics and fiber bridging. Tensile testing shows nylon-12 tubes are notably stronger than PCL ones and while annealing has limited impact on tensile strength, yield, and elastic modulus, it dramatically reduces elongation. The equipment described and material used broadens MEW applications for high melting point polymers and highlights the importance of cooling dynamics for reproducible samples. | Ander Reizabal; Brenna Devlin; Naomi Paxton; Paula Saiz; Ievgenii Liashenko; Simon Luposchainsky; Maria Woodruff; Senentxu Lanceros-Mendez; Paul Dalton | Materials Science; Fibers; Materials Processing | CC BY 4.0 | CHEMRXIV | 2023-07-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ad56039ea64cc167d3f6ce/original/melt-electrowriting-of-nylon-12-microfibers-with-an-open-source-3d-printer.pdf |
67571c7e7be152b1d06e6f84 | 10.26434/chemrxiv-2024-f3b05 | Preparation of Hybrid β-Chitosan – Squid Pen Protein Hydrogel Beads by Ionic Liquid Regeneration for Adsorption of Copper (II) and Zinc (II) from Wastewater | This study explores the use of squid pen protein to enhance the mechanical properties, chemical stability, and heavy metal ion (Cu2+ and Zn2+) affinity of β-chitosan. 1-Butyl-3-methylimidazilium acetate ([BMIM][OAc]) was used to functionalize β-chitosan and prepare hydrogel beads with improved structural integrity and batch uniformity. However, initial experiments noted a reduction in adsorption capacity as the squid pen protein content increased, with Cu2+ and Zn2+ adsorption being particularly inhibited at lower pH levels due to protonation. Subsequent batch adsorption studies identified optimal conditions for Cu2+ and Zn2+ uptake and revealed that adsorption followed pseudo-second-order kinetics, indicating chemisorption. The equilibrium isotherms corresponded with the Langmuir model, suggesting monolayer coverage with maximum adsorption capacities of 70.2 mg g-1 for Cu2+ and 24.0 mg g-1 for Zn2+. The potential of squid pen protein as an economical filler for β-chitosan-based adsorbents was validated alongside the efficiency of using [BMIM][OAc] for the non-toxic functionalization of β-chitosan. Support of green chemistry principles was evidenced by a high atom economy and low environmental impact, indicating a sustainable method for preparing effective biosorbents. | Liyan Moralez; Pedro Nakasu; Jason Hallett | Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Hydrology and Water Chemistry; Natural Resource Recovery; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67571c7e7be152b1d06e6f84/original/preparation-of-hybrid-chitosan-squid-pen-protein-hydrogel-beads-by-ionic-liquid-regeneration-for-adsorption-of-copper-ii-and-zinc-ii-from-wastewater.pdf |
65f16c8be9ebbb4db99c6659 | 10.26434/chemrxiv-2024-sg80r | Analysis of thermodynamics of reactions U+ + CO2, UO+ + O2, and UO+ + CO | With the use of the fundamental law determining the dependence of chemical bond dissociation energy on its length, all values of bond dissociation energy (BDE) U+–O, OU+–O, and U+–CO were calculated. The calculated data are in good agreement depending on integer or fractional quantum numbers. For ion U+–O bond length values are given as follows: 1.8426 and 1.8363 Aº which correspond to equatorial and axial bonds relative to the electron hole. r(OU+–O)= 1.7636Aº and r(U+–CO)= 2.4485Aº are calculated. For bond U+–CO it was shown that for the constant bond length r(U+–CO) the two experimental values (BDE) correspond to two bond types – non-polar covalent and polar donor-acceptor. | Adel Iakubov | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Quantum Computing; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f16c8be9ebbb4db99c6659/original/analysis-of-thermodynamics-of-reactions-u-co2-uo-o2-and-uo-co.pdf |
67abacbd6dde43c9086e8511 | 10.26434/chemrxiv-2025-9tpw3-v2 | Deriving the Isoelectric Point of Amino Acids from Acid-Base Equilibria
| This paper presents a refined method for calculating the isoelectric point (pI) of amino acids, focusing on the dominant zwitterionic form in solution. The approach improves pI calculations and extends to predicting pH values in amphoteric solutions, including titrations of polyprotic acids and bases. | Gayan Senavirathne | Biological and Medicinal Chemistry; Analytical Chemistry; Chemical Education; Analytical Chemistry - General; Biochemical Analysis | CC BY 4.0 | CHEMRXIV | 2025-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67abacbd6dde43c9086e8511/original/deriving-the-isoelectric-point-of-amino-acids-from-acid-base-equilibria.pdf |
60c7537fbb8c1a03db3dc06d | 10.26434/chemrxiv.13502445.v1 | Hydrogen Peroxide-Responsive AIE Probe for Imaging-Guided Organelle Targeting and Photodynamic Cancer Cell Ablation | Hydrogen peroxide (H2O2), as one kind of key reactive oxygen species (ROS), is mainly produced endogenously primarily in the mitochondria. The selective monitoring of H2O2 in living cells is of great significance for understanding diagnosis and pathogenesis of cancers, the Alzheimer’s disease and diabetes. Here, we constructed a versatile AIE probe, TTPy-H2O2, which achieved superb performances in the specifically visualization of H2O2 specifically in various living cells with mitochondria targeting, excellent biocompatibility and photostability, and remarkable ROS generation ability. Red/near-infrared fluorescence firstly located in the mitochondria could light up lipid droplets with bright yellow fluorescence after responding to the H2O2, which can realize both imaging and photodynamic therapy (PDT) for cancer therapy.
<br /> | Qian WU; Youmei Li; Ying Li; Dong Wang; Ben Zhong Tang | Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7537fbb8c1a03db3dc06d/original/hydrogen-peroxide-responsive-aie-probe-for-imaging-guided-organelle-targeting-and-photodynamic-cancer-cell-ablation.pdf |
60c754c6567dfe2e7bec612c | 10.26434/chemrxiv.13726513.v1 | A Versatile New Reagent for Nitrosation under Mild Conditions | We report a new chemical reagent for transnitrosation under mild experimental conditions. This new reagent is stable to air and moisture across a broad range of temperatures, and is effective for transnitrosation in multiple solvents. Compared to traditional nitrosation methods, our reagent shows high functional group tolerance for substrates that are susceptible to oxidation or reversible transnitrosation. Several challenging nitroso-compounds are accessed here for the first time, including 15N isotopologues. X-ray data confirms two rotational isomers of the reagent are configurationally stable at room temperature, although only one isomer is effective for transnitrosation. Computational analysis describes the energetics of rotamer interconversion, including interesting geometry-dependent hybridization ef-fects. | Jordan
D. Galloway; Cristian Sarabia; James
C. Fettinger; Hrant Hratchian; Ryan Baxter | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754c6567dfe2e7bec612c/original/a-versatile-new-reagent-for-nitrosation-under-mild-conditions.pdf |
60c744b84c89193dbcad2884 | 10.26434/chemrxiv.9894416.v1 | Catalytic, Enantioselective Syn-Diamination of Alkenes | The
enantioselective, vicinal diamination of alkenes represents one of the
stereocontrolled additions that remains an outstanding challenge in organic
synthesis. A general solution to this problem would enable the efficient and
selective preparation of widely useful, enantioenriched diamines for
applications in medicinal chemistry and catalysis. In this Article we describe
the first enantioselective, <i>syn-</i>diamination
of simple alkenes mediated by a chiral, enantioenriched organoselenium catalyst
together with a <i>N,N’-</i>bistosyl urea as
the bifunctional nucleophile and <i>N-</i>fluorocollidinium
tetrafluoroborate as the stoichiometric oxidant. Diaryl, aryl-alkyl, and
alkyl-alkyl olefins bearing a variety of substituents are all diaminated in
consistently high enantioselectivities selectivities but variable yields. The
reaction likely proceeds through a Se(II)/Se(IV) redox catalytic cycle
reminiscent of the <i>syn-</i>dichlorination
reported previously. Furthermore, the <i>syn</i>-stereospecificity
of the transformation shows promise for highly enantioselective diaminations of
alkenes with no strong steric or electronic bias. | Zhonglin Tao; Brad Gilbert; Scott Denmark | Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744b84c89193dbcad2884/original/catalytic-enantioselective-syn-diamination-of-alkenes.pdf |
60c74047bdbb89330fa38138 | 10.26434/chemrxiv.7581578.v2 | Triplex hybridization of siRNA with bifacial glycopolymer nucleic acid enables hepatocyte targeted silencing | In this manuscript, we demonstrate the utility of polyacrylates modified with both an artificial base-triple and a sugar (GalNAc) to serve as an siRNA packaging and delivery platform to hepatocytes in culture and in vivo (mice). This work is based upon our previously published finding that base-triple modified polyacrylates can triplex hybridize with oligo T/U DNA/RNA and deliver luciferase-targeted siRNA to HeLa cells engineered to express luciferase (JACS 2015). Herein, we expand on the scope of this work by employing a well-established liver-targeting ligand (GalNAc) to silence an endogenous human target, ApoB, the primary protein component of low density lipoprotein. Our platform was found to be effective in both hepatocyte (HepG2) cell culture as well as in an animal model of cardiac disease that features elevated ApoB levels. This manuscript thus validates the use of a synthetic platform that is designed to integrate both packaging via triplex hybridization with tissue-targeting ligand display. This enabling method could be useful as a new, convenient siRNA platform that accessible through scalable synthesis. Further, this platform would improve the efficiency of screening siRNA sequences for silencing efficacy using the identical glycopolymer carrier, thus alleviating the need for covalent ligand modification of each RNA substrate as typical for competing technologies. | Xin Xia; zhun zhou; chris desantis; John Rossi; Dennis Bong | Bioorganic Chemistry; Supramolecular Chemistry (Org.); Biochemistry; Bioengineering and Biotechnology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74047bdbb89330fa38138/original/triplex-hybridization-of-si-rna-with-bifacial-glycopolymer-nucleic-acid-enables-hepatocyte-targeted-silencing.pdf |
61b0bb63dcbea283759a8e87 | 10.26434/chemrxiv-2021-zgvvm-v2 | Na-β-Al2O3 stabilized Fe2O3 oxygen carriers for chemical looping water splitting: correlating structure with redox stability | Chemical looping is an emerging technology to produce high purity hydrogen from fossil fuels or biomass with the simultaneous capture of the CO2 produced at the distributed scale. This process requires the availability of stable Fe2O3-based oxygen carriers. Fe2O3-Al2O3 based oxygen carriers exhibit a decay in the H2 yield with cycle number due to the formation of FeAl2O4 that cannot be re-oxidized. In this study, the addition of sodium (via a sodium salt) in the synthesis of Fe2O3-Al2O3 oxygen carriers was assessed as a means to counteract the cyclic deactivation of the oxygen carrier. Detailed insight into the oxygen carrier’s structure was gained by combined X-ray powder diffraction (XRD), X-ray absorption spectroscopy (XAS) at the Al, Na and Fe K-edges and scanning transmission electron microscopy/energy-dispersive X-ray spectroscopy (STEM/EDX) analyses. The addition of sodium prevented the formation of FeAl2O4 and stabilized the oxygen carrier via the formation of a layered structure, Na-β-Al2O3 phase. The resulting material, Na-β-Al2O3 stabilized Fe2O3, showed a very high H2 yield of ca. 13.3 mmol/g during 15 cycles. | Nur Sena Yüzbasi; Andac Armutlulu ; Thomas Huthwelker; Paula Abdala; Christoph Müller | Physical Chemistry; Materials Science; Physical and Chemical Processes; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b0bb63dcbea283759a8e87/original/na-al2o3-stabilized-fe2o3-oxygen-carriers-for-chemical-looping-water-splitting-correlating-structure-with-redox-stability.pdf |
63f905c4937392db3d0252de | 10.26434/chemrxiv-2023-0ztw5 | Can we predict ambident regioselectivity using the chemical hardness? | The hard/soft acid/base (HSAB) principle is a cornerstone in our understanding of chemical reactivity preferences. Motivated by the success of the original (e.g., "global") version of this rule, a "local" counterpart was readily proposed to account for regioselectivity preferences, in particular, in ambident reactions. However, ample experimental evidence indicates that the local HSAB principle often fails to provide meaningful predictions. Here we examine the assumptions behind the standard proof of the local HSAB rule, showing that it is based on a flawed premise. By solving this issue, we show that it is critical to consider not only the charge transferred between the different reacting centers but also the charge reorganization within the non-reacting parts of the molecule. We propose different reorganization models and derive the corresponding regioselectivity rules for each. | Ramon Miranda-Quintana; Alberto Vela; Frank De Proft; Jose L Gazquez | Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f905c4937392db3d0252de/original/can-we-predict-ambident-regioselectivity-using-the-chemical-hardness.pdf |
60c754c6469df4878cf44fba | 10.26434/chemrxiv.13726543.v1 | Characterization of Excited States in a Multiple-Resonance-Type Thermally Activated Delayed Fluorescence Molecule Using Time-resolved Infrared Spectroscopy | We have investigated the correlation between the photophysical properties and the excited-state detailed characteristics in a multiple-resonance-type thermally activated delayed fluorescence (TADF) molecule, DABNA-1, using time-resolved infrared vibrational spectroscopy. In comparison of the distinctive vibrational spectra in the fingerprint region, 1000 - 1700 cm<sup>-1</sup>, to the simulated spectra by density functional theory calculations, we found the best calculation condition. On the basis of the calculations, we determined the excited-state geometries and molecular orbitals of the lowest excited singlet (S<sub>1</sub>) and triplet (T<sub>1</sub>) states as well as the ground state (S<sub>0</sub>). We revealed that the similarity of the potential surfaces between T<sub>1</sub> and S<sub>0</sub> suppresses the nonradiative decay and causes the high fluorescence quantum yield via TADF process. | Yuushi Shimoda; Masaki Saigo; Tomohiro Ryu; Takumi Ehara; Kiyoshi Miyata; Ken Onda | Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754c6469df4878cf44fba/original/characterization-of-excited-states-in-a-multiple-resonance-type-thermally-activated-delayed-fluorescence-molecule-using-time-resolved-infrared-spectroscopy.pdf |
60c75598842e659aa6db4351 | 10.26434/chemrxiv.14135138.v1 | Intermolecular Interaction Analyses on SARS-CoV-2 Receptor Binding Domain and Human Angiotensin-Converting Enzyme 2 Receptor-Blocking Antibody/peptide Using Fragment Molecular Orbital Calculation | <p>The spike
glycoprotein (S-protein) mediates SARS-CoV-2 entry via intermolecular interaction
with human angiotensin-converting enzyme 2 (hACE2). The receptor-binding domain
(RBD) of the S-protein has been considered critical for this interaction and
acts as the target of numerous neutralizing antibodies and antiviral peptides.
This study used the fragment molecular orbital (FMO) method to analyze the
interactions between RBD and antibodies/peptides and extracted crucial residues
that can be used to epitopes. The interactions evaluated as inter-fragment interaction energy
(IFIE) values between the RBD and 12 antibodies/peptides showed a fairly good correlation
with the experimental activity pIC<sub>50</sub> (<i>R</i><sup>2</sup> = 0.540). Nine residues (T415, K417, Y421, F456,
A475, F486, N487, N501, and Y505) were confirmed as crucial. Pair interaction energy
decomposition analyses (PIEDA) showed that hydrogen bonds,
electrostatic interactions, and π-orbital interactions are important. Our
results provide essential information for understanding
SARS-CoV-2-antibodies/peptide binding and may play roles in future antibody/antiviral
drug design. </p> | Kazuki Watanabe; Chiduru Watanabe; Teruki Honma; Yu-Shi Tian; Yusuke Kawashima; Norihito Kawashita; Tatsuya Takagi; Kaori Fukuzawa | Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75598842e659aa6db4351/original/intermolecular-interaction-analyses-on-sars-co-v-2-receptor-binding-domain-and-human-angiotensin-converting-enzyme-2-receptor-blocking-antibody-peptide-using-fragment-molecular-orbital-calculation.pdf |
655ecdfecf8b3c3cd7e9e56c | 10.26434/chemrxiv-2023-zmcl9 | Unlocking the Secrets of an Ideal Solid Fast Ion Conductor | All-solid-state battery (ASSB) is a possible alternative to the conventional Li-ion battery (LIB).
ASSB, consisting of solid-fast-ion-conducting electrolytes and electrodes, can surpass LIB in terms of
energy density, battery safety, specific power, and fast-charging capability. A highly conductive solid
electrolyte is a prerequisite part of ASSB. Despite the last couple of decades of research dedicated to
finding suitable materials, only a few have high ionic conductivity near room temperature (RT). To
develop fast ion-conducting materials, both synthesis of novel high-conductivity materials near RT
and a fundamental understanding of their ion transport mechanisms are essential for establishing
suitable guidelines. However, it is a monumental task because of several challenges, such as enormous
variations of the ionic conductivity, even within the same class of materials, indicating the strong
influence of structural modifications on ion transport. In this review, a few selected material classes,
namely layered oxides, polyhedral connections, and cluster anion types, are presented. Emphasis
is placed on the inherent challenges in comprehending the intricate nature of these materials.
Leveraging theoretical frameworks and insights from materials science, strategies to address these
challenges are elucidated. Furthermore, this review covers the systematic trend from the previously
reported results and presents a few new insights. | Kartik Sau; Shigeyuki Takagi; Tamio Ikeshoji; Kazuaki Kisu; Ryuhei Sato; Egon Campos dos Santos; Hao Li; Rana Mohtadi; Shin-ichi Orimo | Materials Science; Energy; Energy Storage; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655ecdfecf8b3c3cd7e9e56c/original/unlocking-the-secrets-of-an-ideal-solid-fast-ion-conductor.pdf |
678935256dde43c908d68dde | 10.26434/chemrxiv-2025-g9rr3 | Niobium Bronzoids as negative Electrodes: Synthesis, Structure and Electrochemical Properties of Li2Nb4P2O16 and Na2Nb4P2O16 | In this study, sodium- and lithium-based phosphate niobium bronzes and bronzoids with the general formula Ax(PO2)2(NbO3)m (where A = Na/Li and m = 4), specifically Na2Nb4P2O16 and Li2Nb4P2O16, are investigated. The crystal structure of Na2Nb4P2O16 is revisited using a combination of laboratory and synchrotron X-ray powder diffraction. It is found to crystallize in the P21/a space group (different from the previously reported P21 space group), with lattice parameters a = 13.2503(6) Å, b = 5.3498(2) Å, c = 19.0807(7) Å, β = 109.9574o (3) and V/Z = 317.833(9) Å3. Additionally, we synthesized and solved the crystal structure of Li2Nb4P2O16 for the first time, introducing it as a lithium-based phosphate niobium bronzoid. It crystallizes in the Pc21n orthorhombic cell with lattice constants a = 6.7031(4) Å, b = 5.1936(2) Å , c = 17.4260(8) Å and V/Z = 303.324(5) Å3. As negative electrodes in Li batteries, Li2Nb4P2O16 and Na2Nb4P2O16 exhibited average discharge capacities of 386 mAh/g and 277 mAh/g, respectively, at C/15 in a voltage window of 3.0 V to 0.1 V. | Jean-Noël Chotard; Nikhil Subash; Amna Rafique; Loic Dupont; Pierre-Etienne Cabelguen; François Fauth; Christian Masquelier | Energy; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678935256dde43c908d68dde/original/niobium-bronzoids-as-negative-electrodes-synthesis-structure-and-electrochemical-properties-of-li2nb4p2o16-and-na2nb4p2o16.pdf |
651d59a745aaa5fdbb49b0d9 | 10.26434/chemrxiv-2023-rgjms-v3 | Structural Dependence of Extended Amide III Vibrations in Two-Dimensional Infrared Spectra | Two-dimensional infrared (2D-IR) spectroscopy is a powerful experimental method for probing the structure and dynamics of proteins in aqueous solution. So far, most experimental studies focus on the amide I vibrations, for which empirical vibrational exciton models provide a means of interpreting such experiments. However, such models are largely lacking for other regions of the vibrational spectrum. To close this gap, we employ an efficient quantum-chemical methodology for the calculation of 2D-IR spectra, which is based on anharmonic theoretical vibrational spectroscopy with localized modes. We apply this approach to explore the potential of 2D-IR spectroscopy in the extended amide III region. Using calculations for a dipeptide model as well as alanine polypeptides, we show that distinct 2D-IR cross-peaks in the extended amide~III region can potentially be used to distinguish \alpha-helix and \beta-strand structures. We propose that the extended amide III region could be a promising target for future 2D-IR experiments. | Julia Brüggemann; Maria Chekmeneva; Mario Wolter; Christoph Jacob | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651d59a745aaa5fdbb49b0d9/original/structural-dependence-of-extended-amide-iii-vibrations-in-two-dimensional-infrared-spectra.pdf |
62335aa75cf719696756cea7 | 10.26434/chemrxiv-2022-4g4bt | Analysis and differentiation of tobacco-derived and synthetic nicotine products: Addressing an urgent regulatory issue | There is significant regulatory and economic need to distinguish analytically between tobacco-derived nicotine (TDN) and synthetic nicotine (SyN) in commercial products. Currently, commercial e-liquid and oral pouch products are available that contain tobacco-free nicotine, which could be either extracted from tobacco or synthesized. While tobacco products that contain TDN are regulated by FDA Center for Tobacco Products, those with SyN are currently not in the domain of any regulatory authority. This regulatory difference provides an economic incentive to use or claim the use of SyN to remain on the market without submitting a Premarket Tobacco Product Application. TDN is ~99.3% (S)-nicotine, whereas SyN can vary from racemic (50/50 (R)/(S)) to ≥ 99% (S)-nicotine, i.e., chemically identical to the tobacco-derived compound. Here we report efforts to distinguish between TDN and SyN in various samples by characterizing impurities, (R)/(S)-nicotine enantiomer ratio, (R)/(S)-nornicotine enantiomer ratio, and carbon-14 (14C) content. Only 14C analysis accurately and precisely differentiated TDN (100% 14C) from SyN (35-38% 14C) in all samples tested. 14C quantitation of nicotine samples by accelerator mass spectrometry is a reliable determinate of nicotine source and can be used to identify misbranded product labelled as containing SyN. This is the first report to distinguish natural, bio-based nicotine from synthetic, petroleum-based nicotine across a range of pure nicotine samples and commercial e-liquid products. | Andrew Cheetham; Susan Plunkett; Preston Campbell; Jacob Hilldrup; Bonnie Coffa; Stan Gilliland; Steve Eckard | Organic Chemistry; Analytical Chemistry; Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62335aa75cf719696756cea7/original/analysis-and-differentiation-of-tobacco-derived-and-synthetic-nicotine-products-addressing-an-urgent-regulatory-issue.pdf |
6422f9e462fecd2a8395101e | 10.26434/chemrxiv-2023-bhmw3 | Solution Synthesis of N = 8 Armchair Graphene Nanoribbons with High Charge Carrier Mobility | Structurally defined graphene nanoribbons (GNRs) have emerged as promising candidates for nanoelectronic devices. Low bandgap (< 1 eV) GNRs are particularly important when considering the Schottky barrier in device performance. Here, we demonstrate the first solution synthesis of 8-AGNRs through a carefully designed arylated polynaphthalene precursor. The efficiency of the oxidative cyclode-hydrogenation of the tailor-made polymer precursor into 8-AGNRs was validated by FT-IR, Raman, and UV-vis-near-infrared (NIR) absorption spectroscopy, and further supported by the synthesis of naphtho[1,2,3,4-ghi]perylene derivatives (1 and 2) as subunits of 8-AGNR, with a width of 0.86 nm as suggested by the X-ray single crystal analysis. The resulting 8-AGNR exhibited a remarkable NIR absorption extending up to ~2400 nm, corresponding to an optical bandgap as low as ~0.52 eV. Moreover, optical-pump TeraHertz-probe spectroscopy revealed a charge-carrier mobility in the dc limit of ∼270 cm2 V–1 s–1 for the 8-AGNR | Xuelin Yao; Heng Zhang; Fanmiao Kong; Masanari Okuno; Peter N. Horton; Simon J. Coles; Lapo Bogani; Mischa Bonn; Hai I. Wang; Klaus Müllen; Akimitsu Narita | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6422f9e462fecd2a8395101e/original/solution-synthesis-of-n-8-armchair-graphene-nanoribbons-with-high-charge-carrier-mobility.pdf |
60c73dd5567dfec72fec371a | 10.26434/chemrxiv.5938177.v2 | Temperature Dependence of the Air/Water Interface Revealed by Polarization Sensitive Sum-Frequency Generation Spectroscopy | <div>
<div>
<div>
<p>The temperature dependence of the vibrational sum-frequency generation (vSFG) spectra of the the air/water interface is investigated using many-body molecular dynamics
(MB-MD) simulations performed with the MB-pol potential energy function. The total vSFG spectra calculated for different polarization combinations are then analyzed
in terms of molecular auto-correlation and cross-correlation contributions. To provide
molecular-level insights into interfacial hydrogen-bonding topologies, which give rise to
specific spectroscopic features, the vSFG spectra are further investigated by separating
contributions associated with water molecules donating 0, 1, or 2 hydrogen bonds to
neighboring water molecules. This analysis suggests that the low frequency shoulder
of the free OH peak which appears at ∼3600 cm−1 is primarily due to intermolecular
couplings between both singly and doubly hydrogen-bonded molecules.
</p>
</div>
</div>
</div> | Daniel R. Moberg; Shelby C. Straight; Paesani Lab | Interfaces; Physical and Chemical Properties; Statistical Mechanics; Structure; Surface; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd5567dfec72fec371a/original/temperature-dependence-of-the-air-water-interface-revealed-by-polarization-sensitive-sum-frequency-generation-spectroscopy.pdf |
64d8ef74dfabaf06ff362c42 | 10.26434/chemrxiv-2022-bzlvv-v2 | Clusters and anisotropic turbulence of gas-particle flow in fluidized risers studied using the four-way coupled second-order moment method | The gas-particle flow in a fluidized bed is characterized as a “core-annulus” pattern with transient clusters moving along the riser. These clusters exist as regions with a higher concentration of particles and are surrounded by dispersed particles at lower concentrations. In this study, clusters and their fluid dynamics were investigated using the four-way coupled second-order moment method of the fluid–particle Eulerian–Eulerian two-fluid model. This model was evidenced in modeling the fluid-particle two phase flow in the previous research, especially when the particles were in medium concentration while the particle turbulence was far from equilibrium to satisfy the Boussinesq approximation. In the simulation, the gas-particle flow in the fluidized risers was predicted. The fluid dynamics of the Geldard B particle clusters in the risers were characterized. In addition, the anisotropic turbulence of either phase in the clusters was studied. According to the turbulence intensity of both the phases, the gas-particle flow in the fluidized riser was classified into six zones. As the volume fraction of the particles increased, the anisotropic ratios of the turbulence intensities in both phases increased in the dispersed zone and decreased in the cluster zone, respectively. | Dan Sun | Chemical Engineering and Industrial Chemistry; Fluid Mechanics; Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d8ef74dfabaf06ff362c42/original/clusters-and-anisotropic-turbulence-of-gas-particle-flow-in-fluidized-risers-studied-using-the-four-way-coupled-second-order-moment-method.pdf |
62b17dc98c552316b21b7c9a | 10.26434/chemrxiv-2021-ffsvz-v2 | Biological activity In vitro, absorption, BBB penetration and tolerability of nanoformulation of BT44, a RET agonist with disease-modifying potential for the treatment of neurodegeneration | BT44 is a novel, second generation glial cell line-derived neurotropic factor (GDNF) mimetic, with improved biological activity and a lead compound for the treatment of neurodegenerative disorders. Like many other small molecules, it suffers from intrinsic poor aqueous solubility, posing significant hurdles at various levels for its preclinical development and clinical translation. Herein, we report a poly(2-oxazoline)s (POx) based BT44 micellar nanoformulation with ultra-high drug loading capacity of 47 wt.%. The BT44 nanoformulation was comprehensively characterized by 1H-NMR spectroscopy, differential scanning calorimetry (DSC), powder X-ray diffraction (XRD), dynamic light scattering (DLS) and cryo-transmission/scanning electron microscopy (cryo-TEM/SEM). The DSC, XRD and redispersion studies collectively confirmed that the BT44 formulation can be stored as a lyophilized powder and can be redispersed upon need. The DLS suggested that the redispersed formulation is suitable for parenteral administration (Dh ≈ 70 nm). The cryo-TEM measurements showed the presence of worm-like structures both in plain polymer and BT44 formulation. The BT44 formulation retained biological activity in immortalized cells and in cultured dopamine neurons. The micellar nanoformulation of BT44 exhibited improved absorption (after subcutaneous injection) and blood-brain barrier (BBB) penetration and no acute toxic effects in mice were observed. In conclusion, herein, we have developed an ultra-high BT44 loaded aqueous injectable nanoformulation, which can be used to pave way for its preclinical and clinical development for the management of neurodegenerative disorders. | Malik Salman Haider; Arun Kumar Mahato; Anastasiia Kotliarova; Stefan Forster; Bettina Böttcher; Philipp Stahlhut; Yulia Sidorova; Robert Luxenhofer | Materials Science; Polymer Science; Nanoscience; Biocompatible Materials; Drug delivery systems; Polymer morphology | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b17dc98c552316b21b7c9a/original/biological-activity-in-vitro-absorption-bbb-penetration-and-tolerability-of-nanoformulation-of-bt44-a-ret-agonist-with-disease-modifying-potential-for-the-treatment-of-neurodegeneration.pdf |
67c851f16dde43c908988412 | 10.26434/chemrxiv-2025-8fvxq | Efficient Ethane Production via SnCl4 Lewis Acid-Enhanced CO2 Electroreduction in a Flow Cell Electrolyser | The development of efficient and selective catalysts for electrochemical CO2 reduction (CO2RR) is critical for advancing sustainable energy solutions. Here, we report a unique catalyst system based on SnCl4 Lewis acid-modified Cu2O, demonstrating enhanced performance in CO2 electroreduction to ethane. The SnCl4 modification introduces chloride ions directly onto the Cu2O surface, creating a synergistic interaction between Sn, Cl, and Cu active sites that optimizes the electronic environment for CO2RR. The catalyst was coated onto a gas diffusion electrode (GDE) and tested in a flow cell electrolyser, with a Fumasep bipolar membrane and a platinum (Pt) foil as the anode. This system achieved a peak Faradaic efficiency of 34.8% for ethane production at -1.0 V vs. RHE, along with 11.3% efficiency for ethylene. Electrochemical studies revealed that the SnCl4-modified Cu2O exhibits low charge transfer resistance and high stability during prolonged electrolysis, with total current densities reaching 74.8 mA cm-2 with a Tafel slope of 92.3 mV/dec at 0.4 V overpotential. Mechanistic investigations, supported by density functional theory, Raman, XRD, and electrochemical Impedance spectroscopy analyses, highlight the critical role of chloride ions in stabilizing CO intermediates and facilitating C-C bond formation, essential for C2 product generation. Operating in a flow cell configuration, the system demonstrated high energy efficiency and selectivity, establishing the SnCl4-modified Cu2O (CTC) as a promising catalyst for CO2RR. These findings offer a scalable and economically viable pathway for renewable hydrocarbon production, paving the way for practical applications in carbon-neutral energy cycles. | Sankeerthana Bellamkonda; Ian Brewis; Venkateswar Rao Gedela; Rana Shahzad; Mohamed Mamlouk; Shahid Rasul | Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Electrocatalysis; Fuels - Energy Science | CC BY 4.0 | CHEMRXIV | 2025-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c851f16dde43c908988412/original/efficient-ethane-production-via-sn-cl4-lewis-acid-enhanced-co2-electroreduction-in-a-flow-cell-electrolyser.pdf |
631a57e7173b5d89f1f6519d | 10.26434/chemrxiv-2022-bkdjs | Chemically Fueled Reinforcement of Polymer Hydrogels | Carbodiimide-fueled anhydride bond formation has been used to enhance the mechanical properties of permanently crosslinked polymer networks, giving materials that exhibit gel-gel-gel transitions. Temporary changes in mechanical properties result from a transient network of anhydride crosslinks which eventually dissipate by hydrolysis. Over an order of magnitude increase in storage modulus is possible through carbodiimide fueling. The time-dependent mechanical properties could be modulated by the concentration of carbodiimide, temperature, and primary chain architecture. Because the materials remain rheological solids, applications such as temporally controlled adhesives and rewritable spatial patterns of mechanical properties are possible. | Chamoni W. H. Rajawasam; Corvo Tran; Michael Weeks; Kathleen S. McCoy; Robert Ross-Shannon; Obed J. Dodo; Jessica L. Sparks; C. Scott Hartley; Dominik Konkolewicz | Organic Chemistry; Polymer Science; Physical Organic Chemistry; Hydrogels; Organic Polymers; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631a57e7173b5d89f1f6519d/original/chemically-fueled-reinforcement-of-polymer-hydrogels.pdf |
667643ca01103d79c5d07cf6 | 10.26434/chemrxiv-2024-7kdxp | Preparation and characterization of liprotides prepared from protein extracts of mung beans (Vigna radiata (L.)) | In recent years, liprotides, which are protein-fatty acid complexes with core-shell structures, have proven to be promising drug carriers for cancer treatment. Due to their novel nature, there are limited studies surrounding liprotides, especially one synthesized from plant-based proteins. Thus, to explore new possibilities for liprotide synthesis, mung bean albumins and globulins were each extracted and combined with oleic acid (OA) at different temperatures (40 °C and 80 °C) to synthesize four variations of plant-based liprotides (Alp40, Alp80, Glp40, and Glp80). These, along with OA and protein controls, were characterized through ATR-FTIR spectroscopy, visual stability testing, particle size analysis, and zeta potential analysis. The IR spectra of the liprotides compared to the controls suggested that the OA molecule was encapsulated within the protein shell as intended. Peak shifts in characteristic absorption bands were also observed, indicating possible structural changes that may or may not be correlated to liprotide formation. Particle size analysis showed that the synthesized liprotides had significantly larger diameters than those indicated in published data and were highly polydispersed (PdI > 0.4). Lastly, zeta-potential analysis of the samples revealed that the oleic acid controls garnered a negative zeta-potential greater than -70 mV. This contrasts the zeta-potential values of both protein controls and liprotides which ranged between -23 mV and -33 mV. | Joshua William Tamayo; Ericsson David; Rafael Espiritu | Polymer Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667643ca01103d79c5d07cf6/original/preparation-and-characterization-of-liprotides-prepared-from-protein-extracts-of-mung-beans-vigna-radiata-l.pdf |
60c7462d9abda21845f8c6d7 | 10.26434/chemrxiv.11012369.v1 | Insights into Charge Transfer at the Cluster/semiconductor Interface for In-Depth Understanding the Role of Atomically Precise Silver Cluster | A cluster/semiconductor model is built for exploring the role of noble
metal clusters in a photocatalytic system. The
incorporation of an atomically precise nanocluster, e.g. Ag<sub>44</sub>(SR)<sub>30</sub>,
onto a large band gap semiconductor such as TiO<sub>2</sub> allows to obtain a
clear interface and thus simplify the system. The composite is employed for
photocatalytic H<sub>2</sub> generation. It’s found that changing the light
source from visible light to simulated sunlight leads to an enhancement by
three orders of magnitude. The H<sub>2</sub> production rate reaches 7.4
mmol/h/g<sub>catalyst</sub> which is five times higher than that of Ag nanoparticles
modified TiO<sub>2</sub> and even comparable to that of the similar conditioned
Pt nanoparticle modified TiO<sub>2</sub>. Energy band alignment and transient
absorption spectroscopy, together with other studies, reveal that the role of
the metal clusters is different from both organometallic complexes and
plasmonic-nanoparticles. A type-II heterojunction charge transfer route is
achieved under UV-vis irradiation, in which the cluster serves as small band
gap semiconductor. The type-II photosystem has a more efficient charge
separation ability, which contributes significantly to the enhanced catalytic
performance. This finding endows the clusters a broad platform as cocatalysts
rather than merely photosensitizers in the applications of light energy
conversion. | Yu Wang; Xiao-He Liu; Qiankun Wang; Martin Quick; Sergey Kovalenko; Qing-Yun Chen; Norbert Koch; Nicola Pinna | Nanostructured Materials - Materials; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7462d9abda21845f8c6d7/original/insights-into-charge-transfer-at-the-cluster-semiconductor-interface-for-in-depth-understanding-the-role-of-atomically-precise-silver-cluster.pdf |
60c75464bb8c1a84aa3dc201 | 10.26434/chemrxiv.13653530.v1 | A Model for Late-Stage Modification of Polyurethane Dendrimers Using Thiol-Ene Click Chemistry | Protecting group free, one-pot multicomponent Curtius reaction was utilized to afford diurethane G-1 dendron. In our synthetic approach, G-1 dendron can undergo late-stage modification using thiol-ene click reaction, which was then attached to the core to furnish a dendrimer. In another approach, the G-1 dendron was attached to the core and so formed dendrimer was surface functionalized using thiol-ene click chemistry. Either way, we can synthesize the dendrimer. | Dhruba Poudel; Richard Taylor | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75464bb8c1a84aa3dc201/original/a-model-for-late-stage-modification-of-polyurethane-dendrimers-using-thiol-ene-click-chemistry.pdf |
66291b3221291e5d1d97b416 | 10.26434/chemrxiv-2024-p5r35-v2 | Radiotherapy Mediated Catalytic Prodrug Therapy with Higher Radiochemical Conversion than Hydrated Electrons | Using radiotherapy to activate chemotherapeutic conversion is a promising approach to reduce off-target toxicity in cancer therapy. Current radiation chemistry mostly relies on substrate to react with the primary species of water radiolysis, with the most abundant being hydrated electron (e−aq) and ·OH. However, only 280 nM e−aq is generated by 1 Gy radiation, fundamentally limiting the yield of conventional radiation chemistry. Here, we show a radiation-mediated catalyst significantly boosts the radiochemical conversion of caged compounds. Palladium precatalyst could be transformed to active Pd(0) by γ-ray of as low as 1 Gy. The radiochemical yield can reach 2750 nM/Gy, which is 10 times that of e−aq. The strategy works even when obstructed by 15 cm of animal tissue. We demonstrate its functionality within live cells, showcasing the synergistic radiation-directed chemotherapy. We anticipate the altered mechanism of action to be a starting point for using bio-compatible dose of ionizing radiation to chemically manipulate deep tissue. | Wei Cao; Jian Wang; Yin Liang; Sijie Wu; Ruotong Deng; Hanjie Zhu | Catalysis; Organometallic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66291b3221291e5d1d97b416/original/radiotherapy-mediated-catalytic-prodrug-therapy-with-higher-radiochemical-conversion-than-hydrated-electrons.pdf |
6740648d7be152b1d053a6f6 | 10.26434/chemrxiv-2024-pctwk | Density Functional Theoretical method for modelling Cobalt-doped g-C3N4 sensor for detecting aniline - a cancer biomarker | Using DFT calculations, we investigated the sensitivity of the lung cancer biomarkers, such as acetone, ethanol, and aniline - on pristine and Cobalt (Co)-doped g-C3N4 systems. The adsorption energy calculations reveal that these biomarkers undergo chemisorption on pristine g-C3N4, resulting in long recovery times, which restricts the suitability of pristine g-C3N4 as a sensor. Alternatively, the band gap of Co-g-C3N4 (0.98 eV) is lower than that of pristine g-C3N4 (1.33 eV), which increases the conductivity of Co-g-C3N4 (5.11 × 10⁻⁹ S/m) compared to pristine g-C3N4 (5.714 × 10⁻¹² S/m) - suggesting obvious selective sensitivity towards the biomarkers. Our results indicate that acetone adsorbs on the Co-g-C3N4 surface via chemisorption process, aniline undergoes physisorption, and ethanol exhibits an intermediate adsorption behaviour. Recovery time analysis revealed that aniline (0.09 s) and ethanol (3.64 s) can be recovered quickly at 398 K, which further accelerates under UV irradiation at 298 K. However, the conductivity calculations revealed that aniline exhibits the highest conductivity of 1.72 × 10-7 and the work function calculations manifested stronger sensitivity of Co-g-C3N4 towards aniline compared to acetone and ethanol. These results predict, Co-g-C3N4 as a superior sensor for aniline biomarker due to its physisorption behaviour, lower recovery time, higher conductivity and significant change in work function. The state-of-the-art analysis of Co-g-C3N4 as a promising reusable sensor for detecting aniline in exhaled breath is hitherto unknow to date. | Sneha Mohanan K; Dhilshada. V. N; Mausumi Chattopadhyaya | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6740648d7be152b1d053a6f6/original/density-functional-theoretical-method-for-modelling-cobalt-doped-g-c3n4-sensor-for-detecting-aniline-a-cancer-biomarker.pdf |
67cb0fb581d2151a0282ed2f | 10.26434/chemrxiv-2025-x484t | Solid State Synthesis of Enzyme and Hydrogen-bonded Organic Framework Biocomposites | Hydrogen-bonded Organic Frameworks (HOFs) emerged as a matrix for preparing higly active and stable enzyme biocomposites in biocompatible synthesis conditions. Here, we demonstrate that a combination of mechanochemistry and accelerated aging processes can be used to synthesize HOF biocomposites with improved enzyme loading, activity, and protection. Advanced characterization techniques, including in situ Wide Angle X-ray Scattering and Transmission Electron Microscopy, provide insights into the formation mechanisms and structural properties of these biocomposites. A comparative analysis with biocomposites prepared via conventional solution synthesis reveals that vapor-induced growth enhances protein loading, ensures a more homogeneous enzyme distribution, and improves protective properties due to distinct growth mechanisms and kinetics. This simple and green synthetic approach could provide a valid alternative toward other protein@HOF biocomposites and unprecedented HOF-based materials. | Michael Hafner; Natalija Pantalon Juraj; Kate Flint; Helmar Wiltsche; Heinz Amenitsch; Christian Doonan; Krunoslav Užarević; Francesco Carraro | Materials Science | CC BY NC 4.0 | CHEMRXIV | 2025-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cb0fb581d2151a0282ed2f/original/solid-state-synthesis-of-enzyme-and-hydrogen-bonded-organic-framework-biocomposites.pdf |
60c73d50337d6ce29ae2612a | 10.26434/chemrxiv.5663623.v1 | Simultaneous Clicknetic Resolution Coetaneous catalytic kinetic resolution of alkynes and azides through asymmetric triazole formation | A non-enzymatic simultaneous kinetic resolution of racemic alkynes and racemic azides utilising an asymmetric CuAAC reaction is reported. The use of a CuCl (R,R)Ph-Pybox catalyst system effects a simultaneous kinetic resolution of two racemic starting materials to give one major triazolic diasteroisomer in the ratio 74:12:4:10 (dr 84:16, 90% ee maj). The corresponding control reaction using an achiral copper catalyst gives the four possible diastereoisomers in a 23:27:23:27 ratio, demonstrating minimal inherent substrate control.<br /> | William D. G. Brittain; Andrew G. Dalling; Zhenquan Sun; Cecile S. Le Duff; Louise Male; Benjamin R. Buckley; John Fossey | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2017-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d50337d6ce29ae2612a/original/simultaneous-clicknetic-resolution-coetaneous-catalytic-kinetic-resolution-of-alkynes-and-azides-through-asymmetric-triazole-formation.pdf |
647422b1e64f843f41ed711b | 10.26434/chemrxiv-2023-3rzs3 | Specificity of thermal stability and reactivity of two-dimensional layered Cu-Fe sulfide - Mg-based hydroxide compounds (valleriites) | We recently synthesized prospective new materials composed of alternating quasi-atomic sheets of brucite-type hydroxide (Mg,Fe)(OH)2 and CuFe1-xS2 sulfide (valleriites). Herein, their thermal behavior important for many potential applications has been studied in inert (Ar) and oxidative (20% O2) atmosphere using TG and DSC analysis and characterization with XRD, XPS, SEM and EDX. In Ar media, the processes are determined by dehydroxylation of the hydroxide layers forming MgO, with the temperature of the major endothermic maximum of the mass loss at 413 °C. Sulfide sheets start to degrade below 500 °C and melt nearby 800 °C, with bornite, chalcopyrite and troilite specified as the final products. In oxidative atmosphere, the exothermic reactions with the mass increase peaked at 345 and 495 °C correspond to a partial and major oxidation of Cu-Fe sulfide layers, respectively. Sulfur oxides captured in magnesium hydroxide layers to form MgSO4 compromised the layer integrity and promoted oxidation of the sulfide entities. The final products contained also minor MgO, Cu2MgO3, Fe3O4 and MgFe2O4 phases. Samples doped with Al, which decreases the content of Fe in hydroxide layers, show notably impeded decay of valleriite in argon but facilitated oxidation of Cu-Fe sulfides, while the impact of Li (it slightly increases the number of the Fe-OH sites) was less expressed. The mutual stabilization of the 2D hydroxide and sulfide layers upon heating in inert atmosphere but not in oxygen as compared with bulk brucite and chalcopyrite was suggested to explain by high thermal resistance across the stacked incommensurate sheets, which slows down the endothermic reactions and accelerates the exothermic oxidation; the high number of Fe atoms in the hydroxide sheets are expected to promote the phonon exchange and heat transfer between the layers. | Maxim Likhatski; Roman Borisov; Olga Fetisova; Anastasia Ivaneeva; Denis Karpov; Evgeny Tomashevich; Anton Karacharov; Sergey Vorobyev; Elena Mazurova; Yuri Mikhlin | Physical Chemistry; Materials Science; Nanoscience; Thermal Conductors and Insulators; Nanostructured Materials - Nanoscience; Physical and Chemical Processes | CC BY NC 4.0 | CHEMRXIV | 2023-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647422b1e64f843f41ed711b/original/specificity-of-thermal-stability-and-reactivity-of-two-dimensional-layered-cu-fe-sulfide-mg-based-hydroxide-compounds-valleriites.pdf |
63ce9e931125966955775988 | 10.26434/chemrxiv-2023-ctmh2 | Direct synthesis of functionalized 3-pyrrolidines and 4-piperidines using the borrowing hydrogen methodology | The Ir(III)-catalyzed synthesis of 3-pyrrolidinols and 4-piperidinols combining 1,2,4-butanetriol or 1,3,5-pentanetriol with primary amines was carried out. This borrowing hydrogen methodology (BH) was further extended to the sequential diamination of triols leading to aza-pyrrolidines and aza-piperidines | Malvina Larduinat; Jordan François; Maiwenn Jacolot; Florence Popowycz | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ce9e931125966955775988/original/direct-synthesis-of-functionalized-3-pyrrolidines-and-4-piperidines-using-the-borrowing-hydrogen-methodology.pdf |
64c53f049ed5166e93b04b57 | 10.26434/chemrxiv-2023-p306g | Phase space perspective on a model for isomerization in an optical cavity | Explanation for the modification of rates and mechanism of reactions carried out in optical cavities still eludes us. Several studies indicate that the cavity-mediated changes in the nature of vibrational energy flow within a molecule may play a significant role. Here we study a model polaritonic system, proposed and analyzed earlier by Fischer, Anders, and Saalfrank[1], comprising of a one dimensional isomerization mode coupled to a single photon mode in a lossless cavity. We show that the isomerization probability in presence of virtual photons, for specific cavity-system coupling strengths and cavity frequencies, can exhibit suppression or enhancement for different choices of the initial reactant vibropolariton wavepacket. We observe qualitative agreement between the classical and quantum average isomerization probabilities in the virtual photon case. A significant part of the effects due to coupling to the cavity can be rationalized in terms of a “chaos-order-chaos” transition of the classical phase space and the phase space localization nature of the polariton states that dominantly participate in the quantum isomerization dynamics. On the other hand, for initial states with zero photons (i.e., a “dark cavity”) the isomerization probability is suppressed when the cavity frequency is tuned near to the fundamental frequency of the reactive mode. The classical-quantum correspondence in the zero photon case is unsatisfactory. In this simple model we find that the suppression or enhancement of isomerization arises due to the interplay between cavity-system energy flow dynamics and quantum tunnelling. | Subhadip Mondal; Srihari Keshavamurthy | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c53f049ed5166e93b04b57/original/phase-space-perspective-on-a-model-for-isomerization-in-an-optical-cavity.pdf |
646c5a71b3dd6a653095b6ec | 10.26434/chemrxiv-2023-j740w | 3D Based Generative PROTAC Linker Design with Reinforcement Learning | Proteolysis targeting chimeras (PROTACs), have emerged as an effective therapeutic modality by harnessing the ubiquitin-proteasome system to selectively induce targeted protein degradation, with the potential to modulate traditional undruggable targets. Due to its hetero-bifunctional characteristics, in which a linker joins warhead binding to a protein of interest, conferring specificity, and E3-ligand binding to an E3 ubiquitin ligase, a PROTAC molecule can form a PROTAC ternary structure for bring the protein of interest to the vicinity of the E3 ligase. The rational PROTAC linker design is challenging due to its relatively large molecular weight and the complexity of maintaining the binding mode of warhead and E3-ligand in the binding pockets of counterpart. Conventional linker generation method can only generate linkers in either 1D SMILES or 2D graph, without taking into account the information of ternary structures. Here we propose a novel 3D linker generative model PROTAC-INVENT which can not only generate SMILES of PROTAC but also its 3D putative binding conformation coupled with the target protein and the E3 ligase. The model is trained jointly with the RL approach to bias the generation of PROTAC structures toward pre-defined 2D and 3D based properties. Examples were provided to demonstrate the utility of the model for generating reasonable 3D conformation of PROTACs. On the other hand, our results show that the associated workflow for 3D PROTAC conformation generation can also be used as an efficient docking protocol for PROTACs. | baiqing li; Hongming Chen | Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646c5a71b3dd6a653095b6ec/original/3d-based-generative-protac-linker-design-with-reinforcement-learning.pdf |
644c189c6ee8e6b5ed4439e7 | 10.26434/chemrxiv-2023-33l70 | Hildebrand Solubility Parameters Revisited - Cohesive Energy or Electrophilicity Densities? | We present certain concepts and expressions from conceptual density functional theory (DFT) for calculating Hildebrand solubility parameters. The original form of the Hildebrand solubility parameter is used to qualitatively estimate solubilities for various apolar and aprotic substances and solvents and is based on the square root of the cohesive energy density. Our revised expression allows the replacement of cohesive energy densities with electrophilicity densities that are numerically accessible through simple DFT calculations. As an extension, the reformulated expression offers a deeper interpretation of the main contributions and particularly emphasizes the importance of charge-transfer mechanisms. All calculated values of the Hildebrand parameters for a large set of common solvents are compared to experimental values and show good agreement for non- or moderately polar aprotic solvents. The observed deviations for more polar and protic solvents define robust limits where the Hildebrand approach is valid. | Ramon Alain Miranda-Quintana; Lexin Chen; Jens Smiatek | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Solution Chemistry; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644c189c6ee8e6b5ed4439e7/original/hildebrand-solubility-parameters-revisited-cohesive-energy-or-electrophilicity-densities.pdf |
62189d377c13f408d85dc24d | 10.26434/chemrxiv-2021-p6t0r-v5 | Hybrid QM/MM free energy evaluation of drug-resistant mutational effect on binding of an inhibitor Indinavir to HIV-1 protease | Human immunodeficiency virus 1 (HIV-1) protease is a homo-dimeric aspartic protease essential for replication of HIV. The HIV-1 protease is a target protein in drug discovery for antiretroviral therapy, and various inhibitor molecules of transition state analog were developed. However, serious drug-resistant mutants have emerged. For understanding molecular mechanism of the drug-resistance, accurate examination of the impacts of the mutations on ligand binding as well as enzymatic activity is necessary. Here, we present a molecular simulation study on the ligand binding of Indinavir, a potent transition state analog inhibitor, to the native protein and a V82T/I84V drug-resistant mutant of HIV-1 protease. We employed a hybrid ab initio quantum mechanical/molecular mechanical (QM/MM) free energy optimization technique which combines highly accurate QM description of the ligand molecule and its interaction with statistically ample conformational sampling of MM protein environment by long-time molecular dynamics simulations. Through free energy calculations of protonation states of catalytic groups at the binding pocket and of ligand binding affinity changes upon the mutations, we successfully reproduced the experimentally observed significant reduction of the binding affinity upon the drug-resistant mutations and elucidated the underlying molecular mechanism. The present study opens the way for understanding the molecular mechanism of drug-resistance through direct quantitative comparison of ligand binding and enzymatic reaction with the same accuracy. | Masahiko Taguchi; Ryo Oyama; Masahiro Kaneso; Shigehiko Hayashi | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62189d377c13f408d85dc24d/original/hybrid-qm-mm-free-energy-evaluation-of-drug-resistant-mutational-effect-on-binding-of-an-inhibitor-indinavir-to-hiv-1-protease.pdf |
6422f3e362fecd2a8394cb9b | 10.26434/chemrxiv-2023-5kkv4 | Drug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations | The initial phases of drug discovery - in silico drug design - could benefit from first principle Quantum Mechanics / Molecular Mechanics (QM/MM) molecular dynamics (MD) simulations in explicit solvent, yet many applications are currently limited by the short time scales that this approach can cover. Developing scalable first principle QM/MM MD interfaces fully exploiting current exascale machines - so far an unmet and crucial goal - will help overcome this problem, opening the way to the study of the thermodynamics and kinetics of ligand binding to protein with first principle accuracy. Here, taking two relevant case studies involving the interactions of ligands with rather large enzymes, we showcase the use of our recently developed massively scalable MiMiC QM/MM framework (currently using DFT to describe the QM region) to investigate reactions and ligand binding in enzymes of pharmacological relevance. We also demonstrate for the first time strong scaling of MiMiC QM/MM MD simulations with parallel efficiency above 70\% with over 40,000 cores. Thus, among many others, the MiMiC interface represents a promising candidate towards exascale applications by combining machine learning with statistical mechanics based algorithms tailored for exascale supercomputers. | Bharath Raghavan; Mirko Paulikat; Katya Ahmad; Lara Callea; Andrea Rizzi; Emiliano Ippoliti; Davide Mandelli; Laura Bonati; Marco De Vivo; Paolo Carloni | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6422f3e362fecd2a8394cb9b/original/drug-design-in-the-exascale-era-a-perspective-from-massively-parallel-qm-mm-simulations.pdf |
6638c27391aefa6ce148bca9 | 10.26434/chemrxiv-2024-d7xbn | Red-shifted two-photon-sensitive phenanthridine photocages: synthesis and characterisation | Herein we describe the synthesis and photophysical study of a novel class of phenanthridine-based, one- and two-photon sensitive, photoremovable protecting groups (PPGs) with absorption wavelengths extending beyond 400 nm. Photocages are indispensable tools for the controlled release of biologically active agents and have found widespread utility in neurophysiology and optogenetics. However, the effectiveness of many PPGs is hindered by their limited absorption of visible light. To address this challenge, we developed a small library of 3-dimethyl amino phenanthridine derivatives through a concise five-step synthetic route. Through comprehensive photophysical and photochemical analysis, coupled with DFT/TD-DFT calculations, we elucidated the key components governing their behaviour. This rational design approach facilitated the development of phenanthridine PPGs with enhanced uncaging quantum yield, paving the way for their broader application in controlled drug delivery and molecular manipulation. | Célest Mordechai Attiach; Amit Kumar; Jonathan Daniel; Mireille Blanchard-Desce ; Antoine Maruani; Peter I. Dalko | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6638c27391aefa6ce148bca9/original/red-shifted-two-photon-sensitive-phenanthridine-photocages-synthesis-and-characterisation.pdf |
65e038ce9138d231614e1067 | 10.26434/chemrxiv-2024-2sjfl | Hyperlocal Air Pollution in London Part 2: NO2
Measured with a Low-Cost Sensor Network and
Mobile Monitoring | Low-cost sensors (LCS) could help extend current air pollution monitoring programs by improving their density and time resolution. We evaluate rapid and hyperlocal pollution gradients in London using a network of LCS nodes and a Mobile Air Pollution Sensing (MAPS) car, focusing on NO2. The measurements were strongly correlated; the R2-value decreased rapidly from 0.80 to 0.19 as the distance between the MAPS car and the LCS nodes increased from 0-5 m to 16-45 m. A maximum variability of 119.0 ppb/min or 181.6 ppb/100 m is seen in urban areas on the roads, with average variability of around 6 ppb/min. Case studies in parks and tunnels revealed that NO2 mixing ratios varied significantly over small distances and times. For example, the mean mixing ratio of NO2 in the urban environment was 21.2 ppb (standard deviation (SD) = 11.8 ppb), whereas it increased to 61.3 ppb (SD = 25.0 ppb) in the Rotherhithe Tunnel, while NO2 increased from a mean of 11.4 ppb (SD = 3.0 ppb) to 22.0 ppb (SD = 16.3 ppb), from the center of Regent's Park to the roads circling around it. This study shows that pollution changes rapidly in urban areas in both space and time, and that high-density networks and mobile monitoring can significantly increase the accuracy of pollution mapping. | Louise B. Frederickson; Hugo S. Russell; Martin O. B. Sørensen; Johan A. Schmidt; Ole Hertel; Matthew S. Johnson | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e038ce9138d231614e1067/original/hyperlocal-air-pollution-in-london-part-2-no2-measured-with-a-low-cost-sensor-network-and-mobile-monitoring.pdf |
67caafd46dde43c908e00c67 | 10.26434/chemrxiv-2025-x1982 | HADDOCK-Guided Modeling and Molecular Simulations of Cereblon-Based Ternary Complexes: Development of novel PROTACs for Ataxia telangiectasia and RAD3-Related (ATR) kinase | Proteolysis-targeting chimeras (PROTACs) offer a novel therapeutic strategy for degrading disease-causing proteins, but designing effective degraders remains challenging. PROTACs function by inducing a ternary complex between the target protein and an E3 ligase, requiring structural insights for rational design. Key factors include linker optimization, attachment points, and warhead refinement. Computational approaches, particularly protein-protein docking, are essential for modeling ternary complexes and predicting critical interactions. However, existing docking methods struggle with cereblon (CRBN)-based ternary complexes. To address this, we introduce a computational approach combining HADDOCK protein-protein docking with induced fit PROTAC docking. Validated against 26 crystal structures from the Protein Data Bank (PDB), this method demonstrated high accuracy, especially for CRBN-based complexes. Additionally, molecular dynamics (MD) simulations of CRBN-BRD4-BD1 complexes (PDB IDs 6BN7, 6BOY) provided insights into complex stability through buried surface area and radius of gyration calculations. This validated approach was then applied to five Ataxia telangiectasia and RAD3-related (ATR) kinase PROTACs, enabling modeling in the absence of experimental structures. Our method provides a robust framework for optimizing and designing novel PROTACs targeting diverse proteins. | Anne-Christin Sarnow; Husam Nassar; Abdallah Alfayomy; Dina Robaa; Wolfgang Sippl | Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67caafd46dde43c908e00c67/original/haddock-guided-modeling-and-molecular-simulations-of-cereblon-based-ternary-complexes-development-of-novel-prota-cs-for-ataxia-telangiectasia-and-rad3-related-atr-kinase.pdf |
65a3b42be9ebbb4db91f8f2d | 10.26434/chemrxiv-2024-51zj6 | Machine learning based knowledge discovery and modeling of silicon content of molten iron from a blast furnace | It is necessary to maintain the silicon content of hot metal in a stipulated range to improve the productivity and energy consumption of a blast furnace. Significant research therefore went into the development of data-driven models to predict hot metal silicon content in real-time. However, these models use only a small subset of blast furnace variables that are chosen using prior process knowledge. As each blast furnace is unique in its operation, using pre-selected variables would lead to sub-optimal models. To address this, a machine learning based ensemble feature selection and modeling approach is proposed. In this approach, all the available furnace variables are ranked using multiple feature selection techniques based on their impact on silicon content. The individual ranks are combined to obtain an ensemble ranking of variables and the top variables in the ranking are used to build data-driven silicon prediction models. This approach is applied to an industrial blast furnace wherein 374 variables are used to obtain the ensemble ranking. While some of the top 100 variables in the ensemble ranking matched those that are commonly used in silicon predictions models, several new variables have also been identified. Silicon prediction models trained using the top 100 variables resulted in a hot rate of ~90% demonstrating the efficacy of the proposed approach. Real-time predictions from the models will enable blast furnace operators to control the silicon content without having to wait for laboratory results. | Sri Harsha Nistala; Jayasree Biswas; Rajan Kumar; Rohan Pandya; Pradeep Rathore; Mahesh Mynam; Venkataramana Runkana; Sristy Raj; Adity Ganguly | Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Quality Control | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a3b42be9ebbb4db91f8f2d/original/machine-learning-based-knowledge-discovery-and-modeling-of-silicon-content-of-molten-iron-from-a-blast-furnace.pdf |
66f65dba51558a15ef4b0dca | 10.26434/chemrxiv-2024-28mwt | Stereoactive Electron Lone Pairs Facilitate Fluoride Ion Diffusion in Tetragonal-BaSnF4 | Solid state ionic conductors are of primary importance for the design of tomorrow's batteries. In lithium ion or sodium ion-based materials, the alkali cations diffuse through three-dimensional channels consisting of interconnected tetrahedral or octahedral sites with low free energy barriers between them. Fluoride ion conductors stand out in this landscape since the materials with the highest conductivities belong to the MSnF4 family (in which M2+ is a divalent cation), which structure is layered and characterized by double-layers of Sn2+ and M2+ cations along a given direction. Importantly, these materials display stereoactive electron lone pairs (LPs) that seemingly play an important role not only in stabilizing of the Sn-Sn layer but also in modulating the fluoride ion diffusive behavior. However, despite previous experimental and simulation studies, the involvement of the LPs in the fluoride ions conduction mechanism remains to be quantitatively understood. In this work, we simulate the BaSnF4 tetragonal structure using machine learning-based molecular dynamics, in which the interaction potential is trained on density functional theory data. We investigate the role of the Sn-LP-Sn layer in lowering the diffusion energy landscape. In particular, we show how the F- ions jump across this layer occur much more frequently than in the Ba-F-Ba one, resulting in the formation of vacancies in the Ba-Sn layers. Concurrently, the LPs stereochemical activity fluctuates to accommodate the F ions jumping. In addition, the presence of the LP layer enhances the flexibility of the Sn ions, which leads to an increase of the two-dimensional diffusion by several orders of magnitude. These results contribute to the understanding of the interplay between LPs and ionic diffusion, helping to explain the good performance of the material in fluoride-ion batteries. | Xiliang Lian; Damien Dambournet; Mathieu Salanne | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Machine Learning; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f65dba51558a15ef4b0dca/original/stereoactive-electron-lone-pairs-facilitate-fluoride-ion-diffusion-in-tetragonal-ba-sn-f4.pdf |
60c75786337d6c7476e29032 | 10.26434/chemrxiv.12854927.v5 | Quantum Chemical Studies and Pharmacophore Modeling for Designing Novel Keap1 Antagonists that Enhance Nrf2 Mediated Neuroprotection | In recent years, the significance of oxidative stress in the pathophysiology of Neurodegenerative/developmental disorders like Attention Deficit Hyperactivity Disorder, Parkinson's and Alzheimer's is being studied at an accelerating pace. Nrf2 activation via Keap1 inhibition is an established strategy for improving the activity of the cellular antioxidant mechanism. In this study, pharmacophore modeling was employed to design efficient Keap1 inhibitors from well-known polypharmacological phytochemicals after extensive structural modifications to improve their pharmacodynamic, pharmacokinetic and drug-likeness qualities (BBB > 0.9, HIA > 0.85). Density functional theory-based quantum chemical calculations at the B3LYP/6-31G (d, p) level of theory were performed for the geometry optimization of the novel ligands and for computing their electronic properties. Resveratrol-4 was found to be the most desirable candidate with an ΔE = 4.24497 eV. HOMO and LUMO distribution of the Resveratrol-4 was found to be very favourable for keap1 binding. Molecular docking studies and comparative interaction analysis also ranked the Resveratrol-4 derivative as the best multi-domain antagonist of the Keap1 protein with a binding affinity of -8 kcal/mole. The following study presents the application of Resveratrol-4 a novel, modified, phytochemical derivative, as an efficient antagonist of the Keap1 protein for enhancing nrf2 mediated neuroprotection from redox insults. | FNU Srinidhi | Bioengineering and Biotechnology; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Quantum Computing; Chemoinformatics - Computational Chemistry; Pharmaceutical Industry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75786337d6c7476e29032/original/quantum-chemical-studies-and-pharmacophore-modeling-for-designing-novel-keap1-antagonists-that-enhance-nrf2-mediated-neuroprotection.pdf |
660e895a21291e5d1d0a0496 | 10.26434/chemrxiv-2024-x9rjg-v2 | Supramolecular-scaffold-directed two-dimensional assembly of pentacene into a configuration to facilitate singlet fission | Molecular assemblies featuring two-dimensionality have attracted increasing attention, whereas such structures are difficult to construct simply relying on spontaneous molecular assembly. Here we present two-dimensional assemblies of acene chromophores achieved using a tripodal triptycene supramolecular scaffold, which have been shown to exhibit a strong ability to assemble molecular and polymer motifs two-dimensionally. We designed pentacene and anthracene derivatives sandwiched by two tripodal triptycene units. These compounds assemble into expected two-dimensional structures, with the pentacene chromophores having both sufficient overlap to cause singlet fission and space for conformational change to facilitate the dissociation of a triplet pair into two free triplets, which is not the case for the anthracene analogue. Detailed spectroscopic analysis revealed that the pentacene chromophore in the assembly undergoes singlet fission with a high quantum yield (ΦSF = 88±5%), giving rise to triplet pairs, from which free triplets are efficiently generated (ΦT = 130±8.8%). This demonstrates the utility of the triptycene-based scaffold to design functional π-electronic molecular assemblies. | Masato Fukumitsu; Tomoya Fukui; Yoshiaki Shoji; Takashi Kajitani; Ramsha Khan; Nikolai Tkachenko; Hayato Sakai; Taku Hasobe; Takanori Fukushima | Physical Chemistry; Photochemistry (Physical Chem.); Physical and Chemical Properties; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660e895a21291e5d1d0a0496/original/supramolecular-scaffold-directed-two-dimensional-assembly-of-pentacene-into-a-configuration-to-facilitate-singlet-fission.pdf |
60c755e29abda20f23f8e459 | 10.26434/chemrxiv.14176835.v1 | NIR Bioluminescence Probe Enables Discovery of Diet-Induced Modulation of the Tumor Microenvironment via Nitric Oxide | <p>Nitric oxide (NO) plays a critical role in acute and
chronic inflammation. NO’s contributions to cancer are of particular interest
due to its context-dependent bioactivities. For example, immune cells initially
produce cytotoxic quantities of NO in response to the nascent tumor. However,
it is believed that this fades over time and reaches a concentration that
supports the tumor microenvironment (TME). These complex dynamics are further
complicated by other factors, such as diet and oxygenation, making it
challenging to establish a complete picture of NO’s impact on tumor progression.
Although many activity-based sensing (ABS) probes for NO have been developed,
only a small fraction have been employed <i>in vivo </i>and fewer yet are
practical in cancer models where the NO concentration is < 200 nM. To overcome
this outstanding challenge, we have developed BL<sub>660</sub>-NO, the first ABS
probe for NIR bioluminescence imaging of NO in cancer. Owing to the low intrinsic
background, high sensitivity, and deep tissue imaging capabilities of our
design, BL<sub>660</sub>-NO was successfully employed to visualize endogenous NO
in cellular systems, a human liver metastasis model, and a murine breast cancer
model. Importantly,
its exceptional performance facilitated the design of a dietary study to examine
the impact of NO on the TME by varying the intake of fat. BL<sub>660</sub>-NO provides
the first direct molecular evidence that intratumoral NO becomes elevated in mice
fed a high-fat diet who became obese with larger tumors compared to control
animals on a low-fat diet. These results indicate that an inflammatory diet can
increase NO production via recruitment of macrophages and overexpression of iNOS which
in turn can drive tumor progression.<br /></p> | Anuj K Yadav; Michael C. Lee; Melissa Lucero; Christopher
J. Reinhardt; ShengZhang Su; Jefferson Chan | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755e29abda20f23f8e459/original/nir-bioluminescence-probe-enables-discovery-of-diet-induced-modulation-of-the-tumor-microenvironment-via-nitric-oxide.pdf |
60c750aeee301c4f03c7a8f2 | 10.26434/chemrxiv.13067147.v1 | Observation of the Reversible Ice III to Ice IX Phase Transition by Using Ammonium Fluoride as Anti-Ice II Agent | Ice III is a hydrogen-disordered phase of ice
that is stable between about 0.2 and 0.35 GPa. Upon cooling, it transforms to
its hydrogen-ordered counterpart ice IX within the stability region of ice II.
Because of this metastability, detailed studies of the ice III to ice IX phase
transition have so far not been carried out. Using ammonium fluoride doping to
prevent the formation of ice II, we now present a detailed study on this phase
transition using in-situ powder neutron diffraction. The <i>a</i> and <i>c</i>
lattice constants are found to expand and contract, respectively, upon hydrogen
ordering yielding an overall negative volume change. Interestingly, the
anisotropy in the lattice constants persists when ice IX is fully formed and
negative thermal expansion is observed. Analogous to the isostructural keatite
and <i>b</i>-spodumenes, the
negative thermal expansion can be explained through the build-up of torsional
strain within in the <i>a</i>-<i>b</i> plane as the helical ‘springs’ within
the structure expand upon heating. The reversibility of the phase transition
was demonstrated for the first time upon heating. The ammonium fluoride doping
induces additional residual hydrogen disorder in ice IX and is suggested to be
a chemical way for ‘excitation’ of the ice-rules configurational manifold.
Compared to ices II and VIII, the induced hydrogen disorder in ice IX is
smaller which suggests a higher density of configurational states close to the
ground state. This study highlights the importance of dopants for exploring water’s
phase diagram and underpins the highly complex solid-state chemistry of ice. | Christoph Salzmann; Zainab Sharif; Ben Slater; Craig L. Bull; Martin Hart | Geological Materials; Solid State Chemistry; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750aeee301c4f03c7a8f2/original/observation-of-the-reversible-ice-iii-to-ice-ix-phase-transition-by-using-ammonium-fluoride-as-anti-ice-ii-agent.pdf |
662f9262418a5379b00614fe | 10.26434/chemrxiv-2024-gd442 | Conformational Dynamics and Energetics of Carbon Nanohoops and their Ring-In-Ring Complexes | Carbon nanohoops are promising precursors for the bottom-up synthesis of carbon nanotubes, whose structural dynamics are not well understood despite their desirable materials properties. Here, we investigate the conformational landscape and energetics of cycloparaphenylenes (CPPs) and similar derivatives, including a methylene-bridged CPP and a carbon nanobelt. These nanohoops can form host-guest complexes with other rings, and understanding the dynamics of such assemblies is crucial for predicting their properties and identifying their potential applications. We used a combination of ion mobility mass spectrometry, tandem mass spectrometry, density-functional theory calculations and collision cross section simulations to characterise the single nanohoops and their ring-in-ring complexes, following their energetics and the conformational landscape of their disassembly from intact complexes to fragment ions. Our results show both rings and ring-in-ring complexes possess structural rigidity and reveal interesting trends in size, packing density, stability, and structure between [6]CPP, the methylene-bridged CPP and the carbon nanobelt as guests in ring-in-ring complexes, showing how mass spectrometry data can help to unravel the rules that govern the formation of such assemblies. | Niklas Geue; Markus Freiberger; Stefan Frühwald; Andreas Görling; Thomas Drewello; Perdita Barran | Physical Chemistry; Organic Chemistry; Analytical Chemistry; Mass Spectrometry; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662f9262418a5379b00614fe/original/conformational-dynamics-and-energetics-of-carbon-nanohoops-and-their-ring-in-ring-complexes.pdf |
6748677bf9980725cf535f7e | 10.26434/chemrxiv-2024-dstp7 | The genesis of OH-stretching vibrational circular dichroism in chiral molecular crystals | The stretching vibration of hydroxyl groups, ν(OH), appears with a strong absorption in the 3 µm region of the infrared (IR) spectrum. In chiral molecular crystals, also vibrational circular dichroism (VCD) can be observed for this band, which is demonstrated by the example of two chiral alcohols crystallising with space groups P2_1 and P3_1 21, respectively. Measurements demonstrate that the VCD bands of the ν(OH) mode show an increased fine structure in comparison to the broad infrared absorption bands. In a computational study, the chiroptical signal can entirely be traced back to non-local terms emerging from the supramolecular environment, determined by the hydrogen-bonded network involving the hydroxyl groups. In turn, the VCD of individual molecules in the crystal related to the ν(OH) mode is almost zero. It can thus be concluded that the entire VCD band in the 3 µm region is determined by the chirality of the crystal, but not by that of the molecules. Further analysis reveals that while vibrational coupling mainly arises from the hydrogen-bonded network, the VCD is strongly influenced by the weaker interactions and long-range order. This highlights the significance of the OH stretching mode as a sensitive probe of supramolecular chirality. | Sascha Jähnigen; Rodolphe Vuilleumier; Anne Zehnacker | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Theory - Computational; Spectroscopy (Physical Chem.); Crystallography – Organic | CC BY NC 4.0 | CHEMRXIV | 2024-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6748677bf9980725cf535f7e/original/the-genesis-of-oh-stretching-vibrational-circular-dichroism-in-chiral-molecular-crystals.pdf |
66e1358e12ff75c3a1012401 | 10.26434/chemrxiv-2024-f4c4k | A Mass Spectrometrical Surface Chemistry Study of Aluminum Nitride ALD from Tris-Dimethylamido Aluminum and Ammonia | Dialkylamido compounds, such as tris-dimethylamido aluminum (TDMAA, Al(NMe2)3) and tetrakis-dimethylamido titanium (TDMAT, Ti(NMe2)4) are interesting precursors for depositing nitrides using atomic layer deposition (ALD) due to their high volatility and reactivity at low temperatures. In this study, we explored surface chemistry using mass spectrometry and discovered that the surface mechanisms involved β-hydride elimination and ligand decomposition, as well as transamination and hydrogenation reactions which facilitate ligand exchange. This is mainly based on the -N(Me)2 and HN(Me)2 detected during both TDMAA and NH3 pulses, and CH4 signals detected during the NH3 pulse stage. The expected reductive elimination of the two dimethylamido ligands, via a direct nitrogen-nitrogen coupling reaction was not observed, suggesting that it is less thermodynamically favorable compared to reduction by NH3. Arrhenius analysis between 150 and 300 °C found activation energies (Ea) = 27-30 kJmol-1 and pre-exponential factors (A) = 3-5 s-1 suggesting for the reaction between TDMAA and NH₃. | Pamburayi Mpofu; Houyem Hafdi; Jonas Lauridsen; Oscar Alm; Tommy Larsson; Henrik Pedersen | Physical Chemistry; Inorganic Chemistry; Kinetics and Mechanism - Inorganic Reactions; Interfaces; Surface; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e1358e12ff75c3a1012401/original/a-mass-spectrometrical-surface-chemistry-study-of-aluminum-nitride-ald-from-tris-dimethylamido-aluminum-and-ammonia.pdf |
66d2b68aa4e53c48763723b9 | 10.26434/chemrxiv-2024-4n2j0 | Phase evolution and thermodynamics of cubic Li6.25Al0.25La3Zr2O12 studied by high-temperature X-ray diffraction | The cubic garnet Li7La3Zr2O12 (LLZO) is a prototypical ceramic electrolyte for solid-state Li-ion batteries. While the electrochemical performance of LLZO is well studied, the thermodynamics of the formation of LLZO is not fully understood and reliable synthesis of phase-pure cubic LLZO requires such knowledge. Here we report a high-temperature X-ray diffraction (HTXRD) study on the crystallization of Al-doped LLZO from an amorphous gel with different amounts of excess Li. Based on the phases
identified in the precursor powders before and during heating, a net chemical reaction for the formation of LLZO is proposed and its thermodynamic properties calculated. The sample thickness, and hence the surface exposure to atmosphere during calcination, strongly affects the phase evolution of cubic LLZO. The configurational entropy of cubic LLZO is estimated be large and necessary to stabilize cubic LLZO. | Øystein Gullbrekken; Kristoffer Eggestad; Maria Tsoutsouva; Benjamin A. D. Williamson; Daniel Rettenwander; Mari-Ann Einarsrud; Sverre Magnus Selbach | Materials Science; Inorganic Chemistry; Ceramics; Materials Processing; Solid State Chemistry; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d2b68aa4e53c48763723b9/original/phase-evolution-and-thermodynamics-of-cubic-li6-25al0-25la3zr2o12-studied-by-high-temperature-x-ray-diffraction.pdf |
66be5c0c20ac769e5fb4b1db | 10.26434/chemrxiv-2024-bg249 | Polymorphism and flexibility of six-porphyrin nanorings in the solid state | Butadiyne-linked porphyrin nanorings are fascinating nanometer-sized platforms for exploring electronic delocalization and aromaticity, and they mimic ultra-fast photosynthetic energy-transfer phenomena in plants and purple bacteria. However, little is known about how they interact in the solid state. Here, we compare the crystal structures of several polymorphs of a six-porphyrin nanoring template complex, and report the structure of the free-base nanoring co-crystallized with C60. The structures differ not only in the molecular packing; they also feature different molecular conformations. The template is slightly too small for the cavity of the nanoring, and this size mismatch can be accommodated by two types of distortion: either the zinc atoms are pulled away from the planes of the porphyrins, or the nanorings contract by adopting a ruffled conformation, with butadiyne links alternatingly above and below the plane of the six zinc centers. The template-bound ring forms sheets and tubular stacks with interdigitated aryl groups. Upon demetallation, the nanoring becomes more flexible, adopting a highly elliptical conformation on co-crystallization with C60. The structure of this free-base nanoring features infinite solvent filled channels with a channel diameter of diameter of 13.5 Å. The high porosity of these materials points towards possible applications as porous light- harvesting frameworks. | Harry Anderson; Wojciech Stawski | Organic Chemistry; Physical Organic Chemistry; Supramolecular Chemistry (Org.); Materials Chemistry; Crystallography – Organic | CC BY 4.0 | CHEMRXIV | 2024-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66be5c0c20ac769e5fb4b1db/original/polymorphism-and-flexibility-of-six-porphyrin-nanorings-in-the-solid-state.pdf |
65ca149e66c138172975f523 | 10.26434/chemrxiv-2024-d352b | Toward GHz-Photodetection with Transition Metal Dichalcogenides | Transition metal dichalcogenides (TMDCs) exhibit favorable properties for optical communication in the GHz regime, such as large mobilities, high extinction coefficients and silicon compatibility. While impressive improvements of their sensitivity have been realized, the bandwidths of these devices have been mostly limited to few MHz. We argue that this shortcoming originates in the relatively large RC constants of TMDC-based photodetectors, which suffer from high surface defect densities, inefficient charge carrier injection at the electrode/TMDC interface and long charging times. However, we show in a series of papers that rather simple adjustments in the device architecture afford TMDC-based photodetectors with bandwidths of several 100s MHz. We rationalize the success of these adjustments in terms of the specific physical-chemical properties of TMDCs, namely their anisotropic in-plane/out-of-plane carrier behavior, large optical absorption, and chalcogenide-dependent surface chemistry. Just one surprisingly simple yet effective pathway to fast TMDC photodetection is the reduction of the photoresistance by using light-focusing optics, which enables bandwidths of 0.23 GHz with an energy consumption of only 27 fJ/bit. By reflecting on the ultrafast intrinsic photoresponse times of few picoseconds in TMDC heterostructures, we motivate the application of more demanding chemical strategies to exploit such ultrafast intrinsic properties for true GHz-operation in real devices. A key aspect in this regard is the management of surface defects, which we discuss in terms of its dependence on the layer thickness, its tunability by molecular adlayers and the prospects of replacing thermally evaporated metal contacts by laser-printed electrodes fabricated with inks of metalloid clusters. We highlight the benefits of combining TMDCs with graphene to heterostructures that exhibit the ultrafast photoresponse and large spectral range of Dirac materials with the low dark current and high responsivities of semiconductors. We introduce the bulk photovoltaic effect in TMDC-based materials with broken inversion symmetry as well as a combination of TMDCs with plasmonic nanostructures as means for increasing the bandwidth and responsivity simultaneously. Finally, we describe the prospects of embedding TMDC photodetectors into optical cavities with the objective of tuning the lifetime of the photoexcited state and increasing the carrier mobility in the photoactive layer. The findings and concepts detailed in this account demonstrate that GHz photodetection with TMDCs is feasible, and we hope that these bright prospects for their application as next-generation optoelectronic material motivates more chemists and material scientists to actively pursue the development of the more complicated material combinations outlined here. | Fabian Strauss; Zhouxiaosong Zeng; Kai Braun; Marcus Scheele | Nanoscience; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ca149e66c138172975f523/original/toward-g-hz-photodetection-with-transition-metal-dichalcogenides.pdf |
65ba6b9666c1381729a7b728 | 10.26434/chemrxiv-2023-lcxn0-v2 | Synergy of Machine Learning and Density Functional Theory Calculations for Predicting Experimental Lewis Base Affinity and Lewis Polybase Binding Atoms | Investigation of Lewis acid-base interactions has been conducted by ab initio calculations and Machine Learning (ML) models. This study aims to resolve two critical tasks that have not been quantitatively investigated. First, ML models developed from Density Functional Theory (DFT) calculations predict experimental BF3 affinity with Pearson correlation coefficients around 0.9 and mean absolute errors around 10 kJ mol-1. The ML models are trained by DFT-calculated BF3 affinity of more than 3000 adducts, with input features readily obtained by rdkit. Second, the ML models have the capability of predicting the relative strength of Lewis base binding atoms in Lewis polybases, which is either an extremely challenging task to conduct experimentally or a computationally expensive task for ab initio methods. The study demonstrates and solidifies the potential of combining DFT calculations and ML models to predict experimental properties, especially those that are scarce and impractical to empirically acquire. | Hieu Huynh; Khanh Le; Linh Vu; Trang Nguyen; Matthew Holcomb; Stefano Forli; Hung Phan | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ba6b9666c1381729a7b728/original/synergy-of-machine-learning-and-density-functional-theory-calculations-for-predicting-experimental-lewis-base-affinity-and-lewis-polybase-binding-atoms.pdf |
620628077d068a64941be366 | 10.26434/chemrxiv-2022-swkw9 | Excited-state properties for extended systems: Efficient hybrid density functional methods. | Time-dependent density functional theory has become state-of-the-art for describing photophysical and photochemical processes in extended materials due to its affordable cost. The inclusion of exact exchange was shown to be essential for the correct description of the long-range asymptotics of electronic interactions and thus a well-balanced description of valence, Rydberg and charge-transfer excitations. Several approaches for an efficient treatment of exact exchange have been established for the ground state, while implementations for excited-state properties are rare. Furthermore, the high computational costs required for excited-state properties in comparison to ground-state computations often hinder large-scale applications on periodic systems with hybrid functional accuracy. We therefore propose two approximate schemes for improving computational efficiency for the treatment of exact exchange. Within the auxiliary density matrix method (ADMM), exact exchange is estimated using a relatively small auxiliary basis and the introduced basis-set incompleteness error is compensated by an exchange density functional correction term. Benchmark results for a test set of 35 molecules demonstrate that the mean absolute error introduced by ADMM is smaller than 0.2 pm for excited-state bond lengths and in the range of 0.02 - 0.06 eV for vertical excitation, adiabatic excitation and fluorescence energies. Computational timings for a series of covalent-organic frameworks demonstrate that a speed-up of at least one order of magnitude can be achieved for ES geometry optimizations in comparison to conventional hybrid functionals. The second method is to use a semi-empirical tight binding approximation for both Coulomb and exchange contributions to the excited-state kernel. This simplified Tamm-Dancoff approximation (sTDA) achieves an accuracy comparable to approximated hybrid density functional theory when referring to highly accurate coupled-cluster reference data. We find that excited-state bond lengths deviate by 1.1 pm on average and mean absolute errors in vertical excitation, adiabatic excitation and fluorescence energies are in the range of 0.2 - 0.5 eV. In comparison to ADMM-approximated hybrid functional theory, sTDA accelerates the computation of broad-band excitation spectra by one order of magnitude, suggesting its potential use for large-scale screening purposes. | Anna-Sophia Hehn; Beliz Sertcan; Fabian Belleflamme; Sergey K. Chulkov; Matthew B. Watkins; Jürg Hutter | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620628077d068a64941be366/original/excited-state-properties-for-extended-systems-efficient-hybrid-density-functional-methods.pdf |
60cc4b9bb912f861cd5a5306 | 10.26434/chemrxiv-2021-zqx4d-v2 | A “Shake ‘n Bake Route” to Functionalised Zr-UiO-66 Metal-Organic Frameworks | We report a novel synthetic procedure for the high-yield synthesis of metal-organic frameworks with UiO-66 topology starting from a range of commercial ZrIV precursors and various substituted dicarboxylic linkers. The syntheses are carried out by grinding in a ball mill the starting reagents, namely Zr salts and the dicarboxylic linkers, in the presence of a small amount of acetic acid and water (1 mL total volume for 1 mmol of each reagent), followed by incubation at either room temperature or 120 °C. Such a “shake ‘n bake” procedure avoids the use of large amounts of solvents generally used for the syntheses of Zr-MOF. Acidity of the linkers and the amount of water are found to be crucial factors in affording materials of quality comparable to that of products obtained in solvo- or hydrothermal conditions. | Roberto D'Amato; Roberto Bondi; Intissar Moghdad; Ferdinando Costantino; Fabio Marmottini; Matthew J. McPherson; Houcine Naili; Marco Taddei | Inorganic Chemistry; Coordination Chemistry (Inorg.); Solid State Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60cc4b9bb912f861cd5a5306/original/a-shake-n-bake-route-to-functionalised-zr-ui-o-66-metal-organic-frameworks.pdf |
60c751c6567dfe10f2ec5b05 | 10.26434/chemrxiv.13207217.v1 | Feshbach-Fano Approach for Calculation of Auger Decay Rates Using Equation-of-Motion Coupled-Cluster Wave Functions: Theory and Implementation | <p>We present a novel methodology to calculate Auger decay rates based on equation-of -motion coupled-cluster singles and doubles (EOM-CCSD) wave function, combined with a simplified continuum orbital describing the outgoing electron. In our approach the Auger process is considered as an autoionization of a resonant electronic state, which can be described with Feshbach-Fano projection technique in order to distill the resonance parameters. To this end, we employ core-valence separation (CVS) scheme as a method to extract the bound part of the decaying many-electronic state. Main advantages of our methodology include (1) flexible EOM-CCSD ansatz enabling to describe various electronic states, (2) simple, yet universal computational setup, (3) fast computations due to fully analytical evaluation of all mixed bound-continuum two-electron integrals, and (4) implementation in general-purpose software package for quantum-chemical calculations.</p> | Wojciech Skomorowski; Anna Krylov | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751c6567dfe10f2ec5b05/original/feshbach-fano-approach-for-calculation-of-auger-decay-rates-using-equation-of-motion-coupled-cluster-wave-functions-theory-and-implementation.pdf |
6494c100a2c387fa9ac8060b | 10.26434/chemrxiv-2023-b649f | Unlimiting Ionic Conduction: Manipulating Hydration Dynamics through Vibrational Strong Coupling of Water | The energy states of molecules and the vacuum electromagnetic field can hybridize to form a strong coupling state. In particular, it has been demonstrated that vibrational strong coupling can be used to modify the chemical dynamics of molecules. Here, we propose
that ion dynamics can be altered through modifications of the dynamic hydration structure in a cavity vacuum field. We conducted investigations on various electrolyte species to explore their impact on ionic conductivity. Infrared spectroscopy of aqueous electrolyte solutions within the cavity confirmed the occurrence of vibrational ultra-strong coupling behavior of water molecules, even in the presence of electrolytes. Interestingly, we observed significant enhancements in ionic conductivity, several times greater for alkali cations, particularly those classified as structure-breaking cations. These enhancements are both feasible and cannot be explained within the current theoretical framework for liquid electrolytes. Our analysis confirmed that the vibrational strong coupling leads to the modification of local dielectric friction experienced by hydrated ions. Additionally, we propose the enthalpic and entropic modifications of ionic conductivity through
systematic investigations of electrolytes and their hydration properties. This study unveiled the potential role of polaritons in opening up possibilities for exploring
uncharted spaces in the design of materials for enhanced ionic conduction. By harnessing the unique properties of strong coupling and its influence on hydration dynamics, we can pave the way for the development of novel electrolytes and advancements in the field of ionic conduction. | Tomohiro Fukushima; Soushi Yoshimitsu; Kei Murakoshi | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study; Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2023-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6494c100a2c387fa9ac8060b/original/unlimiting-ionic-conduction-manipulating-hydration-dynamics-through-vibrational-strong-coupling-of-water.pdf |
60c7496abdbb890bd3a39195 | 10.26434/chemrxiv.12063243.v1 | Molecular Packaging of Biocatalysts Using a Robust Protein Cage | In this paper, we report on the discovery of a
novel, robust protein cage (encapsulin) that we could use for packaging various
biocatalysts. We have elucidated the structure of the stable encapsulin by
electron microscopy and X-ray diffraction. Furthermore, we developed an effective expression system for the encapsulin and a facile protocol for preparing encapsulated enzymes. By packaging and testing
various enzymes (varying in size, oligomeric structure, and cofactor type) we
demonstrate that, through encapsulation, the enzymes become significantly more
stable. We also provide evidence that the pores of the encapsulin, through a
size-exclusion effect, can modulate the substrate acceptance profile of an
encapsulated enzyme. | Nikola Lončar; Henriette J. Rozeboom; Linda E. Franken; Marc C. A. Stuart; Marco Fraaije | Biochemistry; Biocatalysis; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7496abdbb890bd3a39195/original/molecular-packaging-of-biocatalysts-using-a-robust-protein-cage.pdf |
615fa352f718df860bd740c3 | 10.26434/chemrxiv-2021-bm7nj | Direct Observation of Ultrafast Exciton Localization in an Organic Semiconductor with Soft X-ray Transient Absorption Spectroscopy | We report the first demonstration of time-resolved X-ray absorption spectroscopy to track previously undetected photoinduced dynamics of a paradigmatic crystalline conjugated polymer: poly(3-hexylthiophene) (P3HT) commonly used in solar cell devices. The pi to pi* transition, the first step of solar energy conversion, is pumped with a 15 fs optical pulse and the dynamics are probed by an attosecond soft X-ray pulse at the carbon K-edge. We observe direct spectroscopic signatures of the initially hot excitonic state, which is delocalized over multiple polymer chains, undergoing a rapid evolution on a sub 50 fs timescale which can be directly associated with cooling and localization to form the lowest excitonic state on a single polymer chain. This sensitivity of time-resolved X-ray spectroscopy to the primary electron dynamics occurring directly after excitation paves the way for new insights in a wide range of organic optoelectronic materials. | Douglas Garratt; Lukas Misiekis; David Wood; Esben Witting Larsen ; Mary Matthews; Oliver Alexander; Peng Ye; Sebastian Jarosch; Clement Ferchaud; Artem Bakulin; Thomas Penfold; Jon Marangos | Physical Chemistry; Polymer Science; Organic Polymers; Photochemistry (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615fa352f718df860bd740c3/original/direct-observation-of-ultrafast-exciton-localization-in-an-organic-semiconductor-with-soft-x-ray-transient-absorption-spectroscopy.pdf |
6369e9b180c9bf2d658c4ce1 | 10.26434/chemrxiv-2022-7vq8s-v2 | Quantitative and Repetitive Control of Subcellular Protein–Protein Interaction Using a Photochromic Dimerizer | Artificial control of intracellular protein dynamics with high precision provides deep insight into complicated biomolecular networks. Optogenetics and caged compound-based chemically induced dimerization (CID) systems are emerging as tools for spatiotemporally regulating intracellular protein dynamics. However, both technologies face several challenges for accurate control such as the duration of activation, deactivation rate, and repetition cycles. Herein, we report a photochromic CID system that employs the photoisomerization of a ligand so that both association and dissociation are controlled by light, enabling quick, repetitive, and quantitative regulation of the target protein localization upon violet and green light illumination. We also demonstrated the usability of the photochromic CID system as a potential tool to finely manipulate intracellular protein dynamics to study diverse cellular processes. Utilizing this system to manipulate PINK1/Parkin-mediated mitophagy, we showed that PINK1 recruitment to the mitochondria can promote Parkin recruitment to proceed with mitophagy. | Takato Mashita; Toshiyuki Kowada; Hayashi Yamamoto; Satoshi Hamaguchi; Toshitaka Matsui; Shin Mizukami | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6369e9b180c9bf2d658c4ce1/original/quantitative-and-repetitive-control-of-subcellular-protein-protein-interaction-using-a-photochromic-dimerizer.pdf |
632ac2b4e615022f46209d54 | 10.26434/chemrxiv-2021-vtsv9-v4 | Unravelling interactions between active site residues and DMAP in the initial steps of prenylated flavin mononucleotide biosynthesis catalyzed by PaUbiX | Background
Prenylated flavin mononucleotide (prFMN) is a recently discovered, heavily modified flavin compound. It is the only known cofactor that enables enzymatic 1,3-dipolar cycloaddition reactions. It is produced by enzymes from the UbiX family, from flavin mononucleotide and either dimethylallyl mono- or diphosphate. prFMN biosynthesis is currently reported to be initiated by protonation of the substrate by Glu140.
Methods
Computational chemistry methods are applied herein - Constant pH MD, classical MD simulations, and QM cluster optimizations.
Results
Glu140 competes for a single proton with Lys129 prior to prFMN biosynthesis, but it is the latter that adopted a protonated state. Once the prenyl-FMN adduct is formed, Glu140 occurs in a protonated state far more often, while the occupancy of protonated Lys129 does not change. Lys129, Glu140, and Arg122 seem to play a key role in either stabilizing or protonating DMAP’s phosphate group within the PaUbiX active site throughout initial steps of prFMN biosynthesis.
Conclusions
The role of Lys129 in the functioning of PaUbiX is reported for the first time. Glu140 is unlikely to act as a proton donor in prFMN biosynthesis. Instead, Lys129 and Arg122 that fulfil this role. Glu140 still plays a role in contributing to hydrogen-bond network. This behavior is most likely conserved throughout the UbiX family due to the structural similarity of the active sites of those proteins.
Significance
Mechanistic insights into a crucial biochemical process, the biosynthesis of prFMN, are provided. This study, although purely computational, extends and perfectly complements the knowledge obtained in classical laboratory experiments.
| Szymon Zaczek; Agnieszka Dybala-Defratyka | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632ac2b4e615022f46209d54/original/unravelling-interactions-between-active-site-residues-and-dmap-in-the-initial-steps-of-prenylated-flavin-mononucleotide-biosynthesis-catalyzed-by-pa-ubi-x.pdf |
64becfe0b605c6803b48f50b | 10.26434/chemrxiv-2023-8qnvr | Mutate and Conjugate: A Method to Enable Rapid In-Cell Target Validation | Target validation remains a challenge in drug discovery, which leads to a high attrition rate in the drug discovery process, particularly in Phase II clinical trials. Consequently, new approaches to enhance target validation are valuable tools to improve the drug discovery process. Here we report the combination of site-directed mutagenesis and electrophilic fragments to enable the rapid identification of small molecules that selectively inhibit the mutant protein. Using the bromodomain- containing protein BRD4 as an example, we employed a structure-based approach to identify the L94C mutation in the first bromodomain of BRD4 [BRD4(1)] as having minimal effect on BRD4(1) function. We then screen a focused, KAc mimic-containing fragment set, and a diverse fragment library against the mutant and wild-type proteins, and identified a series of fragments that showed high selectivity for the mutant protein. These compounds were elaborated to include an alkyne click tag to enable the attachment of a fluorescent dye. These clickable compounds were then assessed in HEK293T cells, transiently expressing BRD4(1)WT or BRD4(1)L94C, to determine their selectivity for BRD4(1)L94C over other possible cellular targets. One compound was identified that shows very high selectivity for BRD4(1)L94C over all other proteins. This work provides proof-of-concept that the combination of site-directed mutagenesis and electrophilic fragments, in a mutant and conjugate approach, can enable rapid identification of small molecule inhibitors for an appropriately mutated protein of interest. This technology can be used to assess the cellular phenotype of inhibiting the protein of interest, and the electrophilic ligand provides a starting point for non-covalent ligand development. | Adam Thomas; Marta Serafini; Emma Grant; Edward Coombs; Joseph Bluck; Matthias Schiedel; Michael McDonough; Jessica Reynolds; Bernadette Lee; Michael Platt; Vassilena Sharlandjieva; Philip Biggin; Fernanda Duarte; Thomas Milne; Jacob Bush; Stuart Conway | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2023-07-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64becfe0b605c6803b48f50b/original/mutate-and-conjugate-a-method-to-enable-rapid-in-cell-target-validation.pdf |
612f101b66deddafe300d394 | 10.26434/chemrxiv-2021-d8xx1-v2 | Non-halogenated Imidazolium and Phosphonium-based Surface-Active Ionic Liquids as Electrolytes for Supercapacitors | We report a comparative analysis of three novel non-halogenated surface-active ionic liquids (SAILs), which consist of a surface-active anion, 2-ethylhexyl sulfate ([EHS]-), and phosphonium or imidazolium cations: tetrabutylphosphonium ([P4,4,4,4]+), trihexyl(tetradecyl)phosphonium ([P6,6,6,14]+), and 1-methyl-3-hexylimidazolium ([C6C1Im]+). We explored thermal properties (degradation, melting and crystallisation temperatures) of these novel SAILs and their electrochemical properties (ionic conductivity and electrochemical potential window, ECW). These SAILs were tested as electrolytes in a multi-walled carbon nanotubes (MWCNTs)-based supercapacitor at various temperatures from 253 to 373 K and their electrochemical performance as a function of temperature was compared. We found that the supercapacitor cell with [C6C1Im][EHS] as an electrolyte has shown a higher specific capacitance (Celec in F g-1), a higher energy density (E in W h kg-1), and a higher power density (P in kW kg-1) as compared to the other studied SAILs, [P4,4,4,4][EHS], [P6,6,6,14][EHS] and [N8,8,8,8][EHS] (from previous our study) at a temperature range from 253 to 373 K. The supercapacitor with an MWCNT-based electrode and [C6C1Im][EHS], [P4,4,4,4][EHS] and [P6,6,6,14][EHS] as electrolytes showed a specific capacitance of 148, 90 and 47 F g-1 (at the scan rate of 2 mV s-1) with an energy density of 82, 50 and 26 W h kg-1 (at 2 mV s-1), respectively, all at 298 K. For latter three SAILs, the temperature effect can be seen by a two to three-fold increase in the specific capacitance of the cell and the energy density values: 290, 198 and 114 F g-1 (at 2 mV s-1) and 161, 110 and 63 Wh kg-1 (at 2 mV s-1), respectively, at 373 K. The solution resistance (Rs), charge transfer resistance (Rct), and equivalent series resistance (ESR) also decreased with an increase in temperature for all SAILs in this study. These new SAILs can potentially be used for high-temperature electrochemical applications, such as supercapacitors for high energy storage due to a reasonably high specific capacitance and enhanced energy and power density, and wider ECWs as compared to molecular organic and aqueous electrolytes. Specifically, [C6C1Im][EHS] and [P4,4,4,4][EHS], are the best candidates among other “EHS”-based SAILs in this and our previous study, as electrolytes in supercapacitors. | Preeti Jain | Energy; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612f101b66deddafe300d394/original/non-halogenated-imidazolium-and-phosphonium-based-surface-active-ionic-liquids-as-electrolytes-for-supercapacitors.pdf |
678aa1966dde43c908f788d4 | 10.26434/chemrxiv-2025-1nr6z | Meta-analysis of Stoichiometric Changes Before and After the Critical Micelle Concentration Within Lanthanide Solvent Extraction | A dataset derived from 35 sources was used to analyze the changes to acid:extractant and metal:extractant stoichiometric ratios as a function of aqueous acid concentration. The presence and location of the critical micelle concentration is easily identified by sharp changes to the stoichiometric ratios. This is consistent with the proportional increase in aggregate size of extractants surrounding a polar core containing extracted metals. Statistical consistency across the dataset allows for elucidation of outliers, the location of previously unreported CMC conditions, and improved CMC values relative to individual studies. Data dense vs. sparse regions of the composition space are identified and the impact this has upon meta-analysis of extraction data is discussed. | Leonardo da Silva Garcia Leite; Aurora Clark | Inorganic Chemistry; Analytical Chemistry; Separation Science; Lanthanides and Actinides | CC BY 4.0 | CHEMRXIV | 2025-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678aa1966dde43c908f788d4/original/meta-analysis-of-stoichiometric-changes-before-and-after-the-critical-micelle-concentration-within-lanthanide-solvent-extraction.pdf |
660e90fb418a5379b00c3870 | 10.26434/chemrxiv-2024-5c9p3 | Microkinetic Model Fitted with a Genetic Algorithm to Experimental XPS Coverages at High Pressure – CO hydrogenation on Rh(111) | Comparisons to experiments are important when developing kinetic models based on density functional theory (DFT) calculations. The comparisons are, however, often challenging due to the assumed uncertainties in the energies from which the kinetic parameters are calculated. Here, we introduce a genetic algorithm to adjust the DFT-energies to better match experimental XPS data, using CO hydrogenation on Rh(111) as an example. The adjustments are made to adsorption energies, adsorbate-adsorbate interactions, XPS energies and peak shapes. While these parameters improve the experimental agreement considerably, the required changes to the DFT energies are relatively large, which indicates the need for refined treatments of, for example, possible surface species and reaction steps, surface inhomogeneities, or higher levels of electronic structure calculations. We propose the genetic-algorithm based method as a general tool for assessment of computational models. | Mikael Valter-Lithander; Minttu Kauppinen; David Degerman; Gabriel Rodrigues; Henrik Grönbeck; Lars G.M. Pettersson | Theoretical and Computational Chemistry; Catalysis; Heterogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2024-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660e90fb418a5379b00c3870/original/microkinetic-model-fitted-with-a-genetic-algorithm-to-experimental-xps-coverages-at-high-pressure-co-hydrogenation-on-rh-111.pdf |
648ac8a5e64f843f41d008b2 | 10.26434/chemrxiv-2023-0hzxw-v2 | An Activity-Based Sensing Approach to Monitor Nanomaterial-Promoted Changes in Labile Metal Pools in Living Systems | Metal-based nanoparticles are a promising class of materials for diagnosis and treatment of cancer and other diseases. However, mechanisms of action of these nanomedicines remain insufficiently understood due in large part to our limited understanding of the dynamic equilibria between solid metal nanoparticles and labile metal ions generated from these nanoparticles within complex biological milieus. Here we apply activity-based sensing to directly identify and investigate the fate of labile copper pools with metal and oxidation state-specificity generated by anticancer copper nanomedicines. We found that treatment of cells with copper-releasing CuFe2O4 and Cu2Fe(CN)6 nanoparticles alter labile Cu(I)/Cu(II) ratios through an increase in labile Cu(II), while overall labile copper levels decrease. Labile copper release triggers compensatory responses in two major antioxidant pathways, glutathione (GSH) and nuclear factor erythroid 2–related factor 2 (NRF2), as well as in metal homeostasis to limit copper availability via synergistic upregulation of copper export (ATP7B) and downregulation of copper import (CTR1) proteins. These findings establish the value of activity-based sensing as a generalizable approach for labile metal imaging to help decipher molecular mechanisms of bioactive metal nanoparticles and guide the development of more effective nanomedicine diagnostics and therapies to target metal-dependent disease vulnerabilities. | Javier Bonet-Aletá; Aidan Pezacki; Miku Oi; José Luis Hueso ; Jesús Santamaría; Christopher J. Chang | Biological and Medicinal Chemistry; Nanoscience; Nanocatalysis - Catalysts & Materials; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648ac8a5e64f843f41d008b2/original/an-activity-based-sensing-approach-to-monitor-nanomaterial-promoted-changes-in-labile-metal-pools-in-living-systems.pdf |
60c74c3a469df45f82f44044 | 10.26434/chemrxiv.12453644.v1 | Potential Binding Efficiency of Antiviral Drug Lopinavir Targeted to the Catalytic Dyad, His41 - Cys145 of SARS CoV -2 Main Protease | <p>The spread of SARS CoV 2 across the
globe rushed the scientific community to find out the potential inhibitor for
controlling the viral disease. The main protease (Mpro) or Chymotrypsin
protease (3CLpro) is involved in the cleavage of polyproteins, duplication of
intracellular materials and release of nonstructural proteins. Cys-His
catalytic dyad is located in the SARS-CoV Mpro which is the substrate-binding
site located in domains I and II. There
are many approved drugs that have their active protease inhibition
capability. The targeting of the active
site of the main protease is the better option to fight against the viral
population. Lopinavir, ritonavir,
Remdesivir and Chloroquine are some of
the drug candidates considered to be involved in the treatment of SARS CoV 2
under emergency situation as a trial basis.
In the present investigation we used lopinavir as a drug to bind the
catalytic dyad His41, Cys145 of main protease. The minimum binding of energy of -11.45
kcal/mol observed with the binding of Cys145 and -10.93 kcal/mol was noted with
the residue His41. The inhibition constant was also found to be relevant to the
binding efficiency of the drug. This is
considered to be a model drug target which is initiating the finding of many
new drugs to target the current outbreak created by the virus SARS.CoV - 2.</p> | Muthu Raj S; Manohar M; Mohan M; Ganesh P; Marimuthu K | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c3a469df45f82f44044/original/potential-binding-efficiency-of-antiviral-drug-lopinavir-targeted-to-the-catalytic-dyad-his41-cys145-of-sars-co-v-2-main-protease.pdf |
60c74618567dfe45edec457d | 10.26434/chemrxiv.10728128.v1 | Is Preservation of Symmetry Necessary for Coarse-Graining? | This work investigates how preservation of molecular symmetry affects accuracy of coarse-grained (CG) molecular dynamics simulation. We studied 26 mapping operators for 7 molecules to find that it has little effect on accuracy of CG simulations. | Maghesree Chakraborty; Jinyu Xu; Andrew White | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74618567dfe45edec457d/original/is-preservation-of-symmetry-necessary-for-coarse-graining.pdf |
67226049f9980725cf9958f3 | 10.26434/chemrxiv-2024-cchdm | Predicting Emission Wavelengths and Quantum Yields of Diverse Bis-cyclometalated Iridium(III) Complexes Using Machine Learning | Cyclometalated iridium(III) complexes are excellent emitters for phosphorescent organic light-emitting diodes, but the design of such complexes require substantial cost and experimental efforts. In turn, the predictive power of density functional theory calculations is seldom enough for reliable prediction of the excited state properties of iridium(III) complexes. In this work, we aimed at data-driven prediction of the emission energies and photoluminescence quantum yields of such complexes. To this end, we created a database (IrLumDB) that contains experimentally measured luminescence properties for over 1200 literature bis-cyclometalated iridium(III) complexes. Based on this database, we developed machine learning models that are capable of predicting the energy of emission maxima and photoluminescence quantum yields for the iridium phosphors with mean absolute errors of 18.26 nm and 0.129, respectively, requiring only SMILES of ligands. Furthermore, we validated the model for emission wavelength prediction on the set of 33 experimentally obtained luminescence spectra for newly synthesized and characterized iridium(III) complexes. Our data-driven methodology will complement quantum chemical calculations as an efficient alternative approach for the prediction of the excited-state properties of large sets of bis-cyclometalated iridium(III) complexes, facilitating computational discovery of efficient emitters. The emission properties prediction and the dataset exploration are available at https://irlumdb.streamlit.app/. | Sergei Tatarin; Lev Krasnov; Ekaterina Nykhrikova; Maxim Minin; Daniil Smirnov; Andrei Churakov; Stanislav Bezzubov | Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Inorg.); Machine Learning; Ligand Design | CC BY NC 4.0 | CHEMRXIV | 2024-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67226049f9980725cf9958f3/original/predicting-emission-wavelengths-and-quantum-yields-of-diverse-bis-cyclometalated-iridium-iii-complexes-using-machine-learning.pdf |
676d3f0e6dde43c908637d07 | 10.26434/chemrxiv-2024-3fv84 | Wireframe DNA Origami Capable of Vertex-protruding Transformation | Regulating dynamic behavior of the designed molecular structures provides a foundation for the construction of functional molecular devices. DNA nanotechnology allows conformational changes in two-dimensional and three-dimensional DNA origami nanostructures by introducing flexibility between the faces of the structures. However, dynamic transformations in wireframe DNA origami, composed solely of vertices and edges, remain challenging due to vertex-specific flexibility. We report a wireframe DNA origami capable of vertex-protruding transformation from the open- to the closed-form with eight protruding vertices; this transformation is driven by the hybridization of the signal strands with the zipper strands extending from the edges, leading to structural reorganization. Spacer strands between vertices and edges were designed to introduce flexibility. Coarse-grained molecular dynamics simulations demonstrated that a longer spacer increases conformational flexibility and can achieve the narrow angles required for the vertex-protruding transformation. The experimental results showed the successful assembly of the open-form structure under optimized salt conditions, as visualized through transmission electron microscopy images. Furthermore, the transformation from the open-form to the closed- form was demonstrated by adding signal strands, resulting in designed vertex protrusions. This vertex-protruding transformation mechanism will expand the design approach of dynamic DNA nanostructures and help develop functional molecular devices for artificial molecular systems. | Yosuke Ochi; Wataru Kato; Yoichi Tsutsui; Yuki Gomibuchi; Daichi Tominaga; Keisuke Sakai; Takeshi Araki; Suzunosuke Yoshitake; Takuo Yasunaga; Yusuke Morimoto; Kazuhiro Maeda; Junichi Taira; Yusuke Sato | Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676d3f0e6dde43c908637d07/original/wireframe-dna-origami-capable-of-vertex-protruding-transformation.pdf |
649a8da79ea64cc1670a0217 | 10.26434/chemrxiv-2023-0ckx8 | Quantifying Irreversible Entropy Change in Adiabatic Gas Expansion: A Comprehensive Analysis | we calculate the entropy change for irreversible adiabatic expansion for real gas that does not mention in most Physical Chemistry textbook. This often prompts undergrad students, who are customized to study the behavior of real gas and ideal gas in thermodynamic course, to ask about the entropy change in real gases when they are subjected to expand. Change in temperature is also very important in this regard. So how will a student determine the entropy change for irreversible process? This procedure is quite simple according the textbooks. We cannot directly apply the equation ∆S = S2 – S1 = ∫_i^f▒(đQ_rev)⁄T as for irreversible process ∆S may not be necessarily equal to ∫_i^f▒(đQ_irrev)⁄T . Although entropy is a state function, it does not depend on the path how the system changes its course to achieve the final state. First, we have to identify the initial and final states and then find a suitable reversible pathway for the course. The calculations of ideal gases for irreversible pathway are done in textbooks. However, students need to know for the real gases formulas for the entropy change so that one’s expectation matches with the experimental values when done in practical. Here we considered the calculations for irreversible adiabatic expansion (normal and free) and what happens to the temperature of the system when it achieves the final state. | Arnab Halder; Dinesh Kumar Pyne; Soumalya Pramanik | Chemical Education; Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649a8da79ea64cc1670a0217/original/quantifying-irreversible-entropy-change-in-adiabatic-gas-expansion-a-comprehensive-analysis.pdf |
6628a99a91aefa6ce146c728 | 10.26434/chemrxiv-2024-gv3hf | Anisotropic porosity and interface synergy enhanced gas permselectivity in heterolayer metal-organic framework membrane | The pursuit of sustainable, carbon-free separation technology hinges on the efficient separation of gas mixtures with high separation factors and flow rates, i.e. high permselectivity. However, achieving this objective is arduous due to the meticulous engineering at the angstrom scale and intricate chemical manipulation required to design the pores within membranes. To address this challenge, a proof-of-concept for an anisotropic porous membrane has been devised. Employing a meticulous step-by-step methodology, two distinct porous metal-organic frameworks (MOFs) are integrated to form a monolithic anisotropic membrane. By harnessing pore anisotropy (3.4 to 6 Å) aligned with the gas permeation direction and a unique interface characterized by cross-linked pores derived from the two distinct MOFs, this membrane transcends the performance limitations inherent in the individual MOF membranes. This approach not only sheds light on the unprecedented heterolayer membrane design strategy but also elucidates the intricate CO2/N2 permselectivity relationship inherent in the interface structure. | Susmita Kundu; Tanmoy Maity; Suvendu Panda; Ritesh Haldar | Materials Science; Nanoscience; Hybrid Organic-Inorganic Materials; Multilayers; Thin Films; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6628a99a91aefa6ce146c728/original/anisotropic-porosity-and-interface-synergy-enhanced-gas-permselectivity-in-heterolayer-metal-organic-framework-membrane.pdf |
63e0f8c16d032916bb600bd4 | 10.26434/chemrxiv-2023-43zr4-v2 | Temperature dependence of 7Li NMR relaxation rates in Li3InCl6, Li3YCl6, Li1.48Al0.48Ge1.52(PO4)3 and LiPS5Cl | Inorganic solid-state battery electrolytes show high ionic conductivities and enable the fabrication of all solid-state batteries. In this work, we present the temperature dependence of spin-lattice relaxation time (T1), spin-spin relaxation time (T2), and resonance linewidth () of the 7Li nuclear magnetic resonance (NMR) for four solid-state battery electrolytes (Li3InCl6 (LIC), Li3YCl6 (LYC), Li1.48Al0.48Ge1.52(PO4)3 (LAGP) and LiPS5Cl (LPSC) from 173 K to 403 K at a 7Li resonance frequency of 233 MHz, and from 253 K to 353 K at a 7Li resonance frequency of 291 MHz. Additionally, we measured the spin-lattice relaxation rates at an effective 7Li resonance frequency of 133 kHz using a spin-locking pulse sequence in the temperature range of 253 K to 353 K. In LPSC, the 7Li NMR relaxation is consistent with the Bloembergen-Pound-Purcell (BPP) theory of NMR relaxation of dipolar nuclei. In LIC, LYC and LAGP, the BPP theory does not describe the NMR relaxation rates for the temperature range and frequencies of our measurements. The presented NMR relaxation data assists in providing a complete picture of Li diffusion in these four solid-state battery electrolytes. | Darshan Chalise; Carlos Juarez-Yescas; Beniamin Zahiri; Paul Braun; David Cahill | Materials Science; Inorganic Chemistry; Electrochemistry; Magnetism; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e0f8c16d032916bb600bd4/original/temperature-dependence-of-7li-nmr-relaxation-rates-in-li3in-cl6-li3y-cl6-li1-48al0-48ge1-52-po4-3-and-li-ps5cl.pdf |
638e1cfb836ceb115774c21e | 10.26434/chemrxiv-2022-dkzh5-v2 | Origin Invariant Molecular Orbital Decomposition of Optical Rotation | Optical rotation (OR) is a sensitive electronic property for which there are no clear structure-property relations. We proposed an approach to decompose the OR tensor in terms of one-electron transitions between occupied-virtual molecular orbital pairs, called the Sia method. This method allows to select the transitions with the largest magnitude that determine the overall value of the OR for a specific molecule, thus providing useful insights for characterization. However, the individual Sia values are origin-dependent even if the total OR is origin invariant. In this work, we explicitly identify the reason for the origin dependence of the Sia original formulations and we propose two ways to eliminate this spurious effect and define an origin invariant S ̃ia within the modified velocity gauge formalism. One approach is based on averaging the electric and magnetic-perturbed density Sia definitions (which have equal and opposite origin dependence that cancels out in the average), while the second approach is based on the equal distribution of the electronic response to an external field via Cholesky decomposition of the response matrix. Numerical results prove that the new Sia definitions are indeed origin invariant and they provide the same physical picture for the OR tensor decomposition. At the same time, we show that setting the origin of the coordinate system at the center of mass of the molecule also provides the same physical picture when using the original Sia formulation, which confirms that this is a robust approach for investigating structure-property relations in chiral molecules. | Ty Balduf; Marco Caricato | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638e1cfb836ceb115774c21e/original/origin-invariant-molecular-orbital-decomposition-of-optical-rotation.pdf |
65b4120c9138d23161d08aa5 | 10.26434/chemrxiv-2024-06kbz | Isopotential Titration for Quantifying Metal-Adsorbate Charge Transfer | The extent of charge transfer between adsorbed reactants and a catalyst surface plays a key role in determining binding energy and catalytic activity. Here, we describe the technique of ‘isopotential titration’ (IPT) to quantify the magnitude and direction of charge transfer between adsorbates and catalytic surfaces. The method used a ‘catalytic condenser’ device (Pt/C/70 nm HfO2/p++-Si) to evaluate the adsorption of hydrogen on a platinum-on-carbon conductive surface on a HfO2 (70 nm) film on a silicon wafer, with a potentiostat applying fixed (zero) voltage between the conductive Pt/C and silicon wafer layers. Dissociative adsorption of hydrogen on Pt resulted in electron flow through the external circuit from the Pt electrode toward the Si substrate, indicating that adsorbed hydrogen atoms donated electron density to the Pt surface, which then equilibrated with electrons flowing through the potentiostat to the silicon substrate. Desorption of hydrogen from the Pt surface exhibited equal and opposite current flow. The magnitude of the measured charge transfer upon hydrogen adsorption increased with increasing temperature from 100 to 200 °C, consistent with a larger change in H surface coverage at higher temperatures for cycling gaseous H2 partial pressures between 0.5% and 99.999%. Charge transferred from H atoms to the Pt was estimated as 0.17% of an electron donated per adsorbed H atom. The extent of charge transfer was comparable with a computed Bader charge analysis, which calculated an average of 0.4% of an electron transferred from adsorbing H to Pt at high surface coverage. With hydrogen adsorption being an example, isopotential titrations provide a new tool to quantify charge transfer events in heterogeneous catalytic systems. | Justin Hopkins; Shengguang Wang; Kyung-Ryul Oh; Benjamin Page; Jesse Canavan; Nondumiso Chibambo; Amber Walton; Sallye Gathmann; Jason Chalmers; Susannah Scott; Matthew Neurock; Lars Grabow; James McKone; Paul Dauenhauer; Omar Abdelrahman | Materials Science; Catalysis; Chemical Engineering and Industrial Chemistry; Catalysts | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b4120c9138d23161d08aa5/original/isopotential-titration-for-quantifying-metal-adsorbate-charge-transfer.pdf |
60c73dad567dfe002fec36be | 10.26434/chemrxiv.6024893.v1 | Synthesis, PtS-Type Structure, and Anomalous Mechanics of the Cd(CN)2 Precursor Cd(NH3)2[Cd(CN)4] | We report the nonaqueous synthesis of Cd(CN)<sub>2</sub> by oxidation of cadmium metal with Hg(CN)<sub>2</sub> in liquid ammonia. The reaction proceeds <i>via</i> an intermediate of composition Cd(NH<sub>3</sub>)<sub>2</sub>[Cd(CN)<sub>4</sub>], which converts to Cd(CN)<sub>2</sub> on prolonged heating. Powder X-ray diffraction measurements allow us to determine the crystal structure of the previously-unreported Cd(NH<sub>3</sub>)<sub>2</sub>[Cd(CN)<sub>4</sub>], which we find to adopt a twofold interpenetrating PtS topology. We discuss the effect of partial oxidation on the Cd/Hg composition of this intermediate, as well as its implications for the reconstructive nature of the deammination process. Variable-temperature X-ray diffraction measurements allow us to characterise the anisotropic negative thermal expansion (NTE) behaviour of Cd(NH<sub>3</sub>)<sub>2</sub>[Cd(CN)<sub>4</sub>] together with the effect of Cd/Hg substitution; <i>ab initio</i> density functional theory (DFT) calculations reveal a similarly anomalous mechanical response in the form of both negative linear compressibility (NLC) and negative Poisson's ratios. | Andrew Goodwin; Chloe Coates; Joshua Makepeace; Andrew Seel; Mia Baise; Ben Slater | Solid State Chemistry; Theory - Computational; Physical and Chemical Properties; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2018-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dad567dfe002fec36be/original/synthesis-pt-s-type-structure-and-anomalous-mechanics-of-the-cd-cn-2-precursor-cd-nh3-2-cd-cn-4.pdf |
6501f3e3b338ec988a6c2bf4 | 10.26434/chemrxiv-2023-scskq-v2 | Contrast Mechanism of Osmium Staining in
Electron Microscopy of Biological Tissues | Electron imaging of biological samples stained with heavy metals has enabled visualization of nanoscale subcellular structures critical in chemical-, structural-, and neuro-biology. In particular, osmium tetroxide has been widely adopted for selective lipid imaging. Despite the ubiquity of its use, the osmium speciation in lipid membranes and the mechanism for image contrast in electron microscopy (EM) have continued to be open questions, limiting efforts to improve staining protocols and improve high-resolution imaging of biological samples. Following our recent success using photoemission electron microscopy (PEEM) to image mouse brain tissues with a subcellular resolution of 15 nm, we have used PEEM to determine the chemical contrast mechanism of Os staining in lipid membranes. Os (IV), in the form of OsO2, generates aggregates in lipid membranes, leading to a strong spatial variation in the electronic structure and electron density of states. OsO2 has a metallic electronic structure that drastically increases the electron density of states near the Fermi level. Depositing metallic OsO2 in lipid membranes allows for strongly enhanced EM signals of biological materials. This understanding of the membrane contrast mechanism of Os-stained biological specimens provides a new opportunity for the exploration and development of staining protocols for high-resolution, high-contrast EM imaging. | Ruiyu Li; Gregg Wildenberg; Kevin Boergens; Yingjie Yang; Kassandra Weber; Janek Rieger; Ashley Arcidiacono; Robert Klie; Narayanan Kasthuri; Sarah B. King | Physical Chemistry; Biological and Medicinal Chemistry; Materials Science; Biological Materials; Biophysical Chemistry; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6501f3e3b338ec988a6c2bf4/original/contrast-mechanism-of-osmium-staining-in-electron-microscopy-of-biological-tissues.pdf |
60c74f874c8919004bad3bf4 | 10.26434/chemrxiv.12546371.v2 | MDBenchmark: A Toolkit to Optimize the Performance of Molecular Dynamics Simulations | Molecular dynamics simulations resolve biomolecular processes and material properties with incomparable detail. As a result, they consume a significant fraction of worldwide supercomputing resources. With our open source benchmarking software MDBenchmark, expert and novice users alike can easily determine the optimal settings for their specific simulation system, MD engine, software environment, and hardware configuration. Ultimately, saving computation time, energy, and money at essentially no additional cost will produce better science.<br /> | Michael Gecht; Marc Siggel; Max Linke; Gerhard Hummer; Juergen Koefinger | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f874c8919004bad3bf4/original/md-benchmark-a-toolkit-to-optimize-the-performance-of-molecular-dynamics-simulations.pdf |
60c7537c9abda20df2f8dfc2 | 10.26434/chemrxiv.12821492.v2 | Excited State Dynamics of Perylenediimide films with Isopropyl phenyl- and Undecane-Substitution | <p>The aggregation of Perylene Diimide (PDI) and its derivatives strongly depends on the molecular structure, and therefore has great impact on the excited states. By regulating the molecular stacking such as monomer, dimer, J- and/or H-aggregate, the formation of different excited states is adjustable and controllable. In this study, we have synthesized two kinds of PDI derivatives - undecane-substituted PDI (PDI-1) and diisopropylphenyl-substituted PDI (PDI-2), and the films are fabricated with spin-coating method. By employing photoluminescence (PL), time-resolved photoluminescence (TRPL) and transient absorption (TA) spectroscopy, the excited-state dynamics of two PDI amorphous films have been investigated systematically. The result reveals that both films have formed excimer after photoexcitation mainly due to the stronger electronic coupling among molecule aggregate in the amorphous film. It should be noted that the excited state dynamics in PDI-2 shows a singlet fission like process, which is evidenced by the appearance of triplet state absorption. This study provides the dynamics of excited state in amorphous PDI films, and pave the way for better understanding and adjusting the excited state of amorphous films. </p> | Qiu-Shi Ma; Cheng-Wei Ju; Ruihua Pu; Wenjie Zhang; Xian Lin; Yihan Chen; Weimin Liu | Aggregates and Assemblies; Optical Materials; Thin Films; Optics; Photochemistry (Physical Chem.); Physical and Chemical Processes; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7537c9abda20df2f8dfc2/original/excited-state-dynamics-of-perylenediimide-films-with-isopropyl-phenyl-and-undecane-substitution.pdf |
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