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63ea17d19da0bc6b33da603e | 10.26434/chemrxiv-2023-6s3s1 | Sterically Controlled Isodesmic Late-Stage C-H Iodination of Arenes | Aryl iodides are key motifs in organic chemistry due to their versatility as linchpins in metal-mediated cross-coupling reactions for synthesis and drug discovery. These scaffolds are typically prepared indirectly from prefunctionalized starting materials or via electrophilic aromatic iodination protocols. These methods are limited to specific regioisomers by their inherent selectivities and/or the availability of the required starting materials. Herein, we describe the sterically controlled iodination of arenes through an isodesmic C-H/C-I bond metathesis approach enabled by our dual ligand-based catalysts for arene-limited nondirected C-H activation. The protocol gives direct access to a complementary product spectrum with respect to traditional methods. Its synthetic utility is demonstrated by a broad scope and the suitability for late-stage modification. | Manuel van Gemmeren; Mirxan Farizyan; Rita de Jesus; Jyotirmoy Dey | Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ea17d19da0bc6b33da603e/original/sterically-controlled-isodesmic-late-stage-c-h-iodination-of-arenes.pdf |
66b37f55c9c6a5c07a4d206f | 10.26434/chemrxiv-2024-vrsw4-v2 | A Modern Approach to Intermittent Illumination for the Characterization of Chain-Propagation in Photoredox Catalysis | Photoredox catalysis has become an invaluable tool for the construction of organic molecules, allowing for unparalleled control over radical intermediates enabled by the mild conditions achieved through visible-light activation of a photocatalyst. These reactions can be classified under two distinct mechanistic paradigms: closed photocatalytic cycles, and photoinitiated chain reactions. While optimization strategies for each of these classes of reaction differ significantly, organic chemists still lack a straightforward means for probing chain-propagation. In this work, we report a simple and accessible approach to performing intermittent illumination studies for characterizing chain reactions in photoredox catalysis. Using modern LED technologies to precisely control the rate of sample illumination, we were able to validate the presence of product-forming chain reactions in three previously reported photoredox protocols. Furthermore, this technique also allows for the determination of chain-propagating lifetimes through a simple graphical analysis. Given the operational simplicity and ease of accessibility, we believe this intermittent illumination technique will be of great value to practitioners of the field moving forward. | K. A. Viraj Miyuranga; Kaitlin Ashcraft; Spencer Pitre | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photochemistry (Org.); Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b37f55c9c6a5c07a4d206f/original/a-modern-approach-to-intermittent-illumination-for-the-characterization-of-chain-propagation-in-photoredox-catalysis.pdf |
65b0f1b066c138172929aa33 | 10.26434/chemrxiv-2024-xkhqs | Molecular Basis for Chemoselectivity Control in Oxidations of Internal Aryl-Alkenes Catalyzed by Laboratory Evolved P450s | P450 enzymes naturally perform selective hydroxylations and epoxidations of unfunctionalized hydrocarbon substrates, among other reactions. The adaptation of P450 enzymes to a particular oxidative reaction involving alkenes is of great interest for the design of new synthetically useful biocatalysts. However, the mechanism that these enzymes utilize to precisely modulate the chemoselectivity and distinguishing between competing alkene double bond oxidations and allylic hydroxylations is sometimes not clear, which hampers the rational design of specific biocatalysts. In a previous work, a P450 from Labrenzia aggregata (P450LA1) was engineered in the laboratory using directed evolution to catalyze the direct oxidation of trans-b- methylstyrene to phenylacetone. The final variant, KS, was able to overcome the intrinsic preference for alkene epoxidation to directly generate a ketone product via the formation of a highly reactive carbocation intermediate. Here, additional library screening along the evolutionary lineage permitted to serendipitously detect a mutation that overcomes epoxidation and carbonyl formation by exhibiting a large selectivity towards allylic oxidation. A multiscalar computational methodology was applied to reveal the molecular basis towards this hydroxylation preference. Enzyme modelling suggests that introduction of a bulky substitution dramatically changes the accessible conformations of the substrate in the active site, thus modifying the enzymatic selectivity towards terminal hydroxylation and avoiding the competing epoxidation pathway, which is sterically hindered. | Jordi Soler; Sebastian Gergel; Stephan Hammer; Marc Garcia-Borràs | Catalysis; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b0f1b066c138172929aa33/original/molecular-basis-for-chemoselectivity-control-in-oxidations-of-internal-aryl-alkenes-catalyzed-by-laboratory-evolved-p450s.pdf |
60c757fc702a9b30b718cbe2 | 10.26434/chemrxiv.14450007.v2 | Nickel-Catalyzed Reductive Arylation of Redox Active Esters for the Synthesis of α-Aryl Nitriles – Role of a Chlorosilane Additive | <p>A nickel-catalyzed reductive cross-coupling of redox-active <i>N</i>-hydroxyphthalimide (NHP) esters and iodoarenes for the synthesis of α-aryl nitriles is described. The NHP ester substrate is derived from cyanoacetic acid, which allows for a modular synthesis of substituted α-aryl nitriles, an important scaffold in pharmaceutical sciences. Mechanistic studies reveal that decarboxylation of the NHP ester to the reactive radical intermediate is accomplished by a combination of a chlorosilane additive and Zn dust. The reaction exhibits a broad scope as many functional groups are compatible under the reaction conditions, including complex highly functionalized medicinal agents.</p> | Nick Michel; Racquel Edjoc; Emmanuel Fagbola; Jonathan Hughes; Louis-Charles Campeau; Sophie Rousseaux | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757fc702a9b30b718cbe2/original/nickel-catalyzed-reductive-arylation-of-redox-active-esters-for-the-synthesis-of-aryl-nitriles-role-of-a-chlorosilane-additive.pdf |
60c75843702a9b7f8718ccc4 | 10.26434/chemrxiv.14529861.v1 | Predicting Octanol/water Partition Coefficients Using Molecular Simulation for the SAMPL7 Challenge: Comparing the Use of Neat and Water Saturated 1-Octanol | Blind predictions of octanol/water partition coefficients at 298 K for 22 drug-like compounds were made for the SAMPL7 challenge. The octanol/water partition coefficients were predicted using solvation free energies computed using molecular dynamics simulations, wherein we considered the use of both pure and water-saturated 1-octanol to model the octanol-rich phase. Water and 1-octanol were modeled using TIP4P and TrAPPE-UA, respectively, which have been shown to well reproduce the experimental mutual solubility, and the solutes were modeled using GAFF. After the close of the SAMPL7 challenge, we additionally made predictions using TIP4P/2005 water. We found that the predictions were sensitive to the choice of water force field. However, the effect of water in the octanol-rich phase was found to be even more significant and non-negligible. The effect of inclusion of water was additionally sensitive to the chemical structure of the solute. | Spencer J. Sabatino; Andrew Paluch | Computational Chemistry and Modeling; Physical and Chemical Properties; Solution Chemistry; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2021-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75843702a9b7f8718ccc4/original/predicting-octanol-water-partition-coefficients-using-molecular-simulation-for-the-sampl7-challenge-comparing-the-use-of-neat-and-water-saturated-1-octanol.pdf |
6360d8ceac45c7c838a07f63 | 10.26434/chemrxiv-2022-sk07v | Mechanics of Dynamic and Deformable DNA Nanostructures | In DNA nanotechnology, DNA molecules are designed, engineered, and assembled into arbitrary-shaped architectures with predesigned functions. Static DNA assemblies often have delicate designs with structural rigidity to overcome thermal fluctuations, whose design strategies have been studied extensively. Dynamic structures reconfigure in response to external cues. Such transformational mechanisms have been explored to create dynamic nanodevices for environmental sensing, payload delivery, and other applications. However, the precise control of reconfigurable dynamics has been a challenge due partly to flexible single-stranded DNA connections between moving parts. Deformable structures are special dynamic constructs with deformation on double-stranded parts and single-stranded hinges during reconfiguration. These structures often have better controls in programmed deformation. However, related deformability and mechanics, as well as deformation mechanisms are not well understood or documented. In this review, we summarize the development of dynamic and deformable nanostructures from the mechanics perspectives. We present deformation mechanisms such as single-stranded DNA hinges with lock-and-release pairs, jack edges, helicity modulation, and external loading. Theoretical and computational models are discussed for understanding the deformations and mechanics, including commonly used elasticity theory, finite element method, and coarse-grained molecular dynamics models. Other special models are also introduced. We elucidate the pros and cons of each model and recommend design processes based on the models. The design guidelines should be useful for those who have limited knowledge in mechanics as well as expert DNA designers. After presenting unique applications, we conclude with current challenges in dynamic and deformable structures and outlook for the development of the field. | Ruixin Li; Anirudh Madhvacharyula; Yancheng Du; Harshith Adepu; Jong Hyun Choi | Materials Science; Nanoscience; Biological Materials; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6360d8ceac45c7c838a07f63/original/mechanics-of-dynamic-and-deformable-dna-nanostructures.pdf |
63054778f9e99cceec874e87 | 10.26434/chemrxiv-2022-dt7dk | Electrochemical Stability of Thiolate Self-Assembled Monolayers on Au, Pt, and Cu | Self-assembled monolayers (SAMs) of thiolates have increasingly been used for modification of metal surfaces in electrochemical applications including selective catalysis (e.g., CO2 reduction, nitrogen reduction) and chemical sensing. Here, the stable electrochemical potential window of thiolate SAMs on Au, Pt, and Cu electrodes is systematically studied for a variety of thiols in aqueous electrolyte systems. For fixed tail-group functionality, the reductive stability of thiolate SAMs is found to follow the trend: Au < Pt < Cu; this can be understood by considering the combined influences of the binding strength of sulfur and competitive adsorption of hydrogen. The oxidative stability of thiolate SAMs is found to follow the order: Cu < Pt < Au, consistent with each surface’s propensity toward surface oxide formation. The stable reductive and oxidative potential limits are both found to vary linearly with pH, except for reduction above pH ~10, which is independent of potential for most thiol compositions. The electrochemical stability across different functionalized thiols is then revealed to depend on many different factors including SAM defects (accessible surface metal atom sites decrease stability), intermolecular interactions (hydrophilic groups reduce the stability), and SAM thickness (stability increases with alkanethiol carbon chain length), as well as factors such as SAM-induced surface reconstruction, and the ability to directly oxidize or reduce the non-sulfur part of the SAM molecule. | Nathanael Ramos; J. Will Medlin; Adam Holewinski | Physical Chemistry; Catalysis; Energy; Electrochemistry - Mechanisms, Theory & Study; Interfaces; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63054778f9e99cceec874e87/original/electrochemical-stability-of-thiolate-self-assembled-monolayers-on-au-pt-and-cu.pdf |
66c67f4620ac769e5f67c0e9 | 10.26434/chemrxiv-2024-9p6j7-v3 | Reference-Free Thio-Succinimide Isomerization Characterization by Electron-Activated Dissociation | Rationale
Isomerism can be an important aspect in pharmaceutical drug development. Identification of isomers can provide insights into drug pharmacology and contribute to better design of drug molecules. The general approaches to differentiate isomers include Fourier-transform infrared spectroscopy (FTIR), nuclear magnetic resonance (NMR), and circular dichroism. Although proven effective, a commonly used method to differentiate isomers is chromatography coupled with mass spectrometry (MS). Notably, MS is routinely applied in leucine and isoleucine differentiation to facilitate protein sequencing. This work focuses on isomer differentiation of widely applied thio-succinimide structure bridging the antibody backbone and linker-payload of antibody-drug conjugates (ADCs). The hydrolysis of thio-succinimide stabilizes the payload-protein structure while generating a pair of constitutional isomers: thio-aspartyl and thio-isoaspartyl.
Methods
This paper introduces a hybrid method using ligand binding assay (LBA) and liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) to reveal isomerization details of thio-succinimide hydrolysis over time in plasma samples incubated with ADC. By applying two orthogonal dissociation methods, collision-induced dissociation (CID) and electron-activated dissociation (EAD), this pair of isomers showed different MS/MS spectra. This observation enables a unique approach in distinguishing thio-succinimide hydrolysis isomers.
Results
We observed signature [R1+Thio+57+H]+, [R2+Succ+H2O-57+H]+ and [R2+Succ+H2O-44+2H]2+ product ions that differentiated thio-aspartyl and thio-isoaspartyl isomers using EAD. A newly discovered [R2+ThioSucc+H2O-44+2H]2+ ion also served as additional evidence that further supported our findings.
Conclusions
This study is a first-to-date identification of thio-succinimide hydrolysis isomers without using synthesized reference materials. This approach should be applicable to all thio-succinimide-linked molecules. Correct identification of thio-succinimide hydrolysis isomers may eventually benefit the development of ADCs in the future.
| Junyan Yang; Jiaqi Yuan; Yue Huang; Anton Rosenbaum | Analytical Chemistry; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2024-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c67f4620ac769e5f67c0e9/original/reference-free-thio-succinimide-isomerization-characterization-by-electron-activated-dissociation.pdf |
65d04bc49138d231614f7518 | 10.26434/chemrxiv-2024-6q17l | Synthesis of proposed structures and structural revision of marine Roseobacter sulfur amino lipids (SALs) | The Roseobacter Clade Bacteria (RCB) play a crucial role in marine ecosystems, particularly Ruegeria pomeroyi and Phaeobacter inhibens, which utilize organosulfur compounds such as 2,3-dihydroxypropanesulfonate (DHPS) and dimethylsulfoniopropionoate (DMSP). Recently, a new class of sulfonolipids, sulfur amino lipids (SALs), was identified in these bacteria, with possible structures proposed by Smith et al. (ISME Journal, 2021, 15, 2440-2453). This study aims to confirm or revise the proposed structures for SAL-656 and SAL-672. Two candidates for SAL-656 and SAL-672 were synthesized, namely 3-acyloxyacylamides of homotaurine and cysteinolic acid, respectively. Tandem mass spectrometry (MS/MS) analysis of synthetic and natural SALs revealed significant discrepancies, leading to the exclusion of proposed structures. Further exploration of lipid extracts from R. pomeroyi and P. inhibens identified related lipoforms of SAL-656 and SAL-672, which form two distinct families based on LC-MS/MS and molecular network analysis. While the mass spectrometric data allow exclusion of previously proposed structures and provide insights into acyl groups and headgroups, the complete structures of SAL-656 and SAL-672 remain elusive. Nonetheless, the data are consistent with revised structures based on cysteinolic acid or 3-amino-2-hydroxypropanesulfonic acid wherein both hydroxyl and amino groups are acylated. Our findings reveal the SALs as a group of sulfonolipids that are distinct from more studied classes of sulfonolipids, with implications for understanding their biosynthesis and ecological roles in marine environments. | Luca Zudich; Michael Leeming; Luise Pallasdies; Madison Nuske; Gavin Reid; Laura Burchill; Spencer Williams | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Natural Products; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d04bc49138d231614f7518/original/synthesis-of-proposed-structures-and-structural-revision-of-marine-roseobacter-sulfur-amino-lipids-sa-ls.pdf |
60c75939842e65990ddb49bf | 10.26434/chemrxiv.14346182.v2 | Life Cycle Assessment of Direct Air Carbon Capture and Storage with Low-Carbon Energy Sources | Prospective energy scenarios usually rely on carbon dioxide removal (CDR) technologies to achieve the climate goals of the Paris Agreement. CDR technologies aim at removing CO2 from the atmosphere in a permanent way. However, the implementation of CDR technologies typically comes along with unintended environmental side-effects such as land transformation or water consumption. These need to be quantified before large-scale implementation of any CDR option by means of life cycle assessment (LCA). Direct air carbon capture and storage (DACCS) is considered to be among the CDR technologies closest to large-scale implementation, since first pilot and demonstration units have been installed and interactions with the environment are less complex than for biomass related CDR options. However, only very few LCA studies - with limited scope - have been conducted so far to determine the overall life-cycle environmental performance of DACCS. We provide a comprehensive LCA of different low temperature DACCS configurations - pertaining to solid sorbent-based technology - including a global and prospective analysis. | Tom Terlouw; Karin Treyer; christian bauer; Marco Mazzotti | Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75939842e65990ddb49bf/original/life-cycle-assessment-of-direct-air-carbon-capture-and-storage-with-low-carbon-energy-sources.pdf |
66fe1dc412ff75c3a1412054 | 10.26434/chemrxiv-2024-pqjd3 | Paclitaxel Biosynthesis AI Breakthrough | Paclitaxel, C47H51NO14, biosynthesis is an active area of research due to ongoing progress towards more sustainable and environmentally friendly production of the drug compound. Recent literature details the characterization of enzymes that play a role in synthesis, optimization of growth media, and RNA related regulatory mechanisms. The method of PhD students spending excessive time performing literature reviews to discover new findings is obsolete due to faster and high quality state of the art conversational AI. In this study, approximate AI times were obtained regarding how long would it take the fastest human researcher to read, analyze, extract information, and type a high quality 250 word answer; with the fastest time of 1,380 seconds being used as a standard reference. The slowest AI generation in the study was 79.19s by ChatGPT-4o, which was still over 17x faster than the optimal human performance time. Here, a paclitaxel biosynthesis breakthrough was illustrated twice using LLMs and LMMs. In the first instance, full length papers were summarized by AI models – with the finding that AI provided more detailed answers across entire papers, generating over 10x longer descriptions and 12x faster times compared to the manuscript author’s methods to summarize abstracts.
The outputs of individual AI generated answers yielded a 10 Paper Summary with 6,322 words, and served as the input for eight separate prompts, which provided valuable insight regarding both emerging and historical views of paclitaxel retrobiosynthesis, engineering microorganisms, as well as top 10 new research recommendations, and top 10 challenges for this area. The second paclitaxel biosynthesis advancement was demonstrated with a speed of 752 seconds for 36 generations compared to the single optimal human response of 1,380 seconds. Top models received an average AI judge score of 9.5 by ChatGPT-4o for Part A; a score of 9.3 by o1-preview, L3.1-405B, and ChatGPT-4o for Part B; and a score of 9.3 by ChatGPT-4o and 3.5 Sonnet, followed by a score of 9.2 for Wiz8x22B for Part C. These superior results have primarily been afforded by OpenAI, Claude.ai, and Meta AI new model releases in late 2024 that have helped to advance the paclitaxel biosynthesis field. The presence of speedups with more detailed answers over optimal human responses is supported by advanced cloud hardware that processes high dimensional and complex data continually to solve combinatorial problems such as those in this study using 15 different prompts across 163 generations. | Kevin Kawchak | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2024-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fe1dc412ff75c3a1412054/original/paclitaxel-biosynthesis-ai-breakthrough.pdf |
641c5c0a91074bccd0278d77 | 10.26434/chemrxiv-2023-cx09k | The fundamental relation between electrohelicity and molecular optical activity | Electrohelicity arises in molecules such as allene and spiropentadiene when their symmetry is reduced and helical frontier molecular orbitals (MOs) appear. Such molecules are optically active and electrohelicity has been suggested as a possible design principle for increasing the chiroptical response. Here we examine the fundamental link between electrohelicity and optical activity by studying the origin of the electric and magnetic transition dipole moments of the π −π∗ transitions. We show that the helical character of the MOs drives the optical activity in allene, and we use this knowledge to design allenic molecules with increased chiroptical response. We further examine longer carbyne-like molecules. While the MO helicity also contributes to the optical activity in non-planar butatriene, the simplest cumulene, we show there is no relation between the chiroptical response and the helical π-MOs of tolane, a simple polyyne. Finally, we demonstrate that the optical activity of spiropentadiene is inherently linked to mixing of its two π-systems rather than the helical shape of its occupied π-MOs. We thus find that the fundamental connection between electrohelicity and optical activity is very molecule dependent. Although electrohelicity is not the underlying principle, we show that the chiroptical response can be enhanced through insight into the helical nature of electronic transitions. | Marc H. Garner; Clemence Corminboeuf | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties | CC BY 4.0 | CHEMRXIV | 2023-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641c5c0a91074bccd0278d77/original/the-fundamental-relation-between-electrohelicity-and-molecular-optical-activity.pdf |
61aa325a7ce056832b87816f | 10.26434/chemrxiv-2021-jj003 | Reactivity Studies of Thiophosgene and its Halo Versions
towards Diazo Derivatives | The reactions of thiophosgene with diazo derivatives gives dichloro-alkene derivatives and cyclized, 1,2,3-thiadiazoles respectively. The product formation is mainly depending on substitutions on diazo substrates. When its halo versions, CSBr2 and in combination with bromide ion, CSBr2 less reactive than bromide ion with disubstituted diazo, give gem-dihalo derivatives whereas more reactive with mono substituted diazo to gives 1,2,3-thiadiazoles. In case CSI2 irrespective of substitution on diazo, iodide ion is more reactive then CSI2 was observed. | SUDERSHAN GONDI | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2021-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61aa325a7ce056832b87816f/original/reactivity-studies-of-thiophosgene-and-its-halo-versions-towards-diazo-derivatives.pdf |
60c75129bb8c1ac7e03dbc20 | 10.26434/chemrxiv.12988364.v2 | Catalysis of Hydrazone and Oxime Peptide Ligation by Arginine | Hydrazone and oxime peptide ligations are catalyzed by arginine. The catalysis is assisted intramolecularly by the side-chain guanidinium group. Hydrazone ligation in the presence of arginine proceeds efficiently in phosphate buffer at neutral pH but is particularly powerful in bicarbonate/CO<sub>2</sub> buffer. In addition to acting as a catalyst, arginine prevents the aggregation of proteins during ligation. With its dual properties as nucleophilic catalyst and protein aggregation inhibitor, arginine hydrochloride is a useful addition to the hydrazone/oxime ligation toolbox.<br /> | Nathalie Ollivier; Vangelis Agouridas; Benoît Snella; Rémi Desmet; Hervé Drobecq; Jérôme Vicogne; Oleg Melnyk | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Chemical Biology; Acid Catalysis; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75129bb8c1ac7e03dbc20/original/catalysis-of-hydrazone-and-oxime-peptide-ligation-by-arginine.pdf |
6772f6e26dde43c908d1662e | 10.26434/chemrxiv-2024-g62vk | Discrete Brush Polymers Enable Signal Amplification through Architectural Precision | The development of metal-free magnetic resonance imaging agents demands precise control over molecular architecture to achieve optimal performance. Current fluorine-based contrast agents rely on maximizing fluorine content (> 20 wt%) for sensitivity, requiring extensive solubilizing groups that lead to signal-diminishing aggregation. Here we show that discrete brush polymers (Đ = 1.0) with precise backbone lengths and a single terminal fluorine group achieve superior imaging performance through architectural control rather than high fluorine content. This design prevents both intra- and intermolecular fluorine aggregation while maintaining high aqueous solubility, enabling sharper signals and higher sensitivity than conventional systems despite containing less than 7 wt% fluorine. Systematic investigation reveals how backbone length controls fluorine mobility and signal generation, establishing clear structure-property relationships previously obscured by molecular heterogeneity. This work demonstrates how precise architectural control can enhance functional performance beyond traditional approaches, providing new strategies for designing imaging materials. | Nduka Ogbonna; Parikshit Guragain; Venkatesh Mayandi; Cyrus J. Sadrinia; Raman Danrad; Seetharama Jois; JIMMY LAWRENCE | Materials Science; Polymer Science; Biocompatible Materials; Imaging Agents; Polymer brushes; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6772f6e26dde43c908d1662e/original/discrete-brush-polymers-enable-signal-amplification-through-architectural-precision.pdf |
60c74434469df472adf432c8 | 10.26434/chemrxiv.8340857.v2 | Asymptotic behavior of the Hartree-exchange and correlation potentials in ensemble density functional theory | We report on previously unnoticed features of the exact Hartree-exchange and correlation potentials for atoms and ions treated via ensemble density functional theory, demonstrated on fractional ions of Li, C, and F. We show that these potentials, when treated separately, can reach non-vanishing asymptotic constant values in the outer region of spherical, spin unpolarized atoms. In the next leading order, the potentials resemble Coulomb potentials created by effective charges which have the peculiarity of not behaving as piecewise constants as a function of the electron number. We provide analytical derivations and complement them with numerical results using the inversion of the Kohn-Sham equations for interacting densities obtained by accurate quantum Monte Carlo calculations. The present results expand on the knowledge of crucial exact properties of Kohn-Sham systems, which can guide development of advanced exchange-correlation approximations.<br /><br /> | Tim Gould; Stefano Pittalis; Julien Toulouse; Eli Kraisler; Leeor Kronik | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74434469df472adf432c8/original/asymptotic-behavior-of-the-hartree-exchange-and-correlation-potentials-in-ensemble-density-functional-theory.pdf |
60c74d759abda2422cf8d460 | 10.26434/chemrxiv.12536153.v2 | Adsorption of Pd (II) and Au (III) Ions by Commercial Tris(2-Aminoethyl) Amine Polystyrene Polymer Beads | Adsorption of gold, and palladium species containing chlorine ions species onto commercial N-{2-[Bis(2-aminoethyl)amino]ethyl}aminomethyl–polystyrene polymer beads (TRIS) were investigated. The influence of the pH, initial metal ion concentration, and contact time on the adsorption performance was examined in a batch adsorption experiment. Langmuir, Modified Langmuir, Freundlich and Freundlich, Dubinin–Radushkevich isotherm model variables are calculated. The Langmuir monolayer adsorption capacities of the Pd (II), and Au (III) chlorine ions species were found to be 204.5, and 168.5 mg/g, respectively. The two metal adsorption kinetics fit the pseudo-second order kinetic models. In thermodynamic calculations, the choice of different equilibrium constant and withal using dimension containing constant usage are an important problem in the field. To overcome these problems, the Modified Langmuir isotherm equilibrium constant is used at determination of thermodynamic parameters. Adsorption mechanism steps were characterized by using FT-IR, SEM, and EDS. The adsorbent is interacted with each metal ions in HCl solution electrostatic interaction and surface complex formation between the amine groups. The calculation of the thermodynamic parameters using the dimensionless modified Langmuir equilibrium constant calculated more satisfying and more reliable way. All thermodynamic parameters suggested that Pd (II) and Au (III) adsorptions onto TRIS beads was a spontaneous, physisorption. | Merve Özçelik; Mustafa CAN; Mustafa İmamoğlu | Organic Polymers; Spectroscopy (Anal. Chem.); Thermodynamics (Chem. Eng.); Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d759abda2422cf8d460/original/adsorption-of-pd-ii-and-au-iii-ions-by-commercial-tris-2-aminoethyl-amine-polystyrene-polymer-beads.pdf |
60c751a34c8919fe7cad3feb | 10.26434/chemrxiv.13194407.v1 | Photo-Electrochemical Treatment of Disperse Blue1 Dyes in Simulated Textile Effluent: Parameter Optimization Method | <p>In this present
study, a hybrid technique consisting of Electrochemical and UV irradiation is
applied simultaneously to degrade simulated dyeing wastewater containing
Disperse blue 1 dye. Several operational parameters such as the effects of pH,
current intensity, temperature, initial concentration, and kinetic of the dye
concentration on treatment efficiency were studied. </p>
<p>The experimental
results show that the decolourization rate of the wastewater is highest at low
dye concentration consequent on the fact that it gave a percentage
decolourization of 82.1 at a dye concentration of 25mg/L in a short time
interval of 180 minutes. The influence of pH was also evaluated and the result
showed higher efficiency of decolourization at alkaline PH. Similar evaluations
were done for current and temperature. Finally, a comparative study was carried
out to compare the efficiency of decolourization for a single electrochemical
treatment, and the hybrid technique applied here. The result showed a
relatively better efficiency of 89.1% for the photoelectrochemical technique
compared to an88.7% for the electrochemical method. </p>
<p> </p>
<b> Keywords:
</b>Graphite electrodes; Disperse blue1 dye; Photoelectrochemical
degradation; UV-Vis Spectrophotometer | Kelechi Williams Festus; Ephraim chidi Ezeigbo | Electrochemical Analysis; Electrochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751a34c8919fe7cad3feb/original/photo-electrochemical-treatment-of-disperse-blue1-dyes-in-simulated-textile-effluent-parameter-optimization-method.pdf |
60c74165bdbb89395da38309 | 10.26434/chemrxiv.7048781.v2 | Enhancement in the Oxidative Stability of Commercial Gasoline Fuel by the Goethite Nanoparticles | It is well-established that traces of the transition metals strongly accelerate the gasoline oxidation significantly decreasing the gasoline storage time. This paper explores the opposite effect of the goethite nanoparticles on the oxidative stability of the commercial gasoline. | Yevhen Kalishyn; Igor Bychko; E.V. Polunkin; Tetyana Kameneva; Peter Strizhak | Nanostructured Materials - Nanoscience; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74165bdbb89395da38309/original/enhancement-in-the-oxidative-stability-of-commercial-gasoline-fuel-by-the-goethite-nanoparticles.pdf |
6294d6c724011ed4700ff1dd | 10.26434/chemrxiv-2022-xhrd8 | Phosphazenylphosphonium Frameworks: A Novel Main Group Mitochondrial Delivery Vector with Enhanced Properties | Mitochondrial targeting represents an attractive strategy for treating metabolic, degenerative and hyperproliferative diseases, since this organelle plays key roles in essential cellular functions. Triphenylphosphonium (TPP+) moieties – the current “gold standard” – have been widely used as mitochondrial targeting vectors for a wide range of molecular cargo. Recently, further optimisation of the TPP+ platform drew considerable interest as a way to enhance mitochondrial therapies. However, although the modification of this system appears promising, the core structure of the TPP+ moiety remains largely unchanged. Thus, in this study, we explored the use of aminophosphonium (PN+) and phosphazenylphosphonium (PPN+) main group frameworks as novel mitochondrial delivery vectors. The PPN+ moiety was found to be a highly promising platform for this purpose, owing to its unique electronic properties and high lipophilicity. This has been demonstrated by the high mitochondrial accumulation of a PPN+-conjugated fluorophore relative to its TPP+-conjugated counterpart, and has been further supported by density functional theory and molecular dynamics calculations, highlighting the PPN+ moiety’s unusual electronic properties. These results demonstrate the potential of novel phosphorus-nitrogen based frameworks as highly effective mitochondrial delivery vectors over traditional TPP+ vectors | How Chee Ong; João T. S. Coimbra; Maria J. Ramos; Bengang Xing; Pedro A. Fernandes; Felipe Garcia | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Inorganic Chemistry; Bioinorganic Chemistry; Main Group Chemistry (Inorg.); Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6294d6c724011ed4700ff1dd/original/phosphazenylphosphonium-frameworks-a-novel-main-group-mitochondrial-delivery-vector-with-enhanced-properties.pdf |
643589c00784a63aeef14e55 | 10.26434/chemrxiv-2023-q6vlj | Click'n lock: Rapid exchange between asymmetric tetrazines and thiols enables reversible, chemoselective clicking and on demand locking | The late-stage functionalization and diversification of complex structures including biomolecules is often achieved with the help of click chemistry. Besides employing irreversible click-like reactions, many synthetic applications benefit from reversible clicking strategies, so called de-/trans-click approaches. Yet, the combination of both, reversible and irreversible click chemistry – while still respecting the stringent criteria of click transformations – remains so far elusive for modifications of high value structures. Here, we report click’n lock as a concept that enables reversible clicking and on-demand locking of chemical entities, thus switching from reversible to irreversible modifications of complex (bio)molecules. For this purpose, we employ the tetrazine – thiol exchange (TeTEx) reaction as a fully traceless click reaction with second order rate constants k2 up to 25 M-1 s-1 within aqueous environments. Employing TeTEx as a reversible click reaction for the chemoselective modification of biomolecules is made possible by the use of asymmetric 3,6-tetrazines bearing a single sulfide residue. The inherent reactivity of tetrazines towards inverse electron demand Diels – Alder (IEDDA) reactions allows to stabilize the clicked structure, switching from reversible to irreversible systems (click’n lock). | Katerina Gavriel ; Dustin van Doeselaar; Daniëlle Geers; Kevin Neumann | Organic Chemistry; Bioorganic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643589c00784a63aeef14e55/original/click-n-lock-rapid-exchange-between-asymmetric-tetrazines-and-thiols-enables-reversible-chemoselective-clicking-and-on-demand-locking.pdf |
623b5600d6d3ed1a6f9c3501 | 10.26434/chemrxiv-2022-br6r2 | Unravelling free volume in branched-cation ionic liquids based on silicon | We have explored the branching of ionic liquid cation sidechains utilizing silicon as the backbone and found this structural feature to lead to fluids of remarkably low density and viscosity. The relatively low liquid densities suggest a large free volume in these liquids. Argon solubility was measured using a precise saturation method to probe the relative free volumes. We found that argon molar solubilities were slightly higher in ionic liquids with alkylsilane and siloxane groups within the cation, compared to carbon-based branched groups. The anion size, however, showed by far the dominant effect on argon solubility. Thermodynamic solvation parameters were derived from the solubility data and the argon solvation environment was modelled utilizing the polarizable CL&Pol force field. A semiquantitative analysis agrees with trends established from the experimental data. The results of this investigation demonstrate design principles for targeted ionic liquids when optimisation for the free volume is required, and demonstrate the utility of argon as a simple, noninteracting probe. As more ionic liquids find their way into industrial processes of scale, these findings are important for their utilisation in the capture of any gaseous solute, gas separation, or in processes involving the transformation of gases or small molecules. | Eduards Bakis; Kateryna Goloviznina; Inês Vaz; Diana Sloboda; Valda Valkovska; Igors Klimenkovs; Agilio Padua; Margarida Costa Gomes; Daniels Hazens | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Physical and Chemical Properties; Statistical Mechanics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623b5600d6d3ed1a6f9c3501/original/unravelling-free-volume-in-branched-cation-ionic-liquids-based-on-silicon.pdf |
62b7a8de5983a952d66f72ab | 10.26434/chemrxiv-2022-cms3z | Calculation of mass transfer limitations of a gas-phase reaction in an isothermal fixed bed reactor: tutorial and sensitivity analysis | The study of the reactivity of solid catalysts requires assessing chemical kinetics and mechanism in the absence of mass transport artifacts. These artifacts consist of the formation of concentration gradients either on the external or internal (inside nanopores) surface of the solid. Despite the existence of models and criteria for assessing the presence of mass transfer limitations during catalytic tests for gas-phase reactions in isothermal fixed bed reactors, the literature does not present straightforward protocols for performing the latter calculations. In this work, we present a systematic and complete protocol for the calculations above. The developed protocol serves as a tutorial for students and researchers. Particularly, the effectiveness factor for external and the Weisz-Prater number for the internal mass transfer limitations were developed. The oxidation of propane over mixed vanadium-aluminum (hydr)oxides was taken as a case study. Based on these protocols we perform a sensitivity study of the models for the following modifications: (i) the equation of state for modeling the thermodynamic properties of the gas phase, (ii) the particle size, (iii) the conversion of propane at two different temperatures and, (iv) the reactant used as a basis of the calculations; i.e., switching from propane to oxygen. Results showed that the model for calculating the effectiveness factor was poorly sensitive to all the above modifications. Meanwhile, the Weisz-Prater number was much more sensitive to the studied modifications, even reaching deviations up to ~200%. | Julieth García-Sánchez; Rodrigo Valderrama-Zapata; Luisa Acevedo-Córdoba; Sergio Rincón-Ortiz; Víctor Baldovino-Medrano | Catalysis; Chemical Engineering and Industrial Chemistry; Chemical Education; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b7a8de5983a952d66f72ab/original/calculation-of-mass-transfer-limitations-of-a-gas-phase-reaction-in-an-isothermal-fixed-bed-reactor-tutorial-and-sensitivity-analysis.pdf |
6735ee76f9980725cf2beb25 | 10.26434/chemrxiv-2024-z1kkd | Elastic frustration affecting multi-step spin crossover behaviour in two differently interpenetrated FeII-dicyanoargentate 3D Hofmann coordination polymers | The effect of elastic frustration on the multi-step SCO behaviour has been investigated in two differently interpenetrated [Fe(DPyN){Ag(CN)2}2] Hofmann coordination polymers (CPs) (DPyN = 2,6-di(pyridin-4-yl)naphthalene), influenced by argentophilic, ionic and non-covalent interactions. | ARINDAM GUPTA; ABHIK PAUL; DIBYA JYOTI MONDAL; SANJIT KONAR | Inorganic Chemistry; Coordination Chemistry (Inorg.); Magnetism | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6735ee76f9980725cf2beb25/original/elastic-frustration-affecting-multi-step-spin-crossover-behaviour-in-two-differently-interpenetrated-fe-ii-dicyanoargentate-3d-hofmann-coordination-polymers.pdf |
67d1ec9c6dde43c90891ea95 | 10.26434/chemrxiv-2025-ddxpm | Characterizing the content and structure of AAV capsids by size exclusion chromatography and charge detection mass-spectrometry | Adeno-Associated Virus (AAV) is currently the most widely used vector in gene therapy applications. However, a significant challenge in the manufacturing process of recombinant AAV (rAAV) is the presence of empty capsids, AAV aggregates, and partially filled capsids. These components do not provide any therapeutic benefit but add to the overall viral load, which could increase immunogenicity and reduce transduction efficiency. Here, we present a strategy that utilizes size exclusion chromatography (SEC) equipped with multi-angle light scattering (MALS) and a diode-array detector (DAD), followed by charge detection-mass spectrometry (CD-MS). The SEC step was used to separate AAV from aggregates and low molecular weight contaminants. In the second step, we employed direct CD-MS infusion using capillary electrophoresis with a sheath liquid (MS) interface. This approach facilitated automated, reproducible, and robust CD-MS determination of empty-filled capsids. Together, our analytical platform offers a reliable and comprehensive approach for assessing the rAAV purity and characterizing key quality attributes, including capsid aggregation and genome packaging. | Kanchan Pathak; Gustavo Perrotti; Stephen Rosa; Graham Robinett; Lance Kasper; James Xia; Carlos Escalante; Fabio Gomes | Analytical Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d1ec9c6dde43c90891ea95/original/characterizing-the-content-and-structure-of-aav-capsids-by-size-exclusion-chromatography-and-charge-detection-mass-spectrometry.pdf |
60c73f96f96a00cf7e2860e6 | 10.26434/chemrxiv.7397492.v1 | Dispersion-Controlled Regioselective Acid-Catalyzed Intramolecular Hydroarylation of cis-Methindolylstyrenes to Access Tetrahydrobenzo[cd]indoles | Readily prepared <i>cis</i>-<i>β</i>-(<i>α</i>’,<i>α</i>’-dimethyl)-4’-methindolylstyrenes undergo Brønsted acid-catalyzed intramolecular hydroarylation
to afford a variety of 3-aryl-5,5-dimethyl-1,3,4,5-tetrahydrobenzo[<i>cd</i>]indoles. Our experimental and computational
investigations suggest that dispersive interactions between the indole and styrene
preorganize substrates such that 6-membered ring formation occurs via a concerted
hydroarylation step. When dispersability is attenuated (by a substituent or
heteroatom), regioselectivity erodes and competing oligomerization predominates
for <i>cis</i> substrates; all <i>trans</i>-configured substrates that we
evaluated failed to cyclize efficiently. | Xiao Cai; Anargul Tohti; Cristian Ramirez; Hassan Harb; Hrant Hratchian; Ben Stokes | Organic Synthesis and Reactions; Physical Organic Chemistry; Stereochemistry; Computational Chemistry and Modeling; Acid Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f96f96a00cf7e2860e6/original/dispersion-controlled-regioselective-acid-catalyzed-intramolecular-hydroarylation-of-cis-methindolylstyrenes-to-access-tetrahydrobenzo-cd-indoles.pdf |
676e6a8881d2151a0215e455 | 10.26434/chemrxiv-2024-7bz9j | Enhancing Predictive Models for Solubility in Multicomponent Solvent Systems using Semi-Supervised Graph Neural Networks | Solubility plays a critical role in guiding molecular design, reaction optimization, and product formulation across diverse chemical applications. Despite its importance, current approaches for measuring solubility face significant challenges, including time- and resource-intensive experiments and limited applicability to novel compounds. Computational prediction strategies, ranging from theoretical models to machine learning (ML) based methods, offer promising pathways to address these challenges. However, such methodologies need further improvement to achieve accurate predictions of solubilities in multicomponent solvent systems, as expanding the modeling approaches to multicomponent mixtures enables broader practical applications in chemistry. This study focuses on modeling solubility in multicomponent solvent systems, where data scarcity and model generalizability remain key hurdles. We curated a comprehensive experimental solubility dataset (MixSolDB) and examined two graph neural network (GNN) architectures – concatenation and subgraph – for improved predictive performance. By further integrating computationally derived COSMO-RS data via a teacher-student semi-supervised distillation (SSD) framework, we significantly expanded the chemical space and corrected previously high error margins. These results illustrate the feasibility of unifying experimental and computational data in a robust, flexible GNN-SSD pipeline, enabling greater coverage, improved accuracy, and enhanced applicability of solubility models for complex multicomponent solvent systems. | Hojin Jung; Christopher D. Stubbs; Sabari Kumar; Raúl Pérez-Soto; Su-min Song; Yeonjoon Kim; Seonah Kim | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676e6a8881d2151a0215e455/original/enhancing-predictive-models-for-solubility-in-multicomponent-solvent-systems-using-semi-supervised-graph-neural-networks.pdf |
60c75201f96a001084288145 | 10.26434/chemrxiv.13239665.v1 | Augmented Lagrangian Method for Optimizing Non-Orthogonal Orbitals | <p>We applied augmented Lagrangian method to optimize molecular wave function based on non-orthogonal orbitals (Spin coupled wave function; SCWF) for its grand-state energy. </p><p>In contrast to the orthogonal-orbital-based electronic structure theory, SCWF includes spin eigenfunctions to satisfy the eigen states as the operator </p><p>of the square of the spin. </p><p>To obtain the ground-state energy of SCWF, therefore, it is necessary to optimize the orbital and the spin-coupling coefficients simultaneously. </p><p>In this study, the spin-coupling and the orbital coefficients are optimized with the augmented Lagrangian method under the constrain of normality of the wave function.</p><p>We employed this SCWF method to compute dissociative potential energy surfaces (PESs) of H<sub>2</sub>, H<sub>2</sub><sup>-</sup>, He<sub>2</sub><sup>+</sup>, and HLi. The obtained PESs by the SCWF method are close to these by full configuration interaction theory. These results indicate that the augmented Lagrangian method is effective to optimize SCWF.</p> | Masato Sumita; Naruki Yoshikawa | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75201f96a001084288145/original/augmented-lagrangian-method-for-optimizing-non-orthogonal-orbitals.pdf |
60c75315702a9b179418c2f1 | 10.26434/chemrxiv.13385480.v1 | Extensive Exploration of Ayurvedic Herbs to Prioritize Anti-Viral Drugs Alike Phytochemicals Against SARS-CoV-2 Using Network Pharmacology | <div>The novel coronavirus disease (COVID-19), which emerged in Wuhan, China, is continuously spreading worldwide, creating a huge burden on public health and economy. Currently, no specific vaccine or drug exists against SARS-CoV-2 virus, the causative agent of COVID-19. Ayurveda, the oldest healing-schema of Traditional Indian Medicinal (TIM) system, is considered as a promising CAM therapy to combat various diseases and disorders. To explore the regulatory mechanisms of 7,258 Ayurvedic herbs (AHs) against SARS-CoV-2, in this study, multi-targeting and synergistic actions of the constituent 34,472 phytochemicals (APCs) are investigated using a comprehensive approach comprising of network-pharmacology and molecular docking. By evaluating 292 APCs having high-level of similarity with anti-viral drugs in DrugBank for their binding affinity against 24 SARS-CoV-2 proteins, we develop and analyze a high confidence “Bi-regulatory network” of 115 APCs having ability to regulate protein targets in both virus and its host human-system. Immunomodulatory prospects of the antiviral drugs alike potentially effective phytochemicals (PEPs) are presented as a special case study, highlighting the importance of 6 AHs (Zea mays, Cucurbita maxima, Pisum sativum, Thlaspi arvense, Calophyllum inophyllum, Ziziphus jujuba) in eliciting the antiviral immunity at initial stages of infection. The mechanistic actions of PEPs against cardiovascular complications, diabetes mellitus and hypertension are also investigated to address the regulatory potential of Ayurvedic herbs in dealing with COVID-19 associated comorbidities. The study further reports 12 PEPs as promising source of COVID-19 comorbidity regulators.</div> | Neha Choudhary; Vikram Singh | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75315702a9b179418c2f1/original/extensive-exploration-of-ayurvedic-herbs-to-prioritize-anti-viral-drugs-alike-phytochemicals-against-sars-co-v-2-using-network-pharmacology.pdf |
66a4ecc801103d79c5dbe4c6 | 10.26434/chemrxiv-2024-q5f3h | Tailoring Unstrained Pyrrolidines via Reductive C–N Bond Cleavage with Lewis Acid and Photoredox Catalysis | Skeletal remodeling of unstrained azacycles such as pyrrolidine remains a formidable challenge in synthetic chemistry. To achieve such remodeling, continuous development of the cleavage of inert C–N bonds is essential. In this study, we introduce an effective strategy for the reductive cleavage of C–N bond in N-benzoyl pyrrolidine, leveraging a combination of Lewis acid and photoredox catalysis. This method involves single-electron transfer to the amide, followed by site-selective cleavage at C2–N bond. Cyclic voltammetry and NMR studies demonstrated that the Lewis acid is crucial for promoting the single-electron transfer from the photoredox catalyst to the amide carbonyl group. This protocol is widely applicable to various pyrrolidine-containing molecules and enables inert C–N bond cleavage including C–C bond formation via intermolecular radical addition. Furthermore, the current protocol successfully converts pyrrolidines to aziridines, lactones, and tetrahydrofurans, demonstrating the potential to expand synthetic strategies in skeletal remodeling. | Marina Hirao; Kazuhiro Aida; Tsuyoshi Saitoh; Takashi Yamamoto; Yasuaki Einaga; Eisuke Ota; Junichiro Yamaguchi | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2024-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a4ecc801103d79c5dbe4c6/original/tailoring-unstrained-pyrrolidines-via-reductive-c-n-bond-cleavage-with-lewis-acid-and-photoredox-catalysis.pdf |
60c741a9469df45c43f42e8d | 10.26434/chemrxiv.7604663.v3 | Investigations into Sampling Approaches for Chemical Analysis of Latent Fingermark Residue | <div>
<div>
<div>
<p>The quantitative variation in latent fingermark deposits sampled from the same donor (intra-donor) poses
considerable challenges to studies into the chemical composition of latent fingermarks. The work presented
here investigates approaches to the sampling of latent fingermark residues within this context. The amount
of squalene in fingermarks deposited on non-porous surfaces, determined by GC-MS, was used as an
indicator of the amount of non-polar material present. It was found that the percentage difference of
squalene between deposits from two hands at a given time, without controlling the deposition pressure, was
in the range of 4-100 %. This was reduced to 0-44 % in alternative sampling approaches where deposition
pressure was controlled. These results demonstrate the significant influence of sampling on subsequent
chemical analysis of fingermark residues, and offer possible sampling strategies to overcome issues
associated with intra-donor variation.
</p>
</div>
</div>
</div> | Buddhika Dorakumbura; Francesco Busetti; Simon W. Lewis | Analytical Chemistry - General; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741a9469df45c43f42e8d/original/investigations-into-sampling-approaches-for-chemical-analysis-of-latent-fingermark-residue.pdf |
67b81c1b6dde43c908cd37a6 | 10.26434/chemrxiv-2025-s5ndl | Chiral Amplification of Dynamic Helical Polymers through 1:1 Host-Guest Interactions: Theoretical Models for Majority Rule and Sergeants and Soldiers Effects | Chiral amplification is one of the distinctive phenomena of dynamic helical polymers whose helical sense excess is remarkably enhanced with a small amount of chiral units through the strong cooperative interactions among the monomer units. The Ising model for the chiral amplification of the dynamic helical copolymers bearing the chiral side chains has been well-established. However, the theoretical models have not yet been developed for the chiral amplification of the dynamic helical polymers induced by noncovalent intermolecular (host-guest) interactions of the achiral side chains with the chiral/chiral (majority rule effect) and chiral/achiral (sergeants and soldiers effect) guest molecules. In this work, we propose the theoretical models for two types of 1:1 host-guest interactions: the majority rule effect type 1:1 host-guest interaction (MRHG) and sergeants and soldiers effect type 1:1 host-guest interaction (SSHG) models, in which each twisting unit of the dynamic helical polymers is assumed to interact with one guest molecule. The excess energy of the helical reversal state, per unit energy favoring one helical state over the other, and enantioselectivity can be effectively determined using the MRHG model. Moreover, it was revealed that the chiral solvation model reported by Green, Morawetz, and co-workers is a particular solution of the SSHG model. | Nozomu Suzuki; Daisuke Taura; Yusuke Furuta | Physical Chemistry; Organic Chemistry; Polymer Science; Supramolecular Chemistry (Org.); Organic Polymers; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b81c1b6dde43c908cd37a6/original/chiral-amplification-of-dynamic-helical-polymers-through-1-1-host-guest-interactions-theoretical-models-for-majority-rule-and-sergeants-and-soldiers-effects.pdf |
66ad52c6c9c6a5c07ade9a50 | 10.26434/chemrxiv-2024-rgsrh-v2 | Structural Studies of Alloyed and Nanoparticle Transition Metal Dichalcogenides by Selenium-77 Solid-State Nuclear Magnetic Resonance Spectroscopy | Layered transition metal dichalcogenides (TMDCs) such as MoS2, MoSe2, and WSe2 are under intense investigation because they are atomically thin semiconductors with photophysical properties that can be tuned by changing their composition or morphology. Mechanochemical processing has been proposed as a method to obtain alloyed TMDCs in the series Mo1-xWxSySe2-y (x = 0, 1; y = 0, 1, 2). However, elucidating the chemical transformations occurring at the atomic scale following mechanochemical processing can be challenging because the products are often amorphous. To address this challenge, we probe TMDC mixing and alloying by using a combination of powder X-ray diffraction (PXRD), optical (Raman) spectroscopy, 77Se solid-state nuclear magnetic resonance (SSNMR) spectroscopy, and planewave density functional theory (DFT) calculations. The nature of the milling material and reaction atmosphere are shown to be essential factors in limiting the formation of undesired oxide byproducts. We demonstrate acquisition of 77Se SSNMR spectra using different combinations of Carr-Purcell Meiboom-Gill acquisition (CPMG) pulse sequences, magic angle spinning (MAS), and MAS dynamic nuclear polarization (DNP). The combination of SSNMR with the other characterization methods demonstrates that high energy impact ball milling induces molecular level alloying of Mo, W and chalcogen atoms in the family Mo1-xWxSySe2-y. Gauge including projector augmented wave (GIPAW) DFT calculations yield accurate 77Se chemical shift tensor components. 77Se SSNMR spectroscopy was also applied to study the structure of WSe2 nanocrystals intercalated with ethylenediamine. The intercalated WSe2 nanocrystals exhibit a more positive isotropic 77Se chemical shift as compared to bulk WSe2, however, the 77Se chemical shift anisotropy is the same, confirming the WSe2 layers have a similar structure as in their bulk counterparts. | Scott Carnahan; Eunbyeol Gi; Molly Wagner; Anuluxan Santhiran; Elise Amerongen; Hang Yin; Jessica Geisenhoff; Sharifur Rahman; Oleksander Dolotko; Ihor Hlova; Viktor Balema; Emily Smith; Alina Schimpf; Javier Vela; Aaron Rossini | Physical Chemistry; Materials Science; Inorganic Chemistry; Solid State Chemistry; Spectroscopy (Inorg.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ad52c6c9c6a5c07ade9a50/original/structural-studies-of-alloyed-and-nanoparticle-transition-metal-dichalcogenides-by-selenium-77-solid-state-nuclear-magnetic-resonance-spectroscopy.pdf |
678f54e081d2151a02111588 | 10.26434/chemrxiv-2025-3glrp | Deciphering Driving Forces of Biomolecular Phase Separation from Simulations | The formation and modulation of biomolecular condensates as well as their structural and dynamic properties are determined by an intricate interplay of different driving forces, which down at the microscopic scale involve molecular interactions of the biological macromolecules and the surrounding solvent and ions. Molecular simulations are increasingly used to provide detailed insights into the various processes and thermodynamic driving forces at play, thereby yielding mechanistic understanding and aiding the interpretation of experiments at the level of individual amino acid residues or even atoms. Here we summarize recent advances in the field of biocondensate simulations with a focus on coarse-grained and all-atom molecular dynamics (MD) simulations. We highlight possible future challenges concerning computationally efficient and physically accurate simulations of increasingly large and complex biocondensate systems. | Lars Schäfer; Lukas Stelzl | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Biophysical Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678f54e081d2151a02111588/original/deciphering-driving-forces-of-biomolecular-phase-separation-from-simulations.pdf |
60c73d51bdbb89d5f0a37c5d | 10.26434/chemrxiv.5708674.v1 | Which model should be selected to analyze the experimental data among many adsorption kinetic models? | <p>For
many years adsorption kinetics has been investigated, the development of kinetic model has been proceeded in
order to obtain the particular kinetic model which better agree with the
experimental data. As the result, dozens of
kinetic models have been established and used individually despite there are a
certain relationship between them. Students often ask which model should be
selected to analyze their experimental data among different
adsorption kinetic models. In order to clarify dependence relationship and
similar degree between adsorption kinetic models, we calculated and compared. Calculation
results were successfully compared with the correlation between them and an education
method for adsorption kinetic study was proposed. This method can help graduate
students of chemical engineering to understand the calculations on kinetics.</p> | yongson hong; Gwang-Il Kim; Jin-Xi Zhang; Chol-Jin Ri; Gyong-Chol Son; Byong-Suk Kim; Min-U Paek; Il-Hyok Kim; Hyok-Man Rim; Bing-Si Liu | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2017-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d51bdbb89d5f0a37c5d/original/which-model-should-be-selected-to-analyze-the-experimental-data-among-many-adsorption-kinetic-models.pdf |
60c75952bb8c1ad7db3dcbc1 | 10.26434/chemrxiv.14683485.v1 | Siloxy Esters as Traceless Activator of Carboxylic Acids: Boron-Catalyzed Chemoselective Asymmetric Aldol Reaction | The catalytic asymmetric aldol reaction of carboxylic acids is among the most useful reactions for the synthesis of biologically active compounds and pharmaceuticals. Despite the existence of many prominent reports, no general method is available to incorporate the aldol motif into complex carboxylic acids and their derivatives at late stages. Chemoselective catalytic asymmetric aldol reaction of multifunctional carboxylic acids is difficult to achieve, due to the high basicity required for enolization and the poisonous chelation of β-hydroxy acid products to Lewis acid catalysts. Herein, we identified that preconversion of carboxylic acids to siloxy esters facilitated the boron-catalyzed direct aldol reaction, leading to the development of carboxylic acid-selective, catalytic asymmetric aldol reaction applicable to multifunctional substrates. The asymmetric boron catalyst stereodivergently controlled the products’ stereochemistry depending on the catalyst’s chirality, not on the stereochemical bias of substrates. Computational studies rationalized the mechanism of the catalytic cycle and the stereoselectivity, and proposed Si/B enediolates as the active species for the asymmetric aldol reaction. The silyl ester formation facilitated both enolization and catalyst turnover through acidifying the α-proton of substrates and attenuating poisonous Lewis bases to the boron catalyst. | Taiki Fujita; Mina Yamane; W. M. C. Sameera; Harunobu Mitsunuma; Motomu Kanai | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75952bb8c1ad7db3dcbc1/original/siloxy-esters-as-traceless-activator-of-carboxylic-acids-boron-catalyzed-chemoselective-asymmetric-aldol-reaction.pdf |
63cd5141112596b462763635 | 10.26434/chemrxiv-2023-rq2wl | Rapid Detection of Ag (I) via Size Induced Photoluminescence Quenching of Biocompatible Green Emitting L-Tryptophan Scaffolded Copper Nanocluster | Atomically precise metal nanoclusters capped with small molecules like amino acids are highly favoured due to their specific interactions and easy incorporation into biological systems. However, they are rarely explored due to the challenge in surface functionalization of nanocluster with small molecules. Herein, we report the synthesis of green emitting (λ_ex = 380 nm, λ_em = 500 nm) single amino acid (L-tryptophan) scaffolded copper nanocluster (Trp-Cu NC) via one-pot route under mild reaction conditions. The synthesized nanocluster can be used for the rapid detection of heavy metal (Ag(I)) in the nanomolar concentration range in real environmental and biological samples. The strong green photoluminescence intensity of the nanocluster quenched significantly upon addition of Ag(I) due to the formation of bigger nanoparticles, thereby losing its energy quantization. A notable colour change from light yellow to reddish brown can also be observed in the presence of Ag(I) allowing its visual colorimetric detection. Portable paper strips fabricated with Cu-Trp NC can be reliably used for on-site visual detection of Ag(I) in the micromolar concentration range. The Trp-Cu NC possesses excellent biocompatibility making them suitable nanoprobe for cell imaging, thus can act as an in-vivo biomarker. The nanocluster showed a significant spectral overlap with an anticancer drug doxorubicin, thus can be used as an effective FRET pair. FRET results can reveal important information regarding the attachment of the drug to the nanocluster and hence, its role as a potential drug carrier for targeted drug delivery within human body. | Aarya .; Telna Thomas; Bibhu Ranjan Sarangi; Supratik Sen Mojumdar | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63cd5141112596b462763635/original/rapid-detection-of-ag-i-via-size-induced-photoluminescence-quenching-of-biocompatible-green-emitting-l-tryptophan-scaffolded-copper-nanocluster.pdf |
65fc12f5e9ebbb4db92c57d8 | 10.26434/chemrxiv-2023-c75tb-v2 | Elucidating the Influence of Electrolyte Additives on Iron Electroplating Performance | Iron electroplating is a process of great interest for many large-scale industrial and emerging energy applications, such as all-iron redox flow batteries. However, the process efficiency and material lifetime are greatly conditioned and limited by the poorly understood plating process and the presence of competitive reactions. In this work, we propose a methodology to deconvolute the nucleation parameters of iron via a suite of electrochemical techniques, spectroscopy, and analytical models, coupled with microscopic and crystallographic techniques. We perform a systematic analysis with iron-based electrolytes to deconvolute the simultaneous plating and hydrogen evolution reactions, and investigate an array of additives to tune electroplating descriptors. We find that all additives studied are able to regulate the plating process and find that highly stable iron-complexes based on buffers, such as iron-borates or -citrates deliver greater overall electroplating performance. These additives show superior selectivity, with improvements in faradaic efficiencies from 60% to ~90% due to the balanced effects of enhanced nucleation and side reaction suppression. Herewith, the aim of this study is to bridge the knowledge gap between the role of additives, kinetics and efficiency of the electrodeposition reaction, and their interplay defining the quality of the resulting plated layers. | Inmaculada Gimenez-Garcia; Antoni Forner-Cuenca | Physical Chemistry; Materials Science; Energy; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fc12f5e9ebbb4db92c57d8/original/elucidating-the-influence-of-electrolyte-additives-on-iron-electroplating-performance.pdf |
65dd092466c13817299f9d4a | 10.26434/chemrxiv-2022-csn3m-v3 | Examining DNA Structures with In-droplet Hydrogen/Deuterium Exchange Mass Spectrometry | Capillary vibrating sharp-edge spray ionization (cVSSI) combined with hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has been utilized to characterize different solution-phase DNA conformers including DNA G-quadruplex topologies as well as triplex DNA and duplex DNA. In general, G-quadruplex DNA shows a wide range of protection of hydrogens extending from ~12% to ~21% deuterium incorporation. Additionally, the DNA sequences selected to represent parallel, antiparallel, and hybrid G-quadruplex topologies exhibit slight differences in deuterium uptake levels which appear to loosely relate to overall conformer stability. Notably, the exchange level for one of the hybrid sequence sub topologies of G-quadruplex DNA (24 TTG) is significantly different (compared with the others studied here) despite the DNA sequences being highly comparable. For the quadruplex-forming sequences, correlation analysis suggests protection of base hydrogens involved in tetrad hydrogen bonding. For duplex DNA ~19% deuterium incorporation is observed while only ~16% is observed for triplex DNA. This increased protection of hydrogens may be due to the added backbone scaffolding and Hoogsteen base pairing of the latter species. These experiments lay the groundwork for future studies aimed at determining the structural source of this protection as well as the applicability of the approach for ascertaining different oligonucleotide folds, co-existing conformations, and/or overall conformer flexibility. | Kushani Attanayake; Sultan Mahmud; Chandrima Banerjee; Daud Sharif; Mohammad Rahman; Sandra Majuta; Anthony DeBastiani; Mst Nigar Sultana; Samira Hajian Foroushani; Chong Li; Peng Li; Stephen Valentine | Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Chemistry - General; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65dd092466c13817299f9d4a/original/examining-dna-structures-with-in-droplet-hydrogen-deuterium-exchange-mass-spectrometry.pdf |
60c74331567dfe3a52ec4073 | 10.26434/chemrxiv.8969678.v1 | Influenza A M2 Spans the Membrane Bilayer, Perturbs its Organization and Differentiates the Effect of Amantadine and Spiro[pyrrolidine-2,2'-adamantane] AK13 on Lipids | The investigation and observations made for the M2TM, excess aminoadamantane ligands in DMPC were made using the simpler version of biophysical methods including SDC, SAXS and WAXS, MD simulations and ssNMR. 1H, 31P ssNMR and MD simulations, showed that M2TM in apo form or drug-bound form span the membrane interacting strongly with lipid acyl chain tails and the phosphate groups of the polar head surface. The MD simulations showed that the drugs anchor through their ammonium group with the lipid phosphate and occasionally with M2TM asparagine-44 carboxylate groups. The 13C ssNMR experiments allow the inspection of excess drug molecules and the assessment of its impact on the lipid head-group region. At low peptide concentrations of influenza A M2TM tetramer in DPMC bilayer, two lipid domains were observed that likely correspond to the M2TM boundary lipids and the bulk-like lipids. At high peptide concentrations, one domain was identified which constitute essentially all of the lipids which behave as boundary. This effect is likely due, according to the MD simulations, to the preference of AK13 to locate in closer vicinity to M2TM compared to Amt as well as the stronger ionic interactions of Amt primary ammonium group with phosphate groups, compared with the secondary buried ammonium group in AK13.<br /> | Athina Konstantinidi; Maria Chountoulesi; Nikolaos Naziris; Barbara Sartori; Heinz Amenitsch; Gregor Mali; Tomaz Cendak; Maria Plakantonaki; Iro Triantafyllakou; Theodore Tselios; Costas Demetzos; David Busath; Thomas Mavromoustakos; Antonios Kolocouris | Biophysics; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74331567dfe3a52ec4073/original/influenza-a-m2-spans-the-membrane-bilayer-perturbs-its-organization-and-differentiates-the-effect-of-amantadine-and-spiro-pyrrolidine-2-2-adamantane-ak13-on-lipids.pdf |
61722b5fd7e1ee40922dde40 | 10.26434/chemrxiv-2021-rbw7j | Aluminum Foil Anodes for Li-ion Rechargeable Batteries: The Role of Li Solubility within β-LiAl | Li-ion battery (LIB) electrodes contain a substantial amount of electrochemically inactive materials, including binder, conductive agent, and current collectors. These extra components significantly dilute the specific capacity of whole electrodes, and thus have led to efforts to utilize foils, e.g., Al, as the sole anode material. Interestingly, the literature has many reports of fast degradation of Al electrodes, where less than a dozen cycles can be achieved. However, in some studies, Al anodes demonstrate stable cycling life with several hundred cycles. In this work, we present a successful pathway for enabling long-term cycling of simple Al foil anodes: β-LiAl phase grown from Al foil (α-Al) exhibits a cycling life of 500 cycles with a ~96% capacity retention when paired with a commercial cathode. The excellent performance stems from strategic utilization of the Li solubility range of β-LiAl that can be (de-)lithiated without altering its crystal structure. This solubility range at room temperature is determined to be ~6 at%. Consequently, this design circumvents the critical issues associated with the α/β/α phase transformations, such as volume change, mechanical strain, and nanopore formation. Application-wise, the maturity of aluminum industry, combined with excellent sustainability prospects, makes this anode an important option for future devices. | Tianye Zheng; Dominik Kramer; Reiner Mönig; Steven Boles | Materials Science; Energy; Alloys; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61722b5fd7e1ee40922dde40/original/aluminum-foil-anodes-for-li-ion-rechargeable-batteries-the-role-of-li-solubility-within-li-al.pdf |
66697cbf12188379d8ebcf20 | 10.26434/chemrxiv-2024-5p7h6 | Virtual screening for ultra-small NIR emitter with only two isolated hexatomic rings | Unlocking the potential of weak interactions to govern the electronic structure of organic molecules remains a significant challenge. This study constructs a quantitative relationship between conformations and strength of electronic through-space interactions (TSI) for tetraarylethanes (TAEs). To identify long-wavelength emitters, a sophisticated virtual screening is executed for TAE by constructing a TSI-based database. Consequently, an ultra-small emitter (o-2Md), distinguished by a highly concentrated n-electron configuration, is synthesized and shows a remarkable near-infrared (NIR) emission with a luminescence quantum yield of 25% and an emission wavelength extending beyond 800 nm. Notably, the o-2Md stands out as one of the smallest known organic NIR emitters, showcasing the robustness of n-n TSI in designing efficient emitters. This work not only systematically reveals the important role of weak interactions in manipulating the electronic structure at the single-molecule level but also provides a new platform, the TSI database, for designing advanced optoelectronic materials. | Zuping Xiong; Jianyu Zhang; Lei Wang; Xiong Liu; Jing Zhi Sun; Haoke Zhang; Ben Zhong Tang | Materials Science; Aggregates and Assemblies; Dyes and Chromophores; Optical Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66697cbf12188379d8ebcf20/original/virtual-screening-for-ultra-small-nir-emitter-with-only-two-isolated-hexatomic-rings.pdf |
66fa8553cec5d6c142aada39 | 10.26434/chemrxiv-2024-pbp8l | Ultimate Strategy for Preventing Metal Nanoparticle Sintering in Polymer Derived Mesoporous SiCN Ceramics | Polymer-derived ceramics (PDCs) are increasingly recognised as robust supports for high-temperature catalysis. However, the efficiency of these catalysts is often compromised by the sintering of metal nanoparticles, which reduces the surface area available for efficient interaction with reactants. This article introduces a new synthetic approach to prevent nanoparticle sintering through co-polymerization, microphase separation, and pyrolysis. An efficient version of HD-Polyethylene synthesised via Ziegler’s Aufbaureaktion and aminopyridinato gold complex as a porogen block and precursor for the generation of gold nanoparticles respectively. Particularly, a commercially available precursor derived siliconcarbonitride (SiCN) is used as a model PDC to demonstrate effective prevention of gold nanoparticle sintering, in contrast to conventional methods that often lead to particle agglomeration. The successfully synthesised Au@SiCN catalyst overcoming the sintering phenomenon is characterised using transmission electron microscopy, scanning electron microscopy, atomic force microscopy, powder X-ray diffractometry, and nitrogen physisorption techniques. Our findings highlight the effectiveness of this innovative synthetic approach in maintaining nanoparticle dispersion as well as enhancing the performance of PDCs for catalytic and energy applications. | Saravanakumar Thayuman; Rhett Kempe | Catalysis; Polymer Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fa8553cec5d6c142aada39/original/ultimate-strategy-for-preventing-metal-nanoparticle-sintering-in-polymer-derived-mesoporous-si-cn-ceramics.pdf |
637b54ca082129a9f9ff4b72 | 10.26434/chemrxiv-2022-vc1j9 | [2.2.2]Urea cryptand: an easily accessible neutral organic cage for anion binding in water | Binding hydrophilic anions such as sulfate in water is a significant academic challenge, in particular for neutral receptors. To achieve this, typically a large molecular receptor is designed that wraps around a bound anion in a hydrophobic microenvironment. Such receptors require multi-step synthesis and often display selectivity towards hydrophobic anions such as iodide. We here report the one-pot synthesis of a [2.2.2]urea cryptand (cage) and its ability to bind sulfate in water with sub-millimolar affinity achievable by incorporation into micelles. Unlike existing neutral receptors, the cage has >10-fold selectivity for sulfate against hydrophobic anions even in pure water. The cage displays rare slow-exchange NMR responses to divalent anions in DMSO-water allowing for simultaneous analysis of multiple divalent anions in water analogous to an ion chromatography instrument. Our results demonstrate the pre-organization of strong directional NH hydrogen bond donors in a cage scaffold as a synthetically less-demanding, yet effective approach to achieving selective binding of hydrophilic anions in water. | Xin Wu; Jack K. Clegg | Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637b54ca082129a9f9ff4b72/original/2-2-2-urea-cryptand-an-easily-accessible-neutral-organic-cage-for-anion-binding-in-water.pdf |
67b167ca81d2151a02ababba | 10.26434/chemrxiv-2024-hjvh3-v5 | Detection and Quantification of Changes in Oligomeric States of STING at Attomolar Concentrations of Analyte | Few protocols exist today that demonstrate repeatable resolution of small molecule interactions
with target proteins at extremely low analyte levels, particularly at sub-femtomolar levels. We have
developed two approaches for rapid screening and biophysical analysis which leverage changes in protein
oligomer states to study highly potent small molecules. The first protocol employs microscale
thermophoresis (MST) to measure competitive disruption of oligomerization following exposure of the
target protein to its endogenous ligand. The second protocol engages dynamic light scattering (DLS) to
measure the changes in physical size of oligomers after exposure to the endogenous ligand and/or analyte.
STING (stimulator of interferon genes) is a protein that relies on oligomerization after ligand binding for
intracellular signal transduction. Here we demonstrate the utilization of these methods through
measurements of wild type STING oligomerization following exposure to 2’,3’-cGAMP and the compound
clonixeril along with several analogs. Using these techniques, one can now measure small molecule
inhibitor concentrations in the attomolar range when the target protein undergoes oligomerization as part
of its natural biological activity. | William Lawless; Mark Eschenfelder; Robert Sparks; Sarah Lawless; Stephanie Krzypkowski; Kenyon Daniel; Wayne Guida | Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Biochemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b167ca81d2151a02ababba/original/detection-and-quantification-of-changes-in-oligomeric-states-of-sting-at-attomolar-concentrations-of-analyte.pdf |
655fd0965bc9fcb5c93b9812 | 10.26434/chemrxiv-2023-qcdp2 | A Robust Parallel Computing Data Extraction Framework for Nanopore Experiments | The success of a nanopore experiment relies not only on the quality of the experimental design but also on the performance of the analysis program utilized to decipher the ionic perturbations necessary for understanding the fundamental molecular intricacies. We have developed a data extraction and analysis framework that leverages parallel computing, efficient memory management (minimizing data aggregation), and vectorization, yielding significant performance enhancement. The open-seek-read-close data loading architecture running on multiple cores underpins the swift analysis of large files where an ~ ×18 improvement was found for a 100-minute-long file (~4.5 GB in size) compared to the more traditional single (cell) array data loading method. The proposed application was benchmarked against five other analysis platforms showcasing significant performance enhancement (>×6 to ×1120). The integrated provisions for batch analysis enable concurrently analyzing multiple files, a crucial capability notably absent in most existing analysis platforms. The batch-analysis feature is particularly vital for high-bandwidth experiments, wherein data is distributed across several files rather than consolidated into a single large file. Furthermore, the application is equipped with multi-level data fitting based on abrupt changes in the waveform. The ability to condense the extracted events to a single file improves data portability (e.g., 16 GB file acquired at 200 kHz with 28,182 events reduces to 47.9 MB in size—343× reduction in size) and enable a multitude of post-analysis extraction to be done efficiently. In summary, the utilization of parallel computing, efficient memory management, and vectorized operations have led to a fast analysis platform that delivers significant performance enhancement, making it well-suited for multiple and sizeable nanopore data file analysis. | Y. M. Nuwan D. Y. Bandara; Shankar Dutt; Buddini Karawdeniya; Jugal Saharia; Patrick Kluth; Antonio Tricoli | Analytical Chemistry; Nanoscience; Analytical Chemistry - General; Nanofluidics | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655fd0965bc9fcb5c93b9812/original/a-robust-parallel-computing-data-extraction-framework-for-nanopore-experiments.pdf |
60c74f314c89192ef7ad3b6f | 10.26434/chemrxiv.12129318.v3 | Comparison of Chemical and Interpretative Methods: The Carbon-boron π-Bond as a Test Case | Quantum chemical calculations using DFT and NBO, ETS-NOCV, QTAIM and ELF interpretative approaches have been carried out on <b>X</b>-BH<sub>2</sub><sup>+</sup> borenium complexes for 39 divalent C-donor ligands <b>X</b> including various N-heterocyclic carbenes and carbones. The C-B bond length and the barrier of rotation around the C-B bond were calculated and compared with various descriptors of the C-B pi-bond strength obtained from the orbital localization, energy partitioning or topological methods. Two families of descriptors emerged: <i>intrinsic</i> indicators, which measure the intensity of the pi-bond in the investigated molecule, and <i>relative</i> indicators, among them the rotational barrier, which compare the studied molecule with its conformer in which the pi-interaction is prevented. <i>Relative</i> indicators are influenced by other interactions in addition to purely pi-interactions. For both families of descriptors, excellent correlations are obtained, showing that the interpretative methods, despite their conceptual differences, describe the same chemical properties. These results also reveal noticeable shortcomings in these methods, and some precautions that need to be taken to interpret their results adequately.<br /> | Radhika Gupta; Elixabete Rezabal; Golshid Hasrack; Gilles Frison | Physical Organic Chemistry; Bonding; Coordination Chemistry (Inorg.); Ligands (Inorg.); Main Group Chemistry (Inorg.); Theory - Inorganic; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f314c89192ef7ad3b6f/original/comparison-of-chemical-and-interpretative-methods-the-carbon-boron-bond-as-a-test-case.pdf |
66159d5421291e5d1d7aa7c4 | 10.26434/chemrxiv-2024-m37q6-v2 | Quantitative Synthesis of Pt-Si-C Cyclopropane and its Unusual Complexation with Benzene | In this paper, we report the quantitative synthesis of the cyclopropane-type platinum-silene complex and its unusual interaction with benzene in the solid state, revealed by X-ray crystallography. Thus, three platinum complexes "dock" on hydrogens of one benzene molecule via weak van der Waals-type interactions. The cyclopropane nature of the complex in solution was confirmed by 29Si NMR spectroscopy. Also, an unusual 31P NMR spectrum of the complex in hexane was recorded, in which two phosphorus atoms with different chemical environments have similar chemical shifts but different values of J-coupling with platinum. | Gregory Molev; Dmitry Bravo-Zhivotovskii; Yitzhak Apeloig | Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Inorg.); Coordination Chemistry (Organomet.); Main Group Chemistry (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2024-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66159d5421291e5d1d7aa7c4/original/quantitative-synthesis-of-pt-si-c-cyclopropane-and-its-unusual-complexation-with-benzene.pdf |
60c74021469df41004f42bdc | 10.26434/chemrxiv.7637870.v1 | Deconstructing the Behavior of Donor-Acceptor Copolymers in Solution & the Melt: The Case of PTB7 | For organic semiconductors, the solid-state packings of the π-conjugated molecules or polymers dictate the material electronic, optical, and mechanical characteristics. Combinations of solution and solid-state investigations are often used to establish structure–function relationships, though these connections are often loosely correlated, and experiments in different laboratories can lead to widely variable interpretations. Hence, there remains a need to develop a deeper, more robust understanding of the connections between molecular and polymer chemistry, structure, processing, solid-state order, and materials properties to enable judicious materials design principles. Towards this goal, we employ fully-atomistic molecular dynamics (MD) simulations of poly[4,8-bis(5-(2-ethylhexyl)thiophen-2-yl)benzo[1,2-b;4,5-b’]dithiophene-2,6-diyl-alt-(4-(2-ethylhexyl)-3-fluorothieno[3,4-b]thiophene-)-2-carboxylate-2-6-diyl)] (PTB7), a donor–acceptor copolymer that has been widely investigated in the organic solar cell literature, to unravel some of these associations. The MD simulations make use of polymer lengths (masses) and solution concentrations that are consistent with those used in experiment, allowing for a detailed picture to arise as to how variations in the polymer environment can direct polymer structure. Comparisons between experiment and theory suggest that processing history can be an important factor in the polymer structures presumed experimentally that are used to interpret optical and electronic response. The results of these simulations provide specific information into the behavior of PTB7 under different conditions, and showcase how atomistic MD simulations that approach experimentally relevant sizes can be used to develop broader chemical insight that can aid in the design, processing, and characterization of polymer-based organic semiconductors. | Sean M. Ryno; Chad Risko | Carbon-based Materials; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74021469df41004f42bdc/original/deconstructing-the-behavior-of-donor-acceptor-copolymers-in-solution-the-melt-the-case-of-ptb7.pdf |
652e9287bda59ceb9ac52f04 | 10.26434/chemrxiv-2023-t51x7 | Discovering a Herbicide Terminator: The Role of Metals in Eliminating Glyphosate by Metal-Organic Frameworks | The impact of metals within a family of isostructural metal-organic frameworks (MOFs) on the adsorption and photodegradation of the herbicide glyphosate (GP) is presented in this study. Four MOFs, namely Sc-TBAPy, Al-TBAPy, Y-TBAPy, and Fe-TBAPy (TBAPy: 1,3,6,8-tetrakis(p-benzoic acid)pyrene), were characterized and evaluated for their ability to remediate GP from water. Among these materials, Sc-TBAPy demonstrates superior performance in both the adsorption and degradation of GP. Upon light irradiation for 5 min, Sc-TBAPy completely degrades 100% of GP in a 1.5 mM solution. Femtosecond transient absorption spectroscopy reveals that Sc-TBAPy exhibits enhanced charge transfer character compared to the other MOFs, as well as suppressed formation of emissive excimers that could impede photocatalysis. This finding was further supported by hydrogen evolution half-reaction (HER) experiments, which demonstrated Sc-TBAPy’s superior catalytic activity for water splitting. In addition to its faster adsorption and more efficient photodegradation of GP, Sc-TBAPy also exhibits selective oxidation of GP, avoiding the formation of toxic aminomethylphosphonic acid observed with the other M3+-TBAPy MOFs. To investigate the selectivity observed with Sc-TBAPy, electron spin resonance, depleted oxygen conditions, and solvent exchange with D2O were employed to elucidate the role of different reactive oxygen species on GP photodegradation. The findings indicate that singlet oxygen (1O2) plays a critical role in the selective photodegradation pathway achieved by Sc-TBAPy.
Introduction
| Kyriakos Stylianou; Nan Chieh Chiu; Jacob Lessard; Emmanuel Nyela Musa; Logan Lancaster; Clara Wheeler; Taylor Krueger; Cheng Chen; Trenton Gallagher; Makenzie Nord; Hongliang Huang; Paul Ha-Yeon Cheong; Chong Fang | Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652e9287bda59ceb9ac52f04/original/discovering-a-herbicide-terminator-the-role-of-metals-in-eliminating-glyphosate-by-metal-organic-frameworks.pdf |
665f1625418a5379b010d72d | 10.26434/chemrxiv-2024-k035t | Regioselective Photoredox Catalyzed Cycloadditions of Acyclic Carbonyl Ylides | A photoredox catalyzed [3+2] dipolar cycloaddition between acyclic carbonyl ylides generated from 𝛼-cyano epoxides and dipolarophiles is described. This method, influenced by anionic charge localization and temperature control, enabled the synthesis of regioselective functionalized cyclic ethers. By leveraging different dipolarophiles, Lewis acid mediated activation afforded either furan or hydroxy-dihydronaphthalene scaffolds. A direct synthesis of lignan natural products isodiphyllin and diphyllin is achieved by exploiting the nitrile’s reactivity as a directing handle for the desired regioisomer. | Alexandra Millimaci; Antonin Knirsch; Aaron Beeler | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665f1625418a5379b010d72d/original/regioselective-photoredox-catalyzed-cycloadditions-of-acyclic-carbonyl-ylides.pdf |
61a40bbf5f114df58f6a6cf3 | 10.26434/chemrxiv-2021-r9c0c | Acceleration of alkyne metathesis in multicomponent catalytic systems by use of alternative Mo(0) sources under optimised conditions | Abstract. Alkyne metathesis in multicomponent catalytic systems, although subject to changes, is still a domain of molybdenum hexacarbonyl as a source of Mo(0). Our findings show that this coordination compound is relatively inert under metathesis conditions, which results in noticeably long induction of catalytic activity, and the kinetics of this transformation can greatly benefit from switching to more labile Mo(0) complexes. Several easily obtainable ones had been tested and [Mo(CO)3(py)3] has been chosen as the one exhibiting the most desired features, i.e. nearly instant catalytic activity and relative stability in the air. | Maciej Zaranek; Jakub Robaszkiewicz | Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a40bbf5f114df58f6a6cf3/original/acceleration-of-alkyne-metathesis-in-multicomponent-catalytic-systems-by-use-of-alternative-mo-0-sources-under-optimised-conditions.pdf |
66d5644020ac769e5f95c6d8 | 10.26434/chemrxiv-2024-kh8dv | Evaluating ultra-fine friction grinding for the continuous production of nanofibrillated cellulose | Nanofibrillated cellulose (NFC) has applications in many sectors, but economical production of large volumes with a minimized ecological footprint remains challenging. In this study, we have developed a new design to upgrade the Masuko Supermasscolloider from a traditional batch mode to continuous circulation. This upgrade includes a pump-controlled circulating system, an in-line viscosimeter for real-time measurement of cellulose suspension viscosity, and a power meter to monitor and evaluate the energy consumption of both the pump and the grinder throughout the process. These modifications address the limitations of scaling up NFC production, offering a more efficient and effective approach. We investigated the production of NFC from cellulose feedstock derived from miscanthus biomass under various conditions, including different initial cellulose concentrations (1 wt%, 1.5 wt% and 2 wt%) and processing volumes (15L and 25 L) at different grinding time (from 15 minutes to 120 minutes, with 15 minutes intervals). A systematic study on the effect of these processing conditions on the size distribution of NFC particles was conducted using an analytical centrifuge (Lumisizer). A prevalence of particles with equivalent hydrodynamic diameters between ~250 nm and ~300 nm was observed regardless of the processing conditions. Notably, in the context of large-scale NFC production, our approach demonstrated a 70% reduction in specific energy consumption by either increasing the processing volume from 15 L to 25 L and increasing the initial cellulose concentration from 1 wt% to 2 wt%. Additionally, we explored the application of produced NFC as nanofillers in nanocomposite packaging materials. Specifically, NFC particles processed at different grinding times were incorporated into a glycerol-plasticized carboxymethyl cellulose (CMC) matrix to form bio-nanocomposite films. We have found that particles obtained with longer grinding time did not lead to increased mechanical performance. This simplifies the NFC production process by reducing the need for prolonged grinding, thereby saving time and energy while maintaining the desired properties of the nanocomposite samples. | Huy Vu Duc Nguyen; Angus C. L. A. Crampton ; Daniel F Schmidt ; Tim Huber | Materials Science; Chemical Engineering and Industrial Chemistry; Composites; Materials Processing; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d5644020ac769e5f95c6d8/original/evaluating-ultra-fine-friction-grinding-for-the-continuous-production-of-nanofibrillated-cellulose.pdf |
61fab8780aec1ae0ab0fafbc | 10.26434/chemrxiv-2021-3zv3k-v2 | ChemPlot, a Python library for chemical space visualization | Visualizing chemical spaces streamlines the analysis of molecular datasets by reducing the information to human perception level, hence it forms an integral piece of molecular engineering, including chemical library design, high-throughput screening, diversity analysis, and outlier detection. We present here ChemPlot, which enables users to visualize the chemical space of molecular datasets in both static and interactive ways. ChemPlot features structural and tailored similarity methods, together with three different dimensionality reduction methods: PCA, t-SNE, and UMAP. ChemPlot is the first visualization software that tackles the activity/property cliff problem by incorporating tailored similarity. With tailored similarity, the chemical space is constructed in a supervised manner considering target properties. Additionally, we propose a metric, the Distance Property Relationship score, to quantify the property difference of similar (i.e. close) molecules in the visualized chemical space. ChemPlot can be installed via Conda or PyPI (pip) and a web application is freely accessible at https://www.amdlab.nl/chemplot/. | Murat Cihan Sorkun; Dajt Mullaj; J. M. Vianney A. Koelman; Süleyman Er | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61fab8780aec1ae0ab0fafbc/original/chem-plot-a-python-library-for-chemical-space-visualization.pdf |
668448c05101a2ffa830b436 | 10.26434/chemrxiv-2024-gdbgq | Mechanistic Understanding of a Bifunctional Electrolyte Additive as a Solvation-Property Modifier and Polysulfide Mediator for Enhanced Performance in Lithium-Sulfur Battery | Lithium-sulfur (Li-S) batteries stand as promising candidates for next-generation energy storage systems, offering high specific capacity and cost-effectiveness. However, challenges persist due to the sluggish kinetics of polysulfides conversion and migration. Our study, employing operando X-ray absorption spectroscopy (XAS) and operando Raman spectroscopy, reveals that the 16-electron transfer reaction from S8 to Li2S during the sulfur reduction reaction (SRR) remains incomplete, contrary to the prevailing understanding. To address this issue, we introduce a novel bifunctional electrolyte additive, bis(4-nitrophenyl) carbonate (BNC), aimed at enhancing discharge kinetics, particularly for short-chain polysulfides conversion, while simultaneously immobilizing soluble polysulfides. Ab initio molecular dynamics (AIMD) simulations and nuclear magnetic resonance (NMR) spectroscopy confirm that BNC modifies the lithium-ion solvation structure, leading to stronger interactions with Sx2-. The BNC-containing electrolyte exhibits an average reduction of 40.6% in activation energy associated with polysulfide formation compared to the baseline. Additionally, X-ray fluorescence (XRF) mapping corroborated that the addition of BNC reduced sulfur deposition on the anode, thus mitigating the polysulfide shuttling effect. Moreover, via X-ray absorption near-edge structure (XANES) analysis, the cathode with the baseline electrolyte demonstrated a pre-edge peak at 2471.5 eV, indicative of sluggish SRR kinetics. Furthermore, this study explores the optimal concentration of BNC, recognizing that excessive concentrations may exacerbate sulfur depletion and accelerate capacity decay. The 0.01 M BNC-containing electrolyte enhances kinetics and suppresses polysulfide shuttling, standing favorable against literature results with an areal sulfur loading of 4 mg/cm2. These discoveries provide valuable insights into understanding the kinetics of SRR in Li-S batteries and offer significant guidance for developing advanced electrolyte systems. | Huidong Dai; Colin Gallagher; Seong-Min Bak; Luisa Gomes; Kevin Yang; Ruizhi Dong; Srinidi Badhrinathan; Qing Zhao; Yonghua Du; Gaind P. Pandey; Sanjeev Mukerjee | Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Redox Catalysis; Energy Storage | CC BY 4.0 | CHEMRXIV | 2024-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668448c05101a2ffa830b436/original/mechanistic-understanding-of-a-bifunctional-electrolyte-additive-as-a-solvation-property-modifier-and-polysulfide-mediator-for-enhanced-performance-in-lithium-sulfur-battery.pdf |
65f03e26e9ebbb4db98bfcba | 10.26434/chemrxiv-2024-32bcg | Unimolecular Chemiexcited Oxygenation of Pathogenic Amyloids | Pathogenic protein aggregates, called amyloids, are etiological-ly relevant to various diseases, including neurodegenerative Alzheimer disease. Catalytic photooxygenation of amyloids, such as amyloid-β (Aβ), reduces their toxicity; however, the requirement for light irradiation may limit its utility in large animals, including humans, due to the low tissue permeability of light. Here, we report that Cypridina luciferin analogs, dmCLA-Cl and dmCLA-Br, promoted selective oxygenation of amyloids through chemiexcitation without external light irra-diation. Further structural optimization of dmCLA-Cl led to the identification of a derivative with a polar carboxylate functional group and low cellular toxicity: dmCLA-Cl-acid. dmCLA-Cl-acid promoted oxygenation of Aβ amyloid and reduced its cellular toxicity without photoirradiation. The chemiexcited oxygenation developed in this study may be an effective approach to neutralizing the toxicity of amyloids, which can accumulate deep inside the body, and treating amy-loidosis. | Hiroki Umeda; Kayo Suda; Daisuke Yokogawa; Shigehiro A. Kawashima; Harunobu Mitsunuma; Yuki Yamanashi; Motomu Kanai | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f03e26e9ebbb4db98bfcba/original/unimolecular-chemiexcited-oxygenation-of-pathogenic-amyloids.pdf |
6466028cf2112b41e9c09891 | 10.26434/chemrxiv-2023-gpzbp | Two-Steps Halogen Intercalation Mechanism in Dual-Ion Batteries Enabled by Aqueous Biphasic Systems | The electrification of our society requires safer and longer lasting batteries, for which modular electrolytes such as aqueous biphasic systems (ABS) are being developed. ABS, i.e. two-phase systems, were shown to enable high-potential dual-ion aqueous batteries based on Li-ion (de)intercalation at graphite negative electrode and halides (de)intercalation at graphite positive electrode. However, the exact role of ABS in promoting the intercalation of halogens while preventing halogen gas evolution remains unclear. We find that using ABS do not favor halogen intercalation but rather trihalides formation. Electrochemically-generated trihalides are confined in the halide-rich phase of ABS, preventing their diffusion to negative electrode and selfdischarge. We also revealed that confined trihalides spontaneously intercalate in the graphite positive electrode. ABS thus enable a two-steps electrochemical-chemical intercalation mechanism of halogens. This work paves the way toward the design of novel ABS for developing dual-ion batteries or membrane-less redox-flow batteries with independent anodic and cathodic chemistries. | Damien Degoulange; Gwenaëlle Rousse; Alexis Grimaud | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6466028cf2112b41e9c09891/original/two-steps-halogen-intercalation-mechanism-in-dual-ion-batteries-enabled-by-aqueous-biphasic-systems.pdf |
65808ac266c138172982f8a9 | 10.26434/chemrxiv-2024-f5g9p | Radical strain-release photocatalysis for the synthesis of azetidines | The increasing popularity of four-member rings in drug discovery programs has vastly widen the research in synthetic chemistry, guiding the community to progress and reinvent old strategies for their crafting. Recently, the strain-release concept has been effectively used to build complex architectures. However, in contrast to the tens of described strategies accessing small carbocyclic derivatives, azetidine synthesis remains severely underdeveloped. Here, we report a mild visible-light-driven method to access densely functionalised azetidines by subjecting azabicyclo[1.1.0]butanes (ABBs) to radical strain-release (RSR) photocatalysis. We investigated the mechanism of this process using a combination of spectroscopic and optical techniques, and density functional theory (DFT) calculations. The chemistry is orchestrated by the activity of a novel organic photosensitiser, that governs the key energy-transfer process with diverse types of sulfonylimine precursors. The formed radical intermediates are intercepted by the ABB through an RSR process, leading access to azetidines in high chemical yields in a single operation. The power and generality of this photocatalytic method is demonstrated for various azetidine targets, including derivatives of Celecoxib and Naproxen. | Ricardo Rodríguez; Vasco Corti; Lorenzo Rizzo; Stefano Visentini; Marco Bortolus; Mirco Natali; Giorgio Pelosi; Paolo Costa; Luca Dell'Amico; Agnese Amati | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65808ac266c138172982f8a9/original/radical-strain-release-photocatalysis-for-the-synthesis-of-azetidines.pdf |
6509ddb8b927619fe770971f | 10.26434/chemrxiv-2023-8f655 | Understanding the Mechanical Properties of Ultra-Deformable Liposomes Using Molecular Dynamics Simulations | Improving drug delivery efficiency to solid tumor sites is a central challenge in anti-cancer therapeutic research. Our previous experimental study (Guo et al., Nat. Commun. 2018, 9, 130) showed that soft, elastic liposomes had increased uptake and accumulation in cancer cells and tumors in vitro and in vivo respectively, relative to rigid particles. As a first step towards understanding how liposomes’ molecular structure and composition modulates their elasticity, we performed all-atom and coarse-grained classical molecular dynamics (MD) simulations of lipid bilayers formed by mixing a long-tailed, unsaturated phospholipid with a short-tailed saturated lipid with the same head group. The former type of phospholipids considered were 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-dipalmitoleoyl-sn-glycero-3-phosphocholine (termed here DPMPC). The shorter saturated lipids examined were 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC), 1,2-didecanoyl-sn-glycero-3-phosphocholine (DDPC), 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). Several lipid concentrations and surface tensions were considered. Our results show that DOPC or DPMPC systems having 25-35 mol% of the shortest lipids DHPC or DDPC are the least rigid, having area compressibility moduli KA that are ~10% smaller than the values observed in pure DOPC or DPMPC bilayers. These results agree with experimental measurements of the stretching modulus and lysis tension in liposomes with the same compositions. These systems also have lower areas per lipid, form more uneven x-y interfaces with water, the tails of both primary and secondary lipids are more disordered, and the terminal methyl groups in the tails of the long lipids DOPC or DPMPC wriggle more in the vertical direction, compared to pure DOPC or DPMPC bilayers or their mixtures with the longer saturated lipids DLPC or DMPC. These observations confirm our hypothesis that adding increasing concentrations of the short unsaturated lipids DHPC or DDPC to DOPC or DPMPC bilayers, alters lipid packing and thus make the resulting liposomes more elastic and less rigid. No formation of lipid nanodomains was noted in our simulations, and no clear trends were observed in the lateral diffusivities of the lipids as concentration, type of secondary lipid and surface tension were varied. | Jiaming Xu; Vyshnavi Karra; Danielle Large; Debra Auguste; Francisco Hung | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Engineering and Industrial Chemistry; Bioengineering and Biotechnology; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6509ddb8b927619fe770971f/original/understanding-the-mechanical-properties-of-ultra-deformable-liposomes-using-molecular-dynamics-simulations.pdf |
61f1677771868d5a19bf2c79 | 10.26434/chemrxiv-2022-6lpjf | Enzymatic control over reactive intermediates enables direct oxidation of alkenes to carbonyls by a P450 iron-oxo species | The oxidation of alkenes by high-valent iron-oxo active species normally leads to the formation of the corresponding epoxides. Rarely, carbonyl compounds are observed as a side product of the reaction. However, the selective formation of carbonyl compounds from alkenes using iron-oxo species and small molecule catalysts has not yet been achieved. Recently, a new P450-based enzyme (aMOx) has been engineered through laboratory directed evolution to directly oxidize styrenes to their corresponding aldehydes. This transformation uses an enzymatic iron-oxo species as catalytic oxidant and generates aldehydes with high activity and selectivity while suppressing epoxidation.
Here, we combine extensive computational modelling together with experimental mechanistic investigations to study the reaction mechanism and unravel the molecular basis behind the selectivity achieved by the laboratory evolved aMOx enzyme. We found that alkene epoxidation and carbonyl formation pathways diverge from a common covalent radical intermediate generated after the first C–O bond formation. Although both pathways are accessible and very similar in energy, intrinsic dynamic effects determine the strong preference for epoxidation. We discovered that aMOx overrides these intrinsic dynamic preferences by controlling the accessible conformations of the covalent radical intermediate. This disfavors epoxidation and facilitates the formation of a key carbocation intermediate that generates the aldehyde product through a fast 1,2-hydride migration. Computations predicted that the hydride migration is stereoselective due to the conformational control over the intermediate species when formed in the enzyme active site. These predictions were corroborated by experiments using deuterated styrene substrates, which proved that the hydride migration is cis- and enantioselective.
Our results demonstrate that directed evolution tailored a highly specific active site that imposes strong steric control over key fleeting biocatalytic intermediates, which is essential for accessing the carbonyl forming pathway and preventing competing epoxidation. | Jordi Soler; Sebastian Gergel; Stephan Hammer; Marc Garcia-Borràs | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f1677771868d5a19bf2c79/original/enzymatic-control-over-reactive-intermediates-enables-direct-oxidation-of-alkenes-to-carbonyls-by-a-p450-iron-oxo-species.pdf |
6765885c6dde43c908cb2bb3 | 10.26434/chemrxiv-2024-t8znn | First-Principles Molecular Dynamics with
Potential and Charge Fluctuations Applied to
Au(111) in Alkaline Solutions
| Electrified solid-liquid interfaces play a crucial role in energy conversion, storage,
photoconversion, sensors, and corrosion processes. While computational chemistry simulations can provide detailed insight into reaction mechanisms, aligning experimental
and simulation results remains a significant challenge. In this work, we introduce the
FDT-SJM method for ab-initio molecular dynamics simulations under potential control,
where the electrode charge fluctuates around an average value following the fluctuationdissipation theorem (FDT), and electrode charges are screened by the solvated jellium
method (SJM). The FDT-SJM is developed in GPAW, a Python-based, open-source
DFT code. We validate this approach by simulating the Au(111) interface in pure water, KOH, LiOH, Li, and K solutions at several electrode potentials. We analyze water
reorientation in response to changes in the electrode surface charge and demonstrate
that the method enables the estimation of interface capacitance and the potential of
zero charge, yielding values consistent with experimental data. | Renata Sechi; Georg Kastlunger; Arghya Bhowmik; Heine Anton Hansen | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Electrochemistry - Mechanisms, Theory & Study; Interfaces | CC BY 4.0 | CHEMRXIV | 2024-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6765885c6dde43c908cb2bb3/original/first-principles-molecular-dynamics-with-potential-and-charge-fluctuations-applied-to-au-111-in-alkaline-solutions.pdf |
60d448e8926ad00c6e02e5c3 | 10.26434/chemrxiv-2021-w7n78 | Towards Accurate Description of Chemical Reaction Energetics by Using Variational Quantum Eigensolver: A Case Study of the C2v Quasi-Reaction Pathway of Beryllium Insertion to H2 Molecule | We have examined the performance of variational quantum eigensolver along the quasi-reaction pathway of Be insertion to H2 molecule, in which avoided crossing occurs at the transition structure. Numerical simulations revealed that the multireference unitary coupled cluster with partially generalized singles and doubles (MR-UCCpGSD) is a powerful tool to describe the electronic structure of strongly correlated systems. | Kenji Sugisaki; Takumi Kato; Yuichiro Minato; Koji Okuwaki; Yuji Mochizuki | Theoretical and Computational Chemistry; Quantum Computing | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d448e8926ad00c6e02e5c3/original/towards-accurate-description-of-chemical-reaction-energetics-by-using-variational-quantum-eigensolver-a-case-study-of-the-c2v-quasi-reaction-pathway-of-beryllium-insertion-to-h2-molecule.pdf |
60ddb3977d46cdc9f3faf989 | 10.26434/chemrxiv-2021-t1zn7 | Ambient Conversion of Carbon Dioxide into Liquid Fuel by a Heterogeneous Synergetic Dual Single-Atom Catalyst | Ambient conversion of carbon dioxide into various liquid fuels or chemicals is a potential economical solution for reducing CO2 emissions, which may be responsible for recent climate change. Here, we report a highly active dual single-Pd-atom catalyst for ambient conversion of CO2 to formic acid using a step-by-step catalyst design strategy by the density functional theory (DFT) method. The theoretically predicted catalyst is synthesized experimentally and verified to capture a significant amount of CO2 (5.05 mmol/g, 273 K), and it can efficiently convert CO2 to formic acid under ambient conditions (30 °C, 1 bar) with a turnover frequency (TOF) as high as 13.46 h-1, which is the first such report in the field of heterogeneous catalysts. Two major factors contributing to this extraordinary catalytic activity include a pore enrichment effect of the microporous structures of the covalent triazine framework and a ternary synergetic effect among two neighbouring Pd atoms and rich nitrogen environment. Our work may aid the development of heterogeneous catalysts to produce other commonly used fuels from CO2 under ambient conditions. | Guoqing Ren; Jikai Sun; Shengliang Zhai; Li Yang; Tie Yu; Lei Sun; Weiqiao Deng | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60ddb3977d46cdc9f3faf989/original/ambient-conversion-of-carbon-dioxide-into-liquid-fuel-by-a-heterogeneous-synergetic-dual-single-atom-catalyst.pdf |
669138da5101a2ffa83198f2 | 10.26434/chemrxiv-2024-56rks | NaturAr, a collaborative, open source, database of natural products from Argentinian biodiversity for drug discovery and bioprospecting | Since the early stages of modern medicine, natural products have been a source of inspiration for the development of bioactive compounds. Around half of approved small molecule drugs trace their origins to natural products or their derivatives, highlighting the importance of their correct classification and identification. The information generated by the experimental groups is not usually unified, and is available only in publications or general databases, where the compounds are not linked to their natural sources. To address this need, numerous natural product databases specific to distinct geographic regions have emerged. In this work, we introduce NaturAr, a natural products database dedicated to the cataloging of the rich biodiversity of Argentina. At the time of submission, 228 papers were reviewed, leading to a database of more than 1200 compounds from all across the country. A distinctive quality of this database is its collaborative and open-source framework, which promotes contributions from the research community. NaturAr is freely available online at https://naturar.quimica.unlp.edu.ar. | Leandro Martínez-Heredia; Patricia Quispe; Julián Fernández; Martin Lavecchia | Organic Chemistry; Natural Products | CC BY NC 4.0 | CHEMRXIV | 2024-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669138da5101a2ffa83198f2/original/natur-ar-a-collaborative-open-source-database-of-natural-products-from-argentinian-biodiversity-for-drug-discovery-and-bioprospecting.pdf |
670435d751558a15ef66d508 | 10.26434/chemrxiv-2024-7vs8f | Evaluating Cost and Accuracy in Two-Point Complete Basis Set Extrapolation Schemes Using Efficient Diffuse Basis Sets | A widely used procedure for obtaining the complete-basis set (CBS) limit of an electronic structure method is extrapolating results from a sequence of correlation-consistent basis sets. A recent study by Xi et al. trained two-point extrapolation schemes against a new extensive dataset using aug-cc-pVXZ (X = D, T, Q, 5, and 6) basis set pairs. Their results were very promising, providing a significant improvement over previous two-point extrapolation schemes. The present work shows that equally good results can be obtained at lower cost by using the smaller jun-cc-pVXZ or jul-cc-pVXZ basis sets, which contain fewer diffuse functions. Using the smaller jun and jul basis sets to extrapolate to the CBS limit provides a good compromise between accuracy and computational cost. | Aiswarya M. Parameswaran; Antonio Fernández-Ramos; Donald G. Truhlar | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670435d751558a15ef66d508/original/evaluating-cost-and-accuracy-in-two-point-complete-basis-set-extrapolation-schemes-using-efficient-diffuse-basis-sets.pdf |
6710a810cec5d6c14263d351 | 10.26434/chemrxiv-2024-mncv6 | C–S/C–Br metathesis enabled by an Au–Pd alloy nanoparticle catalyst | Metathesis via C–S bond oxidative addition and reductive elimination has recently witnessed considerable development as a functionalization of ubiquitous sulfur-containing molecules with the molecular frameworks intact. Despite the synthetic utilities, C–S/C–Br metathesis has not been reported so far because of the difficulties in managing both reversible C–Br oxidative addition/reductive elimination and sterically sensitive transmetalation between the oxidative adducts. Herein, we report C–S/C–Br metathesis between thioethers and bromoarenes enabled by an Au–Pd alloy nanoparticle catalyst with a high Au/Pd ratio via utilization of unique multiple adsorption/active sites. This catalytic system was applicable to different thioethers and bromoarenes to afford both metathesis products in high yields, and late-stage bromination of C–S bonds in various thioethers possessing bioactive structures and depolymerization of polyphenylene sulfide to 1,4-dibromobenzene were also demonstrated. | Takehiro Matsuyama; Takafumi Yatabe; Kazuya Yamaguchi | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6710a810cec5d6c14263d351/original/c-s-c-br-metathesis-enabled-by-an-au-pd-alloy-nanoparticle-catalyst.pdf |
60c746e9337d6c049ce27254 | 10.26434/chemrxiv.11431878.v1 | Reaction-Diffusion Systems: Self-Balancing Diffusion and the Use of the Extent of Reaction as a Descriptor of Reaction Kinetics | Self-balancing diffusion is a concept which restricts the introduction of extents of reactions. This concept is analyzed in detail for mass- and molar-based balances of reaction-diffusion mixtures, in relation to non-self-balancing cases, and with respect to its practical consequences. A note on a recent generalization of the concept of reaction and diffusion extents is also included.<br /> | Miloslav Pekař | Chemical Kinetics; Thermodynamics (Physical Chem.); Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746e9337d6c049ce27254/original/reaction-diffusion-systems-self-balancing-diffusion-and-the-use-of-the-extent-of-reaction-as-a-descriptor-of-reaction-kinetics.pdf |
67682645fa469535b974f623 | 10.26434/chemrxiv-2024-8b0gb | Polysialosides outperform sulfated analogs for the inhibition of SARS-CoV-2 | Both polysialosides and polysulfates are known to interact with the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. However, a comprehensive site by site analysis of their binding affinities and potential synergistic antiviral effects have not been performed. Here, we report on the synthesis of polysialosides with nanomolar binding affinities to spike proteins of SARS-CoV-2 in solution using microscale thermophoresis (MST). The dendritic polyglycerol based polysialosides dPG500(SA)0.55 and dPG500(SA)0.25, with a dissociation constant Kd of 4.78 nM and 10.85 nM, respectively, bind ~500 times stronger than the high density polysulfated analog dPG500(OSO3Na)0.55, to intact SARS-CoV-2 virus particles or isolated spike protein. In fact, the presence of sulfate groups in a heteromultivalent compound dPG500(SA)0.20(OSO3Na)0.20 weakens the binding to spike proteins. A polycarboxylated analog does not bind to SARS-CoV-2, ruling out that the interaction of polysialoside is simply driven by electrostatic interactions. Furthermore, we found potent nanomolar binding of dPG500(SA)0.55 to SARS-CoV-2 variant B.1.617 (Delta) and B.1.1.529 (Omicron) RBD. Using explicit-solvent all-atom molecular dynamics (MD) simulations and docking studies, we obtain atomistic details on the interaction of different functional groups with the SARS-CoV-2 RBD and their binding affinities. Our data support the conclusion that sialosides interact stronger with RBD than sulfates. Notably, our most affine binder dPG500(SA)0.55 inhibits SARS-CoV-2 (WT, D614G) replication up to 98.6% at low nanomolar concentrations. | Vinod Khatri; Nico Boback; Hassan Abdelwahab; Daniela Niemeyer; Tahlia M. Palmer; Anil Kumar Sahoo; Yannic Kerkhoff; Kai Ludwig; Dilara Balci; Jakob Trimpert; Rainer Haag; Tatyana L. Povolotsky; Roland R. Netz; Christian Drosten; Daniel C. Lauster; Sumati Bhatia | Materials Science; Polymer Science; Nanoscience; Biocompatible Materials; Biopolymers; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67682645fa469535b974f623/original/polysialosides-outperform-sulfated-analogs-for-the-inhibition-of-sars-co-v-2.pdf |
62a0a7938f92d941b949cb3a | 10.26434/chemrxiv-2022-7668b | Can a Finite Chain of Hydrogen Cyanide Molecules Model a Crystal? | When calculating structural or spectroscopic properties of molecular crystals, the question arises whether it is sufficient to simulate only a single molecule or a small molecular cluster or whether the simulation of the entire crystal is indispensable. In this work we juxtapose calculations on the high-pressure structural properties of the (periodic) HCN crystal and chains of HCN molecules of finite length. We find that, in most cases, the behavior of the crystal can be reproduced by computational methods simulating only around 15 molecules. The pressure-induced lengthening of the C-H bond in HCN found in calculations on both the periodic and finite material are explained in terms of orbital interaction. Our results pave the way for a more thorough understanding of high-pressure structural properties of materials and give incentives for the design of materials that expand under pressure. In addition, they shed light on the complementarity between calculations on periodic materials and systems of finite size. | Chieh-Min Hsieh; Björn Grabbet; Felix Zeller; Sanna Benter; Tarek Scheele; Norman Sieroka; Tim Neudecker | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a0a7938f92d941b949cb3a/original/can-a-finite-chain-of-hydrogen-cyanide-molecules-model-a-crystal.pdf |
6489d6d7be16ad5c57ecd765 | 10.26434/chemrxiv-2023-68b5p | Thermal decomposition of 1-ethyl-3-methylimidazolium acetate | To realize the potential applications of ionic liquids as working fluids and solvents one should have knowledge about their long-term stability, which depends on their thermally initiated decomposition. However, the possible decomposition pathways are not yet known accurately. 1-Ethyl-3-methylimidazolium acetate ([C2Mim][OAc]) is widely studied and shows potential in cellulose dissolution. In this study, we investigate possible [C2Mim][OAc] decomposition pathways by combining decomposition experiments and ab initio rate constant computations. Both approaches yield activation energies around 135 kJ·mol-1, which significantly deviate from earlier TGA measurements with open surface yielding 100 - 110 kJ·mol-1 and are probably affected by evaporation. Our study uses an improved TGA measurement protocol with a sealed pan with a tiny hole that fosters measurement of the actual chemical process leading to mass loss. Ab initio computations of this study comprise vapor-liquid equilibria of reactants and products as well as forward and reverse reaction rate constants in the gas and liquid phase. Calculations for the gas phase closely match a first-order analysis of the experiments, but calculations for the liquid phase strongly depend on the quality of solvation modeling. The computations indicate that the SN2 pathway with an activation energy of 140 kJ·mol-1 dominates thermal decomposition of [C2Mim][OAc]. | Dzmitry Zaitsau; Maxim Papusha; Wassja Kopp; Kai Leonhard | Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry; Analytical Apparatus; Chemical Kinetics; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6489d6d7be16ad5c57ecd765/original/thermal-decomposition-of-1-ethyl-3-methylimidazolium-acetate.pdf |
678aa33e81d2151a028c9819 | 10.26434/chemrxiv-2025-m6f1l | Substrate- and Reagent-Controlled Dimerization of Vinyl para-Quinone Methides | Substrate and reagent-controlled dimerization of vinyl para-quinone methides (VPQMs) is reported. When subjected to Brønsted acidic conditions, VPQM dimerization occurs via a formal 1,8-addition to provide griffipavixanthone (GPX)-type congeners. Under optimized Lewis acidic conditions, a change in regioselectivity affords, limonene-containing dimers by a 1,6-addition/cyclization process. This divergent reactivity has been explored on several substrates of differing complexity, providing access to analogues of the natural product griffipavixanthone (GPX) as well as a range of novel, substituted limonene dimers. | John Porco; Ryan Baker; Kyle Reichl; Michael Smith; Michael Ricca; Margaret Ann Mickelberg | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678aa33e81d2151a028c9819/original/substrate-and-reagent-controlled-dimerization-of-vinyl-para-quinone-methides.pdf |
60c7467bbdbb895925a38bfe | 10.26434/chemrxiv.11336993.v1 | Toward Thermodynamically Stable Triplet Carbenes | <p>In
sharp contrast to the widely studied and applied stable singlet carbenes, only
several kinetically persistent triplet carbenes have been studied, and thermodynamically
stable triplet carbenes are much less developed. With the Gibbs free energy of
C-H bond insertion into methane as a probe, DFT calculations were employed to
examine a variety of candidate molecules for stable triplet carbenes. Guided by
these calculations, some molecules with significant stability against C-H
insertion were designed by fine tuning of geometry and electronic structures.
These compounds might be potential candidates for experimental development of
stable triplet carbenes.</p> | Yumiao Ma | Physical Organic Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7467bbdbb895925a38bfe/original/toward-thermodynamically-stable-triplet-carbenes.pdf |
60c73d4fee301cfe5cc78518 | 10.26434/chemrxiv.5594314.v1 | Photodissociation Mass Spectrometry Accurately Localizes Sites of Backbone Deuteration in Peptides | <div>
<p>Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is
now positioned as a routinely used technique to inform on protein structure,
dynamics, and interactions. Localizing the deuterium content on a single
residue basis increases the spatial resolution of this technique enabling
detailed structural analysis. Here we investigate the use of ultraviolet
photodissociation (UVPD) at 213 nm to localize incorporated deuterium with
single residue resolution in HDX-MS experiments. Using a selectively labeled
peptide, we show that UVPD occurs without H/D scrambling as the peptide probe
accurately retains its solution-phase deuterium labeling pattern. Our results
indicate that UVPD provides an attractive alternative to electron mediated
dissociation to increase the spatial resolution of the HDX-MS experiment,
combining high fragmentation efficiency, high fragment ion diversity, and low
charge-state dependency.</p>
</div> | Ulrik Hvid Mistarz; Bruno Bellina; Pernille F. Jensen; Jeffery M. Brown; Perdita E. Barran; Kasper D. Rand | Analytical Chemistry - General; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2017-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d4fee301cfe5cc78518/original/photodissociation-mass-spectrometry-accurately-localizes-sites-of-backbone-deuteration-in-peptides.pdf |
60c74521842e65abefdb25aa | 10.26434/chemrxiv.9974246.v1 | Electrochemical Reduction of Homo– and Hetero–tri(aryl)borohydrides | <p>
Authentic
terminal homo–
and hetero–tri(aryl)borohydrides
of the form [HB(C<sub>6</sub>F<sub>5</sub>)<sub><i>x</i></sub>{<i>m</i>,<i>m</i>–(CF<sub>3</sub>)<sub>2</sub>C<sub>6</sub>H<sub>3</sub>}<sub><i>y</i></sub>(C<sub>6</sub>Cl<sub>5</sub>)<sub><i>z</i></sub>]<sup>−</sup><sup></sup>
have been synthesised by reaction of their parent borane with a
hydride source; their electrochemical properties have been studied,
together
with a computational investigation
using density functional theory (DFT).
The three of these compounds incorporating at least two
pentachlorophenyl rings have been identified as, upon electrochemical
oxidation, regenerating their parent borane, one
of the essential steps (together with rapid cleavage under mild
conditions of H<sub>2</sub>
together with an appropriate Lewis base), in implementing the
electrochemically coupled – frustrated Lewis pair concept. The
resulting mechanism upon oxidation is supported by modelling the
cyclic voltammetry data obtained. The
DFT studies have allowed for the structures of these compounds to be
assessed, along with quantifying their hydride ion affinities (HIAs).</p> | Robin Blagg; Elliot Lawrence; Gregory Wildgoose | Electrochemistry; Frustrated Lewis Pairs; Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74521842e65abefdb25aa/original/electrochemical-reduction-of-homo-and-hetero-tri-aryl-borohydrides.pdf |
60c742ab0f50db4fab395d49 | 10.26434/chemrxiv.8259317.v2 | Enhanced Diffusion of Molecular Catalysts Is Due to Convection | Intriguing reports of enhanced diffusion in enzymes and molecular catalysts have spurred significant interest in experimental and theoretical investigations of this phenomenon, with mechanistic understanding the subject of ongoing and lively debate. Here we use time-resolved diffusion NMR methods to measure the diffusion coefficients of small molecule species involved in chemical reactions with high temporal resolution. We show the enhanced diffusion of small molecules cannot be explained by reaction velocity, and that apparent measurements of enhanced diffusion by small molecules appear to be caused by bulk fluid flow processes such as convection.<br /> | Thomas MacDonald; William S. Price; R. Dean Astumian; Jonathon Beves | Physical Organic Chemistry; Supramolecular Chemistry (Org.); Physical and Chemical Properties; Solution Chemistry; Spectroscopy (Physical Chem.); Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742ab0f50db4fab395d49/original/enhanced-diffusion-of-molecular-catalysts-is-due-to-convection.pdf |
60d62d4667d4914b1295f1ec | 10.26434/chemrxiv-2021-xptgq | Ultrafast Photochemistry of a Molybdenum Carbonyl-Nitrosyl Complex with a Triazacyclononane Coligand | Transition metal complexes capable of releasing small-molecule messengers such as carbon monoxide and nitric oxide upon photoactivation are versatile tools in various fields of chemistry and biology. In this work, we report on the ultrafast photochemistry of [Mo(CO)2(NO)(iPr3tacn)]PF6 (iPr3tacn = 1,4,7-triisopropyl-1,4,7-triazacyclononane), which was synthesized and subsequently characterized in continuous illumination studies and with femtosecond UV-pump/UV-probe and UV-pump/MIR-probe spectroscopy, as well as with stationary calculations. The experimental and theoretical results demonstrate that while the photodissociation of one of the two CO ligands upon UV excitation can be inferred both on an ultrafast timescale as well as under exposure times of several minutes, no evidence of NO release is observed under the same conditions. The binding mode of the diatomic ligands is impacted by the electronic excitation, and excited molecules are observed on a timescale of tens of picoseconds before CO is released from the coordination sphere. Furthermore, based on calculated potential energy scans, we suggest that photolysis of NO could be possible after a subsequent excitation of an electronically excited state with a second laser pulse, or by accessing low-lying excited states that otherwise cannot be directly excited by light. | Niklas Gessner; Anna K. Bäck; Johannes Knorr; Christoph Nagel; Philipp Marquetand; Ulrich Schatzschneider; Leticia González; Patrick Nuernberger | Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Transition Metal Complexes (Inorg.); Theory - Computational; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d62d4667d4914b1295f1ec/original/ultrafast-photochemistry-of-a-molybdenum-carbonyl-nitrosyl-complex-with-a-triazacyclononane-coligand.pdf |
63ced49010cb6a57fce3bbce | 10.26434/chemrxiv-2023-cql2m-v2 | Exploring Eutectic Mixing of Quinones for
Engineering High Energy-Density Electrolytes | Eutectic electrolytes can attain high concentrations of redox-active species, offering a path towards high energy density redox flow batteries. Here we introduce a new entropically-driven eutectic mixing approach using organic small molecules. By mixing chemically similar redox-active species, we engineer highly concentrated, low viscosity liquids composed almost entirely of redox active molecules. Using quinones as a model system, we discover a ternary benzoquinone eutectic mixture and a binary naphthoquinone eutectic mixture which have theoretical redox-active electron concentrations of 16.8 and 8.8 M e−, respectively. We investigate compatibility with protic supporting electrolytes and quantify ionic conductivity and viscosity of quinone eutectic electrolytes across multiple states of charge. A binary naphthoquinone eutectic electrolyte with a protic ionic liquid supporting electrolyte (7.1 M e−, theoretical volumetric capacity 188 Ah L−1) achieves a volumetric capacity of 49 Ah L−1 in symmetric static cell cycling. These preliminary results suggest that entropy-driven eutectic mixing is a promising strategy for developing high energy density flow battery electrolytes. | Emily Penn; Antonio Baclig; Devi Ganapathi; William Chueh | Materials Science; Energy; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ced49010cb6a57fce3bbce/original/exploring-eutectic-mixing-of-quinones-for-engineering-high-energy-density-electrolytes.pdf |
63bc686f5ad3ef3f299266a0 | 10.26434/chemrxiv-2023-6qxhb | Unveiling the Mechanical and Electrochemical Evolution of Nano Silicon Composite Anodes in Sulfide based All-solid-state Batteries | The utilization of silicon (Si) anodes in all-solid-state lithium batteries (ASLBs) provides the potential for high energy density. However, the compatibility of sulfide solid-state electrolytes (SEs) with Si and carbon is often questioned due to potential decomposition. To investigate this, operando X-ray absorption near-edge structure (XANES) spectroscopy, ex-situ scanning electron microscopy (SEM) and ex-situ X-ray nano-tomography (XnT) were utilized to study the chemistry and structure evolution of nano Si composite anodes. Results from XANES demonstrated a partial decomposition of SEs during the first lithiation stage, which was further accelerated by the presence of carbon. But the performance of first three cycles in Si-SE-C was stable, which proved the generated media is ionically conductive. XnT and SEM results showed that the addition of SEs and carbon improved the structural stability of the anode with fewer pores and voids. A chemo-elasto-plastic model revealed that SEs and carbon buffered the volume expansion of Si, thus enhancing mechanical stability. The balance between the pros and cons of SEs and carbon in enhancing reaction kinetics and structural stability enabled the Si composite anode to demonstrate the highest Si utilization with higher specific capacities and better rate than pure Si and Si composite anodes with only SEs. | Daxian Cao; Tongtai Ji; Avtar Singh; Seongmin Bak; Yonghua Du; Xianghui Xiao; Hongyi Xu; Juner Zhu; Hongli Zhu | Materials Science; Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bc686f5ad3ef3f299266a0/original/unveiling-the-mechanical-and-electrochemical-evolution-of-nano-silicon-composite-anodes-in-sulfide-based-all-solid-state-batteries.pdf |
636fac5d92453866038b0e66 | 10.26434/chemrxiv-2022-sgszv | An oligomer approach for blue thermally activated delayed fluorescent emitters based on twisted donor-acceptor units | The development of efficient blue donor-acceptor thermally activated delayed fluorescence (TADF) emitters remains a challenge. To enhance the efficiency of TADF-related processes of the emitter, we targeted a molecular design that would introduce a large number of intermediate triplet states between the lowest energy excited triplet (T1) and singlet (S1) excited states. Here, we introduce an oligomer approach using repetitive donor-acceptor units to gradually increase the number of quasi-degenerate states. In our design, benzonitrile (BN) moieties were selected as acceptors that are connected together via the amine donors, acting as bridges to adjacent BN acceptors. To preserve the photoluminescence emission wavelength across the series, we employed a design based on an ortho substitution pattern of the donors about the BN acceptor that induces a highly twisted conformation of the emitters, limiting the conjugation. Via a systematic photophysical study we show that increasing the oligomer size allows for enhancement of the intersystem crossing and reverse intersystem crossing rates. We attribute the increasing intersystem crossing rate to the increasing number of intermediate triplet states along the series, confirmed by the Time-Dependent Density Functional Theory. Overall, we report an approach to enhance the efficiency of TADF-related processes without changing the blue photoluminescence colour. | Eimantas Duda; Subeesh Madayanad Suresh; David Hall; Sergey Bagnich; Rishabh Saxena; David Cordes; Alexandra Slawin; David Beljonne; Yoann Olivier; Anna Köhler; Eli Zysman-Colman | Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636fac5d92453866038b0e66/original/an-oligomer-approach-for-blue-thermally-activated-delayed-fluorescent-emitters-based-on-twisted-donor-acceptor-units.pdf |
60c747c1ee301c272bc79758 | 10.26434/chemrxiv.11763255.v1 | DP4-AI Automated NMR Data Analysis: Straight from Spectrometer to Structure | <div>
<p>A robust system for automatic processing and
assignment of raw 13C and 1H NMR data DP4-AI has been developed and integrated
into our computational organic molecule structure elucidation workflow.
Starting from a molecular structure with undefined stereochemistry or other
structural uncertainty, this system allows for completely automated structure
elucidation. Methods for NMR peak picking using objective model selection and
algorithms for matching the calculated 13C and 1H NMR shifts to peaks in noisy
experimental NMR data were developed. DP4-AI achieved a 60-fold increase in
processing speed, and near-elimination of the need for scientist time, when
rigorously evaluated used a challenging test set of molecules. DP4-AI
represents a leap forward in NMR structure elucidation and a step-change in the
functionality of DP4. It enables high-throughput analyses of databases and
large sets of molecules, which were previously impossible, and paves the way
for the discovery of new structural information through machine learning. This
new functionality has been coupled with an intuitive GUI and is available as
open-source software at https://github.com/KristapsE/DP4-AI.</p>
</div>
<br /> | Alexander Howarth; Kristaps Ermanis; Jonathan Goodman | Natural Products; Organic Synthesis and Reactions; Spectroscopy (Anal. Chem.); Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747c1ee301c272bc79758/original/dp4-ai-automated-nmr-data-analysis-straight-from-spectrometer-to-structure.pdf |
60c75030bb8c1a0dd23dba90 | 10.26434/chemrxiv.13003010.v1 | Description of Two-particle One-hole Electronic Resonances using Orbital Stabilization Methods | Two-particle one-hole (2p-1h) resonances are elusive to accurate characterization, their decay to the neutral state being a two-electron process.<br />Although in limited cases single reference methods can be used, a proper description of a 2p-1h resonant state entails a multi-configurational treatment of the reference wavefunction. In this work we test the performance of the orbital stabilization method to characterize the 2p-1h resonances found in water and benzene. We employ a set of two multi-reference approaches, namely the restricted active space self-consistent field and multi-reference configuration interaction, as well as, the single reference method, equation of motion for electron attachment coupled-cluster with singles and doubles, in the case of benzene.<br />We further explore the resonant channel mixing in benzene between the B2g shape resonance and 2p-1h resonance, a phenomenon which has been mentioned quite often in experimental studies. | Mushir Thodika; Nathan Mackouse; Spiridoula Matsika | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75030bb8c1a0dd23dba90/original/description-of-two-particle-one-hole-electronic-resonances-using-orbital-stabilization-methods.pdf |
6376399a77ffe7ca38f1f775 | 10.26434/chemrxiv-2022-92418 | Alkyne Polymers from Stable Butatriene Homologues: Controlled Radical Polymerization of Vinylidenecyclopropanes | Controlled polymerization of cumulenic
monomers represents a promising yet underdeveloped strategy towards well-defined alkyne polymers. Here we report a stereoelectronic effect-inspired approach using simple vinylidenecyclopropanes (VDCPs) as butatriene homologues in controlled radical ring-opening polymerizations. While being thermally stable, VDCPs mimic butatrienes via conjugation of the
cyclopropane ring. This leads to exclusive terminal-selective propagation that affords a highly structurally regular alkynebased backbone, featuring complete ring-opening and no backbiting regardless of polymerization conditions. | Bin Wu; Qian-Jun Ding; Zheng-Lin Wang; Rong Zhu | Organic Chemistry; Polymer Science; Organic Synthesis and Reactions; Organic Polymers; Polymerization (Polymers) | CC BY NC 4.0 | CHEMRXIV | 2022-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6376399a77ffe7ca38f1f775/original/alkyne-polymers-from-stable-butatriene-homologues-controlled-radical-polymerization-of-vinylidenecyclopropanes.pdf |
60c7502c702a9b327418bcfc | 10.26434/chemrxiv.12999938.v1 | Understanding Ring Puckering in Small Molecules and Cyclic Peptides | <div>The geometry of a molecule plays a significant role in determining its physical and chemical properties. Despite its importance, there are relatively few studies on ring puckering and conformations, often focused on small cycloalkanes, five- and six-membered carbohydrate rings and specific macrocycle families. We lack a general understanding of the puckering preferences of medium-sized rings and macrocycles. To address this, we provide an extensive conformational analysis of a diverse set of rings. We used Cremer-Pople puckering coordinates to study the trends of the ring conformation across a set of 140,000 diverse small molecules, including small rings, macrocycles and cyclic peptides. By standardizing using key atoms, we show that the ring conformations can be classified into relatively few conformational clusters, based on their canonical forms. The number of such canonical clusters increases slowly with ring size. Ring puckering motions, especially pseudo-rotations, are generally restricted, and differ between clusters. More importantly, we propose models to map puckering preferences to torsion space, which allows us to understand the interrelated changes in torsion angles during pseudo-rotation and other puckering motions. Beyond ring puckers, our models also explain the change in substituent orientation upon puckering. In summary, this work provides an improved understanding of general ring puckering preferences, which will in turn accelerate the identification of low energy ring conformations for applications from polymeric materials to drug binding.</div> | Lucian Chan; Geoffrey Hutchison; Garrett Morris | Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7502c702a9b327418bcfc/original/understanding-ring-puckering-in-small-molecules-and-cyclic-peptides.pdf |
675fa7cc7be152b1d018fccf | 10.26434/chemrxiv-2024-g0dxz | Quantum Spin Transport through Blatter’s Di- and Tri-Radicals | A single unpaired electron in an organic molecule residing in the singly occupied molecular orbital (SOMO) renders it an organic radical. It incorporates exchange splitting in the frontier occupied and unoccupied orbitals, separating the alpha and beta-orbitals. This fact enormously impacts the electron transport properties in the organic radicals by promoting spin-polarized current and significantly enhanced conductance as compared to their closed shell counterparts. Exploring these phenomena, several mono-radicals have been investigated by molecular spintronic experiments and theories. In this work, we addressed the impact of increasing number of of radical centers on the transport properties of the multi-radical molecular species by considering di- and tri-radicals based on a stable Blatter’s radical. With the increasing number of radical centers, the number of SOMOs increases. Does the increased number of frontier SOMOs provide larger exchange splitting and better transport properties? Here, we have observed that the spatial distributions of SOMOs and their coupling with electrodes play a decisive role compared to the presence of multiple unpaired electrons in the molecular systems. | Ashima Bajaj; Shahjad Ali; Rishu Khurana; Md. Ehesan Ali | Physical Chemistry; Physical and Chemical Properties; Quantum Mechanics; Transport phenomena (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675fa7cc7be152b1d018fccf/original/quantum-spin-transport-through-blatter-s-di-and-tri-radicals.pdf |
6579b274bec7913d2780fe36 | 10.26434/chemrxiv-2023-qr76m | Reservoir Computing with Colloidal Mixtures of ZnO and Proteinoids | Liquid computers use incompressible fluids for computational processes. Here we present experimental laboratory prototypes of liquid computers using colloids composed of zinc oxide (ZnO) nanoparticles and microspheres containing thermal proteins (proteinoids). The choice of proteinoids is based on their distinctive neuron-like electrical behaviour and their similarity to protocells. In addition, ZnO nanoparticles are chosen for their non-trivial electrical properties. Our research demonstrates the successful extraction of 2-, 4- and 8-bit logic functions in ZnO proteinoid colloids. Our analysis shows that each material has a distinct set of logic functions, and that the complexity of the expressions is directly related to each material present in a mixture. These findings provide a basis for the development of future hybris liquid devices capable of general purpose computing. | Raphael Fortulan; Noushin Raeisi Kheirabadi; Panagiotis Mougkogiannis; Alessandro Chiolerio; Andrew Adamatzky | Materials Science; Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6579b274bec7913d2780fe36/original/reservoir-computing-with-colloidal-mixtures-of-zn-o-and-proteinoids.pdf |
644087e57be842788ded5215 | 10.26434/chemrxiv-2023-kjrcr | Fluorosulfide La2+xSr1−xF4+xS2 with Triple-fluorite Layer Enabling Interstitial Fluoride-ion Conduction | Fluoride-ion conducting solid materials are applicable as solid electrolytes for sensing devices and next generation rechargeable batteries. Most of the previously reported materials have limited to the single-anion compounds such as fluorite-type, tysonite-type, and perovskite-type structures. These are suffered from further improvements by crystal structure modification which derives a paradigm shift in the material tailoring. Fluoride and sulfide ions prefer respective coordination environments because of the different ionic radii and electronegativity. This feature implies that fluorosulfide mixed-anion compounds have potential to form anion-ordering crystal structures with new fluoride-ion conducting layers. Herein, we have found that the fluorosulfide La2+xSr1−xF4+xS2 exhibits fluoride ion conduction. The presence of multiple anions results in the formation of anion-ordering two-dimensional crystal lattice with triple fluorite layers, which cannot be realized for metal fluorides. Sulfide ions in the crystal structure increases the number of interstitial sites of fluoride ions, forming fluoride ion conduction pathway. | Shintaro Tachibana; Chengchao Zhong; Kazuto Ide; Hisatsugu Yamasaki; Takeshi Tojigamori; Hidenori Miki; Takashi Saito; Takashi Kamiyama; Keiji Shimoda; Yuki Orikasa | Materials Science; Inorganic Chemistry; Electrochemistry; Solid State Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644087e57be842788ded5215/original/fluorosulfide-la2-x-sr1-x-f4-x-s2-with-triple-fluorite-layer-enabling-interstitial-fluoride-ion-conduction.pdf |
6591ea689138d23161ea0c93 | 10.26434/chemrxiv-2022-j8rgj-v3 | Multistate, polarizable QM/MM embedding scheme based on the direct reaction field method: Solvatochromic shifts, analytical gradients and optimization of conical intersections in solution | We recently introduced a polarizable embedding scheme based on an integral-exact reformulation of the direct reaction field method (IEDRF) that accounts for differential solvation of ground and excited states in QM/MM simulations. The polarization and dispersion interactions between the quantum-mechanical (QM) and molecular-mechanical (MM) regions are described by the DRF Hamiltonian, while the Pauli repulsion between explicitly treated QM electrons and the implicit electron density around MM atoms is modeled with effective core potentials. A single Hamiltonian is used for all electronic states, so that Born-Oppenheimer states belonging to the same geometry are orthogonal and state crossings are well-defined. In this work, we describe the implementation of the method using graphical processing unit acceleration in TeraChem, where it is combined with multiple electronic structure methods, including Hartree-Fock, Time-dependent Density Functional Theory, and Complete Active Space Self-Consistent Field. In contrast with older implementations of the DRF method, integrals of the polarization operators are evaluated exactly. Expressions for ingredients needed to construct analytical gradients and non-adiabatic coupling vectors are derived and tested by optimizing a conical intersection between two excited states in the presence of a polarizable solvent shell. The method is applied to estimating the solvent shifts of absorption energies of a series of donor-acceptor dyes having low-lying charge-transfer states. Even for a non-polar solvent such as n-hexane, the inclusion of its static polarizability leads to non-negligible shifts that improve the agreement to essentially quantitative levels (0.03 eV) with full-system calculations. Good agreement with the positions of experimental absorption maxima measured in solution is also observed. | Alexander Humeniuk; William J. Glover | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6591ea689138d23161ea0c93/original/multistate-polarizable-qm-mm-embedding-scheme-based-on-the-direct-reaction-field-method-solvatochromic-shifts-analytical-gradients-and-optimization-of-conical-intersections-in-solution.pdf |
627570a343d1f04643226c5e | 10.26434/chemrxiv-2022-93bbn | Cell-level Comparisons between Literature and Industry for Lithium-Sulfur, Lithium-Ion, Lithium-Oxygen, and other Next-Generation Batteries | A set of 212 lithium-sulfur, lithium-ion, lithium-oxygen, and other next-generation experimental battery articles was reviewed, and 15 articles provided at least one cell-level performance metric and/or a complete set of information to calculate it. This subset was compared against 27 commercial technologies in key metrics across various energy storage applications using an Excel database tool. While many high cell-level specific energy batteries are reported in the literature, there is a lack of demonstrated high cell-level specific power batteries for any chemistry. Li-S applications are comparable to Li-ion in terms of specific power and generally have higher specific energy, but also exhibit lower cycle life. In future work and as more articles include cell-level information, this tool can be expanded to include thousands of data points, enabling development of new models via machine learning and other methods to predict relationships between battery structure and performance. Additionally, the tool would become more useful for industry experts to effectively search and sort through the vast amount of knowledge accessible in research journals. | Sterling Baird | Energy; Energy Storage | CC BY 4.0 | CHEMRXIV | 2022-05-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627570a343d1f04643226c5e/original/cell-level-comparisons-between-literature-and-industry-for-lithium-sulfur-lithium-ion-lithium-oxygen-and-other-next-generation-batteries.pdf |
667079f4c9c6a5c07aaccc30 | 10.26434/chemrxiv-2024-22skh | Head Group Dependence and Kinetic Bottlenecks of Gas- phase Thermal PFAS Destruction | Varying and sometimes con[icting temperatures and products have been reported from studies addressing thermal PFAS destruction, often because decomposition pathways are highly dependent on the respective experimental system. Here we applied highest-level coupled cluster calculations to isolate and identify the major processes during thermal PFAS destruction in the gas phase with relevance to incineration, thermal oxidation, and other thermal treatment technologies in which PFAS and their volatile decomposition products desorb into the gas phase. All investigated per[uoroalkyl acids decompose via unimolecular head group loss, either through HF elimination or homolytic bond cleavage as a function of head group type. In contrast, all investigated [uorotelomers undergo initial hydrogen abstraction from the characteristic C2H4 moiety by hydroxyl radicals under representative incineration conditions, followed by radical decomposition. Subsequent formation of per[uoroalkanes including CF4 can then be prevented by supplying su`cient hydrogen donors such as hydrocarbon fuel and water as well as by scavenging released [uorine. This leads to the generation of stable 1H-per[uoroalkanes. While parent PFAS decomposition proceeds at gas-phase temperatures ≤700 °C, carbon-carbon cleavage of 1H-per[uoroalkanes requires up to ~950 °C at 2 seconds gas residence time, making this step the kinetic bottleneck on the way to complete thermal PFAS mineralization. | Jens Blotevogel; Justin Joyce; Olivia Hill; Anthony Rappe | Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667079f4c9c6a5c07aaccc30/original/head-group-dependence-and-kinetic-bottlenecks-of-gas-phase-thermal-pfas-destruction.pdf |
6308ade9f9e99c45988ab9f8 | 10.26434/chemrxiv-2022-b66w2 | Systematic Evaluation of Counterpoise Correction in Density Functional Theory | A widespread belief persists that the Boys-Bernardi function counterpoise (CP) procedure "overcorrects" supramolecular interaction energies for the effects of basis-set superposition error. To the extent that this is true for correlated wave function methods, it is usually an artifact of low-quality basis sets, but the question has not been considered systematically in the context of density functional theory (DFT) where basis-set convergence is
generally less problematic. We present a systematic assessment of the CP procedure for a representative set of functionals and basis sets, considering both benchmark data sets of small dimers as well as larger supramolecular complexes including layered composite polymers with ~150 atoms and ligand--protein models with ~300 atoms. We find that intermolecular interaction energies approaching complete-basis quality can be obtained using only double-zeta basis sets, provided that CP correction is applied. This is less expensive as compared to using triple-zeta basis sets without CP correction. CP-corrected interaction energies are also less sensitive to the presence of diffuse basis functions as compared to uncorrected energies, which is important given that diffuse functions are expensive and often numerically problematic for large systems. Our results upend the conventional wisdom that CP "overcorrects" for basis-set incompleteness. In small basis sets, CP correction is mandatory in order to demonstrate that the results do not rest on error cancellation. | Montgomery Gray; Paige Bowling; John Herbert | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6308ade9f9e99c45988ab9f8/original/systematic-evaluation-of-counterpoise-correction-in-density-functional-theory.pdf |
60c74265842e65261cdb2059 | 10.26434/chemrxiv.8259095.v1 | Optical Spectra in the Condensed Phase: Capturing Anharmonic and Vibronic Features Using Dynamic and Static Approaches | <p>Simulating optical spectra in the condensed phase remains a challenge for theory due to the need to capture spectral signatures arising from anharmonicity and dynamical effects, such as vibronic progressions and their induced asymmetry. As such, numerous simulation methods have been developed that invoke different approximations and vary in their ability to capture different physical regimes. Here we use several models of chromophores in the condensed phase and ab initio molecular dynamics simulations to rigorously assess the applicability of methods to simulate optical absorption spectra. Specifically, we focus on the ensemble scheme, which can address anharmonic potential energy surfaces but relies on the applicability of extreme nuclear-electronic timescale separation; the Franck-Condon method, which includes dynamical effects but only at the harmonic level; as well as the recently introduced ensemble zero-temperature Franck-Condon approach, which straddles these limits. We also devote particular attention to the performance of methods derived from a cumulant expansion of the energy gap fluctuations and test the ability to approximate the requisite time correlation functions using classical dynamics with quantum correction factors. These results provide insights as to when these methods are applicable and able to capture the features of condensed phase spectra qualitatively and, in some cases, quantitatively across a range of regimes.<br /></p> | Tim Zuehlsdorff; Andres Montoya-Castillo; Joseph Anthony Napoli; Thomas E. Markland; Christine Isborn | Dyes and Chromophores; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74265842e65261cdb2059/original/optical-spectra-in-the-condensed-phase-capturing-anharmonic-and-vibronic-features-using-dynamic-and-static-approaches.pdf |
6370238b924538cddb8b9651 | 10.26434/chemrxiv-2022-wf59b | A Review on Self-Assembled Colloidal Nanoparticle Clusters, Patterns and Films: Emerging Synthesis Techniques and Applications | The colloidal synthesis of functional nanoparticles have gained tremendous scientific attention in the last decades. In parallel to these advancements, another rapidly growing area is the self-assembly of these colloidal nanoparticles into greater periodic arrangements. Firstly, the organization of nanoparticles into ordered structures is important for obtaining functional interfaces that extend or even amplify the intrinsic properties of the constituting nanoparticles at a larger scale. The synthesis of large-scale interfaces using complex or intricately designed nanostructures as building blocks, requires highly controllable self-assembly techniques down to the nanoscale. In certain cases, for example, when dealing with plasmonic nanoparticles, the assembly of the nanoparticles further enhances their properties by coupling phenomena. In other cases, the process of self-assembly itself is useful in the final application such as in sensing and drug delivery, amongst others. In view of the growing importance of this field, this review provides a comprehensive overview of the recent developments in the field of self-assembly of different nanostructures and their applications. For clarity, the self-assembled nanostructures are classified into two broad categories: finite clusters/patterns, and infinite films. Different state-of-the-art techniques to obtain these nanostructures are discussed in detail, before discussing the applications where the self-assembly significantly enhances the performance of the process. | Rituraj Borah; Karthick Raj AG; Antony Charles Minja; Sammy Verbruggen | Materials Science; Nanoscience; Aggregates and Assemblies; Multilayers; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6370238b924538cddb8b9651/original/a-review-on-self-assembled-colloidal-nanoparticle-clusters-patterns-and-films-emerging-synthesis-techniques-and-applications.pdf |
60c74d360f50db9c6d396fcc | 10.26434/chemrxiv.12598655.v1 | Modulation of Immune Cell Reactivity with Cis-Binding Siglec Agonist | Primary inflammatory pathologies caused by phagocytes lead to numerous debilitating conditions, including chronic pain and blindness due to age-related macular degeneration. Many members of the sialic acid-binding immunoglobulin-like lectin (Siglec) family are immunoinhibitory receptors whose agonism is an attractive approach to for anti-inflammatory therapy. Here, we show that synthetic lipid-conjugated glycopolypeptides can insert into cell membranes and engage Siglec receptors in cis, leading to inhibitory signaling. Specifically, we construct a cis-binding agonist of Siglec-9 and show that it modulates MAPK signaling in reporter cell lines, immortalized macrophage and microglial cell lines, and primary human macrophages. These cis-binding agonists of Siglecs present a new modality for therapeutic suppression of immune cell reactivity. | Corleone Delaveris; Shannon Chiu; Nicholas Riley; Carolyn Bertozzi | Biochemistry; Bioengineering and Biotechnology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d360f50db9c6d396fcc/original/modulation-of-immune-cell-reactivity-with-cis-binding-siglec-agonist.pdf |
674455c9f9980725cfceaf70 | 10.26434/chemrxiv-2024-2pd87 | Visible light-mediated 1,3-acylative chlorination of cyclopropanes employing benzoyl chloride as bifunctional reagents in NHC catalysis | Chlorine-substituted ketones are essential intermediates in organic synthesis and commercially available benzoyl chloride participates in acyl chlorination, which provides an atom-and-step economic route for their synthesis. While atom-transfer radical addition (ATRA) is an efficient method for 1,2-acyl chlorination, achieving efficient 1,3-acyl chlorination remains a significant challenge. In this work, we developed an NHC/PC dual-catalyzed system for the 1,3-acyl chlorination of cyclopropanes using benzoyl chloride as a bifunctional reagent. Furthermore, it enables the synthesis of acyl-cyclopropanes featuring quaternary carbon centers through the nucleophilic annulation process. The practical utility of the approach is demonstrated by large-scale synthesis, product derivatization, and the preparation of analogs to antipsychotics such as haloperidol and melperone. | Mingrui Li; Xiao Song; Xueyun Lu; Jiuli Xia; Guangfan Zheng; Qian Zhang | Organic Chemistry; Photochemistry (Org.) | CC BY NC 4.0 | CHEMRXIV | 2024-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674455c9f9980725cfceaf70/original/visible-light-mediated-1-3-acylative-chlorination-of-cyclopropanes-employing-benzoyl-chloride-as-bifunctional-reagents-in-nhc-catalysis.pdf |
65c3ac359138d231619ff143 | 10.26434/chemrxiv-2024-3lt8b | Synthesis and anti-Chagas activity profile of a novel redox-active lead 3-benzylmenadione revealed by high-content imaging | Chagas’ disease or American trypanosomiasis is a neglected tropical disease, which is a top priority target of the World Health Organization. The disease, caused by the protozoan Trypanosoma cruzi, is endemic in Latin America and has spread around the globe due to human migration. There are multiple transmission routes, from vectorial, congenital, oral to iatrogenic. Less than 1% of patients have access to treatment, limited to two old redox-active drugs, but these have poor pharmacokinetics and severe adverse effects. Hence, the priorities for the next steps of R&D include i) the discovery of new drugs/chemical classes for clinical trials; ii) filling the pipeline with drug candidates that have new mechanisms of action, iii) the need for more research and access to new chemical entities. In the present work, we first identified a hit (4a), from a library of 3-benzylmenadiones, that had potent anti-T.cruzi activity. We then designed a synthetic strategy to build a library of 49 3-(4-mono-amino)benzylmenadione derivatives, via reductive amination to obtain diazacyclic benz(o)ylmenadiones. Among them, we identified an anti-amastigote “early lead” 11b (henceforth called cruzidione) by high content imaging with optimized pharmacokinetic properties and better specificity. Studies in a yeast model revealed that a cruzidione metabolite, the 3-benzoylmenadione (cruzidione oxide), enters redox-cycling with the NADH-dehydrogenase, generating reactive oxygen species, as hypothesized for the early hit (4a). | Nathan Trometer; Jeremy Pecourneau; Liwen Feng; José A. Navarro-Huerta; Danielle Lazarin-Bidóia; Sueli de Oliveira Silva Lautenschlager; Louis Maes; Amanda F. Francisco; John M. Kelly; Brigitte Meunier; Monica Cal; Pascal Mäser; Marcel Kaiser; Elisabeth Davioud-Charvet | Biological and Medicinal Chemistry; Cell and Molecular Biology; Microbiology | CC BY 4.0 | CHEMRXIV | 2024-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c3ac359138d231619ff143/original/synthesis-and-anti-chagas-activity-profile-of-a-novel-redox-active-lead-3-benzylmenadione-revealed-by-high-content-imaging.pdf |
660762589138d23161b764d6 | 10.26434/chemrxiv-2024-dqvbp | Insights into controlling bacterial cellulose nanofiber film properties through balancing thermodynamic interactions and colloidal dynamics | In recent years, nanocellulose has emerged as a sustainable and environmentally friendly alternative to traditional petroleum-derived structural polymers. Sourced either from plants, algae, or bacteria, nanocellulose can be processed into colloid, gel, film and fiber forms. However, the required fundamental understanding of process parameters that govern the morphology and structure-property relationships of nanocellulose systems, from colloidal suspensions to bulk materials, has not been developed and generalized for all forms of cellulose. This further hinders the more widespread adoption of this biopolymer in applications. Our study investigates the dispersion of cellulose nanofibers (CNFs) produced by a bacterial-yeast co-culture, in solvents, highlighting the role of thermodynamic interactions in influencing their colloidal behavior. By adjusting Hansen solubility parameters, we controlled the thermodynamic relationship between CNFs and solvents across various concentrations, studying the dilute to semi-dilute regimes. Rheological measurements revealed that the threshold at which a concentration-based regime transition occurs is distinctly solvent-dependent. Complementing rheological analysis with small angle X-ray scattering and zeta potential measurements, our findings reveal that enhancing CNF-solvent interactions increases excluded volume in the dilute regime, emphasizing the importance of the balance between fiber-fiber and fiber-solvent interactions. Moreover, we investigated the transition from colloidal to solid state by creating films from dispersions with varying interaction parameters in semi-dilute regimes. Through mechanical testing and scanning electron microscopy imaging of the fracture surfaces, we highlight the significance of electrokinetic effects in such transitions, as dispersions with higher electrokinetic stabilization gave rise to stronger and tougher films despite having less favorable thermodynamic interaction parameters. Our work provides insights into the thermodynamic and electrokinetic interplay that governs bacterial CNF dispersion, offering a foundation for future application and a deeper understanding of nanocellulose's colloidal and structure-property relationships. | Aban Mandal; Kuotian Liao; Hareesh Iyer; Junhao Lin; Xinqi Li; Shuai Zhang; Eleftheria Roumeli | Materials Science; Chemical Engineering and Industrial Chemistry; Biological Materials; Fibers; Materials Processing | CC BY NC 4.0 | CHEMRXIV | 2024-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660762589138d23161b764d6/original/insights-into-controlling-bacterial-cellulose-nanofiber-film-properties-through-balancing-thermodynamic-interactions-and-colloidal-dynamics.pdf |
628ee4cf6b12b649cf7fc3c6 | 10.26434/chemrxiv-2022-7jzv6 | Pitfalls of quantifying intersystem crossing rates in singlet-fission chromophore solutions | Singlet fission (SF), a process that produces two triplet excitons from one singlet exciton, has attracted recent interest for its potential to circumvent the detailed-balance efficiency limit of single-junction solar cells. For the potential of SF to be fully realized, accurate assignment and quantification of SF is necessary. Intersystem crossing (ISC) is another process of singlet to triplet conversion that is important to distinguish from SF to avoid either over- or under-estimation of SF triplet production. Here, we quantify an upper bound on the rate of ISC in two commonly studied SF chromophores, TIPS-pentacene and TIPS-tetracene, by using transient absorption spectroscopy of solutions of varying concentrations in toluene. We show that SF in solutions of these acenes has previously been misidentified as ISC, and vice versa. By determining a bimolecular SF rate constant in concentrated solutions in which SF dominates over ISC, we distinguish triplet formation due to SF from triplet formation due to ISC, and show that the characteristic time scale of ISC must be longer than 325 ns in TIPS-pentacene, while it must be longer than 118 ns in TIPS- tetracene. We additionally note that no excimer formation is observed in the relatively dilute (up to 8 mM) solutions studied here, indicating that previous excimer formation observed at much higher concentrations may be partially due to aggregate formation. This work highlights that an accurate quantification of ISC is crucial as it leads to accurate determination of SF rate constants and yields. | Alexandra Stuart; Patrick Tapping; Tak Kee; David Huang | Physical Chemistry; Chemical Kinetics; Physical and Chemical Processes; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628ee4cf6b12b649cf7fc3c6/original/pitfalls-of-quantifying-intersystem-crossing-rates-in-singlet-fission-chromophore-solutions.pdf |
67c6fa1581d2151a020902a8 | 10.26434/chemrxiv-2025-65t1h | Mechanochemical Solid Form Screening of Zeolitic Imidazolate Frameworks using Structure-Directing Liquid Additives | We demonstrate a systematic application of the mechanochemical liquid-assisted grinding (LAG) methodology to screen for forms of zinc imidazolate (ZnIm2), of fundamental importance as the simplest member of the zeolitic imidazolate framework materials family. The exploration of 45 different liquid additives, selected based on their molecular structure and physicochemical properties has resulted in seven different ZnIm2 topologies, appearing in 12 structurally distinct solid forms (including two previously unknown forms of the crb (BCT) topology), amorphous phases, and the interrupted moc topology material. All prepared topologies were also explored computationally, using dispersion-corrected periodic density functional theory (DFT) calculations, enabling the rationalization of screening outcomes, and setting the stage for future prediction of additive-directed MOF synthesis. This first systematic exploration of LAG in screening for three-dimensional metal-organic frameworks demonstrates the potential of the liquid additive to not only accelerate materials synthesis, but also to direct it towards topologically different frameworks. The ability to discover novel forms in a material that already exhibits at least 21 crystalographically and functionally different forms provides a strong testimony on the power of mechanochemistry in metal-organic materials discovery. | Ivana Brekalo; Katarina Lisac; Joseph R. Ramirez; Petra Pongrac; Yizhi Xu; Michael Ferguson; Joseph M. Marrett; Mihails Arhangelskis; Tomislav Friščić; K. Travis Holman | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c6fa1581d2151a020902a8/original/mechanochemical-solid-form-screening-of-zeolitic-imidazolate-frameworks-using-structure-directing-liquid-additives.pdf |
654cd9c42c3c11ed711023f0 | 10.26434/chemrxiv-2023-wqcsq | Low-cost Vibrational Free Energies in Solid Solutions with Machine Learning Force Fields | The rational design of alloys and solid solutions relies on accurate computational predictions of phase diagrams. The cluster expansion method with effective cluster interactions fitted to energies from first principles calculations has proven to be a valuable tool for studying disordered crystals. However, the effects of vibrational entropy are commonly neglected due to their additional computational cost. Here, we devise a method for including vibrational free energy in cluster expansions at a very low computational cost by fitting a machine learning force field (MLFF) to the relaxation trajectories already available from the cluster expansion construction. We demonstrate our method for two (pseudo)binary systems, Na1-xKxCl and Ag1-xPd_x, for which accurate phonon dispersions and vibrational free energies are derived from the MLFF. For both systems, inclusion of vibrational effects results in significantly better agreement with miscibility gaps in experimental phase diagrams. This methodology can allow routine inclusion of vibrational effects in calculated compositional phase diagrams, and thus more accurate predictions of properties and stability for materials mixtures. | Kasper Tolborg; Aron Walsh | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Thermodynamics (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654cd9c42c3c11ed711023f0/original/low-cost-vibrational-free-energies-in-solid-solutions-with-machine-learning-force-fields.pdf |
60c743b0f96a00fa9f286857 | 10.26434/chemrxiv.7269287.v3 | 6-(N,N-Dimethylamino)fulvene: A Potential Precursor for a New Class of Fingermark Detection Reagents for Paper Surfaces | <div><div><div><p>The ability to detect latent fingermarks on porous surfaces, such as paper-based documents, is extremely important in resolving criminal cases. Detection methods that target amino acids present in latent fingermark deposits have achieved widespread use due to the binding of these acids to paper fibres resulting in a good representation of the fingermark. This communication is the first report of 6-(N,N-dimethylamino)fulvene (DMAF) as a novel reagent for the detection of latent fingermarks on porous surfaces. Through observation of undergraduate students showing poor laboratory hygiene, we noted that exposure to DMAF leads to brown staining on the students’ skin. We discovered that indeed it can develop latent fingermarks on paper surfaces as pale pink impressions, which are luminescent when illuminated at 505 nm and viewed through orange goggles. The procedure is simple, requiring treatment of the specimen with a solution of DMAF in hexane with subsequent heat treatment. Preliminary experiments indicate that DMAF is reacting with the amino acids present in the latent fingermark.</p></div></div></div> | Jason Wells; Zachary Parsons; Renee Jelly; Alan Payne; Simon W. Lewis | Analytical Chemistry - General; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743b0f96a00fa9f286857/original/6-n-n-dimethylamino-fulvene-a-potential-precursor-for-a-new-class-of-fingermark-detection-reagents-for-paper-surfaces.pdf |
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