id
stringlengths 24
24
| doi
stringlengths 28
32
| title
stringlengths 8
495
| abstract
stringlengths 17
5.7k
| authors
stringlengths 5
2.65k
| categories
stringlengths 4
700
| license
stringclasses 3
values | origin
stringclasses 1
value | date
stringdate 1970-01-01 00:00:00
2025-03-24 00:00:00
| url
stringlengths 119
367
⌀ |
|---|---|---|---|---|---|---|---|---|---|
63244ee4ba8a6dd5b85185e4 | 10.26434/chemrxiv-2022-scv2t | Thiamine Analogues as Tools to Study Pyruvate Dehydrogenase in Cancer: Biochemical, Computational and Cellular Analyses | Pyruvate dehydrogenase complex (PDHc) suppression has long been regarded as a mechanism for cancer cells to manifest the well-known Warburg effect. However, in recent years, it has been proposed that whether PDHc is suppressed or activated in cancer development is context-dependent. The PDHc E1 subunit (PDH E1), a thiamine pyrophosphate (TPP)-dependent enzyme, catalyses the first and rate-limiting step of the complex so there is a need for selective PDH E1 inhibitors. Using thiamine/TPP analogues, we have developed potent and selective inhibitors of mammalian PDH E1. These inhibitors will aid work on understanding of the oncogenic role of PDHc and, ultimately, the development of anticancer strategies. | Finian James Leeper; Alex Chan; Terence Ho; Daniel Parle | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2022-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63244ee4ba8a6dd5b85185e4/original/thiamine-analogues-as-tools-to-study-pyruvate-dehydrogenase-in-cancer-biochemical-computational-and-cellular-analyses.pdf |
60c9e3b11fd5332f3f56ac82 | 10.26434/chemrxiv.14776449.v1 | In Situ-Formed Cobalt Nanoparticles Embedded Within Carbonaceous Matrix as Highly Efficient and Selective Catalysts for the Hydrogenation of Nitroarenes | Inhibiting the side reactions (such as dehalogenation) while promoting both/transfer hydrogenation are the main target for the production of functional anilines from nitroarenes; consequently, the preparation of an ideal catalyst to improve reaction selectivity stays as the fundamental direction for this field. In this work, we provided an easy-to-prepared heterogeneous catalyst with multilayered graphene shells where cobalt nanoparticles were encapsulated inside and distributed uniformly. This as-prepared catalysts were fabricated via one-pot pyrolysis by using mixture of citrate acid and cobalt acetate as C source and Co source, respectively. First of all, structural features of catalyst were characterized by a series of analytic techniques involving XPS, SEM/EDS, TEM as well as elemental mapping, to reveal its unique properties in relation to the catalytic mechanisms; in simple terms, the outer graphitic shell could be activated by the electronic interaction between the inner metallic nanoparticles and the outer graphene layer. Subsequently, the catalytic performance was tested in hydrogenation of nitrobenezene by using H2 as hydrogen source, so as to optimize the preparation process as well as the reaction conditions. Other nitro aromatics with functional groups such as halogen atoms, methyl or hydroxyl were also tolerated under very mild industrially viable and scalable conditions (60 °C, 2 h, and 2 MPa H2). More surprisingly, this catalyst could still exhibit excellent yields over 96 % in gram-scale test for the selected substrates, and could also be easily separated from the aqueous system due to its magnetic properties. The determined yields of target products were not decreased even after eight cycles, suggesting a potential for future industrial application in the selective hydrogenation of nitroarenes to the corresponding amines. | Xiuzheng Zhuang; Jianguo Liu; Shurong Zhong; Longlong Ma; 修政 庄 | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c9e3b11fd5332f3f56ac82/original/in-situ-formed-cobalt-nanoparticles-embedded-within-carbonaceous-matrix-as-highly-efficient-and-selective-catalysts-for-the-hydrogenation-of-nitroarenes.pdf |
66fc06b951558a15efb4496b | 10.26434/chemrxiv-2024-ptq46 | Ligand-Solvent Library Design for Tailoring Interparticle Interactions in Colloidal Nanocrystals | This study explores the critical role of nonpolar ligand-solvent in modulating interparticle interactions in colloidal nanocrystals, which profoundly affects colloidal stability and enables bottom-up precision self-assembly. We created a library comprising 28 distinct ligands and three different solvents to investigate how the position of various modifications—specifically double bond, branched chain, benzene ring, and naphthalene ring—influence ligand crystallinity and interparticle attraction in nonpolar solvents. Through explicit solvent simulations, we demonstrated that placing molecular fragments near the head group or in the midsection of the ligand chain leads to disordered ligand structure, diminishing interparticle attraction, while terminal positioning fosters ordered ligand packing and attractive interactions. By fine-tuning fragment positions or combining two fragments, we achieved control over the crystallinity of ligand bundles, thereby influencing the attraction in the "touch" mode. Additionally, we examine the effects of solvent size on solvation, revealing its potential to independently control attraction in the "lock" mode. These findings enhance our understanding of ligand-solvent dynamics and lay the groundwork for the precise manipulation of nanocrystal self-assembly. | Meng Deng; Chuncheng Li; Lei Liu; Zhaochuan Fan | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Computational Chemistry and Modeling; Self-Assembly; Surface | CC BY 4.0 | CHEMRXIV | 2024-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fc06b951558a15efb4496b/original/ligand-solvent-library-design-for-tailoring-interparticle-interactions-in-colloidal-nanocrystals.pdf |
64a3b775ba3e99daef7b7a01 | 10.26434/chemrxiv-2023-psth7 | Human and environmental safety of carbon nanotubes across their life cycle | Carbon nanotubes are a large family of carbon-based hollow cylindrical structures with unique physicochemical properties that have motivated research for diverse applications; some have reached commercialization. Recent actions in the European Union that propose to ban this entire class of materials highlight an unmet need to precisely define carbon nanotubes, to better understand their toxicological risk effects on human health and the environment throughout their life cycle, and to communicate science-based policy-driving information comprising their taxonomy, safe sourcing, processing, production, manufacturing, handling, use, transportation, and disposal. In this review, we discuss current information and knowledge gaps regarding these issues. We highlight the significance of life cycle assessments of carbon nanotubes and provide a framework to inform policy decisions. | Mijin Kim; Dana Goerzen; Prakrit Jena; Jia Zeng; Rachel Meidl; Daniel Heller | Materials Science; Nanoscience; Earth, Space, and Environmental Chemistry; Carbon-based Materials; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a3b775ba3e99daef7b7a01/original/human-and-environmental-safety-of-carbon-nanotubes-across-their-life-cycle.pdf |
60c749f5469df42aacf43c68 | 10.26434/chemrxiv.12128292.v1 | Self-Adjusting Binding Pockets Enhance H₂ and CH₄ Adsorption in a Uranium-Based Metal–Organic Framework | A new, air-stable, permanently porous uranium(IV) metal–organic framework U(bdc)<sub>2</sub> (<b>1</b>, bdc<sup>2−</sup> = 1,4-benzenedicarboxylate) was synthesized and its H<sub>2</sub> and CH<sub>4</sub> adsorption properties were investigated. Low temperature adsorption isotherms confirm strong adsorption of both gases in the framework at low pressures. In situ gas-dosed neutron diffraction experiments with different D2 loadings revealed a rare example of cooperative framework contraction (Δ<i>V</i> = −7.8%), triggered by D<sub>2</sub> adsorption at low pressures. This deformation creates two optimized binding pockets for hydrogen (<i>Q</i><sub>st</sub> = −8.6 kJ/mol) per pore, in agreement with H<sub>2</sub> adsorption data. Analogous experiments with CD<sub>4</sub> (<i>Q</i><sub>st</sub> = −24.8 kJ/mol) and N,N-dimethylformamide as guests revealed that the binding pockets in <b>1</b> adjust by selective framework contractions that are unique for each adsorbent, augmenting individual host-guest interactions. Our results suggest that the strategic combination of binding pockets and structural flexibility in metal–organic frameworks holds great potential for the development of new adsorbents with an enhanced substrate affinity.<br /> | Dominik P. Halter; Ryan A. Klein; Michael A. Boreen; Benjamin A. Trump; Craig M. Brown; Jeffrey R. Long | Hybrid Organic-Inorganic Materials; Hydrogen Storage Materials; Lanthanides and Actinides; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749f5469df42aacf43c68/original/self-adjusting-binding-pockets-enhance-h2-and-ch4-adsorption-in-a-uranium-based-metal-organic-framework.pdf |
63d1045011259678e379f19d | 10.26434/chemrxiv-2023-5qgth | Inhibition of Thiamine Diphosphate (ThDP)-dependent Enzymes by Triazole-based Thiamine Analogues | Thiamine (vitamin B1) is metabolised into the coenzyme thiamine diphosphate (ThDP). Interrupting thiamine-utilisation leads to disease states and thiamine/ThDP analogues are commonly used as antagonists of thiamine-utilisation pathways to investigate the underlying pathophysiology. Oxythiamine, a thiamine analogue, uses the thiamine-utilising pathways for conversion into oxythiamine diphosphate (OxThDP), which binds to ThDP-dependent enzymes but lacks the catalytic activity of ThDP. Oxythiamine has been used to validate thiamine utilisation as an antimalarial drug target. However, high oxythiamine doses are often needed in vivo because 1) of its rapid clearance and 2) its potency decreases dramatically with thiamine levels. We report herein thiamine analogues possessing a triazole ring and a hydroxamate tail in place of the thiazolium ring and diphosphate group, respectively, of ThDP. We characterise their broad-spectrum inhibition of ThDP-dependent enzymes in biochemical and computational studies, and establish their ThDP-competitive action using Plasmodium falciparum as a model. We demonstrate how the cellular thiamine-utilisation pathway can be probed in mechanistic studies using our compounds and oxythiamine in parallel. | Alex H. Y. Chan; Terence C. S. Ho; Imam Fathoni; Rebecca Pope; Kevin J. Saliba; Finian James Leeper | Biological and Medicinal Chemistry; Chemical Biology; Microbiology | CC BY NC 4.0 | CHEMRXIV | 2023-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d1045011259678e379f19d/original/inhibition-of-thiamine-diphosphate-th-dp-dependent-enzymes-by-triazole-based-thiamine-analogues.pdf |
649ae6c1ba3e99daef1f7404 | 10.26434/chemrxiv-2023-fhfbr | Synthesis and Biophysical Studies of High Affinity Morpholino Oligomers Containing G-clamp Analogs | Synthesis of chlorophosphoramidate morpholino monomers containing tricyclic cytosine analogs phenoxazine, G-clamp, and G8AE-clamp were achieved and incorporated into 12-mer oligonucleotides using trityl-chemistry by automated synthesizer. Phosphorodiamidate morpholino oligomers containing a single G-clamp had significantly enhanced affinity for complementary RNA and DNA relative to unmodified oligomers. The G-clamp-modified oligomers adopt a B-type helical conformation as per CD spectra. Binding affinities were sequence and position dependent. | SURAJIT SINHA; Arnab Das; Atanu Ghosh; Jayanta Kundu; Martin Egli; Muthiah Manoharan | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649ae6c1ba3e99daef1f7404/original/synthesis-and-biophysical-studies-of-high-affinity-morpholino-oligomers-containing-g-clamp-analogs.pdf |
6759a196085116a1330fc54c | 10.26434/chemrxiv-2024-9bdxz-v2 | Computational Insights into the Energetics of Single C2-C10 Aliphatic Moieties Adsorbed on Hydrogenated Silicon (111) Surface | Silicon's versatility as a semiconductor renders it indispensable across various domains, including electronics, sensors, and photovoltaics. Modifying Hydrogen-terminated Silicon surfaces with moieties adsorption offers a method to tailor the material’s properties for specific applications. In this study, we employ ab initio density functional theory calculations to explore the energetics of single alkyl, 1-alkenyl and 1-alkynyl moieties chemisorbed on Hydrogen-terminated Silicon (111) surface. We analyse the interfacial dipole induced by Si–C bond formation that determines the Schottky barrier and examine the alignment of the frontier orbitals energy levels with Silicon band structure to investigate the charge transfer based on tunnelling mechanism. Our findings provide valuable insights into how aliphatic moiety functionalization affects interfacial electronic properties, offering clues for optimizing Silicon-based devices. | Francesco Buonocore; Sara Marchio; Simone Giusepponi; Massimo Celino | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Hybrid Organic-Inorganic Materials; Computational Chemistry and Modeling; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6759a196085116a1330fc54c/original/computational-insights-into-the-energetics-of-single-c2-c10-aliphatic-moieties-adsorbed-on-hydrogenated-silicon-111-surface.pdf |
64348509a41dec1a56d8902b | 10.26434/chemrxiv-2023-p8jvp | Electrically Conductive [Fe4S4]-based Organometallic Polymers | Tailoring the molecular components of hybrid organic-inorganic materials enables precise control over their electronic properties. Designing electrically conductive coordination materials, e.g. metal-organic frameworks (MOFs), has relied on single-metal nodes because the metal-oxo clusters present in the vast majority of MOFs are not suitable for elec- trical conduction due to their localized electron orbitals. Therefore, the development of metal-cluster nodes with delocal- ized bonding would greatly expand the structural and electrochemical tunability of conductive materials. Whereas the cuboidal [Fe4S4] cluster is a ubiquitous cofactor for electron transport in biological systems, few electrically conductive artificial materials employ the [Fe4S4] cluster as a building unit due to the lack of suitable bridging linkers. In this work, we bridge the [Fe4S4] clusters with ditopic N-heterocyclic carbene (NHC) linkers through charge-delocalized Fe-C bonds that enhance electronic communication between the clusters. [Fe4S4Cl2(ditopic NHC)] exhibits a high electrical conductivity of 1 mS cm−1 at 25 oC, surpassing the conductivity of related but less covalent materials. These results highlight that synthetic control over individual bonds is critical to the design of long-range behavior in semiconductors. | Kentaro Kadota; Tianyang Chen; Eoghan Gormley; Christopher Hendon; Mircea Dinca; Carl Brozek | Inorganic Chemistry; Coordination Chemistry (Inorg.); Polymers; Solid State Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64348509a41dec1a56d8902b/original/electrically-conductive-fe4s4-based-organometallic-polymers.pdf |
60cc4e4da5b6af1a487566d5 | 10.26434/chemrxiv-2021-09srz | A fast alternative to the galvanostatic intermittent titration technique | The galvanostatic intermittent titration technique (GITT) has been regarded as the go-to method for determining the diffusion coefficients of Li-ions in insertion electrode materials at various states of charge (SoC). However, the
method is time-consuming. In this work, the intermittent current interruption (ICI) method is demonstrated to provide comparably accurate measurements of diffusion coefficients with a drastically reduced experimental time. Theoretically, it is derived from Fick’s laws that the ICI method renders essentially the same information as GITT. Experimentally, both GITT and ICI are then compared side-by-side in a three-electrode half-cell of LiNi0.8Mn0.1Co0.1O2 (NMC811). It is shown that the results from both methods match where the assumption of semi-infinite diffusion applies. Moreover, the benefit of the
non-disruptive ICI method to operando characterization methods is demonstrated via correlation of changes in the continuously monitored diffusion coefficient of Li+ in NMC811 to structural changes in the material by operando X-ray diffraction (XRD). | Yu-Chuan Chien; Haidong Liu; Ashok S. Menon; William R. Brant; Daniel Brandell; Matthew J. Lacey | Materials Science; Inorganic Chemistry; Energy; Electrochemistry; Kinetics and Mechanism - Inorganic Reactions; Energy Storage | CC BY 4.0 | CHEMRXIV | 2021-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60cc4e4da5b6af1a487566d5/original/a-fast-alternative-to-the-galvanostatic-intermittent-titration-technique.pdf |
6687df15c9c6a5c07a5d8d8c | 10.26434/chemrxiv-2024-pd863 | LIBX-A401: A Novel Selective Inhibitor of Acyl-CoA Synthetase Long Chain Family Member 4 (ACSL4) and Its Binding Mode | Lipid metabolism affects many cellular processes essential for homeostasis, and its disruption is linked to various diseases. A key enzyme in these processes, acyl-coenzyme A synthetase long-chain family member 4 (ACSL4), is a promising target for treating conditions involving ferroptosis and certain cancers. Rosiglitazone (ROSI) is a known ACSL4 inhibitor but its potent activity on peroxisome proliferator-activated receptor gamma (PPARγ), a nuclear receptor strongly involved in lipid metabolism constitutes an important limitation. This study focuses on developing novel ACSL4 inhibitors derived from ROSI, which lack PPARγ activity. Binding of the most potent compound of this series (9) relies on the prior binding of ATP. Hydrogen-Deuterium Exchange Mass Spectrometry (HDx-MS) demonstrated that ATP binding stabilizes the ACSL4 C-terminus, an effect enhanced by compound 9, which also alters important peptide sequences, including the fatty acid gate-domain. Photoaffinity Labeling (PAL) with a diazirine-based probe identified residue A329 in the fatty acid pocket. Molecular dynamics simulations and site-directed mutagenesis highlighted Q302 as critical for compound 9 binding. Thus, compound 9 (LIBX-A401) is a promising tool for studying ACSL4 in ferroptosis-related diseases and cancer, and the elucidation of its binding mode paves the way to the rational design of optimized inhibitors | Darius Mazhari Dorooee; Severine Ravez; Didier Vertommen; Nicolas Renault; Nicolas Papadopoulos; Romain Marteau; Emeline Charnelle; Karine Porte; Alexandre Gobert; Nathalie Hennuyer; Gaetan Herinckx; Bart Staels; Patricia Melnyk; Stefan Constantinescu; Raphael Frederick; Jamal El Bakali | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6687df15c9c6a5c07a5d8d8c/original/libx-a401-a-novel-selective-inhibitor-of-acyl-co-a-synthetase-long-chain-family-member-4-acsl4-and-its-binding-mode.pdf |
67abd90e6dde43c90874d79d | 10.26434/chemrxiv-2025-74hf0 | From Non-Classical to Classical: Crystallization Seeds Reshape Nucleation Mechanisms
| Crystalline seeds are widely employed in crystallization to accelerate nucleation and control product polymorphs, yet their impact on nucleation mechanisms remains poorly understood. While homogeneous nucleation of crystals from solution often proceeds through non-classical pathways involving amorphous intermediates, it is unclear how seeds that promote heterogeneous nucleation reshape these mechanisms and govern polymorph selection. Here, we provide the first direct evidence that crystalline seeds can bypass amorphous intermediates, converting non-classical nucleation mechanisms into classical, monomer-by-monomer crystallization pathways. Using molecular dynamics simulations of zeolite synthesis, we uncover a complex reaction network of competing nucleation processes mediated by intermediate interfacial polymorphs. The interplay between thermodynamic stability and kinetic favorability of these interfacial polymorphs dictates nucleation outcomes, creating a dynamic tension between interfacial polymorph stability and crystallization rates. Fur-thermore, we show that the synthesis environment—whether monomers or aggregates serve as reactants—profoundly impacts these pathways. At moderate supersaturation, seeds eliminate amorphous intermediates and promote classical nucleation, whereas high super-saturation or aggregate-based reactants favor non-classical pathways, even in the presence of a seed. These findings establish a general framework for understanding how seeds govern crystallization mechanisms, with broad implications for controlling nucleation kinetics, polymorph selection, and material properties. While focused on zeolites, this work reveals insights applicable to biominerals, pharmaceu-ticals, functional materials, and catalysts, providing a basis for engineering crystallization pathways in diverse applications. | Carlos Chu-Jon; Eli Martinez; Andressa Bertolazzo; Aditya Koneru; Subramanian Sankaranarayanan; Jeffrey Rimer; Valeria Molinero | Theoretical and Computational Chemistry; Physical Chemistry; Interfaces; Physical and Chemical Processes; Self-Assembly; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67abd90e6dde43c90874d79d/original/from-non-classical-to-classical-crystallization-seeds-reshape-nucleation-mechanisms.pdf |
670497bccec5d6c142887f8e | 10.26434/chemrxiv-2024-b05bz | Sonochemistry and Sonocatalysis: Current Progress, Existing Limitations, and Future Opportunities in Sustainable Chemistry | Sonocatalysis is a specialised field within sonochemistry that leverages the interaction between ultrasound and solid catalysts to enhance the rate and selectivity of chemical reactions. As a non-traditional catalytic activation method, sonocatalysis can profoundly modify reaction mechanisms and unlock novel activation pathways that are not typically accessible through standard catalysis. This unique approach offers new opportunities for driving reactions under milder conditions while potentially improving selectivity and efficiency. This review highlights the recent progress in sonocatalytic applications aligned with several United Nations Sustainable Development Goals, including environmental remediation, sonotherapy, and biomass conversion. In these applications, we explore the underlying sonocatalytic mechanisms and the interaction between solid catalysts and ultrasound, which drive the enhanced reactivity. A key feature of this manuscript is its comprehensive analysis of the primary technical challenges in sonocatalysis, specifically its low energy efficiency and the complexity of reaction control. To address these hurdles, we examine various effective strategies, such as the incorporation of nanostructured catalytic cavitation agents and the design of advanced microfluidic sonoreactors. These innovations improve energy transfer, control bubble dynamics, and enhance catalytic activity under ultrasound. Furthermore, we implement molecular modelling to gain fundamental insights into the mechanisms fundamental to the effectiveness of sonocatalysts. This approach provides a deeper understanding of how nanostructured catalysts interact with ultrasonic fields, guiding the design of next-generation catalytic materials. The integration of nanostructured catalytic cavitation agents, microfluidic reactor technologies, and computational molecular modelling forms a trilateral synergistic platform that unlocks new potential in sonocatalysis. This multidisciplinary framework paves the way for significant advancements in sustainable chemistry, offering innovative solutions to global challenges in energy, health, and environmental sustainability. | Quang Thang Trinh; Nicholas Golio; Yuran Cheng; Haotian Cha; Kin Un Tai; Lingxi Ouyang; Jun Zhao; Tuan Sang Tran; Tuan-Khoa Nguyen; Jun Zhang; Hongjie An; Zuojun Wei; Francois Jerome; Prince Nana Amaniampong; Nam-Trung Nguyen | Materials Science; Catalysis; Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670497bccec5d6c142887f8e/original/sonochemistry-and-sonocatalysis-current-progress-existing-limitations-and-future-opportunities-in-sustainable-chemistry.pdf |
64c3a3999ed5166e939d4801 | 10.26434/chemrxiv-2023-48ll0-v2 | Increasing the robustness of SIFT-MS volatilome fingerprinting by introducing notional analyte concentrations | Selected-ion-flow-tube-mass-spectrometry (SIFT-MS) is an analytical technique for volatile detection and quantification. SIFT-MS can be applied in a ‘white box’ approach, measuring concentrations of target compounds, or as a ‘black box’ fingerprinting technique, scanning all product ions during a full scan. Combining SIFT-MS full scan data acquired from multi-batches or large-scale experiments remains problematic due to signal fluctuation over time. The standard approach of normalizing full scan data to total signal intensity was insufficient. This study proposes a new approach to correct SIFT-MS fingerprinting data. In this concept, all the product ions from a full scan are considered individual compounds for which notional concentrations can be calculated. Converting ion count rates into notional analyte concentrations accounts for any changes in instrument parameters. The benefits of the proposed approach are demonstrated on three years of data from both multi-batches and long-term experiments showing a significant reduction of system-induced fluctuations providing a better focus on the changes of interest. | Amina Benchennouf; Matthias Corion; Angelica Dizon; Yijie Zhao; Jeroen Lammertyn; Barbara De Coninck; Bart Nicolaï; Joeri Vercammen; Maarten Hertog | Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c3a3999ed5166e939d4801/original/increasing-the-robustness-of-sift-ms-volatilome-fingerprinting-by-introducing-notional-analyte-concentrations.pdf |
60c74ff20f50dbe9a13974d3 | 10.26434/chemrxiv.12966737.v1 | From Zero- to Three-Dimensional Heterobimetallic Coordination Polymers with the [Pt{SSC-N(CH2COO)2}2]4– Metalloligand | <br />Heterobimetallic compounds of the type M’2[Pt(L)2] (L = N-dithioato-iminodiacetate, {SSC-N(CH2COO)2}3–) containing different bivalent, oxophilic metals M’ were prepared in a straightforward manner from [Pt(H2L)2] and the respective metal acetates, M’(OAc)2 (M’ = Mg–Ba, M–Cu, Cd). X-ray structure determination revealed that the products exist as zero- (Mg), one- (Mn), two- (Fe, Co, Ni, Cd), or three-dimensional (Sr) assemblies in the solid state. As a result, the water solubilities and thermal stabilities of the products cover much wider ranges than it has been seen with M’2[M(L)2] compounds having different thiophilic metal centers (M = Ni, Pd, Pt). While most of the compounds show a typical diamagnetic (Mg–Ba, Cd) or paramagnetic (Mn, Co, Ni, Cu) behaviour at ambient temperature, for Fe2[Pt(L)2] ·4 H2O an antiferromagnetic interaction of the Fe atoms is assumed. <br /> | Phil Liebing; Florian Oehler; Juliane Witzorke; Marten Schmeide | Coordination Chemistry (Inorg.); Solid State Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ff20f50dbe9a13974d3/original/from-zero-to-three-dimensional-heterobimetallic-coordination-polymers-with-the-pt-ssc-n-ch2coo-2-2-4-metalloligand.pdf |
615124cbaeaa6ef7ecfb6e01 | 10.26434/chemrxiv-2021-pk4xk-v2 | A Free Aluminylene with Diverse σ-Donating and Doubly σ/π-Accepting Ligand Features for Transition Metals | We report herein the synthesis, characterization, and coordination chemistry of a free N-aluminylene, namely a carbazolylaluminylene 2b. This species is prepared via a reduction reaction of the corresponding carbazolyl aluminium diiodide. The coordination behavior of 2b towards transition metal centers (W, Cr) is shown to afford a series of novel aluminylene complexes 3-6 with diverse coordination modes. We demonstrate that the Al center in 2b can behave as: 1. a σ-donating and doubly π-accepting ligand; 2. a σ-donating, σ-accepting and π-accepting ligand; and 3. a σ-donating and doubly σ-accepting ligand. Additionally, we show ligand exchange at the aluminylene center providing access to the modulation of electronic properties of transition metals without changing the coordinated atoms. Investigations of 2b with IDippCuCl (IDipp = 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene) show an unprecedented aluminylene-alumanyl transformation leading to a rare terminal Cu-alumanyl complex 8. The electronic structures of such complexes and the mechanism of the aluminylene-alumanyl transformation are investigated through density functional theory (DFT) calculations. | Xin Zhang; Liu Leo Liu | Inorganic Chemistry; Main Group Chemistry (Inorg.); Organometallic Compounds | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615124cbaeaa6ef7ecfb6e01/original/a-free-aluminylene-with-diverse-donating-and-doubly-accepting-ligand-features-for-transition-metals.pdf |
641aec24aad2a62ca12a5f0d | 10.26434/chemrxiv-2022-t3srw-v3 | A Resource to Support Decolonization of the Undergraduate Chemistry Curriculum | In our taught chemistry curricula, the majority of individuals who are used to illustrate historical aspects of chemistry topics are white western chemists. Decolonizing the undergraduate chemistry curricula is increasingly recognized as an important step towards developing a more inclusive higher-education environment for students from minoritized ethnic backgrounds. Here, we provide the first openly accessible resource that can be used to decolonize an undergraduate chemistry course. In particular, the resource provides examples of both individual scientists and groups that can be used to illustrate chemistry teaching, and hence provide role model examples of scientists from different cultures. The resource presented provides a significant body of examples for chemistry lecturers to use as they begin working towards decolonizing their curricula. | Ogochukwu Kelechi Uleanya; Sam Furfari; Leonie C. Jones; Kgato P. Selwe; Amelia B. Milner; Caroline E. H. Dessent | Chemical Education; Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641aec24aad2a62ca12a5f0d/original/a-resource-to-support-decolonization-of-the-undergraduate-chemistry-curriculum.pdf |
67a8e02881d2151a02c531e9 | 10.26434/chemrxiv-2024-fc23q-v2 | Auger-excited Photoluminescence from Gold Nanoflowers | Photoluminescence from metal nanostructures offers a promising means for studying excited charge processes in metal nanostructures. Moreover, it has many potential applications in sensing, imaging, and nanothermometry. However, a general understanding of the emission from metal nanoparticles has not yet been achieved. In particular, the possible presence of sequential emission mechanisms involving the excitation of conduction band electrons via Auger scattering remains unclear. In this article, we provide spectroscopic evidence for Auger-excited intraband emission from gold nanoflowers. We employ a combination of photoluminescence and photoluminescence excitation spectroscopy to investigate the excitation pathways in films of gold nanoflowers. While on the one hand, the excitation spectrum clearly demonstrates absorption by interband transitions, the emission spectra can be unequivocally assigned to intraband recombination. The combination of these two observations can only be conclusively explained by Auger-excited intraband emission. This results suggest that Auger excitation is a promising route to generate energetic non-thermal electrons with energies substantially above the Fermi level. Exploiting this effect could strongly benefit applications for nano-luminescent probes and the progress of plasmon catalysis. | Wouter Koopman; Jan Kutschera; Felix Stete; Matias Bargheer | Physical Chemistry; Materials Science; Nanoscience; Nanostructured Materials - Materials; Plasmonic and Photonic Structures and Devices; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2025-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a8e02881d2151a02c531e9/original/auger-excited-photoluminescence-from-gold-nanoflowers.pdf |
625f27d2742e9f9470644f24 | 10.26434/chemrxiv-2022-g2mjt-v2 | An aerial field trial of methane detection technologies at oil and gas production sites | Methane emissions from >100 tank battery sites in the Permian Basin of west Texas were quantified using two different aircraft-based measurement platforms deployed asynchronously, but within a 5-day period. Emissions were detected by aircraft with rates ranging from 0.71 kg/hr to >750 kg/hr. On-site emission measurements were also made using a drone-based technology at a representative sample of 33 sites and were compared to engineering estimates of emission rates. A large fraction of total emissions from the sites sampled by the aircraft systems (90%±6%) were accounted for by sites with emissions greater than 10 kg/hr, when engineering estimates of emissions were assigned to sites with no emissions detected by aircraft. At least half of the sites with emission rates above 10 kg/hr had emissions that did not persist longer than a few days, and consequently, site by site comparisons of asynchronous aircraft measurements showed poor agreement. The two aircraft systems differed in their estimates of total emissions from the ensembles of sites sampled, and in the percentage of sites with emissions greater than 10 kg/hr. The differences in frequencies of detection between the two aircraft based platforms are attributed to a combination of factors, however, both aircraft-based emission measurement systems attribute a large fraction of emissions to sites with emission rates >10 kg/hr. | Shannon Stokes; Erin Tullos; Linley Morris; Felipe J. Cardoso-Saldaña; Mackenzie Smith; Stephen Conley; Brendan Smith; David T. Allen | Energy; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Atmospheric Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625f27d2742e9f9470644f24/original/an-aerial-field-trial-of-methane-detection-technologies-at-oil-and-gas-production-sites.pdf |
61af3e42dce179cdc703e991 | 10.26434/chemrxiv-2021-gstjz | Structure-Guided Optimization of Small-Molecule Folate Uptake Inhibitors Targeting the Energy-Coupling Factor Transporters | Here, we report on a potent class of substituted ureidothiophenes targeting energy-coupling factor (ECF) transporters, an unexplored target, which is not addressed by any antibiotic on the market. Since the ECF module is crucial for the vitamin transport mechanism, prevention of substrate uptake should ultimately lead to cell death. By utilizing a combination of virtual and functional whole-cell screening of our in-house library, the membrane-bound protein mediated uptake of folate could be effectively inhibited. Structure-based optimization of our hit compound yielded low-micromolar inhibitors, whereby the most active compounds showed in addition potent antimicrobial activities against a panel of clinically relevant Gram-positive pathogens without significant cytotoxic effects. | Alexander F. Kiefer; Spyridon Bousis; Mostafa M. Hamed; Eleonora Diamanti; Jörg Haupenthal; Anna K. H. Hirsch | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2021-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61af3e42dce179cdc703e991/original/structure-guided-optimization-of-small-molecule-folate-uptake-inhibitors-targeting-the-energy-coupling-factor-transporters.pdf |
6269c7181033885338fd38ae | 10.26434/chemrxiv-2022-b8xj8 | Impact of Polymer Rigidity on Thermoresponsive Luminescence and Electron Spin Resonance of Polyester-Tethered Single Radicals | Stable organic radicals represent a unique type of functional materials for a broad scope of applications in optoelectronic and spintronic devices. A central challenge towards these applications is how to suppress the inter-radical aggregation that often causes aggregation-induced photoluminescence quenching and limits the correlation lifetime of the electron spins from the radicals. Here we report an effective approach to fine-tuning luminescence and spin dynamics using a series of polyester-tethered single radicals, with a common core of carbazole-triphenylmethyl radical but different chains of polyesters with distinct glass transition temperature and rigidity. The rigidity of the polymeric matrices plays a critical role in tuning the luminescence and electron spin resonance of the radicals. The tunable properties of luminescence and electron spin dynamics as well as robust photostability of such polymer-tethered single radicals represent important attributes for cutting-edge applications in optoelectronic devices and quantum information technologies. | Liman Hou; Hongxue Xu; Xuanyu Zhang; Rui Chen; Zhaoyu Zhang; Mingfeng Wang | Physical Chemistry; Materials Science; Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6269c7181033885338fd38ae/original/impact-of-polymer-rigidity-on-thermoresponsive-luminescence-and-electron-spin-resonance-of-polyester-tethered-single-radicals.pdf |
60c749a0f96a003b432872ce | 10.26434/chemrxiv.12086493.v1 | Synthesis of Clustered Mn3O4 Nanoparticles through a Polymer Surfactant Mediated Route on Few-Layer Graphene Nanoplatelet Surface and its Application for Electrochemical Energy Storage: Lithium-ion Battery Anode | <p>Composites synthesized through the deposition of Mn<sub>3</sub>O<sub>4</sub>
on graphene, carbon nanotube and other carbon based materials have attracted
much attention recently as potential electrode materials for different
electrochemical applications such as pseudocapacitor; Lithium-ion battery; and catalysis. The primary reason Mn<sub>3</sub>O<sub>4</sub>
is grown on these substrates in spite of having high charge storage capacity as pseudocapacitor or Lithium-ion battery electrodes on its own is to enhance its electrical conductivity and/or to impart flexibility to the electrode, which is
difficult for a fully metallic electrode. Higher electrical conductivity
prolongs the cycle life of an electrode. In addition, the substrate contributes
capacity and thus, enhances the overall energy density of an electrode. Mn<sub>3</sub>O<sub>4
</sub>acts as a spacer and keeps graphene nanosheets separated when used as the
substrate for capacitor electrode fabrication. This helps retain the high
surface area of graphene nanosheets in the electrode which contributes
additional capacitance. Mn<sub>3</sub>O<sub>4 </sub>supported on graphene and
other carbon substrates have recently been investigated as catalyst for
methanol electro-oxidation in alkaline media; CO oxidation; and
Oxygen reduction reaction (ORR). High surface area substrate uniformly
distributes metal particles and prevents their agglomeration and dissolution
during catalytic process. In addition, high electrical conductivity of graphene
and carbon substrates enhances the electronic conductivity of Mn<sub>3</sub>O<sub>4</sub>
which is of importance for superior catalytic activity. Composite of Mn<sub>3</sub>O<sub>4</sub>
combined with carbon based substrate has also found non-electrochemical
application such as the removal of Pb and Cu ions from aqueous solution because
of their adsorptive behaviour.<b></b></p>
<p>A myriad of procedures have been adopted for the synthesis
of Mn<sub>3</sub>O<sub>4</sub> on graphene or other carbonaceous substrates. All of these methods
involve one or more of the following factors that complicate the process, such
as: long synthesis time; high synthesis temperature; use of hazardous/toxic
chemicals; multistep process and the requirement for sophisticated device or
highly controlled environment. In fact, the complicacies associated with the
synthesis of Mn<sub>3</sub>O<sub>4</sub> have already been acknowledged and
investigations have been directed at finding relatively simpler route such as
the use of microwave technique. <b></b></p>
<p>In this research, we report the synthesis of clusters of
nearly octahedral shapedn Mn<sub>3</sub>O<sub>4</sub> nanoparticles on few-layer
graphene nanoplatalet (GnP) surface through a simple, wet-chemical,
polyethyleneimine (PEI) mediated route. Few-layer graphene nanoplatelets are
ultrathin particles of graphite prepared through proprietary intercalation and
exfoliation method (XG Sciences, Inc., Lansing, MI, USA). The components
involved in this synthesis method are manganese salts (KMnO<sub>4</sub> and MnSO<sub>4</sub>.H<sub>2</sub>O); water; PEI; and GnP as the substrate. The
synthesis is carried out at a temperature of 80°C only and in open air. Highly
crystallized Mn<sub>3</sub>O<sub>4</sub> particles, as observed by X-Ray
Diffraction (XRD), can be synthesized on GnP surface. It has also been observed
that PEI acts as a reducing agent and as a capping agent on a continuous
network of ribbon-like Birnessite-MnO<sub>2</sub> (IV) to produce a nearly
octahedral shaped nanoparticles of Mn<sub>3</sub>O<sub>4</sub> (II, III). It
has already been mentioned that composites of Mn<sub>3</sub>O<sub>4</sub> on
graphene or other carbonaceous substrates find a myriad of applications. Thus,
our research findings to synthesize GnP-Mn<sub>3</sub>O<sub>4</sub> composite
through a simple method should be of interest to a broad group of researchers.
In this research, we have investigated the performance of this composite system
as a Lithium-ion battery anode only. Our preliminary investigations reveal that
the Mn<sub>3</sub>O<sub>4</sub> composite synthesized through this method has
just as much potential as the ones prepared through other alternative methods.</p> | Debkumar Saha; Lawrence T. Drzal | Carbon-based Materials; Nanostructured Materials - Materials; Surfactants | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749a0f96a003b432872ce/original/synthesis-of-clustered-mn3o4-nanoparticles-through-a-polymer-surfactant-mediated-route-on-few-layer-graphene-nanoplatelet-surface-and-its-application-for-electrochemical-energy-storage-lithium-ion-battery-anode.pdf |
64f08e00dd1a73847fe311fb | 10.26434/chemrxiv-2023-g4w7b-v2 | Ruptures in Mixed Monolayers Under Tension and Supercooling: Implications for Plant Nanobubbles | Mixed phospholipid and glycolipid monolayers likely coat the surfaces of pressurised gas nanobubbles within the hydraulic systems of plants. The lipid coatings bond to water under negative pressure and are thus stretched out of equilibrium. In this work, we have used molecular dynamics simulations to produce trajectories of a biologically relevant mixed monolayer, pulled at mild negative pressures (−1.5 to −4.5 MPa). Pore formation within the monolayer is observed at both 270 and 310 K, and proceeds as an activated process once the lipid tails fully transition from liquid condensed/liquid expanded coexistence to the liquid expanded phase. Pressure : area isotherms showed reduced surface pressure in the undercooled trajectory at all observed areas per lipid. Rayleigh-Plesset simulations were used to predict evolving nanobubble size using the calculated pressure : area isotherms as dynamic surface tensions. We confirm the existence of a critical radius with respect to runaway growth, above the homogeneous cavitation radius, coinciding with the area per lipid at which pore formation occurs. | Stephen Ingram; Bernhard Reischl; Timo Vesala; Hanna Vehkamäki | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Interfaces | CC BY NC 4.0 | CHEMRXIV | 2023-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f08e00dd1a73847fe311fb/original/ruptures-in-mixed-monolayers-under-tension-and-supercooling-implications-for-plant-nanobubbles.pdf |
665486f191aefa6ce11caa2e | 10.26434/chemrxiv-2024-tjfj7-v2 | On the continuous modeling of fluid and solid states | For over 150 years, the “holy grail” of thermodynamic modeling has been to express the free energy of matter as a single analytical expression from where all other thermodynamic properties can be derived. This vision was partially achieved with the pioneering suggestion of J. D. van der Waals of modeling the gas and liquid states with a continuous polynomial. van der Waals' work spawned a century of development of equations of state (EoSs) for fluid phases and fluid phase equilibria. However, the extension to include the solid phase has largely been ignored, presumably out of the inherent difficulties in expressing the corresponding thermodynamic surface analytically. In this contribution, we resolve this century-old problem by presenting a procedure where an equation of state based on artificial neural networks is built based on an extensive database of accurate molecular dynamics data. The use of this EoS is exemplified here for the Mie particle, providing a single thermodynamically consistent model that continuously represents the fluid (gas, liquid and supercritical) and crystalline states. Apart from accurately predicting the derivative properties, the equation exhibits metastable regions characterized by van der Waals loops that correctly quantify the existence of vapor-liquid, solid-liquid, and solid-vapor equilibria along with the position of the critical and triple points. This new paradigm in EoS development is a pathway for the rapid deployment of models for complex matter and its interpretation opens doors to studying the transition regions between different aggregation states. | Gustavo Chaparro; Erich A. Müller | Physical Chemistry; Chemical Engineering and Industrial Chemistry; Thermodynamics (Chem. Eng.); Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665486f191aefa6ce11caa2e/original/on-the-continuous-modeling-of-fluid-and-solid-states.pdf |
60c742b50f50db7cbe395d91 | 10.26434/chemrxiv.8521955.v1 | Impact of Stereo- and Regiochemistry on Energetic Materials | The synthesis, physical properties and calculated performances of six stereo- and regioisomeric cyclobutane nitric ester materials is described. While the calculated performances of these isomers, as expected, were similar, their physical properties were found to be extremely different. By altering the stereo- and regiochemistry, complete tunability in the form of low-or high-melting solids, standalone melt-castable explosives, melt-castable explosive eutectic compounds, and liquid propellant materials were obtained. This study demonstrates that theoretical calculations should not be the main factor in driving the design and synthesis of new materials, and that stereo- and regiochemistry offer a new dimension to consider when designing compounds of potential relevance to energetic formulators.<br /> | Lisa M. Barton; Jacob T. Edwards; Eric C. Johnson; Eric J. Bukowski; Rosario C. Sausa; Edward F. C. Byrd; Joshua A. Orlicki; Jesse J. Sabatini; Phil Baran | Organic Synthesis and Reactions; Stereochemistry; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742b50f50db7cbe395d91/original/impact-of-stereo-and-regiochemistry-on-energetic-materials.pdf |
60e2a4a6f7373f34eb451ccc | 10.26434/chemrxiv-2021-0dt3n | A systematic comparison of the structural and dynamic properties of commonly used water models for molecular dynamics simulations | Water is a unique solvent that is ubiquitous in biology and present in a variety of solutions, mixtures, and materials settings. It therefore forms the basis for all molecular dynamics simulations of biological phenomena, as well as for many chemical, industrial, and materials investigations. Over the years, many water models have been developed, and it remains a challenge to find a single water model that accurately reproduces all experimental properties of water simultaneously. Here, we report a comprehensive comparison of structural and dynamic properties of 30 commonly used 3-point, 4-point, 5-point, and polarizable water models simulated using consistent settings and analysis methods. For the properties of density, coordination number, surface tension, dielectric constant, self-diffusion coefficient, and solvation free energy of methane, models published within the past two decades consistently show better agreement with experimental values compared to models published earlier, albeit with some notable exceptions. However, no single model reproduced all experimental values exactly, highlighting the need to carefully choose a water model for a particular study, depending on the phenomena of interest. Finally, machine learning algorithms quantified the relationship between the water model force field parameters and the resulting bulk properties, providing insight into the parameter-property relationship and illustrating the challenges of developing a water model that can accurately reproduce all properties of water simultaneously. | Sachini P. Kadaoluwa Pathirannahalage; Nastaran Meftahi; Aaron Elbourne; Alessia C. G. Weiss; Chris F. McConville; Agilio Padua; David A. Winkler; Margarida Costa Gomes; Tamar L. Greaves; Quinn A. Besford; Tu C. Le; Andrew J. Christofferson | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2021-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e2a4a6f7373f34eb451ccc/original/a-systematic-comparison-of-the-structural-and-dynamic-properties-of-commonly-used-water-models-for-molecular-dynamics-simulations.pdf |
6610c02891aefa6ce1ec47d9 | 10.26434/chemrxiv-2024-v10t8 | ABC of Kd Accuracy | The equilibrium dissociation constant (Kd) is a major characteristic of affinity complexes and one of the most frequently determined physicochemical parameters. Despite its significance, the values of Kd obtained for the same complex under similar conditions often exhibit considerable discrepancies and sometimes vary by orders of magnitude. These inconsistencies highlight the susceptibility of Kd determination to large systematic errors, ultimately leading to misconceptions and significant misallocation of research and development resources. It is imperative to both minimize and quantitatively assess the systematic errors inherent in Kd determination. Traditionally, Kd values are determined through nonlinear regression of binding isotherms. This analysis utilizes three variables: concentrations of two reactants and a fraction R of unbound limiting reactant. The systematic errors in Kd arise directly from systematic errors in these variables. In this study, we thoroughly analyze the sources of systematic errors within these variables, aiming to mitigate their impact on Kd accuracy. Through this analysis, we illustrate how each source contributes to inaccuracies in Kd determination. Additionally, we propose a method for quantitatively assessing the confidence interval of systematic errors in concentrations, a crucial step towards quantitatively evaluating Kd accuracy. While presenting original findings, this paper also reiterates the fundamentals of Kd determination, hence, guiding researchers across all proficiency levels. By shedding light on the sources of systematic errors and offering strategies for their mitigation, our work will help researchers to enhance the accuracy of Kd determination thereby making binding studies more reliable. | Tong Ye Wang; Jean-Luc Rukundo; Zhiyuan Mao; Sergey N. Krylov | Physical Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Chemical Biology; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6610c02891aefa6ce1ec47d9/original/abc-of-kd-accuracy.pdf |
65f333299138d2316176262d | 10.26434/chemrxiv-2024-jg1wl | High-efficiency 99Tc separation from contaminated liquid waste using some anion exchange resins | 99Tc removal from contaminated aqueous solution was explored using some commercially available anion exchange resins with various specifications. Various combinations of physicochemical parameters like polymeric network, pore diameter, percent cross-linking, bead size etc. were selected to appraise their impact on 99Tc uptake. Fundamental extraction properties such as effect of solution pH, equilibration time, effect of temperature were determined for obtaining the optimum extraction condition. The resins were characterized using BET, SEM, EDS, XPS, TG, FTIR spectroscopy to decipher the structure-extraction correlation and extraction mechanism. In order to quantify the loading capacity (745 mg/g as maximum) and ascertain the reaction mechanism, non-radioactive surrogate of TcO4-, i.e, ReO4- have been used. ReO4- quantity in solution was measured using UV-Vis spectrophotometry with λmax at 204 nm. 4M HNO3 was found be an effective reagent towards desorption from the loaded resins. The capture performance was found to deteriorate with γ-radiation particularly at higher absorbed dose (500 kGy onwards). Competition studies with most common anions found in ground water as well as soil such as Cl-, NO3-, SO42-, CO32-, PO43- indicate that, even in presence of high concentration (1:10000 molar ratio) of these interfering anions, TcO4- can be selectively extracted by the resins confirming their effectiveness towards the decontamination of real ground water with respect to 99Tc. | DEBASISH DAS | Inorganic Chemistry; Chemical Engineering and Industrial Chemistry; Polymers; Process Control; Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f333299138d2316176262d/original/high-efficiency-99tc-separation-from-contaminated-liquid-waste-using-some-anion-exchange-resins.pdf |
67bd124afa469535b9ca0580 | 10.26434/chemrxiv-2024-wbf7n-v3 | Dyeing to Know: Harmonising Nile Red Staining Protocols for Microplastic Identification | With the escalation of microplastic (MPs) pollution and the laborious nature of existing MPs identification methods, new approaches for large-scale sampling of MPs in the environment are necessary. A promising solution lies in the fluorescence staining of Nile Red (NR), whose fluorescence is polarity-dependent, offering the potential for classification based on fluorescence. However, the choice of carrier solvents to dissolve NR remains unstandardised, and methods to represent and differentiate the fluorescent behaviour of MPs are lacking. This study addresses these gaps by testing eight NR-carrier solvents (n-hexane, chloroform, acetone, methanol, ethanol, acetone/hexane, acetone/ethanol, and acetone/water) applied to ten most common polymer-types of MPs (HDPE, LDPE, PP, EPS, PS, PC, ABS, PVC, PET, and PA). The fluorescence behaviour, including fluorescence intensity and Stokes shift, was compared across solvents, and their effects on polymer degradation were evaluated. Additionally, the effectiveness of various polarity measures with the proposed HSV colour spaces in reflecting Stokes shift for MPs identification was assessed. To differentiate natural organic materials (e.g., eggshells, fingernails, wood, and cotton) from polymers, Fenton oxidation was found to quench the fluorescence of natural organic matter with minimal changes observed in NR-stained MPs. The findings identified acetone/water [25% (v/v)] as the best compromise, effectively mitigating the adverse effects of acetone while maintaining strong fluorescence behaviour suitable for identification. | Derek Ho; Julie Masura | Materials Science; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Environmental Analysis; Imaging | CC BY NC 4.0 | CHEMRXIV | 2025-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bd124afa469535b9ca0580/original/dyeing-to-know-harmonising-nile-red-staining-protocols-for-microplastic-identification.pdf |
63b5b3cde9d0fd568a359785 | 10.26434/chemrxiv-2023-4q5xv | Synthesis and Reactivity of Dithienopyrazines | Heteroacenes developed to widely used building blocks in organic semiconductors for application in organic electronics due to their tunable structures and properties concomi¬ant with inherent stability. Here, we report efficient preparation and investigation of so far unknown heterotriacenes, basic anti- and syn-dithienopyrazines 5 and 6. The comparison of the two isomers with respect to electronic properties and follow-up reactions gives insights into structure-property and -reactivity relationships. Examples of tran¬sition metal-catalyzed C-C cross-coupling reactions of corresponding halogenated derivatives show the practical impact for extended pi-conjugated systems applied in optoelectronic devices. | Peter Baeuerle; Elena Mena-Osteritz; Franziska Kreuzer | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2023-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b5b3cde9d0fd568a359785/original/synthesis-and-reactivity-of-dithienopyrazines.pdf |
63ad129516e9a8132138579a | 10.26434/chemrxiv-2023-clz1b | Allosteric Regulation of SARS-CoV-2 Spike Protein Revealed by Contrastive Machine Learning | Allosteric regulation is common in protein-protein interactions and thus can be used in drug design. Nevertheless, the mechanism of allosteric regulation remains elusive for most proteins, including SARS-CoV-2 spike protein, despite extensive experimental endeavors over the past years. In the present computational study, the route of allosteric regulation of SARS-CoV-2 is examined by all-atom explicit solvent molecular dynamics simulations in conjunction with contrastive machine learning. It was found that peptide binding to the polybasic cleavage sites, especially the one at the first monomer of the trimeric SARS-CoV-2, activates the fluctuation of the spike protein’s backbone. This fluctuation eventually propagates to a nitrogen-terminal domain and its neighboring receptor-binding domain, remarkably weakening the latter’s binding affinity to the human cell receptor ACE2. Our study justifies the presence of allosteric regulation in SARS-CoV-2, paving the way for the systematic design of allosteric antibody inhibitors. | Yong Wei; Amy Chen; Yuewei Lin; Tao Wei; Baofu Qiao | Theoretical and Computational Chemistry; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ad129516e9a8132138579a/original/allosteric-regulation-of-sars-co-v-2-spike-protein-revealed-by-contrastive-machine-learning.pdf |
6433adbf0784a63aeedf28eb | 10.26434/chemrxiv-2023-dklsp | Robust Chemoenzymatic Synthesis of the Keratinimicin Aglycone Facilitated by the Structure and Selectivity of OxyB | The emergence of multidrug-resistant pathogens poses a threat to public health and requires new antimicrobial agents. As the archetypal glycopeptide antibiotic (GPA) used against drug-resistant Gram-positive pathogens, vancomycin provides a promising starting point. Peripheral alterations to the vancomycin scaffold have enabled the development of new GPAs. However, modifying the core remains challenging due to the size and complexity of this compound family. The recent successful chemoenzymatic synthesis of vancomycin suggests that such an approach can be broadly applied. Herein, we describe the expansion of chemoenzymatic strategies to encompass type II GPAs bearing all aromatic amino acids through the production of the aglycone analogue of keratinimicin A, a GPA that is five-fold more potent than vancomycin against Clostridioides difficile. In the course of these studies, we found that the cytochrome P450 enzyme OxyBker boasts both broad substrate tolerance and remarkable selectivity in the formation of the first aryl ether crosslink on the linear peptide precursors. The X-ray crystal structure of OxyBker, determined to 2.8 Å, points to structural features that may contribute to these properties. Our results set the stage for using OxyBker broadly as a biocatalyst toward the chemoenzymatic synthesis of diverse GPA analogues. | Nicole Hauser; Kendra Ireland; Vasiliki Chioti; Katherine Davis; Mohammad Seyedsayamdost | Biological and Medicinal Chemistry; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6433adbf0784a63aeedf28eb/original/robust-chemoenzymatic-synthesis-of-the-keratinimicin-aglycone-facilitated-by-the-structure-and-selectivity-of-oxy-b.pdf |
649b5d0aba3e99daef25c79b | 10.26434/chemrxiv-2023-1l9cr | Modelling the Fluorescence Quantum Yields of Aromatic Compounds: Benchmarking the Machinery to Compute Intersystem Crossing Rates | The from-first-principles calculation of fluorescence quantum yields (FQYs) and lifetimes of organic dyes remains very challenging. In this manuscript we extensively test the static machinery to calculate FQYs. Specifically, we perform an extensive analysis on the parameters influencing the intersystem crossing (ISC), internal conversion (IC), and fluorescence rates calculations. The impact of i) the electronic structure (chosen exchange-correlation functional and spin-orbit Hamiltonian), ii) the vibronic parameters (coordinate system, broadening function, and dipole expansion), and iii) the excited-state kinetic models, are systematically assessed for a series of seven rigid aromatic molecules. Our studies provide more insights into the choice of parameters and the expected accuracy for the computational protocols aiming to deliver FQYs values. Some challenges are highlighted, such as, on the one hand, the difficulty to benchmark against the experimental non-radiative rates, for which the separation between the IC and ISC contributions is often not provided in the literature and, on the other hand, the need to go beyond the harmonic approximation for the calculation of the IC rates. | Koen Veys; Manon H. E. Bousquet; Denis Jacquemin; Daniel Escudero | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Photochemistry (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2023-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649b5d0aba3e99daef25c79b/original/modelling-the-fluorescence-quantum-yields-of-aromatic-compounds-benchmarking-the-machinery-to-compute-intersystem-crossing-rates.pdf |
60c7405a4c8919715dad20e1 | 10.26434/chemrxiv.7184876.v2 | Enhancing Sidechain Rotamer Sampling Using Non-Equilibrium Candidate Monte Carlo | <div>Molecular simulations are a valuable tool for studying biomolecular motions and thermodynamics. However, such motions can be slow compared to simulation timescales, yet critical. Specifically, adequate sampling of sidechain motions in protein binding pockets proves crucial for obtaining accurate estimates of ligand binding free energies from molecular simulations. The timescale of sidechain rotamer flips can range from a few ps to several hundred ns or longer, particularly in crowded environments like the interior of proteins. Here, we apply a mixed non-equilibrium candidate Monte Carlo (NCMC)/molecular dynamics (MD) method to enhance sampling of sidechain rotamers. The NCMC portion of our method applies a switching protocol wherein the steric and electrostatic interactions between target sidechain atoms and the surrounding environment are cycled off and then back on during the course of a move proposal. Between NCMC move proposals, simulation of the system continues via traditional molecular dynamics. Here, we first validate this approach on a simple, solvated valine-alanine dipeptide system and then apply it to a well-studied model ligand binding site in T4 lysozyme L99A. We compute the rate of rotamer transitions for a valine sidechain using our approach and compare it to that of traditional molecular dynamics simulations. Here, we show that our NCMC/MD method substantially enhances sidechain sampling, especially in systems where the torsional barrier to rotation is high (>10 kcal/mol). These barriers can be intrinsic torsional barriers or steric barriers imposed by the environment.</div><div>Overall, this may provide a promising strategy to selectively improve sidechain sampling in molecular simulations.</div> | Kalistyn H. Burley; Samuel C. Gill; Nathan M. Lim; David Mobley | Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2019-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7405a4c8919715dad20e1/original/enhancing-sidechain-rotamer-sampling-using-non-equilibrium-candidate-monte-carlo.pdf |
60c740204c89190ba6ad208f | 10.26434/chemrxiv.7233152.v2 | Conformational Sampling and Polarization of Asp26 in pKa Calculations of Thioredoxin | Thioredoxin is a protein that has been used as model system by various computational methods to predict the p<i>K<sub>a</sub></i> of aspartate residue Asp26 which is 3.5 units higher than a solvent exposed one (e.g Asp20). Here, we use extensive atomistic molecular dynamics simulations of two different protonation states of Asp26 in combination with conformational analysis based on RMSD clustering and principle component analysis to identify representative conformations of the protein in solution. For each conformation the Gibbs free energy of proton transfer between Asp26 and Asp20, which is fully solvated in a loop region of the protein, is calculated with the Amber99sb force field in alchemical transformations. The varying polarization of the two residues in different molecular environments and protonation states is described by Hirshfeld-I (HI) atomic charges obtained from the averaged polarized electron density. Our results show that the Gibbs free energy of proton transfer is dependent on the protein conformation, the proper sampling of the neighbouring Lys57 residue orientations and on water molecules entering the hydrophobic cavity upon deprotonating Asp26. The inclusion of the polarization of both aspartate residues in the free energy cycle by the HI atomic charges improves the results from the nonpolarizable force field and reproduces the experimental p<i>K<sub>a</sub></i> value of Asp26.<br /> | Aharon Gomez Llanos; Esteban Vöhringer-Martinez | Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740204c89190ba6ad208f/original/conformational-sampling-and-polarization-of-asp26-in-p-ka-calculations-of-thioredoxin.pdf |
653944df48dad23120520486 | 10.26434/chemrxiv-2023-nh3jb-v2 | Investigation of the Stability of D5SIC-DNAM-Incorporated DNA duplex in Taq Polymerase Binary system: A Systematic Classical MD Approach | DNA polymerases are fundamental enzymes that play a crucial role in processing DNA with high fidelity and accuracy ensuring the faithful transmission of genetic information. The recognition of unnatural base pairs (UBPs) by polymerases, enabling their replication, represents a significant and groundbreaking discovery with profound implications for genetic expansion. Romesberg et al. examined the impact of DNA containing 2,6-dimethyl-2H-isoquiniline-1-thione: D5SIC (DS) and 2-methoxy-3-methylnaphthalene: DNAM (DN) UBPs bound to T. aquaticus DNA polymerase (Taq) through crystal structure analysis. Here, we have used polarizable and nonpolarizable classical molecular dynamics (MD) simulations to investigate the structural aspects and stability of Taq in complex with a DNA duplex including a DS-DN pair in the terminal templating and priming positions. Our results suggest that the flexibility of UBP-incorporated DNA in the terminal position is arrested by the polymerase, thus preventing fraying and mispairing. Our investigation also reveals that the UBP remains in an intercalated conformation inside the active site, exhibiting two distinct orientations in agreement with experimental findings. Our analysis pinpoints particular residues responsible for favorable interactions with the UBP, with some relying on van der Waals interactions while others on Coulombic forces. | Tanay Debnath; G. Andrés Cisneros | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2023-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653944df48dad23120520486/original/investigation-of-the-stability-of-d5sic-dnam-incorporated-dna-duplex-in-taq-polymerase-binary-system-a-systematic-classical-md-approach.pdf |
60c74331702a9b7a4318a585 | 10.26434/chemrxiv.8108105.v2 | Biomimetic Composites with Enhanced Toughening Using Silk Inspired Triblock Proteins and Aligned Nanocellulose Reinforcements | Silk and cellulose are biopolymers that show a high potential as future
sustainable materials.They also have complementary properties, suitable
for combination in composite materials where cellulose would form the
reinforcing component and silk the tough matrix. Therein, a major
challenge concerns balancing structure and properties in the assembly
process. We used recombinant proteins with triblock architecture
combining structurally modified spider silk with terminal cellulose
affinity modules. Flow-alignment of cellulose nanofibrils and triblock
protein allowed a continuous fiber production.The protein assembly
involved phase separation into concentrated coacervates, with subsequent
conformational switching from disordered structures to beta sheets.
This gave the matrix a tough adhesiveness, forming a new composite
material with high strength and stiffness combined with increased
toughness. We show that versatile design possibilities in protein
engineering enable new fully biological materials, and emphasize the key
role of controlled assembly at multiple length scales for realization. | Pezhman Mohammadi; A. Sesilja Aranko; Christopher P. Landowski; Olli Ikkala; Wolfgang Wagermaier; Markus Linder | Biological Materials; Composites; Fibers; Materials Processing; Biopolymers; Cellulosic materials; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74331702a9b7a4318a585/original/biomimetic-composites-with-enhanced-toughening-using-silk-inspired-triblock-proteins-and-aligned-nanocellulose-reinforcements.pdf |
67a38cb3fa469535b92920bb | 10.26434/chemrxiv-2025-2x123 | Smart Surface Engineering in Microcarriers: Towards Applications in Cancer Therapy | Despite significant advances in cancer treatment, several challenges persist in optimizing effective cargo
delivery, including enhancing bioavailability, improving targeted delivery, and overcoming biological barriers for improved tumor tissue penetration. There is an urgent need for versatile carriers capable of dual
or multi-functional targeting within a single system without compromising functionality. Here, we present
a microcarrier employing a dual surface modification strategy to enhance therapeutic efficacy through
controlled, site-specific drug release. This functionalized microcarrier (potential microrobotic platform)
integrates two distinct pH-sensitive polymeric nanoreservoirs with different membrane permeability. One
nanoreservoir is engineered to release the antitumor agent curcumin in response to the acidic tumor microenvironment, while the second is designed to degrade the tumor extracellular matrix via enzymatic
activity, facilitating deeper penetration of therapeutic agents. This dual surface modification approach
represents a significant advancement in the customizable integration of multifunctional nanoreservoirs.
By leveraging dual compartmentalization, it prevents deactivation and cross-process interference, enabling precise nanoscale combination therapies for microrobotic cancer treatment. These surface-engineered microrobots hold promise for overcoming physiological barriers, ensuring stable cargo transport,
and broadening the applicability of microrobotic platforms across diverse cancer types. | Fatemeh Rajabasadi; Silvia Moreno ; Mercedes Gonzalez Rico; Pedro Viñola; Kristin Fichna; Franziska Hebenstreit; Susanne Boye ; Andreas Janke; Dietmar Appelhans; Mariana Medina Sanchez | Materials Science; Polymer Science; Nanoscience; Controlled-Release Systems; Nanostructured Materials - Materials; Drug delivery systems | CC BY 4.0 | CHEMRXIV | 2025-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a38cb3fa469535b92920bb/original/smart-surface-engineering-in-microcarriers-towards-applications-in-cancer-therapy.pdf |
63516fbc31107239d6e88ba6 | 10.26434/chemrxiv-2022-6kjvc | United atom and coarse grained models for crosslinked polydimethylsiloxane with applications to the rheology of silicone fluids | Siloxane systems consisting primarily of polydimethylsiloxane (PDMS) are versatile, multifaceted materials that play a key role in diverse applications. However, open questions exist regarding the correlation between their varied atomic-level properties and observed macroscale features. To this effect, we have created a systematic workflow to determine coarse-grained simulation models for crosslinked PDMS in order to further elucidate the effects of network changes on the system's mechanical properties. Our approach leverages a fine-grained united atom model for linear PDMS, which we extend to include crosslinking terms, and applies iterative Boltzmann inversion to obtain a coarse-grain ``bead-spring-type'' model. We then perform extensive molecular dynamics simulations to explore the effect of crosslinking on the rheology of silicone fluids, where we compute systematic increases in both density and shear viscosity that compare favorably to experiments that we conduct here. The kinematic viscosity of partially crosslinked fluids follows an empirical linear relationship that is surprisingly consistent with Rouse theory, which was derived for systems comprised of a uniform distribution of linear chains. The models developed here serve to enable quantitative bottom-up predictions for curing- and age-induced effects on macroscale mechanical and rheological properties, allowing for accurate prediction of material properties based on fundamental chemical data. | Aditi Khot; Rebecca Lindsey; James Lewicki; Amitesh Maiti; Nir Goldman; Matthew Kroonblawd | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63516fbc31107239d6e88ba6/original/united-atom-and-coarse-grained-models-for-crosslinked-polydimethylsiloxane-with-applications-to-the-rheology-of-silicone-fluids.pdf |
60c75995337d6c126fe29421 | 10.26434/chemrxiv.14714838.v1 | Origins of Internal Regioselectivity in Copper-Catalyzed Borylation of Terminal Alkynes | <p>Installation of a boron functionality into a more substituted carbon of terminal alkynes has been a challenging issue in chemical synthesis, since inherently Lewis acidic boron moieties, in principle, favor their attachment to a terminal carbon. Herein, we report on the highly internal-selective borylation of terminal alkynes under copper catalysis, wherein diminishment of boron-Lewis acidity and ligand-derived steric bulk around a copper center are the key to the success. In particular, the use of an anthranilamide-substituted boron moiety [B(aam)] is of high synthetic significance, because its properly diminished Lewis acidity enabled the internal regioselectivity and the Suzuki–Miyaura cross-coupling activity to be compatibly achieved. This method provided direct and universal approach to variously substituted branched alkenylboron compounds, regardless of electronic and steric properties of a substituent on terminal alkynes.</p> | Takumi Tsushima; Hideya Tanaka; Kazuki Nakanishi; Masaaki Nakamoto; Hiroto Yoshida | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75995337d6c126fe29421/original/origins-of-internal-regioselectivity-in-copper-catalyzed-borylation-of-terminal-alkynes.pdf |
60c749ccf96a007203287301 | 10.26434/chemrxiv.12034296.v2 | Activation and Functionalization of C–C σ-Bonds of Alkylidene Cyclopropanes at Main Group Centers | Aluminum(I) and magnesium(I) compounds are reported for the C–C s-bond activation of strained alkylidene cyclopropanes. These reactions result in the formal addition of the C–C s-bond to main group center either at a single site (Al) or across a metal–metal bond (Mg–Mg). Mechanistic studies suggest that rather than occurring by a concerted oxidative addition, these reactions involve stepwise processes in which substrate binding to the main group metal acts as a precursor to a- or b-alkyl migration steps that break the C–C s-bond. This mechanistic understanding is used to develop the magnesium-catalyzed hydrosilylation of the C–C s-bonds of alkylidene cyclopropanes. | Mark Crimmin; Richard Y Kong | Coordination Chemistry (Inorg.); Main Group Chemistry (Inorg.); Organometallic Compounds; Small Molecule Activation (Inorg.); Theory - Inorganic; Bond Activation; Catalysis; Kinetics and Mechanism - Organometallic Reactions; Main Group Chemistry (Organomet.); Small Molecule Activation (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749ccf96a007203287301/original/activation-and-functionalization-of-c-c-bonds-of-alkylidene-cyclopropanes-at-main-group-centers.pdf |
642cf41816782ec9e65c3f26 | 10.26434/chemrxiv-2023-bclq3 | Taming the Dichalcogenides: Isolation, Characterization, and Reactivity of Elusive Perselenide, Persulfide, Thioselenide, and Selenosulfide Anions | Reactive sulfur species (RSS) and reactive selenium species (RSeS) play integral roles in hydrogen sulfide (H2S) and hydrogen selenide (H2Se) biological signaling pathways, and dichalcogenide anions are proposed transient intermediates that facilitate a variety of biochemical transformations. Herein we report the selective synthesis, isolation, spectroscopic and structural characterization, and fundamental reactivity of persulfide (RSS–), perselenide (RSeSe–), thioselenide (RSSe–), and selenosulfide (RSeS–) anions. The isolated chalcogenides do not rely on steric protection for stability and have steric profiles analogous to cysteine (Cys). Simple reduction of S8 or Se by potassium benzyl thiolate (KSBn) or selenolate (KSeBn) in the presence of 18-crown-6 afforded [K(18-crown-6)][BnSS] (1), [K(18-crown-6)][BnSeSe] (2) [K(18-crown-6][BnSSe] (3), and [K(18-crown-6][BnSeS] (4). The chemical structure of each dichalcogenide was confirmed by X-ray crystallography and solution state 1H, 13C, and 77Se NMR spectroscopy. To advance our understanding of the reactivity of these species, we demonstrated that reduction of 1-4 by PPh3 readily generates E=PPh3 (E: S, Se), and reduction of 1, 3, and 4 by DTT readily produces HE–/H2E. Furthermore, 1-4 reacts with CN– to produce ECN–, which is consistent with the detoxifying effects of dichalcogenide intermediates in the Rhodanese enzyme. Taken together, this work provides new insights into the inherent structural and reactivity characteristics of dichalcogenides relevant to biology and advances our understanding of the fundamental properties of these reactive anions. | Keyan Li; Lev Zakharov; Michael Pluth | Biological and Medicinal Chemistry; Inorganic Chemistry; Bioinorganic Chemistry; Main Group Chemistry (Inorg.); Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642cf41816782ec9e65c3f26/original/taming-the-dichalcogenides-isolation-characterization-and-reactivity-of-elusive-perselenide-persulfide-thioselenide-and-selenosulfide-anions.pdf |
60c7480d842e651e21db2ad4 | 10.26434/chemrxiv.11852241.v1 | Scope of 3D Shape-Based Approaches in Predicting the Macromolecular Targets of Structurally Complex Small Molecules Including Natural Products and Macrocyclic Ligands | A plethora of similarity-based, network-based, machine learning and docking approaches for predicting the macromolecular targets of small molecules are available today and recognized as valuable tools for providing guidance in early drug discovery. With the increasing maturity of target prediction methods, researchers have started to explore ways to expand their scope to more challenging molecules such as structurally complex natural products and macrocyclic small molecules. In this work we systematically explore the capacity of an alignment-based approach to identify the targets of structurally complex small molecules (including large and flexible natural products and macrocyclic compounds) based on the similarity of their 3D molecular shape to non-complex molecules (i.e. more conventional, "drug-like", synthetic compounds). For this analysis, query sets of ten representative, structurally complex molecules were compiled for each of 35 pharmaceutically relevant proteins. Subsequently, ROCS, a leading shape-based screening engine, was utilized to generate rank-ordered lists of the potential targets of the 35x10 queries according to the similarity of their 3D molecular shape with that of compounds from a knowledge base of 272 640 non-complex small molecules active on a total of 3642 different proteins. Four of the scores implemented in ROCS were explored for target ranking, with the TanimotoCombo score consistently outperforming all others. The score successfully recovered the targets of 29% and 40% of the 350 queries among the top-5 and top-20 positions, respectively. For 29 out of the 35 investigated targets (83%), the method correctly assigned the first rank (out of 3642) to the target of interest for at least one of the ten queries. The shape-based target prediction approach showed remarkable robustness, with good success rates obtained even for compounds that are clearly distinct from any of the ligands present in the knowledge base. However, complex natural products and macrocyclic compounds proved to be challenging even with this approach, although cases of complete failure were recorded only for a small number of targets. | Ya Chen; Neann Mathai; Johannes Kirchmair | Chemoinformatics; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2020-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7480d842e651e21db2ad4/original/scope-of-3d-shape-based-approaches-in-predicting-the-macromolecular-targets-of-structurally-complex-small-molecules-including-natural-products-and-macrocyclic-ligands.pdf |
626836b8368ab655418e3c7f | 10.26434/chemrxiv-2022-2l1m9 | The COMPAS Project: A Computational Database of Polycyclic Aromatic Systems.
Phase 1: cata-condensed Polybenzenoid Hydrocarbons | Chemical databases are an essential tool for
data-driven investigation of structure-property
relationships and design of novel functional
compounds. We introduce the first phase of the
COMPAS Project – a COMputational database
of Polycyclic Aromatic Systems. In this phase,
we have developed two datasets containing the
optimized ground-state structures and a selec-
tion of molecular properties of 34k and 9k cata-
condensed polybenzenoid hydrocarbons (at the
GFN2-xTB and B3LYP-D3BJ/def2-SVP lev-
els, respectively), and have placed them in the
public domain. Herein we describe the process
of the dataset generation, detail the informa-
tion available within the datasets, and show
the fundamental features of the generated data.
We analyze the correlation between the two
types of computation as well as the structure-
property relationships of the calculated species.
The data and the insights gained from them can
inform rational design of novel functional aro-
matic molecules for use in, e.g., organic elec-
tronics, and can provide a basis for additional
data-driven machine- and deep-learning studies
in chemistry. | Alexandra Wahab; Lara Pfuderer; Eno Paenurk; Renana Gershoni-Poranne | Theoretical and Computational Chemistry; Organic Chemistry; Physical Organic Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626836b8368ab655418e3c7f/original/the-compas-project-a-computational-database-of-polycyclic-aromatic-systems-phase-1-cata-condensed-polybenzenoid-hydrocarbons.pdf |
63bd37f21f125830f2981cd3 | 10.26434/chemrxiv-2023-d5pxk | Ethanol dehydrogenation to acetaldehyde with mesoporous Cu-SiO2 catalysts prepared by aerosol-assisted sol-gel | Copper based catalysts are central for carrying dehydrogenation reactions. However, these materials are prone to deactivation by sintering and coke deposition. Irreversible sintering occurring during reaction (under the effect of temperature) is known to decrease both activity and selectivity, where the unwanted dehydration activity of the support might also play an important role. From this perspective, the quite unreactive silica supports may be attractive. However, using classical catalyst preparation methods (e.g. impregnation), it is a challenge to obtain a stable and homogeneous dispersion of Cu over SiO2 owing to the weak support-active phase interactions. Taking a sidestep, aerosol-assisted sol-gel is a promising alternative for the facile preparation of mesostructured metallosilicates with high metal dispersion. Here we report, for the first time, Cu-SiO2 made by the aerosol-assisted sol-gel method and exploited in the ethanol non-oxidative dehydrogenation to acetaldehyde. These catalysts are compared with a series of catalysts made by impregnation to investigate, through a thorough characterization survey, the effect of the synthesis procedure as well as the effect of Cu loading. We show that aerosol-made catalysts do not suffer heavy sintering, reach high ethanol conversions with acetaldehyde selectivity above 75%, and only slowly deactivate upon time due to a (reversible) coking phenomenon. | Giovanni Pampararo; Gabriella Garbarino; Paola Riani; Vit Vykoukal; Guido Busca; Damien Debecker | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bd37f21f125830f2981cd3/original/ethanol-dehydrogenation-to-acetaldehyde-with-mesoporous-cu-si-o2-catalysts-prepared-by-aerosol-assisted-sol-gel.pdf |
60c74805702a9b839918aed6 | 10.26434/chemrxiv.9939008.v2 | Site-selective and Re-writable Labeling of DNA through Enzymatic, Reversible and Click Chemistries | <p>Current methods for bioconjugation rely on the introduction of stable linkers that lack the required versatility to perform sequential functionalizations. However, sequential manipulations are an increasing requirement in chemical biology because they can underpin multiple analyses of the same sample to provide a wider understanding of cell behavior. Here, we present a new method to site-selectively <i>write</i>, <i>remove</i> and <i>re-write</i> chemical functionality to a biomolecule, DNA in this case. Our method combines the precision and robustness of methyltransferase-directed labeling with the reversibility of acyl hydrazones and the efficiency of click chemistry. Underpinning the method is a new S-adenosyl-l-methionine derivative to site-selectively label DNA with a bifunctional chemical handle containing an acyl hydrazone-linker and a terminal azide. Functional <i>tags</i> are conjugated via the azide, and can be <i>removed (i.e. un-tagged)</i> when needed at the acyl hydrazone via exchange with hydroxyl amine. The formed hydrazide-labeled DNA is a versatile intermediate that can be either <i>re-written</i> to reset the original chemical handle, or covalently reacted with a <i>permanent tag</i>. This ability to <i>write</i>, <i>tag</i>, <i>un-tag</i> and <i>permanently tag</i> DNA is exploited to sequentially introduce two fluorescent dyes on DNA. Finally, we demonstrate the potential of the method by developing a protocol to sort labeled DNA using magnetic beads, with subsequent amplification of the sorted DNA sample for further analysis. The presented method opens new avenues for site-selective bioconjugation and should underpin integrative approaches in chemical biology where sequential functionalizations of the same sample are required.<br /></p> | Andrew A. Wilkinson; Elodie Jagu; Krystian Ubych; Steven Coulthard; Ashleigh E. Rushton; Jack Kennefick; Qiang Su; Robert K. Neely; Paco Fernandez-Trillo | Bioorganic Chemistry; Supramolecular Chemistry (Org.); Biological Materials; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74805702a9b839918aed6/original/site-selective-and-re-writable-labeling-of-dna-through-enzymatic-reversible-and-click-chemistries.pdf |
6560c531cf8b3c3cd70785eb | 10.26434/chemrxiv-2023-nzr36 | A versatile optimization framework for porous electrode design | Porous electrodes are performance-defining components in electrochemical devices, such as redox flow batteries, as they govern the electrochemical performance and pumping demands of the reactor. Yet, conventional porous electrodes used in redox flow batteries are not tailored to sustain convective-enhanced electrochemical reactions. Thus, there is a need for electrode optimization to enhance the system performance. In this work, we present an optimization framework to carry out the bottom-up design of porous electrodes by coupling a genetic algorithm with a pore network modeling framework. We introduce geometrical versatility by adding a pore merging and splitting function, study the impact of various optimization parameters, geometrical definitions, and objective functions, and incorporate electrode structures and flow field with well-defined geometries. Moreover, we show the need for optimizing electrodes for specific reactor architectures and operating conditions to design next-generation electrodes, by analyzing the genetic algorithm optimization for initial starting geometries with diverse morphologies (cubic and a tomography-extracted commercial electrode), flow field designs (flow-through and interdigitated), and redox chemistries (VO2+/VO2+ and TEMPO/TEMPO+). We found that for kinetically sluggish electrolytes with high ionic conductivity, electrodes with numerous small pores and high internal surface area provide enhanced performance, whereas for kinetically facile electrolytes with low ionic conductivity, low through-plane tortuosity and high hydraulic conductance are required. The computational tool developed in this work can guide the design of high-performance electrode materials for a broad range of operating conditions, electrolyte chemistries, reactor designs, and electrochemical technologies. | Maxime van der Heijden; Gabor Szendrei; Victor de Haas; Antoni Forner-Cuenca | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6560c531cf8b3c3cd70785eb/original/a-versatile-optimization-framework-for-porous-electrode-design.pdf |
6735c3f1f9980725cf27865b | 10.26434/chemrxiv-2024-r3thp | PyCPET - Computing Heterogeneous 3D Protein Electric Fields and Their Dynamics | Electrostatic preorganization is an exciting mode to understand the catalytic function of enzymes, yet limited tools exist to computationally analyze it. In particular, no methods exist to interpret the geometry, dynamics, and fundamental components of 3-D electric fields, E(r), in protein active sites. Here we present PyCPET (Python Computation of Electric Field Topologies), a comprehensive, open-source toolbox to analyze E(r), in enzymes. We designed it to be computationally efficient and user friendly with both CPU and GPU accelerated codes. Our aim is to provide a set of functions for rich, descriptive analysis of enzyme systems including dynamics, benchmarking, distribution of streamlines analysis in 3-D E(r), computation of point E(r), principal component analysis, and 3-D field visualization. Finally, we demonstrate its versatility by exploring the nature of electrostatic preorganization and dynamics in three cases: Cytchrome C, Co-substituted Liver Alcohol Dehydrogenase, and HIV Protease. These test systems, along with previous work, establish PyCPET as an essential toolkit for the in-depth analysis and visualization of electric fields in enzymatic systems, unlocking new avenues for understanding electrostatic contributions to enzyme catalysis. | Pujan Ajmera; Santiago Vargas; Shobhit Chaturvedi; Matthew Hennefarth; Anastassia Alexandrova | Theoretical and Computational Chemistry; Catalysis; Theory - Computational; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2024-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6735c3f1f9980725cf27865b/original/py-cpet-computing-heterogeneous-3d-protein-electric-fields-and-their-dynamics.pdf |
6177e1db5c433d1d448b81c0 | 10.26434/chemrxiv-2021-ftrfx | Developing simple boranes as phase transfer catalysts for nucleophilic fluorination using CsF | Despite the general high fluorophilicity of boron, simple organoboranes such as BEt3 and 3,5-(CF3)2C6H3–BPin are shown herein for the first time, to our knowledge, to be effective phase-transfer catalysts for the fluorination of organohalides with CsF. Significant chiral induction during nucleophilic fluorination to form -fluoroamines using oxazaborolidine (CBS) (pre)catalysts and CsF also can be achieved. Screening different boranes revealed a correlation between calculated fluoride affinity of the borane and nucleophilic fluorination reactivity, with sufficent fluoride affinity required for boranes to react with CsF and form Cs[fluoroborate] salts, but too high a fluoride affinity leading to fluoroborates that are poor at transferring fluoride to an electrophile. Fluoride affinity is only one component controlling reactivity in this context; effective fluorination also is dependent on the ligation of Cs+ which effects the [Cs⋯F⋯BR3] interaction and thus the B–F bond strength. Effective ligation of Cs+ (such as by [2.2.2]-cryptand) weakens the Cs⋯FB interaction which strengthens the B–F bond - thus disfavours fluoride transfer to an electrophile. Combined these findings enables optimal fluorination outcomes to be expected using robust (to the fluorination conditions) boranes with fluoride affinity of ca. 110 kJ mol-1 (relative to Me3Si+) under conditions where a signficant Cs⋯F–B interaction persists. | Sven Kirschner; Matthew Peters; Kang Yuan; Marina Uzelac; Michael Ingleson | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Organocatalysis; Main Group Chemistry (Organomet.) | CC BY 4.0 | CHEMRXIV | 2021-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6177e1db5c433d1d448b81c0/original/developing-simple-boranes-as-phase-transfer-catalysts-for-nucleophilic-fluorination-using-cs-f.pdf |
65794886fd283d7904e26d7f | 10.26434/chemrxiv-2023-rf93d | Mechanochemically Accelerated Deconstruction of
Chemically Recyclable Plastics | Here, we show that when polymers are deconstructed as solids in a reaction medium that swells the polymer, the rate of chain cleavage is accelerated beyond that for bond cleavage in small molecule analogues. Moreover, by tailoring the reactive medium to promote swelling via kosmotropic and chaotropic principles, we show that the initial rates of deconstruction can be accelerated by up to 90%. | Mutian Hua; Zhengxing Peng; Rishabh Guha; Xiaoxu Ruan; Ka Chon Ng; Jeremy Demarteau; Shira Haber; Sophia Fricke; Jeffrey Reimer; Miquel Salmeron; Kristin Persson; Cheng Wang; Brett Helms | Theoretical and Computational Chemistry; Polymer Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65794886fd283d7904e26d7f/original/mechanochemically-accelerated-deconstruction-of-chemically-recyclable-plastics.pdf |
62f14df91803730ec19e1fed | 10.26434/chemrxiv-2022-80fgz | A Statistical Modeling Approach to Catalyst Generality Assessment in Enantioselective Synthesis | Selecting the optimal catalyst to impart high levels of enantioselectivity in a new transformation is challenging because the ideal molecular requirements of the catalyst for one reaction do not always simply translate to another. In these reaction scenarios practitioners typically use the most general catalyst structure as a starting point for optimization. However, for many reaction systems and catalyst chemotypes the most general catalyst structure may be largely unknown presenting a significant limitation
in catalyst application to new reaction space. Herein, we demonstrate that comprehensive statistical models can be applied to identify the most general catalyst for many chemical systems. These inclusive statistical models that encompass many reaction types can provide information about the relevant structural requirements necessary for high enantioselectivity across a broad reaction range.
By validating this approach on diverse regions of organocatalyzed reaction space we discovered structurally distinct catalysts can in some cases provide similar levels of enantioselectivity. The second curious finding determined that the best and most popular catalyst
systems may not be equivalent. Validation of this approach on a multi-catalytic dearomatization reaction resulted in the discovery that our general catalyst findings allowed for streamlined reaction development for highly complex transformations. | Junshan Lai; Jiajing Li; Isaiah Betinol; Yutao Kuang; Jolene Reid | Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f14df91803730ec19e1fed/original/a-statistical-modeling-approach-to-catalyst-generality-assessment-in-enantioselective-synthesis.pdf |
6291c7926209e03c3554aeee | 10.26434/chemrxiv-2022-l34t8 | Cherry-picking resolvents: Recovering the valence contribution in X-ray two-photon absorption within the core--valence-separated equation-of-motion coupled-cluster response theory | Calculations of first-order response wave functions in the X-ray regime often diverge within correlated frameworks such as equation-of-motion coupled-cluster singles and doubles (EOM-CCSD), a consequence of the coupling with the valence ionization continuum. Here, we extend our strategy of introducing a hierarchy of approximations to the EOM-EE-CCSD resolvent (or, inversely, the model Hamiltonian) involved in the response equations for the calculation of X-ray two-photon absorption (X2PA) cross sections. We exploit the frozen--core core--valence--separation (fc-CVS) scheme to first decouple the core and valence Fock spaces, followed by a separate approximate treatment of the valence resolvent. We demonstrate the robust convergence of X-ray response calculations within this framework and compare X2PA spectra of small benchmark molecules with the previously reported density functional theory results. | Josefine Andersen; Kaushik Nanda; Anna Krylov; Sonia Coriani | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6291c7926209e03c3554aeee/original/cherry-picking-resolvents-recovering-the-valence-contribution-in-x-ray-two-photon-absorption-within-the-core-valence-separated-equation-of-motion-coupled-cluster-response-theory.pdf |
60c746754c8919f5b1ad2b42 | 10.26434/chemrxiv.11323742.v1 | Visible-Light-Driven Reductive Carboarylation of Styrenes with CO2 and Aryl Halides | The first example of
visible-light-driven reductive carboarylation of styrenes with CO<sub>2</sub>
and aryl halides in a regioselective manner has been achieved. A broad range of aryl iodides and bromides were compatible with this reaction. <a>Moreover, pyridyl halides, alkyl halides and even aryl
chlorides were also viable with this method.</a> These findings may stimulate
the exploration of novel visible-light-driven Meerwein arylation-addition reactions
with user-friendly aryl halides as the radical sources and the photocatalytic utilization of CO<sub>2.</sub> | Hao Wang; yuzhen gao; Chunlin Zhou; Gang Li | Organic Synthesis and Reactions; Photochemistry (Org.); Homogeneous Catalysis; Catalysis; Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746754c8919f5b1ad2b42/original/visible-light-driven-reductive-carboarylation-of-styrenes-with-co2-and-aryl-halides.pdf |
60c74688469df4ad09f43696 | 10.26434/chemrxiv.11347040.v1 | Ultrafast Formation of the Charge-Transfer State of Prodan Reveals Unique Aspects of the Chromophore Environment | <div>Lipiophilic dyes such as Laurdan and Prodan are widely used in membrane biology due to a strong bathochromic shift in emission that reports structural parameters of the membrane such as area per molecule. Disentangling the factors which control the spectral shift is complicated by the stabilization of a charge-transfer-like excitation of the dye in polar environments. Predicting the emission therefore requires modeling both the relaxation of the environment and the corresponding evolution of the excited state. Here an approach is presented in which (i) the local environment is sampled by classical molecular dynamics (MD) simulation of the dye and solvent; (ii) the electronically excited state of Prodan upon light absorption is predicted by numerical quantum mechanics (QM); (iii) iterative relaxation of the environment around the excited dye by MD coupled with evolution of the excited state is performed; (iv) the emission properties are predicted by QM. The QM steps are computed using many-body Green's functions theory in the GW approximation and the Bethe-Salpeter Equation with the environment modeled as fixed point charges, sampled in the MD simulation steps. Comparison to ultrafast time resolved transient absorption measurements demonstrates that the iterative MM/QM approach agrees quantitatively with both the polarity dependent shift in emission and the timescale over which the charge transfer state is stabilized. Together the simulations and experimental measurements suggest that evolution into the charge-transfer state is slower in amphiphilic solvents.</div> | Swapnil Baral; Matthew Phillips; Han Yan; Joseph Avenoso; Lars Gundlach; Björn Baumeier; Edward Lyman | Computational Chemistry and Modeling; Theory - Computational; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74688469df4ad09f43696/original/ultrafast-formation-of-the-charge-transfer-state-of-prodan-reveals-unique-aspects-of-the-chromophore-environment.pdf |
60c73fe3567dfe0a0eec3ae0 | 10.26434/chemrxiv.7556690.v1 | Dilute Solution Structure of Bottlebrush Polymers | <div>Bottlebrush polymers are a class of macromolecules that has recently found use</div><div>in a wide variety of materials, ranging from lubricating brushes and</div><div>nanostructured coatings to elastomeric gels that exhibit structural color. These</div><div>polymers are characterized by dense branches extending from a central backbone,</div><div>and thus have properties distinct from linear polymers. It remains a challenge</div><div>to specifically understand conformational properties of these molecules, due to</div><div>the wide range of architectural parameters that can be present in a system, and</div><div>thus there is a need to accurately characterize and model these molecules. In</div><div>this paper, we use a combination of viscometry, light scattering, and computer</div><div>simulations to gain insight into the conformational properties of dilute</div><div>bottlebrush polymers. We focus on a series of model bottlebrushes consisting of</div><div>a poly(norbornene) (PNB) backbone with poly(lactic acid) (PLA) side chains. We</div><div>demonstrate that intrinsic viscosity and hydrodynamic radius are experimental</div><div>observations \emph{sensitive} to molecular architecture, exhibiting distinct</div><div>differences with different choices of branch and backbone lengths. Informed by</div><div>the atomistic structure of this PNB-PLA system, we rationalize a coarse-grained</div><div>simulation model that we evaluate using a combination of Brownian Dynamics and</div><div>Monte Carlo simulations. We show that this exhibits quantitative matching to</div><div>experimental results, enabling us to characterize the overall shape of the</div><div>bottlebrush via a number of metrics that can be extended to more general</div><div>bottlebrush architectures.</div> | Sarit Dutta; Matthew A. Wade; Dylan J. Walsh; Damien Guironnet; Simon A. Rogers; Charles E. Sing | Polymer brushes; Polymer chains | CC BY 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fe3567dfe0a0eec3ae0/original/dilute-solution-structure-of-bottlebrush-polymers.pdf |
62eff61cfad4850c9b6531ae | 10.26434/chemrxiv-2022-mwf0b | Atomistic Insights into the Oxidation of Flat and Stepped Platinum Surfaces Using Large-Scale Machine Learning Potential-based Grand-Canonical Monte Carlo | Understanding catalyst surface structure changes under reactive conditions has become an important topic with the increasing interest in operando measurement and modelling. In this work, we develop a workflow to build machine learning potentials (MLPs) for simulating complicated chemical systems with large spatial and time scales, in which the committee model strategy equips the MLP with uncertainty estimation, enabling active learning protocol. The methods are applied to constructing PtOx MLP based on explored configurations from bulk oxides to amorphous oxidised surfaces, which cover most ordered high-oxygen-coverage platinum surfaces within an accessible energy range. This MLP is used to perform large-scale grand canonical Monte Carlo simulations to track detailed structure changes during oxidations of flat and stepped Pt surfaces, which is normally inaccessible to costly ab initio calculations. These structural evolution trajectories reveal the stages of surface oxidation without laboriously manual construction of surface models. We identify the building blocks of oxide formation and elucidate the surface oxide formation mechanism on Pt surfaces. The insightful interpretations of the oxide formation are likely to be general for other metal surfaces. We demonstrate that these large-scale simulations would be a powerful tool to investigate realistic structures and the formation mechanisms of complicated systems. | Jiayan Xu; Wenbo Xie; Yulan Han; Peijun Hu | Theoretical and Computational Chemistry; Materials Science; Catalysis; Computational Chemistry and Modeling; Machine Learning; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62eff61cfad4850c9b6531ae/original/atomistic-insights-into-the-oxidation-of-flat-and-stepped-platinum-surfaces-using-large-scale-machine-learning-potential-based-grand-canonical-monte-carlo.pdf |
60c75647ee301c4d5dc7b31b | 10.26434/chemrxiv.14103740.v2 | Electronic Structure of Ytterbium(III) Solvates – A Combined Spectro-scopic and Theoretical Study | The wide range of optical and magnetic properties of the lanthanide(III) ions is associated to their intricate electronic structures, which in contrast to lighter elements is characterized by strong relativistic effects and spin-orbit coupling. Nevertheless, computational methods are now capable of describing the ladder of electronic energy levels of the simpler trivalent lanthanide ions, as well as the lowest energy term of most of the series. The electronic energy levels result from electron configurations that are first split by spin-orbit coupling into groups of energy levels denoted by the corresponding Russel-Saunders terms. Each of these groups are then split by the ligand field into the actual electronic energy levels known as microstates or sometimes mJ levels. The ligand field splitting directly informs on coordination geometry, and is a valuable tool for determining structure and thus correlating the structure and properties of metal complexes in solution. The issue with lanthanide complexes is that the determination of complex structures from ligand field splitting remains a very challenging task. In this manuscript, the optical spectra – absorption, luminescence excitation and luminescence emission – of ytterbium(III) solvates were rec-orded in water, methanol, dimethyl sulfoxide and N,N-dimethylformamide. The electronic energy levels, that is the microstates, were resolved experimentally. Subsequently, density functional theory (DFT) calculations were used to model the structures of the solvates and ab initio relativistic complete active space self-consistent field (CASSCF) calculations were employed to obtain the microstates of the possible structures of each solvate. By comparing experimental and theoretical data, it was possible to determine both the coordination number and solution structure of each solvate. In water, methanol and N,N-dimethylformamide the solvates were found to be eight-coordinated and to have a square anti-prismatic coordination geometry. In DMSO the speciation was found to be more complicated. The robust methodology developed for comparing experimental spectra and computational results allows the solution structures of lanthanide complexes to be determined, paving the way for the design of complexes with predetermined properties. <br /> | Nicolaj Kofod; Patrick Nawrocki; Carlos Platas-Iglesias; Thomas Just Sørensen | Coordination Chemistry (Inorg.); Lanthanides and Actinides; Spectroscopy (Inorg.); Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75647ee301c4d5dc7b31b/original/electronic-structure-of-ytterbium-iii-solvates-a-combined-spectro-scopic-and-theoretical-study.pdf |
63f05bc51d2d184063aec927 | 10.26434/chemrxiv-2023-qv422-v2 | N-Borane-Substituted Cyclic Phosphine Imides (BCPIs) | Phosphine imides are ubiquitous nucleophiles/Lewis bases in modern organic chemistry. The introduction of unexplored substituents on the phosphine imidoyl nitrogen and/or phosphorus atoms should facilitate the discovery of unprecedented utility for phosphine imides. Herein, we have designed and prepared a novel class of phosphine imides known as N-borane-substituted cyclic phosphine imides (BCPIs). Experimental and theoretical analyses of the electronic structure of BCPIs demonstrate the existence of substantial negative hyperconjugation between the nitrogen and the phosphorus atoms. Given a characteristic nucleophilic/Lewis basic reactivity of BCPIs, we represent the first experimental demonstration that a 5-oxazaphosphetane species is a key intermediate in the transformation of CO2 using phosphine imides. Moreover, although it has been previously considered unlikely, the spontaneous heterolysis of a BCl bond in a BCPI-coordinated chloroborane has been directly observed, suggesting that such process is a plausible key step in the Lewis acid-promoted generation of borenium species from chloroboranes. These results thus provide evidence of two species that have been missing in contemporary organic chemistry. | Shun Nagai; Takaya Hinogami; Sensuke Ogoshi; Yoichi Hoshimoto | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2023-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f05bc51d2d184063aec927/original/n-borane-substituted-cyclic-phosphine-imides-bcp-is.pdf |
60c748b2567dfe6855ec4a4a | 10.26434/chemrxiv.11956518.v1 | Solvation Effects Drive the Selectivity in Diels-Alder Reaction Under Hyperbaric Conditions | High pressure effects on the Diels-Alder reaction in condensed phase are investigated by means oftheoretical methods, employing advanced multiscale modeling approaches based on physically groundedmodels. The simulations reveal how the increase of pressure from 1 to 10000 atm does not affect thestability of the reaction products, modifying the kinetics of the process by lowering considerably thetransition state energy. The reaction profile at high pressure remarkably differs from that at 1 atm,showing a submerged TS and a pre–TS structure lower in energy. The different solvation between endoand exo pre–TS is revealed as the driving force pushing the reaction toward a much higher preferencefor the endo product at high pressure. | Daniele Loco; Riccardo Spezia; François Cartier; Isabelle Chataigner; Jean-Philip Piquemal | Organic Synthesis and Reactions; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748b2567dfe6855ec4a4a/original/solvation-effects-drive-the-selectivity-in-diels-alder-reaction-under-hyperbaric-conditions.pdf |
60c743eff96a0091f92868c8 | 10.26434/chemrxiv.9177146.v1 | Excitation Emission Matrix Fluorescence Spectroscopy for Combustion Generated Particulate Matter Source Identification | The inhalation of particulate matter (PM) is a significant health risk associated with reduced life expectancy due to increased cardio-pulmonary disease and exacerbation of respiratory diseases such as asthma and pneumonia. PM originates from natural and anthropogenic sources including combustion engines, cigarettes, agricultural burning, and forest fires. Identifying the source of PM can inform effective mitigation strategies and policies, but this is difficult to do using current techniques. Here we present a method for identifying PM source using excitation emission matrix (EEM) fluorescence spectroscopy and a machine learning algorithm. We collected combustion generated PM2.5 from wood burning, diesel exhaust, and cigarettes using filters. Filters were weighted to determine mass concentration followed by extraction into cyclohexane and analysis by EEM fluorescence spectroscopy. Spectra obtained from each source were used as machine learning training data for source identification in mixed samples. This method can predict the presence or absence of the three laboratory sources with an overall accuracy of 89% when the threshold for classifying a source as present is 1.1 µg/m3 in air over a 24-hour sampling time. We apply this method to a small set of field samples to evaluate its effectiveness.<br /> | Jay Rutherford; Neal Dawson-Elli; Anne M. Manicone; Gregory V. Korshin; Igor V. Novosselov; Edmund Seto; Jonathan D. Posner | Environmental Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743eff96a0091f92868c8/original/excitation-emission-matrix-fluorescence-spectroscopy-for-combustion-generated-particulate-matter-source-identification.pdf |
60c74062ee301c862ec78a82 | 10.26434/chemrxiv.7718522.v1 | Uncatalysed Oxidative C‒H Amination of 9,10-Dihydro-9-Heteroanthracenes: A Mechanistic Study | A new method for the one-step C‒H amination of xanthene and thioxanthene with sulfonamides is reported, without the need for any metal catalyst. A benzoquinone is employed as a hydride (or two-electron and one-proton) acceptor. Moreover, a previously unknown and uncatalysed reaction between iminoiodanes and xanthene, thioxanthene and dihydroacridines (9,10-dihydro-9-hetero-anthracenes or dihydroheteroanthracenes) is disclosed. The reactions proceed via hydride transfer from the heteroarene substrate to the iminoiodane or benzoquinone, followed by conjugate addition of the sulfonamide to the oxidized heteroaromatic compounds. These findings may have important mechanistic implications for metal-catalysed C‒H amination processes involving nitrene transfer from iminoiodanes to dihydroheteroanthracenes. Due to the weak C‒H bond, xanthene is an often-employed substrate in mechanistic studies of C‒H amination reactions, which are generally proposed to proceed via metal-catalysed nitrene insertion, especially for reactions involving nitrene or imido complexes that are less reactive (i.e. less strongly oxidizing). However, these substrates clearly undergo non-catalysed (proton-coupled) redox coupling with amines, thus providing alternative pathways to the widely assumed metal-catalysed pathways. | Nicolaas P. van Leest; Lars grooten; Jarl Ivar van der Vlugt; Bas de Bruin | Organic Synthesis and Reactions; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74062ee301c862ec78a82/original/uncatalysed-oxidative-c-h-amination-of-9-10-dihydro-9-heteroanthracenes-a-mechanistic-study.pdf |
67cf1ec56dde43c9084bf140 | 10.26434/chemrxiv-2025-d3jzq | The key to reducing steel emissions may be using aluminum instead | Steelmaking is a major source of difficult-to-abate carbon dioxide (CO2) emissions. Here, we analyze decarbonization pathways for both aluminum and steel by considering five production routes, including the fossil fuel-based processes that are used today and fully-electrified processes under development. We find that on a $/t CO2 basis, aluminum is cheaper to decarbonize than steel over a wide range of projected electricity costs and carbon intensities. Projections for the year 2050 suggest aluminum abatement costs of $9/t CO2 and steel abatement costs of $363/t CO2 by electrification. Furthermore, we observe that if renewable electricity costs decrease enough for green steel to compete with conventional steel, aluminum may be a cost-effective substitute in many applications. Thus, in contrast to the dominant theory of change, an important option for reducing steel emissions may be substitution with low-carbon aluminum. | Samuel Faucher; Steven Davis; Ian McKay | Energy; Chemical Engineering and Industrial Chemistry; Industrial Manufacturing | CC BY 4.0 | CHEMRXIV | 2025-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cf1ec56dde43c9084bf140/original/the-key-to-reducing-steel-emissions-may-be-using-aluminum-instead.pdf |
65e1f60666c1381729f43f28 | 10.26434/chemrxiv-2024-87tgr | Surface-induced Self-Assembly of Amphiphilic Block Copolymers into Functional Bilayer Thin Films. | An scalable method for the fabrication of symmetric and asymmetric BC bilayers on solid support of any type, shape and size is proposed, in order to overcome the specific limitations of currently available techniques (notably Langmuir-Blodgett (LB) deposition and polymersome vesicle fusion (VF)). We demonstrated that this fabrication process is viable by developing a proof of concept on silicon wafers, flat and macro-scopic substrates that allow the use of a wide range of complementary state-of-the-art techniques to precisely characterize the different steps of the assembly. This type of assembly, however, is potentially possible on colloidal objects, as showed by preliminary results. The proposed fabri-cation method was done using polystyrene-block-poly(acrylic acid) block copolymer and consists of two steps: i) the formation of a monolayer of BCs by the establishment of non-covalent interactions between the substrate and the hydrophilic blocks in a non-selective solvent ii) the controlled addition of a selective solvent (water) which triggers the assembly of the second layer through hydrophobic interactions between the free and previously adsorbed hydrophobic blocks resulting in the formation of a self-assembled bilayer of BCs on a solid support. A final rinsing step allows to eliminate the excess of aggregates (micelles) generated in the solution during the second step. BC monolayers and bilayers on solid supports were obtained and characterized using various surface characterization techniques. The ability of these bilayers to encapsulate hydrophobic actives of interest for specific applications has also been highlighted using gold nanoparticles (AuNPs). Finally, the possibility to form asymmetric bilayers was demonstrated on a PS-b-PAA/PS-b -poly(vinyl pyridine) (PS-b-P2VP) system. | Jean-Paul Chapel; Christophe Schatz; Fabrice Cousin; Thierry BUFFETEAU; Martin Fauquignon; Alliny Naves; Flavia Mesquita Cabrini | Physical Chemistry; Polymer Science; Nanoscience; Polymer brushes; Self-Assembly; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e1f60666c1381729f43f28/original/surface-induced-self-assembly-of-amphiphilic-block-copolymers-into-functional-bilayer-thin-films.pdf |
640a63cfcc600523a3f102e6 | 10.26434/chemrxiv-2023-0tp5j | Structural Characterization and Bonding Analysis of [Hg{Fe(CO)5}2]2+ [SbF6]-2 | The non-classical carbonyl complex [Hg{Fe(CO)5}2]2+ [SbF6]-2 is prepared by reaction of Hg(SbF6)2 and excess Fe(CO)5 in anhydrous HF. The single-crystal X-ray structure reveals a linear Fe-Hg-Fe moiety as well as an eclipsed conformation of the eight basal CO ligands. Interestingly, the Hg-Fe bond length of 2.5745(7) Angstrom is relatively similar to the corresponding Hg-Fe bonds in literature-known [Hg{Fe(CO)4}2]2- dianions (2.52-2.55 Angstrom) which intrigued us to analyze the bonding situation in both the dications and dianions with the EDA-NOCV method. Both species are best described as Hg(0) compounds which are also confirmed by the shape of the HOMO-4 and HOMO-5 of the dication and dianion, respectively, in which the electron pair is located mainly at the Hg. Furthermore, for the dication and the dianion the sigma-backdonation from Hg into the [Fe(CO)5]22+ or the [Fe(CO)4]22- fragment is the most dominant orbital interaction and surprisingly these interaction energies are also very similar even in absolute values. The fact that both iron-based fragments are missing two electrons explains their prominent sigma-acceptor properties. | Susanne Margot Rupf; Sudip Pan; Amina Leoni Moshtaha; Gernot Frenking; Moritz Malischewski | Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Bonding; Organometallic Compounds; Crystallography – Inorganic | CC BY 4.0 | CHEMRXIV | 2023-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640a63cfcc600523a3f102e6/original/structural-characterization-and-bonding-analysis-of-hg-fe-co-5-2-2-sb-f6-2.pdf |
61851b89e04a8e1d2c2800f8 | 10.26434/chemrxiv-2021-x171c | Heterologous Biosynthesis and Genomics-Driven Derivatization of Fungal Bioactive Sesterterpenoid Variecolin | The biosynthetic gene cluster of fungal bioactive sesterterpenoids, variecolin (1) and variecolactone (2), was identified in Aspergillus aculeatus ATCC 16872. Heterologous production of 1 and 2 was achieved in Aspergillus oryzae by expressing the sesterterpene synthase VrcA and the cytochrome P450 VrcB. Intriguingly, the replacement of VrcB with homologous P450s from other fungal terpenoid pathways yielded three new variecolin analogues, one of which exhibited potent anticancer activity comparable to that of 1. | Dexiu Yan; Jemma Arakelyan; Teng Wan; Tsz Ki Chan; Dohyun Ahn; Tsz Kiu Cheung; Ho Ching Chan; Inseo Choi; Pui Yi Ho; Feijun Hu; Yujeong Kim; Hill Lam Lau; Ying Lo Law; Chi Seng Leung; Ritvik Raina; Chun Yin Tong; Kai Kap Wong; Wing Lam Yim; Maria V. Babak; Richard Y. C. Kong; Yudai Matsuda | Biological and Medicinal Chemistry; Organic Chemistry; Natural Products | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61851b89e04a8e1d2c2800f8/original/heterologous-biosynthesis-and-genomics-driven-derivatization-of-fungal-bioactive-sesterterpenoid-variecolin.pdf |
663643cf91aefa6ce12453a3 | 10.26434/chemrxiv-2024-g54bp | Identification of Novel Target DCTPP1 for Colorectal Cancer Therapy with the Natural Small-molecule Inhibitors Regulating Metabolic Reprogramming | Colorectal cancer (CRC) is one of the most common malignant tumors. Identification of new effective drug targets for CRC and exploration of bioactive small-molecules are clinically urgent. The human dCTP pyrophosphatase 1 (DCTPP1) is a newly identified pyrophosphatase regulating the cellular nucleotide pool but remains unexplored as potential target for CRC treatment. Here, twelve unprecedented chemical architectures terpene-nonadride heterodimers (1–12) and their monomers (13–20) were isolated from endophyte Bipolaris victoriae S27. Compounds 1–12 represented the first example of terpene-nonadride heterodimers, in which nonadride monomers of 1 and 2 were also first example of 5/6 bicyclic nonadrides. A series of assays showed that 2 could repress proliferation and induce cell cycle arrest, apoptotic and autophagic CRC cell death in vitro and in vivo. Clinical cancer samples data revealed that DCTPP1 was a novel target associated with poor survival in CRC. DCTPP1 was also identified as a new target protein of 2. Mechanistically, compound 2 bound to DCTPP1, inhibited its enzymatic activity, intervened with amino acid metabolic reprogramming, and exerted anti-CRC activity. Our study demonstrates that DCTPP1 was a novel potential biomarker and therapeutic target in CRC, and 2 was the first natural anti-CRC drug candidate targeting DCTPP1. | Li Feng; Xinjia Wang; Xinrui Guo; Liyuan Shi; Shihuang Su; Xinjing Li; Jia Wang; Ninghua Tan; Yi Ma; Zhe Wang | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663643cf91aefa6ce12453a3/original/identification-of-novel-target-dctpp1-for-colorectal-cancer-therapy-with-the-natural-small-molecule-inhibitors-regulating-metabolic-reprogramming.pdf |
6634c77191aefa6ce10ee886 | 10.26434/chemrxiv-2024-vghrz | How Cations - Silica Surface Interactions Affect Water Dynamics in Nanoconfined Electrolyte Solutions | Probing electrolytes behavior at the atomic level provides valuable insights into understanding the reactive transport of electrolyte solutions in nanoconfinement and help explaining and predicting the macroscopic properties of industrial or natural nanoporous materials. In this study, we focused on the behavior of water and ions in 2.6 nm silica nanocylinders filled with electrolyte solutions, XCl at 1M with X = Li, Na and Cs, monovalent cations presenting various kosmotropic/chaotropic properties. Using a combination of experiments and theoretical modeling, we analyzed the water dynamics based on three primary effects: the confinement, the electrolyte, and the interfacial ions-porous material surface interaction. Comparing the water dynamics obtained with divalent cations previously studied by Baum et al., we highlight that monovalent cations present weaker interactions with silica surfaces than divalent cations. This significantly impacts the water dynamics in addition to the confinement and electrolyte effects. This study pinpoints the importance of ions behavior within the interfacial layer and its impact on water transport in nanoconfinement. | Hassan Khoder; Bertrand Siboulet; Jacques Ollivier; Béatrice Baus-Lagarde; Diane Rébiscoul | Physical Chemistry; Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6634c77191aefa6ce10ee886/original/how-cations-silica-surface-interactions-affect-water-dynamics-in-nanoconfined-electrolyte-solutions.pdf |
679a8f11fa469535b958a862 | 10.26434/chemrxiv-2025-dc28b | Collective Intelligence of Specialized Language Models Guides Realization of de novo Chemical Synthesis | While hundreds of thousands of new chemical reactions are reported annually, efficient use of this vast collection of synthetic knowledge remains a persistent challenge in modern chemistry. Recent applications of large language models (LLMs) have shown promise, but systems that reliably work for de novo compounds and molecular transformations have remained elusive. Here we introduce MOSAIC (Multiple Optimized Specialists for AI-Driven Chemical Prediction), a computational framework that enables chemists to harness the collective knowledge of millions of reaction protocols. In contrast to existing approaches relying on agentic models, MOSAIC leverages the open-source Llama3.1-8B-instruct architecture. By training 2,489 specialized chemical experts on Voronoi-clustered reaction spaces, we establish a scalable paradigm that delivers reproducible and human-readable experimental protocols for complex syntheses. Experimental validation demonstrates MOSAIC's ability to predict and execute previously unreported transformations, including challenging reactions via Buchwald-Hartwig amination, Suzuki coupling, and olefin metathesis. We validate this approach through the successful synthesis of over 35 novel compounds spanning pharmaceuticals, materials, agrochemicals, and cosmetics. This framework establishes a new relationship between computational and experimental chemistry, providing a foundation for accelerated chemical discovery across disciplines. | Haote Li; Sumon Sarkar; Wenxin Lu; Patrick Loftus; Tianyin Qiu; Yu Shee; Abbigayle Cuomo; John-Paul Webster; H. Ray Kelly; Vidhyadhar Manee; Sanil Sreekumar; Frederic Buono; Robert Crabtree; Timothy Newhouse; Victor Batista | Theoretical and Computational Chemistry; Organic Chemistry; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Process Chemistry; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679a8f11fa469535b958a862/original/collective-intelligence-of-specialized-language-models-guides-realization-of-de-novo-chemical-synthesis.pdf |
63c835ea5ab3135f8eac3f4a | 10.26434/chemrxiv-2023-w286t | A Scalable Total Synthesis of Portimine A and B Reveals the Basis of Their Potent and Selective Anti-cancer Activity | Marine derived cyclic imine toxins, portimine A and B, have attracted extensive attention owing to their intriguing chemical structure and promising anti-cancer therapeutic potential. However, access to large quantities is currently unfeasible and the molecular mechanism behind their potent activity is unknown. To address this, a scalable 15-step total synthesis of portimines is presented, which benefits from the logic used in two-phase terpenoid synthesis along with unique tactics such as exploiting ring-chain tautomerization and skeletal reorganization to minimize protecting group chemistry through “self-protection”. Critically, this total synthesis enabled a structural reassignment of portimine B and an in-depth functional evaluation of portimine A, revealing that it induces apoptosis selectively in human cancer cell lines with high potency. Finally, practical access to the portimines and analogs thereof simplified the development of photoaffinity analogs, which were used in chemical proteomic experiments to identify a primary target of portimine A as the 60S ribosomal export protein NMD3. | Junchen Tang; Weichao Li; Tzu-Yuan Chiu; Zengwei Luo; Christine Chong; Qijia Wei; Francisco Martínez-Peña; Nathalia Gazaniga; Yi Yang See; Luke Lairson; Christopher Parker; Phil Baran | Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Organic Synthesis and Reactions; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2023-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c835ea5ab3135f8eac3f4a/original/a-scalable-total-synthesis-of-portimine-a-and-b-reveals-the-basis-of-their-potent-and-selective-anti-cancer-activity.pdf |
61e00def4a603d65552ea644 | 10.26434/chemrxiv-2022-983h7 | Mechanochemically Synthesised Dicyanamide Hybrid Organic-Inorganic Perovskites and their Melt-Quenched Glasses | Here we present efficient and scalable mechanochemical formation of hybrid organic-inorganic perovskites of the form [TPrA][M(dca)₃] (M = Mn²⁺, Co²⁺) and the subsequent formation of their bulk melt-quenched glass samples. The thermal, chemical and adsorptive properties of the materials are also investigated. | Lauren N. McHugh; Michael F. Thorne; Ashleigh M. Chester; Martin Etter; Krunoslav Užarević; Thomas D. Bennett | Materials Science; Inorganic Chemistry; Hybrid Organic-Inorganic Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e00def4a603d65552ea644/original/mechanochemically-synthesised-dicyanamide-hybrid-organic-inorganic-perovskites-and-their-melt-quenched-glasses.pdf |
61a390b3c481c3360dfbc1e8 | 10.26434/chemrxiv-2021-7wchd | Dynamical Component Exchange in a Model Phase Separating System: an NMR-based Approach | Biomolecular phase separation plays a key role in spatial organization of cellular activities. Dynamic formation and rapid component exchange between phase separated cellular bodies and their environment are crucial for their function. Here, we employ a well-established phase separating model system, namely, triethylamine (TEA)-water mixture, and develop an NMR approach to detect the exchange of scaffolding TEA molecules between separate phases and determine the underlying exchange rate. We further demonstrate how the advantageous NMR properties of fluorine nuclei provide access to otherwise inaccessible exchange processes of a client molecule. The developed NMR-based approach allows quantitative monitoring of the effect of regulatory factors on component exchange and facilitates “exchange”-based screening and optimization of small molecules against druggable biomolecular targets located inside condensed phases. | Christian F. Pantoja; Markus Zweckstetter; Nasrollah Rezaei-Ghaleh | Physical Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Biophysical Chemistry; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a390b3c481c3360dfbc1e8/original/dynamical-component-exchange-in-a-model-phase-separating-system-an-nmr-based-approach.pdf |
60c74d37842e6540aedb3428 | 10.26434/chemrxiv.12360722.v2 | On the Local Charge Inhomogeneity and Lithium Distribution in the Superionic Argyrodites Li6PS5X (X = Cl, Br, I) | The lithium-argyrodites Li<sub>6</sub>PS<sub>5</sub><i>X</i> (<i>X</i> = Cl, Br, I) exhibit high lithium-ion conductivities, making them promising candidates for use in solid-state batteries. These solid electrolytes can show considerable substitutional <i>X</i><sup>−</sup>/S<sup>2−</sup> anion-disorder, with greater disorder typically correlated with higher lithium-ion conductivities. The atomic-scale effects of this anion site-disorder within the host lattice—in particular how lattice disorder modulates the lithium substructure—are not well understood. Here, we characterize the lithium substructure in Li<sub>6</sub>PS<sub>5</sub><i>X</i> (<i>X </i>= Cl, Br, I) as a function of temperature and anion site-disorder, using Rietveld refinements against temperature-dependent neutron diffraction data. Analysis of these high-resolution diffraction data reveals an additional lithium position previously unreported for Li<sub>6</sub>PS<sub>5</sub><i>X</i>argyrodites, suggesting that the lithium conduction pathway in these materials differs from the most common model proposed in earlier studies. Analysis of the Li<sup>+</sup> positions and their radial distributions reveals that greater inhomogeneityof the local anionic charge, due to <i>X</i><sup>−</sup>/S<sup>2−</sup> site-disorder, is associated with more spatially-diffuse lithium distributions. This observed coupling of site-disorder and lithium distribution provides a possible explanation for the enhanced lithium transport in anion-disordered lithium argyrodites, and highlights the complex interplay between anion configuration and lithium substructure in this family of superionic conductors. | Nicolo Minafra; Marvin Kraft; Tim Bernges; Cheng Li; Roman Schlem; Benjamin Morgan; Wolfgang Zeier | Solid State Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d37842e6540aedb3428/original/on-the-local-charge-inhomogeneity-and-lithium-distribution-in-the-superionic-argyrodites-li6ps5x-x-cl-br-i.pdf |
62b58c395983a931c66d2eaf | 10.26434/chemrxiv-2022-3tvpq | Thermally induced oxygen vacancies in BiOCl nanosheets and their impact on photoelectrochemical performance | Oxygen vacancies (OVs) have been reported to significantly alter the photocatalytic properties of BiOCl nanosheets. However, their formation mechanism and their role in the enhancement of photoelectrochemical performance remain unclear. In this work, thermally induced oxygen vacancies are introduced in BiOCl nanosheets by annealing in He atmosphere at various temperatures and their formation mechanism is investigated by in-situ diffuse reflectance infrared (DRIFTS) measurements. The influence of OVs on band offset, carrier concentrations and photoelectrochemical performance are systematically studied. The results show that (1) the surface of BiOCl nanosheets is extremely sensitive to temperature and defects are formed at temperatures as low as 200 °C in inert atmosphere. (2) The formation of bulk OVs in BiOCl is identified by a combination of XPS and EPR experiments. (3) The photocurrent of BiOCl is limited by the concentration of charge carriers and shallow defect states induced by bulk oxygen vacancies, while the modulation of these parameters can effectively increase light absorption and carrier concentration leading to an enhancement of photoelectrochemical performance of BiOCl. | Xiaofeng Wu; Freddy E. Oropeza; Daan den Boer; Peter Kleinschmidt; Thomas Hannappel; Dennis G. H. Hetterscheid; Emiel J. M. Hensen; Jan Philipp Hofmann | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b58c395983a931c66d2eaf/original/thermally-induced-oxygen-vacancies-in-bi-o-cl-nanosheets-and-their-impact-on-photoelectrochemical-performance.pdf |
62011f60e0f52961deaa45b1 | 10.26434/chemrxiv-2021-ttc5g-v2 | An expanded palette of fluorogenic HaloTag probes with enhanced contrast for targeted cellular imaging | We report the development of HaloTag fluorogens based on dipolar flexible molecular rotor structures. By modulating the electron donating and withdrawing groups, we have tuned the absorption and emission wavelengths to design a palette of fluorogens with emissions spanning the green to red range. The probes were studied in glycerol and in presence of HaloTag and exhibited good fluorogenic properties thanks to a viscosity-sensitive emission. In live-cell confocal imaging, the fluorogens yielded only a very low non-specific signal that enabled wash-free targeted imaging of intracellular organelles and proteins with good contrast. | Sylvestre Bachollet; Yuriy Shpinov; Fanny Broch; Hela Benaissa; Arnaud Gautier; Jean-Maurice Mallet; Blaise Dumat | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62011f60e0f52961deaa45b1/original/an-expanded-palette-of-fluorogenic-halo-tag-probes-with-enhanced-contrast-for-targeted-cellular-imaging.pdf |
671bf31983f22e421433b46a | 10.26434/chemrxiv-2024-zq14j | A Reliable, Colloidal Syntheses Method of the Chalcogenide Perovskite, BaZrS3, and Related ABS3 Nanomaterials (A = Sr, Ba; B = Ti, Zr, Hf): Towards Thin-Film Device Applications | Recently, chalcogenide perovskites, of the form ABX3, where typically A = alkaline earth metals Ca, Sr, or Ba; B = group IV transition metals Zr or Hf; and X = chalcogens S or Se, have become of interest for their potential optoelectronic properties. In this work, we build upon recent studies and show a general synthesis protocol, involving the use of carbon disulfide insertion chemistry, to generate highly reactive precursors that can be used towards the colloidal synthesis of numerous ABS3 nanomaterials, including BaTiS3, BaZrS3, BaHfS3, α-SrZrS3 and α-SrHfS3. We overcome the shortcomings in the current literature where BaZrS3 nanoparticles are synthesized in separate phases via colloidal methods and lack a reproducible protocol for orthorhombic perovskite nanoparticles. We present a high-temperature, hot-injection method that reliably controls the formation of the colloidal BaZrS3 nanoparticles with the Pnma orthorhombic distorted perovskite structure. We show that the alternate phase, most notably denoted by its extra peaks in the pXRD pattern, is distinct from the distorted perovskite phase as it has a different bandgap value obtained via UV-vis measurements. We also show that the reaction byproducts, resulting from the use of oleylamine and CS2, have their own photoluminescence (PL) and their residual presence on the surface of the nanoparticles complicates the interpretation of PL from the nanoparticles. The utility of these nanomaterials is also assessed via the measurement of their absorption properties and in the form of highly stable colloidal inks for the fabrication of homogeneous, crack-free thin films of BaZrS3 nanoparticles. | Daniel Hayes; Shubhanshu Agarwal; Kiruba Catherine Vincent; Izoduwa Aimiuwu; Apurva Pradhan; Madeleine Uible; Suzanne Bart; Rakesh Agrawal | Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671bf31983f22e421433b46a/original/a-reliable-colloidal-syntheses-method-of-the-chalcogenide-perovskite-ba-zr-s3-and-related-abs3-nanomaterials-a-sr-ba-b-ti-zr-hf-towards-thin-film-device-applications.pdf |
60c73d76842e656f60db1794 | 10.26434/chemrxiv.5813979.v1 | Non-Plasmonic SERS with Silicon: Is It Really Safe? New Insights into Opto-Thermics of Core/Shell Microbeads | <p>Here we
investigate for the first time the opto-thermal behavior of SiO<sub>2</sub>/Si
core/shell microbeads (Si-rex) irradiated with three common Raman laser sources
(lambda=532, 633, 785 nm) under real working conditions. We obtained an
experimental proof of the critical role played by bead size and aggregation in
heat and light management, demonstrating that in the case of strong
opto-thermal coupling the temperature can exceed that of the melting points of
both core and shell components. In addition, we also show that weakly coupled
beads can be utilized as stable substrates for plasmon-free SERS experiments.</p> | Nicolò Bontempi; Irene Vassalini; Stefano Danesi; Matteo Ferroni; Paolo Colombi; Ivano Alessandri | Core-Shell Materials; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2018-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d76842e656f60db1794/original/non-plasmonic-sers-with-silicon-is-it-really-safe-new-insights-into-opto-thermics-of-core-shell-microbeads.pdf |
67a32debfa469535b920425b | 10.26434/chemrxiv-2025-lj16r-v2 | Surface charge overrides protein corona formation in determining the cytotoxicity, cellular uptake, and biodistribution of silver nanoparticles | Silver nanoparticles (AgNPs) hold great promise in biomedical applications due to their unique properties and potential for specific tissue targeting. However, the clinical translation of nanoparticle-based therapeutics remains challenging, primarily due to an incomplete understanding of how nanoparticle properties influence interactions at the nano-bio interface, as well as the role of surface-adsorbed proteins (i.e. protein corona) in modulating nanoparticle-cell interactions.
This study demonstrates that surface charge has a greater influence than protein corona formation in determining the cytotoxicity, cellular uptake, and biodistribution of AgNPs. Using negatively and positively charged AgNPs, we show that while protein corona formation is essential for ensuring nanoparticle availability for cellular interactions, the adsorption of biomolecules is non-specific and independent of surface charge. Conversely, surface charge significantly influences the interactions of AgNPs with cells. Positively charged nanoparticles exhibit enhanced cellular uptake, preferential accumulation in lysosomes, and pronounced mitochondrial damage compared to their negatively charged counterparts, resulting in greater cytotoxic effects. This effect is particularly evident in human breast cancer cells, where negatively charged nanoparticles show minimal uptake and cytotoxicity. These findings demonstrate that surface charge is the primary factor governing nanoparticle-cell interactions, rather than protein corona formation. Nonetheless, the protein corona plays a critical role in stabilizing nanoparticles within physiological environments.
| Marianna Barbalinardo; Francesca Chiarini; Gabriella Teti; Francesca Paganelli; Elisa Mercadelli; Andrea Bartoletti; Andrea Migliori; Manuela Piazzi; Jessika Bertacchini; Paola Sena; Alessandra Sanson; Mirella Falconi; Carla Palumbo; Massimiliano Cavallini; Denis Gentili | Materials Science; Nanoscience; Biological Materials; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a32debfa469535b920425b/original/surface-charge-overrides-protein-corona-formation-in-determining-the-cytotoxicity-cellular-uptake-and-biodistribution-of-silver-nanoparticles.pdf |
60c77416bdbb89f583a3b1ba | 10.26434/chemrxiv.14368838.v2 | Surface Molecule Manipulated Pt/TiO2 Catalysts for Selective Hydrogenation of Cinnamaldehyde | <p>Surface
states—the electronic states emerging as a solid material terminates at a
surface—are usually vulnerable to contaminations and defects. This fundamental
limitation has prohibited systematic studies of the potential role of surface
states in surface reactions and catalysis, especially in more realistic
environments. Herein, we use selective hydrogenation of <a>cinnamaldehyde</a>
(CAL) on <a>platinum-covered titanium oxide</a> (Pt@P25) as
a prototype reaction, and show that the competitive exchange of extra-introduced
species (sodium hydroxide and sodium formate) with spontaneously formed weak
bound carbonate and bicarbonate anions at Pt NPs can reconstruct the surface
states, which directs the preferred adsorption of the conjugated C=O and C=C
double bonds of CAL, and consequently, results in highly efficient synthesis of
unsaturated alcohol cinnamyl alcohol (COL) and saturated aldehyde
hydrocinnamaldehyde (HCAL) with high selectivity of 98.9% and 99.5%, respectively.
Our concept of restructured surface states to tune the chemoselectivity of α, β-unsaturated
aldehydes triggered by the selective adsorption of alien molecules may lead to
new design principles of heterogeneous catalysts, beyond the conventional
d-band theory.</p> | Ran Tao; Bing-Qian Shan; Hao-Di Sun; Meng Ding; Qing-Song Xue; Jin-Gang Jiang; Wu Peng; Kun Zhang | Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c77416bdbb89f583a3b1ba/original/surface-molecule-manipulated-pt-ti-o2-catalysts-for-selective-hydrogenation-of-cinnamaldehyde.pdf |
60c745d8f96a0066b9286c53 | 10.26434/chemrxiv.10274408.v1 | Amorphous Carbon Against Reduced Graphene Oxide in Li- and Na-Ion Electrochemical Storage Devices: The Case of Nb2O5 | Two-dimensional (2D)
reduced graphene oxide (rGO) is often combined with metal oxides for
energy-storage applications, owing to its unique properties. Here, we show that
amorphous carbon sources, such as organic molecules, can be more efficient in
controlling the size of small metal oxide particles and in achieving uniform
carbon-oxide contacts, which benefits the energy-storage performance. A
composite made of Nb<sub>2</sub>O<sub>5</sub> and amorphous carbon (using
1,3,5-triphenylbenzene as carbon source) outperforms the Nb<sub>2</sub>O<sub>5</sub>-rGO
counterpart as high rate anode electrode material in Li-ion and Na-ion
half-cells and hybrid supercapacitors, delivering specific capacities of 134
mAh g<sup>-1</sup> at 25C against 98 mAh g<sup>-1</sup> for the rGO-based
composite (in Li electrolyte) and 125 mAh g<sup>-1</sup> at 20C against 98 mAh
g<sup>-1</sup> (in Na electrolyte). These findings suggest that amorphous
carbon sources and the development of amorphous carbon-based composites for
Li-ion and Na-ion energy-storage devices are worthy of more attention and
research efforts than those currently given compared to 2D rGO-based
composites. | Xianying Han; Patrícia Russo; Claudia Triolo; Saveria Santangelo; Nicolas Goubard-Bretesché; Nicola Pinna | Nanostructured Materials - Nanoscience; Electrochemistry; Solid State Chemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745d8f96a0066b9286c53/original/amorphous-carbon-against-reduced-graphene-oxide-in-li-and-na-ion-electrochemical-storage-devices-the-case-of-nb2o5.pdf |
648e344d4f8b1884b772472b | 10.26434/chemrxiv-2023-f23m6 | Understanding Catalytic Mechanisms and Cathode Interface Kinetics in Non-Aqueous Mg-CO2 Batteries | We leverage first-principles density functional theory (DFT) calculations to understand the electrocatalytic processes in Mg-CO2 batteries, considering ruthenium oxide (RuO2) as an archetypical cathode catalyst. Our goal is to establish a mechanistic framework for understanding the charging and discharging reaction pathways and their influence on overpotentials. Interestingly, we discover that Mg adsorption energies are enhanced, leading to the activation of CO2. On the RuO2 (211) surface, we predict that MgC2O4 will form as the discharge product due to its lower overpotential compared to MgCO3. However, MgC2O4 is thermodynamically unstable and expected to decompose into MgCO3, MgO, and carbon (C) as final discharge products. Through Bader charge analysis, we investigate the covalent interactions between intermediates and catalyst sites. We find that CO2 is inactivated due to negligible electron transfer, making the formation of carbonate (CO32-) and oxalate (C2O42-) intermediates thermodynamically unfavorable. Moreover, we study the electrochemical free energy profiles of the most favorable reaction pathways and determine discharge and charge overpotentials of 1.30 V and 1.35 V, respectively. Our results underscore the importance of catalyst design for the cathode material to overcome performance limitations in non-aqueous Mg-CO2 batteries. | Rahul Jayan; Md Mahbubul Islam | Theoretical and Computational Chemistry; Catalysis; Energy; Theory - Computational; Electrocatalysis; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2023-06-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648e344d4f8b1884b772472b/original/understanding-catalytic-mechanisms-and-cathode-interface-kinetics-in-non-aqueous-mg-co2-batteries.pdf |
6701695812ff75c3a18ac11a | 10.26434/chemrxiv-2024-hzx0w-v2 | On the Relativistic Nature of Light: From the Relativistic Interpretation of Planck’s Equation to Theoretical Estimation of Photon’s Intrinsic Properties | This study highlights a previously unnoticed peculiarity of the relativistic Doppler effect, which arises when considering the indistinguishability of photons that are identical in one reference frame but differ across others. To address this issue, the Light Intrinsic Frame of Reference (LIFOR) is proposed, defined as a specific frame where a photon is observed with its intrinsic properties, including a specific wavelength, period, and energy-equivalent-mass. The proposed theory maintains the constancy of the speed of light, aligns fully with special relativity, and explains frequency shifts via Lorentz transformations. Additionally, it provides a relativistic interpretation for Planck’s radiation energy quantization, and enables experimental quantification of photons' intrinsic properties. | Amin Alibakhshi | Theoretical and Computational Chemistry; Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6701695812ff75c3a18ac11a/original/on-the-relativistic-nature-of-light-from-the-relativistic-interpretation-of-planck-s-equation-to-theoretical-estimation-of-photon-s-intrinsic-properties.pdf |
6562552a29a13c4d47fb560a | 10.26434/chemrxiv-2023-r1qn9 | Diagram-based Input for Large Language Models to Support Accessible STEM Learning | To meet the accessibility needs of students who are blind or have low vision (BLV), detailed textual descriptions of STEM diagrams within interactive learning tools are cre-ated in real-time and correspond to the configurations of the interactive software system. The descriptions are read by screen readers as alternative (alt) text to provide infor-mation for BLV students to compose mental representa-tions of the diagram. These descriptions provide a unique bridge from the visual language of STEM diagrams to natural language of Large Language Models (LLMs). By interfacing with an LLM, these descriptions are used for personalized exploration by the BLV user and to guide all learners through a defined pedagogical pathway. Results from a usability study with four BLV adults are reported. | Sarah E. Wegwerth; Alexa Urrea; Julia Winter | Chemical Education | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6562552a29a13c4d47fb560a/original/diagram-based-input-for-large-language-models-to-support-accessible-stem-learning.pdf |
64472acee4bbbe4bbf33711b | 10.26434/chemrxiv-2023-42rq1-v2 | Electronic Couplings for Singlet Fission Processes Based on The Fragment Particle-Hole Densities | A new diabatization scheme is proposed to calculate the electronic couplings for the singlet fission process in multichromophoric systems. In this approach, a robust descriptor that treats single and multiple excitations on an equal footing is adopted to quantify the localization degree of the particle and hole densities of the electronic states. By maximally localizing the particles and holes in terms of predefined molecular fragments, quasi-diabatic states with
well-defined characters (locally excited, charge transfer, correlated triplet pair, etc.) can be automatically constructed as the linear combinations of the adiabatic ones, and the electronic couplings can be directly obtained. This approach is very general in that it applies to electronic
states with various spin multiplicities and can be combined with various kinds of preliminary electronic structure calculations. Due to the high numerical efficiency, it is able to manipulate more than 100 electronic states in diabatization. The applications to the tetracene dimer
and trimer reveals that high-lying multiply-excited charge transfer states have significant influences on both the formation and separation of the correlated triplet pair, and can even enlarge the coupling for the latter process by one order of magnitude. | Yu-Chen Wang; Shishi Feng; Yi Kong; Xunkun Huang; WanZhen Liang; Yi Zhao | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2023-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64472acee4bbbe4bbf33711b/original/electronic-couplings-for-singlet-fission-processes-based-on-the-fragment-particle-hole-densities.pdf |
60c75113842e653ed6db3b20 | 10.26434/chemrxiv.13110710.v1 | Redesigning a “Writing for Chemists” Course Using Specifications Grading | The Department of Chemistry at the University of California, Irvine (UCI) instituted an
upper-division “Writing for Chemists” course in fall 2017 that fulfills part of UCI’s writing
graduation requirement. During the 2019-2020 school year, we re-designed the course using a
specifications grading system with the following goals: 1) to teach students how to develop their
own writing practice, while mastering chemistry discipline-specific writing conventions, 2) to
provide students with frequent and constructive instructor and teaching assistant (TA)
feedback by providing ample revision opportunities, 3) to increase transparency in how
students can achieve course SLOs, and 4) to provide students with consistent and clear
assessment rubrics. This specifications grading approach uses a high-pass, low-pass,
unsatisfactory system predicated on whether students meet a certain number of criteria for
each assignment. Achievement of Student Learning Outcomes (SLOs) was assessed using
criteria instead of points so that instructors and students could more objectively measure
student learning. Standardized rubrics and a student grade tracker helped students
understand the relationship between meeting criteria, achieving SLOs, and earning grades.
Students completed surveys at the end of the course to determine if their writing habits and
attitudes towards writing changed. After the course, students self-reported increased
propensities to pre-write and edit, and several students mentioned that they appreciated the
transparency of the specifications rubrics and the control the specifications system gave them
over their grades. | Stephen Mang; Kate J. McKnelly; Michael Morris | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75113842e653ed6db3b20/original/redesigning-a-writing-for-chemists-course-using-specifications-grading.pdf |
646e2707e64f843f41b37340 | 10.26434/chemrxiv-2023-kqf82 | Quantitative prediction of excited-state decay rates for radical anion photocatalysts | We present a computational approach for predicting key properties of organic radical anions, including excited-state lifetimes and redox potentials. The approach shows good agreement with experimental data and has potential for in silico screening to facilitate the rational design of photocatalysts. | Leandro D. Mena ; Jose L. Borioni ; Sofia Caby; Patrick Enders; Miguel Argüello Cordero ; Franziska Fennel ; Robert Francke ; Stefan Lochbrunner ; Javier Ivan Bardagi | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Photocatalysis; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646e2707e64f843f41b37340/original/quantitative-prediction-of-excited-state-decay-rates-for-radical-anion-photocatalysts.pdf |
67aa7e516dde43c9085379a7 | 10.26434/chemrxiv-2025-dndx6 | What can be learned from the electrostatic environments within nitrogenase enzymes? | Nitrogen fixation is a fundamental, and yet challenging, chemical transformation due to the intrinsic inertness of dinitrogen (N₂). Whereas industrial ammonia synthesis relies on the energy-intensive Haber–Bosch process, nitrogenase enzymes achieve this transformation under ambient conditions—yet at the expense of a remarkably high ATP demand. Understanding their mode of operation could inspire the development of more efficient synthetic catalysts. In this study, we scrutinize the role of electrostatics in nitrogenase’s active site, surrounding the so-called M-cluster. Strikingly, all M-clusters reveal similar trends, exhibiting distinct electrostatic environments at the metal sites that have been proposed as potential N2-coordination sites. Specifically, a strong local electric field pointing away from the Fe2 site favors the cleavage of the Fe6–S–Fe2 sulfido bridge, exposing the Fe6 center for N₂ binding. Moreover, an oriented long-range electric field along the Fe2–Fe6 axis is identified, which may assist in N₂ activation towards hydrogenation, once the nitrogen takes on a bridging configuration between both metal sites. Our findings suggest that nitrogenases likely exploit electrostatic effects in an unconventional manner; rather than directly favoring the coordination of N2 to the M-cluster, they primarily modulate the kinetics (and thermodynamics) of key mechanistic steps preceding, and following, the absorption step. Overall, this study highlights the importance of local electric fields in enzymatic catalysis, even for substrates that have only limited susceptibility to electric fields, and provides insights that could inform the design of improved nitrogen fixation catalysts. | Thijs Stuyver; Olena Protsenko; Davide Avagliano; Thomas Ward | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Biology; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2025-02-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67aa7e516dde43c9085379a7/original/what-can-be-learned-from-the-electrostatic-environments-within-nitrogenase-enzymes.pdf |
6554a402dbd7c8b54b4ece25 | 10.26434/chemrxiv-2023-l4t9j-v2 | The tautomer-specific excited state dynamics of 2,6-diaminopurine using REMPI and quantum chemical calculations | 2,6-diaminopurine (2,6-dAP) is an alternative nucleobase that potentially played a role in prebiotic chemistry. We studied its excited state dynamics in the gas phase by REMPI, IR-UV hole burning, and ps pump-probe spectroscopy and performed quantum chemical calculations at the SCS-ADC(2) level of theory to interpret the experimental results. We found the 9H tautomer to have a small barrier to ultrafast relaxation via puckering of its 6-membered ring. The 7H tautomer has a larger barrier to reach a conical intersection and also has a sizable triplet yield. These results are discussed relative to other purines, for which 9H tautomerization appears to be more photostable than 7H and homosubstituted purines appear to be less photostable than heterosubstituted or singly substituted purines. | Gregory Gate; Ann Williams; Samuel Boldissar; Jiri Sponer; Rafał Szabla; Mattanjah de Vries | Physical Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6554a402dbd7c8b54b4ece25/original/the-tautomer-specific-excited-state-dynamics-of-2-6-diaminopurine-using-rempi-and-quantum-chemical-calculations.pdf |
66c35bec20ac769e5f14055c | 10.26434/chemrxiv-2024-gql2x | Au···I Coinage Bonds: Boosting the Efficiency of Photoluminescence and Solid-State Molecular Motion | Coinage bonds, a type of non-covalent interaction, occur between group 11 elements (Au, Ag, Cu) with electron donor groups. Despite theoretical validation, empirical evidence has been limited. In this study, an AIE-active gold(I) complex, [(4-ClPh)3PAuI] (ITCPAu), which exhibits Au···I coinage bonds, was revealed based on the single-crystal X-ray diffraction and theoretical calculations. Further examination of the luminescence properties of the ITCPAu revealed multi-switchable behaviors, including mechanochromism and thermochromism. Nearly pure white light emission was achieved with Commission Internationale de L’Eclairage (CIE) 1931 chromaticity coordinates of (0.30, 0.31) by grinding the green-emissive ITCPAu monomer crystals. Moreover, visualization and manipulation of solid-state molecular motions (SSMMs) in the yellow-emissive ITCPAu dimer crystals, driven by the robust Au···I coinage bonds, were revealed through a combination of crystal engineering and luminescent properties. Furthermore, to support the robust Au···I coinage bonds, a versatile carrier for small solvent molecules in crystal lattices was developed for uptake and release. Our findings provide experimental and theoretical evidence for Au···I coinage bonds, highlighting their ability to boost photoluminescence quantum yield (PLQY) and SSMMs, emphasizing their potential in developing smart materials with stimuli-responsive properties. | Xueqian Zhao; Junyi Gong; Zikang Li; Linli Xu; Herman H. Y. Sung; Ian D. Williams; Jacky W. Y. Lam; Zheng Zhao; Ben Zhong Tang; Wai-Yeung Wong | Organic Chemistry; Materials Science; Aggregates and Assemblies | CC BY NC 4.0 | CHEMRXIV | 2024-08-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c35bec20ac769e5f14055c/original/au-i-coinage-bonds-boosting-the-efficiency-of-photoluminescence-and-solid-state-molecular-motion.pdf |
664c8f2291aefa6ce195ef6f | 10.26434/chemrxiv-2024-83qmp | Machine-learning prediction of facet-dependent CO coverage on Cu electrocatalysts | Copper-based electrocatalysts, which hold great promise in selectively reducing CO2 into multicarbon products, have attracted a lot of recent interest, both experimentally and theoretically. While many studies have suggested a strong dependence of catalytic selectivity on the concentration of the *CO reaction intermediate on Cu surface, it remains challenging for a direct experimental probe of the CO coverage. This necessitates a reliable computational method that can accurately establish the theoretical coverage-dependent phase diagram of CO adsorbates on the catalyst. Here we propose a scheme composed of density functional theory (DFT) calculations, machine-learning force fields (MLFF) and graph neural networks (GNN) as a solution. This method enables a fast screening of 7 million adsorption configurations based on a small set of DFT data, with a balance between accuracy and efficiency tuned by the combinatorial use of MLFF and GNN models. We have investigated 8 different Cu facets, and discovered that the high-index facets such as (310), (210) and (322) exhibit a much higher CO coverage than the low-index counterparts such as (111), leading to an increased opportunity for C-C coupling for the former. Our results can provide a new perspective for the understanding of the fundamental role of CO coverage on Cu surface for electrochemical CO2 reduction. | Shanglin Wu; Shisheng Zheng; Wentao Zhang; Mingzheng Zhang; Shunning Li; Feng Pan | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664c8f2291aefa6ce195ef6f/original/machine-learning-prediction-of-facet-dependent-co-coverage-on-cu-electrocatalysts.pdf |
60c74db49abda2e79cf8d4ea | 10.26434/chemrxiv.9640814.v4 | Deep Learning for Variational Multi-Scale Molecular Modeling | Molecular simulations are widely applied in the study of chemical and bio-physical systems. However, the<br />accessible timescales of atomistic simulations are limited, and extracting equilibrium properties of systems<br />containing rare events remains challenging. Two distinct strategies are usually adopted in this regard: either<br />sticking to the atomistic level and performing enhanced sampling, or trading details for speed by leveraging<br />coarse-grained models. Although both strategies are promising, either of them, if adopted individually,<br />exhibits severe limitations. In this paper we propose a machine-learning approach to ally both strategies so<br />that simulations on different scales can benefit mutually from their cross-talks: Accurate coarse-grained (CG)<br />models can be inferred from the fine-grained (FG) simulations through deep generative learning; In turn, FG<br />simulations can be boosted by the guidance of CG models via deep reinforcement learning. Our method<br />defines a variational and adaptive training objective which allows end-to-end training of parametric<br />molecular models using deep neural networks. Through multiple experiments, we show that our method is<br />efficient and flexible, and performs well on challenging chemical and bio-molecular systems.
<br /> | Jun Zhang; Yaokun Lei; Yi Isaac Yang; Yi Qin Gao | Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74db49abda2e79cf8d4ea/original/deep-learning-for-variational-multi-scale-molecular-modeling.pdf |
64147a7b2bfb3dc251ed2424 | 10.26434/chemrxiv-2023-8w6k6 | Cytoplasmic accumulation and permeability of antibiotics in Gram positive and Gram negative bacteria visualized in real-time via a fluorogenic tagging strategy | In this study, we describe a real-time live cell assay for compound accumulation and permeability in both Gram positive and Gram negative bacteria. The assay utilizes a novel fluorogenic tagging strategy that permits direct visualization of compound accumulation dynamics in the cytoplasm of live cells, unobscured by washing or other processing steps. Quantitative differences could be reproducibly measured by flow cytometry at compound concentrations below the limit of detection for MS-based approaches. We establish the fluorogenic assay in E. coli and B. subtilis and compare the intracellular accumulation of two antibiotics, ciprofloxacin and ampicillin, with related pharmacophores in these model Gram negative and Gram positive bacteria. | Scott Squire; Sepehr Sebghati; Ming Hammond | Biological and Medicinal Chemistry; Organic Chemistry; Bioengineering and Biotechnology; Chemical Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64147a7b2bfb3dc251ed2424/original/cytoplasmic-accumulation-and-permeability-of-antibiotics-in-gram-positive-and-gram-negative-bacteria-visualized-in-real-time-via-a-fluorogenic-tagging-strategy.pdf |
60c7553bbdbb8992baa3a7bd | 10.26434/chemrxiv.14055398.v1 | Spatial and Temporal Distributions of Polycyclic Aromatic Hydrocarbons in Sediments from the Canadian Arctic Archipelago | <p>The concentrations of 23 polycyclic aromatic hydrocarbons (PAHs; 16 parent and 7 alkylated PAHs) in 113 surface marine sediment samples, 13 on-land sediment samples and 8 subsampled push cores retrieved from the Canadian Arctic Archipelago (CAA) were calculated. PAHs were extracted via accelerated solvent extraction (ASE) and quantified via gas chromatography-mass spectrometry (GC-MS). The sums of the concentrations 16 PAHs in the surface sediments ranged from 7.8 to 247.7 ng g<sup>-1</sup> (dry weight [dw]) basis). The PAH inputs to the sediments have remained constant during the last century and agree with the results obtained for the surface sediments. Diagnostic ratios indicated that the PAHs in the CAA mainly originate from natural petrogenic sources, with some pyrogenic sources. Temporal trends did not indicate major source shifts and largely indicated petrogenic inputs. Overall, the sediments retrieved from the CAA have low PAH concentrations that are mainly natural.</p> | Anne Corminboeuf; Jean-Carlos Montero-Serrano; Richard St-Louis | Geochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7553bbdbb8992baa3a7bd/original/spatial-and-temporal-distributions-of-polycyclic-aromatic-hydrocarbons-in-sediments-from-the-canadian-arctic-archipelago.pdf |
60c751e4337d6c2a53e2861a | 10.26434/chemrxiv.13224596.v1 | Brillouin Light Scattering Study of Microscopic Structure and Dynamics in Pyrrolidinium Based Ionic Liquids | <p>Pyrrolidinium
based ionic liquids are known to be good ionic conductors even in solid-state
around room temperature, which is attributed to the highly disordered plastic
crystalline phase. Moreover, these ionic liquids are characterized by multiple
phase transitions which include plastic, structural glass, and glassy crystal phases
with varying levels of molecular disorder. Temperature-dependent Brillouin
light scattering is used to investigate the phase transitions in a series of
alkylmethylpyrrolidinium Bis(trifluoromethanesulfonyl) imides (P<i><sub>1n</sub></i>TFSI, n=1,2,4). Brillouin spectral
features such as the number of acoustic modes, their shape, and linewidth
provide the picture of different disordered phases resultant of dynamics at the
microscopic scale. The longitudinal and transverse acoustic velocities in
different phases are determined from the corresponding acoustic mode
frequencies (Brillouin shift). Extremely low acoustic velocities in the solid
phase of P<i><sub>11</sub></i>TFSI and P<i><sub>12</sub></i>TFSI are a consequence of a
high degree of disorder and plasticity present in the system. Anomalous
temperature-dependent behavior of linewidth and asymmetric (Fano) line shape of
acoustic modes observed in certain phases of P<i><sub>1n</sub></i>TFSI could be due to the strong coupling between the
Brillouin central peak and the acoustic phonons. The present results establish
that the Brillouin light scattering technique can be efficiently used to understand
the complex phase behavior, microscopic structure, and dynamics of ionic
liquids.</p> | Supti Das; Dhanya Radhakrishnan; Venkata. S. Bhadram; Chandrabhas Narayana; Aninda J. Bhattacharyya | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751e4337d6c2a53e2861a/original/brillouin-light-scattering-study-of-microscopic-structure-and-dynamics-in-pyrrolidinium-based-ionic-liquids.pdf |
60c742da4c89193008ad2531 | 10.26434/chemrxiv.8709566.v1 | Predicting Intermetallic Surface Energies with High-Throughput DFT and Convolutional Neural Networks | Surface energy of inorganic crystals is crucial in understanding experimentally-relevant surface properties and thus important in designing materials for many applications including catalysis. Predictive methods and datasets exist for surface energies of monometallic crystals but predicting these properties for bimetallic or more complicated surfaces is an open challenge. Here we present a workflow for predicting surface energies \textit{ab initio} using high-throughput DFT and a machine learning framework. We calculate the surface energy of 3,285 intermetallic alloys with combinations of 36 elements and 47 space groups. We used this high-throughput workflow to seed a database of surface energies, which we used to train a crystal graph convolutional neural network (CGCNN). The CGCNN model was able to predict surface energies with a mean absolute test error of 0.0082 eV/angstrom^2 and can qualitatively reproduce nanoparticle surface distributions (Wulff constructions). Our workflow provides quantitative insights into which surfaces are more stable and therefore more realistic. It allows us to down-select interesting candidates that we can study with robust theoretical and experimental methods for applications such as catalysts screening and nanomaterials synthesis. | Aini Palizhati; Wen Zhong; Kevin Tran; Zachary Ulissi | Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742da4c89193008ad2531/original/predicting-intermetallic-surface-energies-with-high-throughput-dft-and-convolutional-neural-networks.pdf |
65410faa48dad23120c6fb44 | 10.26434/chemrxiv-2023-v2ntf-v2 | Broken Edge Spin-Symmetry Induces Spin-polarized Current in Graphene Nanoribbon | Zig-zag graphene nanoribbons (ZGNRs) are known to possess spin moments at the hydrogen- terminated edge carbon atoms, thus the spin-polarized electron transmission is expected while the current is longitudinally passed through the ZGNRs. However, in pristine ZGNRs, the spin polarized transmission is not observed due to symmetric anti-parallel distributions of the spin densities between the edges. Here, the hypothesis is, any physical or chemical process that breaks such anti-parallel spin-symmetry can induce spin-polarized transmission in the ZGNRs. In this work, we have established this proof-of-concept by depositing the trimethylenemethane (TMM) radical on 6ZGNRH and investigating the quantum transport properties by employing the density functional theory in conjunction with nonequilibrium Green’s function (DFT-NEGF) method. Although TMM has a high magnetic moment (2 µB ), it does not induce magnetization in 6ZGNRH when TMM is physisorbed. But, during the chemisorption of TMM, it forms the π − π bond with the 6ZGNRH in a particular geometric configuration where the pz orbitals of carbon atoms of TMM have maximum overlap with the pz orbitals of carbon atoms of 6ZGNRH. The chemisorption of TMM transfers the spin moment to 6ZGNRH, which breaks the edge spin-symmetry of pristine 6ZGNRH. The adsorption of TMM radical results in transmission dips in the transmission spectra due to interference between localized states of TMM and 6ZGNRH states. This induces spin-polarized transmission with 60% spin-filtering efficiency (SFE) at zero bias, which can further be enhanced up to 92% by applying the bias voltage of 1.0 V. | Shahjad Ali; Md. Ehesan Ali | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Computational Chemistry and Modeling; Physical and Chemical Properties; Transport phenomena (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65410faa48dad23120c6fb44/original/broken-edge-spin-symmetry-induces-spin-polarized-current-in-graphene-nanoribbon.pdf |
60c749d9567dfe7444ec4c76 | 10.26434/chemrxiv.12056154.v2 | A NOVEL COMPUTATIONALLY DESIGNED DRUG TO TREAT THE COVID -19 PANDEMIC | A computationally designed drug to treat Covid-19 | Chikoo Cherian | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749d9567dfe7444ec4c76/original/a-novel-computationally-designed-drug-to-treat-the-covid-19-pandemic.pdf |
61f2b20771868d1242c050b0 | 10.26434/chemrxiv-2022-612pc | On the effects of the degrees of freedom on calculating diffusion properties in nanoporous materials | If one carries out a molecular simulation of N particles using periodic boundary conditions, linear momentum is conserved and hence the number of degrees of freedom is set to 3N-3. In most programs, this number of degrees of freedom is the default setting. However, if one carries out a molecular simulation in an external field, one needs to ensure that degrees of freedom are changed from this default setting to 3N, as in an external field the velocity of the center of mass can change. Using the correct degrees of freedom is important in calculating the temperature and in some algorithms to simulate at constant temperature.
For sufficiently large systems, the difference between 3N and 3N-3 is negligible in the way. However, there are systems in which the comparison with experimental data requires molecular dynamics simulations of a small number of particles. In this work, we illustrate the effect of an incorrect setting of degrees of freedom in molecular dynamic simulations studying the diffusion properties of guest molecules in nanoporous materials. We show that previously published results have reported a surprising diffusion dependence on the loading, which could be traced back to an incorrect setting of the degrees of freedom. As the correct settings are convoluted and counter-intuitive in some of the most commonly used molecular dynamics programs, we carried out a systematic study on the consequences of the various commonly used (incorrect) settings. Our conclusion, is that for systems smaller than 50 particles the results are most likely unreliable as these are either performed at an incorrect temperature or the temperature is incorrectly used in some of the results.
Furthermore, a novel and efficient method to calculate diffusion coefficients of guest molecules into nanoporous materials at zero loading conditions is introduced. | Henglu Xu; Raffaela Cabriolu; Berend Smit | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f2b20771868d1242c050b0/original/on-the-effects-of-the-degrees-of-freedom-on-calculating-diffusion-properties-in-nanoporous-materials.pdf |
61a07119784805081c9b532b | 10.26434/chemrxiv-2021-nxbn4 | Orthogonal activation of metabotropic glutamate receptor using coordination chemogenetics | Cell-surface receptors play a pivotal role as transducers of extracellular input. Although different cell types express the same receptor, the physiological roles of the receptor are highly dependent on cell type. To understand each role, tactics for cell-specific activation of the target receptor are in high demand. Herein, we developed an orthogonal activation method targeting metabotropic glutamate receptor 1 (mGlu1), a G-protein coupled receptor. In this method, direct activation via coordination-based chemogenetics (dA-CBC) was adopted, where activation of mGlu1 was artificially induced by a protein conformational change in response to the coordination of a metal ion or metal-ion complex. Our structure-based protein design and screening approach identified mGlu1 mutants that were directly activated by the coordination of Cu2+ or Zn2+, in addition to our previous Pd-complex-sensitive mGlu1 mutant. Notably, the activation of the mutants was mutually orthogonal, resulting in cell-type selective activation in a model system using HEK293 cells. | Akinobu Senoo; Yutaro Yamada; Kento Ojima; Tomohiro Doura; Itaru Hamachi; Shigeki Kiyonaka | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a07119784805081c9b532b/original/orthogonal-activation-of-metabotropic-glutamate-receptor-using-coordination-chemogenetics.pdf |
66c9dc71f3f4b05290fbc394 | 10.26434/chemrxiv-2024-k846p | OpenQP: A Quantum Chemical Platform Featuring MRSF-TDDFT with an Emphasis on Open-source Ecosystem | The OpenQP (Open Quantum Platform) is a new open-source quantum chemistry library developed to tackle sustainability and interoperability challenges in the field of computational chemistry. OpenQP provides various popular quantum chemical theories as autonomous modules such as energy and gradient calculations of HF, DFT, TDDFT, SF-TDDFT, and MRSF-TDDFT, thereby allowing easy interconnection with third-party software. A scientifically notable feature is the innovative Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory (MRSF-TDDFT) and its customized exchange-correlation functionals such as DTCAM series of VAEE, XI, XIV, AEE, and VEE, which significantly expands the applicability scope of DFT and TDDFT. OpenQP also supports parallel execution and is optimized with BLAS and LAPACK for high performance. Future enhancements such as EKT-MRSF-TDDFT and SOC-MRSF-TDDFT will further expand OpenQP’s capabilities. Additionally, a Python wrapper PyOQP is provided that performs tasks such as geometry optimization, conical intersection searches, and nonadiabatic coupling calculations, among others, by prototyping the modules of OpenQP library in combination with third-party libraries. Overall, OpenQP aligns with modern trends in high-performance scientific software development by offering flexible prototyping and operation while retaining the performance benefits of compiled languages like Fortran and C. They enhance the sustainability and interoperability of quantum chemical software, making OpenQP a crucial platform for accelerating the development of advanced quantum theories like MRSF-TDDFT. | Vladimir Mironov; Konstantin Komarov; Jingbai Li; Igor Gerasimov; Hiroya Nakata; Mohsen Mazaheri; Kazuya Ishimura; Woojin Park; Alireza Lashkaripour; Minseok Oh; Miquel Huix-Rotllant; Seunghoon Lee; Cheol Ho Choi | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c9dc71f3f4b05290fbc394/original/open-qp-a-quantum-chemical-platform-featuring-mrsf-tddft-with-an-emphasis-on-open-source-ecosystem.pdf |
66e75a1b12ff75c3a16e9d00 | 10.26434/chemrxiv-2024-zk6hp-v2 | Real-space machine learning of correlation density functionals | Machine learning (ML) has started to play a pivotal role in extending the reach of quantum chemistry methods for both molecules and materials. However, in density functional theory — the primary workhorse for quantum simulations—using ML to address the limitations of human-designed density functional approximations (DFAs) remains elusive, as ML-based approximations suffer from severely limited transferability to unseen chemical systems. We apply real-space ML of DFAs to address this challenge, where energy is learned point-by-point in space through energy densities. Central to our real-space learning is the derivation and implementation of correlation energy densities from regularized perturbation theory. This allows us to pursue two directions for real-space ML of DFAs from these energy densities. First, we introduce the Local Energy Loss (LES), where model energy densities are trained against our implemented counterparts at every point in space. By expanding each system’s single energy data point into thousands, LES dramatically enhances the transferability of ML DFAs compared to traditional global energy training. Second, we use spin-resolution of our correlation energy density to build a real-space, ML-based, and regularized extension of Spin-Component-Scaled second-order M\o ller-Plesset perturbation theory. We then show how the resulting model opens up new avenues for the construction of transferable ML DFAs.
| Elias Polak; Heng Zhao; Stefan Vuckovic | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY 4.0 | CHEMRXIV | 2024-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e75a1b12ff75c3a16e9d00/original/real-space-machine-learning-of-correlation-density-functionals.pdf |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.