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
⌀ |
|---|---|---|---|---|---|---|---|---|---|
678f32106dde43c90877502f | 10.26434/chemrxiv-2025-8fvf1 | Interplay Between Organic Solvent Geometry and Divalent Cation Dynamics in Divalent Metal Batteries | This study investigates the interplay between organic solvent geometry and divalent cation dynamics in liquid electrolytes, emphasizing their relevance for energy storage systems. Using molecular dynamics simulations, the structural and transport properties of Mg²⁺ and Ca²⁺ were evaluated in cyclic (ethylene carbonate, EC; propylene carbonate, PC) and linear (ethyl methyl carbonate, EMC) solvents in the presence of TFSI⁻ anions across a range of temperatures. Results reveal that Mg²⁺ exhibits superior diffusion compared to Ca²⁺ due to its smaller ionic radius and weaker ion-pair interactions. Diffusion increases with temperature, following the solvent trend EC > EMC > PC. Coordination analysis showed compact solvation shells for both cations, with Ca²⁺ forming denser structures and demonstrating higher residence times compared to Mg²⁺. Solvent geometry significantly influenced solvation dynamics, with cyclic solvents enhancing ion coordination and linear solvents reducing solvation due to steric hindrance. These findings underscore the critical role of solvent structure and ion dynamics in optimizing divalent-ion battery performance, positioning Mg²⁺ as a promising candidate for sustainable energy storage solutions. | Nazifa Jahan Pranti; Sharifa Faraezi; Tomonori Ohba; Argyrios V. Karatrantos; Md Sharif Khan | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Theory - Computational; Energy Storage; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678f32106dde43c90877502f/original/interplay-between-organic-solvent-geometry-and-divalent-cation-dynamics-in-divalent-metal-batteries.pdf |
65c06c43e9ebbb4db9b0d3a2 | 10.26434/chemrxiv-2024-t8cvk | Metal Ions-Induced Unusual Stability of the Metastable Vesicle-like Intermediates Evolving in the Self-Assembly Process of Phenylalanine: The Role of Hydrophobic Interaction, Metal-Coordination, and Surface Charge Inversion | The underlying mechanism and the intermediates formation in the self-assembly of aromatic amino acids, peptides and proteins remain elusive despite numerous reports. We, for the first time, report that one can modulate the stability of the intermediates by tuning the metal ions-amino acid interaction of carboxybenzyl (Z)-protected phenylalanine (ZF). The microscopic and spectroscopic investigations reveal that the bivalent metal ions lead to the formation of fibrillar networks after a certain interval similar to blank ZF, whereas the trivalent ions develop vesicle-like intermediates which do not undergo fibrillation for a prolonged time. The time-lapse measurement of surface charge reveals that the surface charge of blank ZF and in the presence of bivalent metal ions alters from negative value to zero implying unstable intermediates leading to the fibril network. Strikingly, a prominent charge inversion from an initial negative to a positive value in the presence of trivalent metal ions imparts unusual stability to the metastable intermediates. | DEBANJAN BAGCHI; AVIJIT MAITY; ANJAN CHAKRABORTY | Physical Chemistry; Interfaces; Physical and Chemical Processes; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c06c43e9ebbb4db9b0d3a2/original/metal-ions-induced-unusual-stability-of-the-metastable-vesicle-like-intermediates-evolving-in-the-self-assembly-process-of-phenylalanine-the-role-of-hydrophobic-interaction-metal-coordination-and-surface-charge-inversion.pdf |
60c7581b702a9bcc2218cc3a | 10.26434/chemrxiv.14494383.v1 | A General Approach to Convert Hemicyanine Dyes into Highly Optimized Photoacoustic Scaffolds for Analyte Sensing | <p>In the context of
deep-tissue disease biomarker detection and analyte sensing of biologically
relevant species, the impact of photoacoustic imaging has been profound. However,
most photoacoustic imaging agents to date are based on the repurposing of
existing fluorescent dye platforms that exhibit non-optimal properties for photoacoustic applications (e.g., high
fluorescence quantum yield). Herein, we introduce two effective modifications to
the hemicyanine dye to afford PA-HD, a new dye scaffold optimized for photoacoustic
probe development. We observed a significant increase in the photoacoustic
output, representing an increase in sensitivity of 4.8-fold and a red-shift of
the λ<sub>abs</sub> from 690 nm to 745 nm to enable ratiometric
imaging. Moreover, to demonstrate the generalizability and utility of our
remodeling efforts, we developed three probes using common analyte-responsive
triggers for beta-galactosidase activity (PA-HD-Gal), nitroreductase activity (PA-HD-NTR),
and hydrogen peroxide (PA-HD-H<sub>2</sub>O<sub>2</sub>). The performance of
each probe (responsiveness, selectivity) was evaluated <i>in vitro</i> and <i>in
cellulo</i>. To showcase the enhance properties afforded by PA-HD for <i>in
vivo</i> photoacoustic imaging, we employed an Alzheimer’s disease model to detect
H<sub>2</sub>O<sub>2</sub>. In particular, the photoacoustic signal at 735 nm in
the brains of 5xFAD mice (a murine model of Alzheimer’s disease) increased by
1.72 ± 0.20-fold relative to background indicating the
presence of oxidative stress, whereas the change in wildtype mice was
negligible (1.02 ± 0.14). These results were
confirmed via ratiometric calibration which was not possible using the parent
HD platform.</p> | Sarah Garder; Catharine Brady; Cameron Keeton; Anuj K Yadav; Sharath C Mallojjala; Melissa Lucero; ShengZhang Su; Zhengxin Yu; Jennifer S. Hirschi; Liviu M. Mirica; Jefferson Chan | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7581b702a9bcc2218cc3a/original/a-general-approach-to-convert-hemicyanine-dyes-into-highly-optimized-photoacoustic-scaffolds-for-analyte-sensing.pdf |
673babd15a82cea2fa945927 | 10.26434/chemrxiv-2024-lpm8c | Ab initio predictions of adsorption in flexible metal-organic frameworks for water harvesting applications. | Recently, metal-organic frameworks like MOF-303 and MOF-LA2-1 have demonstrated exceptional performance for water harvesting applications. To enable a reticular design of such materials, an accurate prediction of the adsorption properties with chemical accuracy and fully accounting for the flexibility is crucial. The computational prediction of water adsorption properties of metal-organic frameworks (MOFs) has become standard practice. However their predictive power to design new materials is hindered by the limited accuracy of the used interatomic potential and the limitations on how to account for the framework flexibility. In this work, we showcase a methodology to obtain chemically accurate adsorption isotherms that fully account for the framework flexibility. The method is founded on very accurate and efficiently trained machine learning potentials and transition matrix Monte Carlo simulations to account for framework flexibility. By first benchmarking the reference electronic level of theory used for the training, quantitatively accurate adsorption isotherms are obtained for MOF-303, a highly topical MOF being investigated for its potential use in water harvesting applications. We show that both an accurate level of theory and a proper inclusion of local and global framework flexibility is vital in the prediction of the adsorption properties of MOF-303. The broader applicability of our methodology is demonstrated through the study of related linker-exchanged materials, MOF-333 and MOF-LA2-1. Analyses of the density profiles of water adsorbed in these MOFs yields deeper insight into the origins and differences of the observed isotherms. An optimal water harvester should have initial seeding sites with intermediate adsorption strength, to prevent detrimental low-pressure water uptake. To increase the working capacity, linker extension strategies can be used while maintaining the initial seeding sites, as was done in the MOF-LA2-1. The proposed methodology is applicable to other guest molecules and MOFs, paving the way to future rational design of MOFs with specific adsorption properties for the application at hand. | Ruben Goeminne; Veronique Van Speybroeck | Theoretical and Computational Chemistry; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673babd15a82cea2fa945927/original/ab-initio-predictions-of-adsorption-in-flexible-metal-organic-frameworks-for-water-harvesting-applications.pdf |
67ac29c881d2151a02169df6 | 10.26434/chemrxiv-2025-x885b | Organoids Producing Materials | Self-organizing tissues, such as organoids, offer transformative potential beyond healthcare by enabling the sustainable production of advanced materials. Resource scarcity and global warming drive the need for innovative fabrication solutions. This prospective review explores developmental biology as a manufacturing process, where the material (e.g. spider silk) and its production unit are self-organized (e.g. silk glands). Biological systems orchestrate the emergence of hierarchical materials with superior mechanical properties and biodegradability, using abundant and renewable resources. Tissue engineering enables the creation of biological systems that surpass current synthetic designs in complexity.
We highlight application opportunities, focusing on spider silk as a model to demonstrate how organs synthesize and assemble next-generation materials. The concept of growing both a material and its organ production units is exemplified by hair-bearing organoids, self-organized from induced pluripotent stem cells (iPSCs).
Key challenges in expanding organoid research to new model species and scaling-up production are discussed alongside potential solutions. We propose a simplified description of these complex systems to help address key challenges. Furthermore, synthetic and hybrid approaches are explored, considering the ethical, societal, and technological impacts.
Though still in their infancy, material-producing organoids present a promising avenue for sustainable, high-value products, fostering new interdisciplinary collaborations among bioengineers, developmental biologists, and material scientists. This work aims to inspire further exploration into the applications of self-organized biological systems in addressing global challenges. | Quentin Moana Perrin; Ali Miserez | Biological and Medicinal Chemistry; Materials Science; Biological Materials; Bioengineering and Biotechnology; Cell and Molecular Biology; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ac29c881d2151a02169df6/original/organoids-producing-materials.pdf |
60c75194702a9b2b7218bf82 | 10.26434/chemrxiv.13134785.v1 | Collaborative Virtual Screening to Elaborate an Imidazo[1,2-A]pyridine Hit Series for Visceral Leishmaniasis | An
innovative pre-competitive virtual screening collaboration was engaged to
validate and subsequently explore an imidazo[1,2-a]pyridine screening hit for
visceral leishmaniasis. Parasitology and early ADME data is presented. | Benjamin Perry; yuichiro akao; Stacie Canan; Yafeng Cao; Kevin Condroski; Ola Engkvist; sachiko itono; rina kaki; chiaki kimura; Thierry Kogej; Charles E. Mowbray; kazuya nagaoka; Akira Naito; Hiromi Nakai; Garry Pairaudeau; Constantin Radu; Ieuan Roberts; mitsuyuki shimada; David Shum; Nao-aki Watanabe; huanxu xie; Shuji Yonezawa; Osamu Yoshida; Ryu Yoshida | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75194702a9b2b7218bf82/original/collaborative-virtual-screening-to-elaborate-an-imidazo-1-2-a-pyridine-hit-series-for-visceral-leishmaniasis.pdf |
628e7bb3f053df7c4828ff0b | 10.26434/chemrxiv-2022-xz6vh | Solvent-free Route to High-performance Electrode Materials for Li/Na Storage from Mechanochemically Synthetised MOFs/MXene Composites | The development of new energy-related materials is the pinnacle to attaining a sustainable society based on renewable energy. Over the past decades, plenty of electrode materials have been investigated seeking better energy storage properties. However, the often tedious synthetic procedures and large amounts of solvents utilized during their syntheses incur in high costs and severe environmental pollution. Here we present a solvent-free approach to metal-organic-frameworks/MXene-derived carbonaceous metal selenide/MXene composites with unique nanostructures rich in mesopores and macropores. These species can be readily transformed into high-performance electrode materials with enhanced Li/Na ion storage properties compared with their solution-based counterparts. Our results provide an environmentally benign production process of metal-organic framework/MXene-derived high-performance electrode materials for advanced lithium/sodium storage applications | Xiaoyan Shi; Weiquan Liang; Weikun Lin; Bin Chen; Lianyi Shao; Zhipeng Sun; Felipe Garcia | Inorganic Chemistry; Energy; Solid State Chemistry; Energy Storage; Fuel Cells; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628e7bb3f053df7c4828ff0b/original/solvent-free-route-to-high-performance-electrode-materials-for-li-na-storage-from-mechanochemically-synthetised-mo-fs-m-xene-composites.pdf |
60c74268469df460ccf42f99 | 10.26434/chemrxiv.8266745.v1 | Multi-Resolution Autoregressive Graph-to-Graph Translation for Molecules | The problem of accelerating drug discovery relies heavily on automatic tools to optimize precursor molecules to afford them with better biochemical properties. Our work in this paper substantially extends prior state-of-the-art on graph-to-graph translation methods for molecular optimization. In particular, we realize coherent multi-resolution representations by interweaving trees over substructures with the atom-level encoding of the original molecular graph. Moreover, our graph decoder is fully autoregressive, and interleaves each step of adding a new substructure with the process of resolving its connectivity to the emerging molecule. We evaluate our model on multiple molecular optimization tasks and show that our model outperforms previous state-of-the-art baselines by a large margin. | Wengong Jin; Regina Barzilay; Tommi S Jaakkola | Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74268469df460ccf42f99/original/multi-resolution-autoregressive-graph-to-graph-translation-for-molecules.pdf |
646780a4a32ceeff2de83820 | 10.26434/chemrxiv-2023-fdwc6 | Near-infrared clusteroluminescence in amine-capped polyesters | Near-infrared (NIR) luminophores has many advantages in practical applications,
however, the fabrication of NIR clusteroluminogens (CLgens) from nonconjugated luminescent
polymers is still a big challenge owing to uncontrollable structures and photophysical properties.
Herein, the first example of amine-capped aliphatic polyesters with full-spectrum CL from blue to
NIR region based on amine-ester complexes is reported. Experimental and theoretical calculation
results prove that, in addition to the blue CL (~470 nm) generated by n−π* transitions of isolated
ester groups, the new red-to-NIR CL (600~780 nm) originate from short-range and long-range
amine-ester complexes based on through-space charge transfer (TSCT), respectively. Compared
with small molecules, the unique and abundant microstructures of polymer chains directly
generate long-range complexes and induces NIR CL. Meanwhile, the intensity ratios of these CL
peaks are easily manipulated by molar contents and types of amines, chain structures of polyesters.
This work not only constructs a novel platform to design high-efficiency, controllable,
full-spectrum CLgens and breaks though the wavelength limitation of CLgens for the first time,
but also enriches the relationship of polymer structures and CL properties. | Chu Bo; Liu Xiong; Xiong Zuping; Zhang Ziteng; Liu Bin; Sun Jingzhi; Yang Qing; Zhang Haoke; Zhang Chengjian; Zhang Xinghong; Tang Benzhong | Organic Chemistry; Polymer Science; Nanoscience; Organic Polymers; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646780a4a32ceeff2de83820/original/near-infrared-clusteroluminescence-in-amine-capped-polyesters.pdf |
65b6bba7e9ebbb4db92a9985 | 10.26434/chemrxiv-2024-8k45x | Seamless integration of GEM, a density based-force field, for QM/MM simulations via LICHEM, Psi4 and Tinker-HP | Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have become an essential tool in computational chemistry, particularly for analyzing complex biological and condensed phase systems. Building on this foundation, our work presents a novel implementation of the Gaussian Electrostatic Model (GEM), a polarizable density-based force field, within the QM/MM framework. This advancement provides seamless integration, enabling efficient and optimized QM/GEM calculations in a single step using the LICHEM Code. We have successfully applied our implementation to water dimers and hexamers, demonstrating the ability to handle water systems with varying numbers of water molecules. Moreover, we have extended the application to describe the double proton transfer of the aspartic acid dimer in a box of water, which highlights the method's proficiency in investigating heterogeneous systems. Our implementation offers the flexibility to perform on-the-fly density fitting or to utilize pre-fitted coefficients to estimate exchange and Coulomb contributions. This flexibility enhances efficiency and accuracy in modeling molecular interactions, especially in systems where polarization effects are significant. | Jorge Nochebuena; Andrew C. Simmonett; G. Andrés Cisneros | Physical Chemistry; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b6bba7e9ebbb4db92a9985/original/seamless-integration-of-gem-a-density-based-force-field-for-qm-mm-simulations-via-lichem-psi4-and-tinker-hp.pdf |
676eede1fa469535b900025f | 10.26434/chemrxiv-2024-k9psr | Revealing the hidden polysulfides in solid-state Na-S batteries: How pressure and electrical transport control kinetic pathways | Room temperature operation of Na-S batteries with liquid electrolytes is plagued by fundamental challenges stemming from polysulfide solubility and their shuttle effects. Inorganic solid electrolytes offer a promising solution by acting as barriers to polysulfide migration, mitigating capacity loss. While the sequential formation of cycling products in molten-electrode and liquid electrolytes-based Na-S batteries generally aligns with the expectations from the Na-S phase diagram, their presence, stability, and transitory behavior in systems with inorganic solid electrolytes at room temperature, remain poorly understood. To address this, we employed operando scanning micro-beam X-ray diffraction and ex-situ X-ray absorption spectroscopy to investigate the sulfur conversion mechanisms in Na-S cells with Na3PS4 and Na4(B10H10)(B12H12) electrolytes. Our findings reveal the formation of crystalline and amorphous polysulfides, including those predicted by the Na-S phase diagram (e.g., Na2S5, Na2S4, Na2S2, Na2S), high-order polysulfides observed in liquid-electrolyte systems (e.g., Na2Sx, where x = 6–8), and phases like Na2S3 typically stable only under high-temperature or high-pressure conditions. We demonstrate that these transitions are governed by diffusion-limited kinetics and localized stress concentrations, emphasizing the critical role of pressure, which serves as both a thermodynamic variable, as well as a design parameter, for optimizing solid-state Na-S battery performance necessary for pushing these cells closer to the commercial frontier. | Hung Quoc Nguyen; Mikael Dahl Kanedal; Juraj Todt; Feng Jin; Quyen Do; Dora Zalka; Alexey Maximenko; Dragos Stoian; Norbert Schell; Wouter van Beek; Steven Boles; Jozef Keckes; Daniel Rettenwander | Physical Chemistry; Materials Science; Energy; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Structure | CC BY NC 4.0 | CHEMRXIV | 2024-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676eede1fa469535b900025f/original/revealing-the-hidden-polysulfides-in-solid-state-na-s-batteries-how-pressure-and-electrical-transport-control-kinetic-pathways.pdf |
6185826f9b583a27daed01b6 | 10.26434/chemrxiv-2021-v79sv | Ferromagnetic 1H-LaBr2 monolayer: a promising 2D piezoelectric | Abstract The discovery of two dimensional (2D) materials that have excellent piezoelectric response along with intrinsic magnetism is promising for nanoscale multifunctional piezoelectric or spintronic devices. Piezoelectricity requires non-centrosymmetric structures with an electric band-gap, whereas magnetism demands broken time-reversal symmetry. Most of the well-known 2D piezoelectric materials – e.g., 1H-MoS2 monolayer – are not magnetic. Being intrinsically magnetic, semiconducting 1H-LaBr2and 1H-VS2 monolayers can combine magnetism and piezoelectricity. We compare piezoelectric properties of 1H-MoS2, 1H-VS2 and 1H-LaBr2 using density functional theory. Our results show that ferromagnetic 1H-LaBr2 2D monolayer displays a larger piezoelectric strain co-efficient (d_{11}= -4.527 pm/V, which is close to d_{11}= 4.104 pm/V of 1H-VS2 monolayer) compared to that of well-known 1H-MoS2 monolayer (d_{11}= 3.706 pm/V), while 1H-MoS2 monolayer has a larger piezoelectric stress co-efficient (e_{11}= 370.675 pC/m) than the 1H-LaBr2 monolayer (e_{11}= -94.175 pC/m, which is also lower than e_{11}= 298.100 pC/m of 1H-VS2 monolayer). These in-plane piezoelectric d_{11} coefficients are quite comparable with piezo-response of bulk wurtzite nitrides – e.g., d_{33} of GaN is about 3.1 pm/V. The large d_{11} for 1H-LaBr2 monolayer originates from the low elastic constants, C_{11}= 30.338 N/m and C_{12} = 9.534 N/m. Interestingly, the sign of the piezoelectric co-coefficients for 1H-LaBr2 monolayer is different to that of the 1H-MoS2 or 1H-VS2 monolayers. The negative sign arises from the negative ionic contribution of e_{11}, which dominates in the 1H-LaBr2 monolayer, whereas the electronic part of e_{11} dominates in 1H-MoS2 and 1H-VS2. Furthermore, we explain the origin of this large ionic contribution of e_{11} for 1H-LaBr2 in terms of the Born effective charges (Z_{11}) and the sensitivity of the atomic positions to the strain (\frac{du}{d\eta}). Surprisingly, we observe a sign reversal in the Z_{11} of Mo and S compared to the nominal oxidation states, which makes both the electronic and ionic parts of e_{11} positive, and results in the high value of e_{11}. Additionally, our interatomic bond analysis using crystal orbital Hamilton populations indicates that the weaker covalent bond in 1H-LaBr2 monolayer is responsible for large \frac{du}{d\eta} and elastic softening (lower elastic constants). | Mohammad Noor A-Alam; Michael Nolan | Theoretical and Computational Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6185826f9b583a27daed01b6/original/ferromagnetic-1h-la-br2-monolayer-a-promising-2d-piezoelectric.pdf |
67d1bbfa81d2151a02229629 | 10.26434/chemrxiv-2025-gr39c | A computational study to assess the influence of elastic strains on the catalytic activity of Au surfaces for the HER and ORR including the effect of coverage | The influence of different surface coverages and the effect of biaxial elastic strains on the catalytic properties for the hydrogen evolution reaction (HER) and the oxygen reduction reaction (ORR) were analyzed on the example of a Au fcc(111) surface. The adsorption energies of H, O, and OH for the corresponding intermediate reactions were obtained by density functional theory calculations. While for H and O the adsorption energy increases with coverage, for OH the lowest adsorption energy was observed at 0.5~ML. Then, after applying elastic strains, the trends observed for the unstrained slab were maintained for the three adsorbates. Although neither tension nor compression modified the optimum coverage, they do change the differences in relative energies. This is considered to be a consequence of the deformations promoted on the surface. Finally, the catalytic activity of the HER and ORR was computed for the distinct coverages and elastic strains. Volcano plots confirmed for both reactions that the more favorable adsorption energy promoted by tensile strains leads to an increment of the activity and that the most active coverage is 0.25~ML. Furthermore, an analysis of the free energies of each step of the dissociative mechanism of the ORR unveils that both coverage and elastic strains can modify the rate-limiting step and, therefore, the catalytic activity of a material. The results presented in this work provide an ample characterization of Au fcc(111) surface as a catalyst for the HER and ORR, and offer, for the first time, an analysis of the influence of both coverage and elastic strain engineering on the catalytic activity. | Diego Schaefer-Dalmau; Carmen Martínez-Alonso; Javier LLorca; Valentin Vassilev-Galindo | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d1bbfa81d2151a02229629/original/a-computational-study-to-assess-the-influence-of-elastic-strains-on-the-catalytic-activity-of-au-surfaces-for-the-her-and-orr-including-the-effect-of-coverage.pdf |
60c757370f50db4c2f398227 | 10.26434/chemrxiv.14372015.v1 | A QuantCrit investigation of society’s educational debts due to racism and sexism in chemistry student learning | <div>
<div>
<div>
<p>The American Chemical Society holds supporting diverse student populations engaging in chemistry
as a core value. We analyzed chemical concept inventory scores from 4,612 students across 12
institutions to determine what inequities in content knowledge existed before and after introductory
college chemistry courses. We interpreted our findings from a Quantitative Critical (QuantCrit)
perspective that framed inequities as educational debts that society owed students due to racism,
sexism, or both. Results showed that society owed women and Black men large educational debts
before and after instruction. Society’s educational debts before instruction were large enough that
women and Black men’s average scores were lower than White men’s average pretest scores even after
instruction. Society would have to provide opportunities equivalent to taking the course up to two and
a half times to repay the largest educational debts. These findings show the scale of the inequities in
the science education systems and highlight the need for reallocating resources and opportunities
throughout the K-16 education system to mitigate, prevent, and repay society’s educational debts from
sexism and racism. </p>
</div>
</div>
</div> | Ben Van Dusen; jayson nissen; Robert Talbot; Hannah Huvard; Mollee Shultz | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757370f50db4c2f398227/original/a-quant-crit-investigation-of-society-s-educational-debts-due-to-racism-and-sexism-in-chemistry-student-learning.pdf |
671a48fe98c8527d9e3548e8 | 10.26434/chemrxiv-2024-6j8vr-v2 | Large scale compartmental model-based study of preclinical pharmacokinetic data and its impact on compound triaging in drug discovery | Reliable and robust human dose prediction plays a pivotal role in compound optimization and advancement in drug discovery. The prediction of human dose in discovery requires proper modelling of preclinical intravenous (IV) pharmacokinetic (PK) data which is usually achieved either through non-compartmental analysis (NCA) or compartmental analysis. While NCA is straightforward, it loses valuable information about the shape of PK curves. In contrast, compartmental analysis offers a more comprehensive interpretation but poses challenges in scaling up for high-throughput applications in discovery. To address this challenge, we developed computational frameworks, termed Compartmental PK (CPK) and Automated Dose Prediction (ADP), to enable automated compartmental model-based IV PK data modeling, translation, and simulation for human dose prediction in compound triage and optimization. With CPK and ADP, we analyzed compounds with data collected at MRL between 2013 and 2023 to quantitatively characterize the impact of different PK modeling and simulation methods on human dose prediction. Our study revealed that, despite minimal impact on estimating animal PK parameters, different methods significantly impacted predicted human dose, exposure, and Cmax, driven more by different simulation assumptions than by the PK modeling itself. CPK-ADP therefore enables us to efficiently perform complex human dose predictions on a large scale while integrating the latest and best information available on absorption, distribution, and clearance to support decision making in discovery. | Peter Zhiping Zhang; Xiang Yu; Christopher Gibson ; Jeanine Ballard ; Dustin Smith ; Facundo Esquivel Fagiani | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671a48fe98c8527d9e3548e8/original/large-scale-compartmental-model-based-study-of-preclinical-pharmacokinetic-data-and-its-impact-on-compound-triaging-in-drug-discovery.pdf |
63a5aee5ff4651907134f7c5 | 10.26434/chemrxiv-2022-fwgr0 | Transient imine as a directing group for the Pd-catalyzed anomeric C(sp)3-H arylation of 3-aminosugars | The first example of Pd(II)-catalyzed anomeric arylation of 3-aminosugars is reported by using an L,X-type transient directing groups (TDG) approach combined with an external 2-pyridone ligand. The released free amine was in situ transformed into an azide function, which was then exploited in a CuAAC to increase the molecular complexity and prepare a variety of complex substituted C3-triazolo C-glycosides in good yields. | Juba Ghouilem; Sokna Bazzi; Nicolas Grimblat; Pascal Retailleau; Vincent Gandon; Samir MESSAOUDI | Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a5aee5ff4651907134f7c5/original/transient-imine-as-a-directing-group-for-the-pd-catalyzed-anomeric-c-sp-3-h-arylation-of-3-aminosugars.pdf |
62601071368ab66bd986bf14 | 10.26434/chemrxiv-2022-9m4jh | Grouped representation of interatomic distances as a similarity measure for crystal structures | Determining how similar two materials are in terms of both atomic composition and crystallographic structure remains a challenge, the solution of which would enable generalised machine learning using crystal structure data. We demonstrate a new method of describing crystal structures based on interatomic distances, termed the Grouped Representation of Interatomic Distances (GRID). This fast to compute descriptor can equally be applied to crystalline or disordered materials, and encodes additional information beyond pairwise distances, such as coordination environments. Combined with earth mover’s distance as a measure of similarity, we show that GRID is able to quantitatively compare materials involving both short- and long-range structural variation. Using this new material descriptor, we show that it can accurately predict bulk moduli using a simple nearest-neighbour model, and that the resulting similarity shows good generalisability across multiple materials properties. | Ruizhi Zhang; Sohan Seth; James Cumby | Theoretical and Computational Chemistry; Materials Science; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62601071368ab66bd986bf14/original/grouped-representation-of-interatomic-distances-as-a-similarity-measure-for-crystal-structures.pdf |
672668e25a82cea2fad470ad | 10.26434/chemrxiv-2024-6g0h2 | Galvanic Corrosion Underlies Coulombic Efficiency Differences in High-Performing Lithium Metal Battery Electrolytes | Current guidelines for electrolyte engineering in lithium metal batteries are based on design metrics such as lithium morphology, electrolyte transport properties, solid electrolyte interphase (SEI) characteristics, and lithium-electrolyte reactivity. In our work, we show that those design metrics fail to account for performance differences in new high-performing electrolytes whereas galvanic corrosion does. This insight regarding the importance of galvanic corrosion is enabled by the combination of machine learning with rigorous experimental characterization. First, we partition our electrolyte data into low and high Coulombic efficiency (CE) segments to obtain an interpretable machine learning model which informs the design of high-performing (high CE) electrolytes. We design new model-guided, high-performing electrolytes and use spectroscopy and electroanalytical methods to demonstrate the weak correlation between common design metrics and performance in the high-performing electrolytes. Our work results in the design of a high-performing electrolyte with a Coulombic efficiency (CE) of 99.6%, a new understanding that common performance indicators are not sufficient for informing the development of high-performing electrolytes, and the identification of galvanic corrosion as an important performance driver in high-performing electrolytes. | Solomon T. Oyakhire; Sang Cheol Kim; Wenbo Zhang; Sanzeeda Baig Shuchi; Yi Cui; Stacey F. Bent | Physical Chemistry; Energy; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Interfaces; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672668e25a82cea2fad470ad/original/galvanic-corrosion-underlies-coulombic-efficiency-differences-in-high-performing-lithium-metal-battery-electrolytes.pdf |
64b12f6eb605c6803bb16e34 | 10.26434/chemrxiv-2023-4z3jc | Revealing the Structural Evolution of Electrode/Electrolyte Interphase Formation during Magnesium Plating and Stripping with operando EQCM-D | Rechargeable magnesium batteries could provide future energy storage systems with high energy density. One remaining challenge is the development of electrolytes compatible with the negative Mg electrode enabling uniform plating and stripping with high Coulombic efficiencies. Often improvements are hindered by a lack of fundamental understanding of processes occurring during cycling as well as the existence and structure of a formed interphase layer at the electrode/electrolyte interface. Here, a magnesium model electrolyte based on magnesium bis(trifluoromethanesulfonyl)imide (Mg(TFSI)2) and MgCl2 with a borohydride as additive, dissolved in dimethoxyethane (DME), was used to investigate the initial galvanostatic plating and stripping cycles under operation conditions using electrochemical quartz crystal microbalance with dissipation monitoring (EQCM-D). We show that side reactions lead to the formation of an interphase of irreversibly deposited Mg during the initial cycles. EQCM-D based hydrodynamic spectroscopy reveals the growth of a porous layer during Mg stripping. After the first cycles, the interphase layer is in a dynamic equilibrium between the formation of the layer and its dissolution, resulting in a stable thickness upon further cycling. This study provides operando information of the interphase formation, its changes during cycling and the dynamic behavior, helping to rationally develop future electrolytes and electrode/electrolyte interfaces and interphases. | Benjamin W. Schick; Xu Hou; Viktor Vanoppen; Matthias Uhl; Matthias Kruck; Erik J. Berg; Timo Jacob | Physical Chemistry; Energy; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b12f6eb605c6803bb16e34/original/revealing-the-structural-evolution-of-electrode-electrolyte-interphase-formation-during-magnesium-plating-and-stripping-with-operando-eqcm-d.pdf |
634ebc041df68826a99504de | 10.26434/chemrxiv-2022-9tb5p-v2 | A Redox-active Manganate(0) Dicarbene Metalloradical | We report a rare redox-active Mn0 metalloradical [Mn(CO)3(Ph2B(tBuNHC)2)]- (NHC = N-heterocyclic carbene) with countercations [K([2.2.2]cryptand)]+, [Na([2.2.2]cryptand)]+, or [Li(DME)(12-crown-4)]+, all characterized via single crystal X-ray diffraction. Cyclic voltammograms reveal solvation-dependent MnI/0 redox potentials that are modeled using the Born equation. | Ageliki Karagiannis; Alexei Tyryshkin; Roger Lalancette; Denis Spasyuk; Asmaa Washington; Demyan Prokopchuk | Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Organomet.); Electrochemistry - Organometallic; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634ebc041df68826a99504de/original/a-redox-active-manganate-0-dicarbene-metalloradical.pdf |
65feeebf66c1381729a343d5 | 10.26434/chemrxiv-2024-mv02m | Are polymer gels synthesized by free radical
polymerization with cleavable crosslinkers really
degradable? | Using cleavable crosslinkers is a straightforward way to impart degradability to gels/networks
from vinyl polymers. However, if synthesized by conventional free-radical polymerization
(FRP), such networks are often resistant to degradation, despite containing cleavable bonds.
Indeed, the literature contains conflicting reports, suggesting a more complex relationship
between the polymer type, preparation conditions and the ability of a network to degrade. To
address this, we present a systematic study on the degradation of a series of polymer networks
synthesized via FRP and containing disulfide crosslinkers. Poly(methyl methacrylate)
(PMMA), polystyrene (PS), poly(methyl acrylate) (PMA), and poly(N,N-dimethylacrylamide)
(PDMAm) networks were synthesized under standardized polymerization conditions and
subjected to degradation by thiol-disulfide exchange. Interestingly, PMMA and PS networks
fully degraded and dissolved, however only at relatively low crosslinker loadings (< 2 mol%
vs monomer). In contrast, PMA and PDMAm networks were found not to degrade at any
crosslinking densities. By analysis of the polymerization kinetics, equilibrium swelling ratios
pre- and post- attempted degradation and theoretical studies, we show that the inability of the
FRP networks to fully degrade results from the presence of microclusters that form due to the
rapid polymerization and extensive intramolecular cyclization. These heterogeneous structures
do not swell, which prevents a small fraction of the disulfide bonds from being cleaved.
Furthermore, degradability can be afforded to these networks by significantly reducing the
initial monomer concentration, however at the expense of effective crosslinking density, thus
explaining the literature discrepancies. Alternatively, strand-cleaving comonomers can be
employed instead of cleavable crosslinkers to make the FRP networks fully degradable. | Gavin Irvine; Frances Dawson; Aimee George; Maciej Kopeć | Polymer Science; Hydrogels; Polymerization (Polymers); Polymerization kinetics; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65feeebf66c1381729a343d5/original/are-polymer-gels-synthesized-by-free-radical-polymerization-with-cleavable-crosslinkers-really-degradable.pdf |
60f6e570537d1022887e53e7 | 10.26434/chemrxiv-2021-lf2zd-v2 | Geographical Distribution of Amino Acid Mutations in Human SARS-CoV-2 Orf1ab Poly-Proteins Compared to the Equivalent Reference Proteins from China | The amino acid mutations among 28,345 poly-protein sequences corresponding to human SARS-CoV-2 orf1AB gene representing the six geographical locations; Africa, Asia, Europe, North America, Oceania and South America were identified by comparing with the equivalent reference poly-protein sequences derived from the first human SARS-CoV-2 genome sequence, reported from Wuhan-Hu-1, China. The mutations were analysed according to the following three datasets; i) 27,956 poly-proteins comprising 7,096 amino acid residues, ii) 373 poly-proteins comprising between 7,051-7,095 amino acid residues and iii) 16 poly-proteins comprising between 7,097-7,099 amino acid residues. In all, 3,204 distinct mutation sites were observed among the poly-proteins comprising 7,096 amino acid residues contributing to ~45% of the poly-protein sequence in SARS-CoV-2 orf1AB gene that have undergone mutations since the outbreak of COVID-19 pandemic disease in December 2019. Fifteen proteins of the poly-protein sequence were associated with mutations and the mutation propensities for the “leader protein”, nsp2, nsp3, nsp6, nsp7, nsp8, endoRNAse proteins was higher (> 1) compared to nsp4, nsp9, nsp10, 3C-like proteinase, RdRp, helicase, 3’-to-5’ exonuclease and 2’-O-ribose methyltransferase proteins. Relatively higher mutation percentages were observed for the RdRp (35.32%), nsp2 (26.42%), nsp3 (11.73%) and helicase (7.88%) proteins, whereas, mutation percentages for the remaining proteins ranged between 0.16% for nsp10 protein to 4.11% for the 3’ -to-5’ exonuclease proteins. Five mutations; T265I in nsp2 protein, T1246I in nsp3, G3278S in 3C-like proteinase, L3606F in nsp6 and P4715L in RdRp were common across all six geographical locations. The P4715L RdRp mutation was predominant in all geographical locations, except Africa, where G5215S mutation was predominant. The maximum number of distinct mutation sites were observed for the nsp3 protein. In 373 orf1AB poly-protein sequences comprising between 7,051-7,095 amino acid residues, deletion mutations were observed that were associated with “leader protein” between positions; 82-86 (GHVMV) and positions 141-143 (KSF). Among 16 orf1AB poly-proteins comprising between 7,097-7,099 amino acid residues, certain insertion mutations were observed that were associated with the nsp2 (517K), nsp3 (938E, 1901Y), 2’ -O-ribose methyltransferase (7046F) and nsp6 (3610F, 3611L) proteins. In this work, all mutations observed among the 28,345 orf1AB poly-proteins of human SARS CoV-2 relative to the reference sequences are presented. | Kunchur Guruprasad | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f6e570537d1022887e53e7/original/geographical-distribution-of-amino-acid-mutations-in-human-sars-co-v-2-orf1ab-poly-proteins-compared-to-the-equivalent-reference-proteins-from-china.pdf |
614dd3fb87a02dd657470f4d | 10.26434/chemrxiv-2021-l3jm1-v2 | Signal responsive transient coacervation in complex coacervate core micelles | Triggered coacervate phase (de)stabilisation in complex coacervate core micelles (C3Ms) has traditionally been limited to changes in pH and salt concentration, limiting options in responsive C3M material design. To expand this toolbox, we have developed C3Ms, that, at constant physiological pH, assemble and disassemble by coupling to a chemical reaction network (CRN) driven by the conversion of electron deficient allyl acetates and thiol or amine nucleophiles. This CRN produces transient quaternization of tertiary amine-functionalised block copolymers, which can then form the complex coacervate phase. We demonstrate triggered C3M assembly using two different allyl acetates, resulting in dramatically different assembly rates from hours to days. These are applied in various combinations with selected nucleophiles, demonstrating sequential signal induced C3M formation and deformation, as well as transient non-equilibrium (de)formation. We expect that timed and signal-responsive control over coacervate phase formation at physiological pH will find application in nucleic acid delivery, nano reactors and protocell research. | Reece W. Lewis; Benjamin Klemm; Mariano Macchione; Rienk Eelkema | Organic Chemistry; Materials Science; Polymer Science; Core-Shell Materials; Nanostructured Materials - Materials; Polyelectrolytes - Polymers | CC BY NC 4.0 | CHEMRXIV | 2021-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614dd3fb87a02dd657470f4d/original/signal-responsive-transient-coacervation-in-complex-coacervate-core-micelles.pdf |
60c756e69abda2cb69f8e5ea | 10.26434/chemrxiv.14345843.v1 | Contribution of C−H⋯π Interactions to Polymorphic Transitions of a Molecular Crystal with Disordered Fragments | Polymorphic transition is important for the functionality of crystalline materials. However, the
underlying mechanism remains unclear, especially when the crystal structure contains disordered
fragments. We report that C−H⋯π interactions play an important role in polymorphic transitions in
a molecular crystal with disordered fragments. The crystal has three phases, namely the a (< -80°C),
β (-80-40°C), and γ (< 40°C) phases, which are reversible through single-crystal-to-single-crystal
transformation in association with temperature change. Disorder of bulky tert-butyl substituents
appears at high-temperature in the β and γ phases. Intermolecular interaction analysis based on
Hirshfeld surfaces and related fingerprint plots revealed that the proportion of π⋯π interactions
decreased, while that of C−H⋯π interactions increased, at the transition from a to β phase. The
proportion of C−H⋯π interactions also increased at the transition from β to γ phase, but continuously
decreased in the β phase due to elevated temperature. Intermolecular interaction energies clarified the
contribution of C−H⋯π interactions to the stability of high-temperature crystal β and γ phases via polymorphic transitions. Our results potentially lead to design molecular crystals with polymorphic
transitions. | Takuya Taniguchi; Daisuke Takagi; Toru Asahi | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756e69abda2cb69f8e5ea/original/contribution-of-c-h-interactions-to-polymorphic-transitions-of-a-molecular-crystal-with-disordered-fragments.pdf |
63a12c4be8047a634bef12c2 | 10.26434/chemrxiv-2022-dc750 | The role of electrochemistry and surface chemistry in water-induced electricity generation from electrically conductive solids | Water-induced electricity generators (WIEGs) based on solid-water interactions are considered as promising next-generation power sources due to the abundance and sustainability of water. Nevertheless, the contributions of electrochemistry and solid surface chemistry to the electricity generation of WIEGs have not gained enough attention. Here, a series of WIEGs is designed to investigate the effects of different pairings of electrically conductive solids, device configurations, solid surface chemistry, and electrolytes in water on the electricity generation. It is revealed that the electricity generated from these devices is mainly ascribed to the electrochemical reactions involved by the conductive solids, dissolved oxygen, and liquid water that convert chemical energy into electricity. The dissociation of surface functional groups also affects the generated voltage in different electrolytes. The output performance can be enhanced by using more active solids and salty/acidic electrolytes. Finally, a semi-solid-state portable WIEG capable of producing stable voltage for at least 30 days was constructed, demonstrating great potential for driving portable/wearable/flexible electronics and internet of things devices. | Lingyi Lan; Shaohua Chen; Xiaoxue Liu; Jiaqing Xiong; Jianfeng Ping; Yibin Ying | Energy; Power; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a12c4be8047a634bef12c2/original/the-role-of-electrochemistry-and-surface-chemistry-in-water-induced-electricity-generation-from-electrically-conductive-solids.pdf |
62c4dbb3253021e6d98a8500 | 10.26434/chemrxiv-2021-6wbv4-v2 | Direct Observation of Peptide Hydrogel Self-Assembly | The characterization of self-assembling molecules presents significant experimental challenges, especially when associated with phase separation or precipitation. Transparent window infrared (IR) spectroscopy leverages site-specific probes that absorb in the “transparent window” region of the biomolecular IR spectrum. Carbon-deuterium (C-D) bonds are especially compelling transparent window probes since they are non-perturbative, can be readily introduced site selectively into peptides and proteins, and their stretch frequencies are sensitive to changes in the local molecular environment. Importantly, IR spectroscopy can be applied to a wide range of molecular samples regardless of solubility or physical state, making it an ideal technique for addressing the solubility challenges presented by self-assembling molecules. Here, we present the first continuous observation of transparent window probes following stopped-flow initiation. To demonstrate utility in a self-assembling system, we selected the MAX1 peptide hydrogel, a biocompatible material that has significant promise for use in drug delivery and medical applications. C-D labeled valine was synthetically introduced into five distinct positions of the twenty- residue MAX1 β-hairpin peptide. Consistent with current structural models, steady-state IR absorption frequencies and linewidths of C-D bonds at all labeled positions indicate that these side chains occupy a hydrophobic region of the hydrogel and that the motion of side chains located in the middle of the hairpin is more restricted than those located on the hairpin ends. Following a rapid change in ionic strength to initiate self-assembly, the peptide absorption spectra were monitored as function of time, allowing determination of site-specific time constants. We find that within the experimental resolution, MAX1 self-assembly occurs as a cooperative process. These studies suggest that stopped-flow transparent window FTIR can be extended to other time-resolved
applications, such as protein folding and enzyme kinetics. | Zoë Adams; Erika Olson; Zhengwen Lian; Audrey Kim; Matthew Holcomb; Jörg Zimmermann; Ramkrishna Adhikary; Philip Dawson | Physical Chemistry; Biological and Medicinal Chemistry; Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c4dbb3253021e6d98a8500/original/direct-observation-of-peptide-hydrogel-self-assembly.pdf |
60c75194ee301c499ac7aae3 | 10.26434/chemrxiv.13181117.v1 | Insilico Identification of Potential Antivirals and Molecular Dynamics Against SARS-CoV2 Main Protease and RBD of Spike Protein | <p>A coronavirus identified as 2019 novel coronavirus (COVID-19) is the etiological agent
responsible for the 2019-2020 viral pneumonia outbreak that commenced in Wuhan has been
declared as a pandemic by the World Health Organization. The virus is predominantly spread
from person-to-person mainly through airborne, fomite, contact, and droplet from the infected
patients. Also, the lack of definitive treatment is another concern that needs consideration. The
novel 2019 SARS-CoV-2 enters the host cell by binding of the viral surface spike glycoprotein
(S-protein) to angiotensin-converting enzyme 2 (ACE2). Mpro is a key coronavirus enzyme,
which plays a pivotal role in mediating viral replication and transcription, making it an attractive
drug target for this virus. Considering the importance of these two proteins in the viral infection,
these were preferred as a potential drug target against Covid19. In this study, we screened
potential antiviral drugs from the Pubchem database and natural antiviral agent quercetin for
induced fit docking against these two key proteins. The identified top hit was further evaluated
through molecular dynamic simulations. Our results suggest that the antiviral drugs Indinavir and
Famciclovir could be a potential drug against Covid19. <br /></p> | Vijayakumar Rajendran; Saravanan Kandasamy; Ankita Gupta; Jagannathan Selvaraj; Kukkaler Channappa Shivanandappa | Biochemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75194ee301c499ac7aae3/original/insilico-identification-of-potential-antivirals-and-molecular-dynamics-against-sars-co-v2-main-protease-and-rbd-of-spike-protein.pdf |
6449a175df78ec5015707a77 | 10.26434/chemrxiv-2023-lnfq8 | Identifying Coarse-Grained Representations for Electronic Predictions | Coarse-grained (CG) simulations are an important computational tool in chemistry and materials science. Recently, systematic ``bottom-up" CG models have been introduced to capture electronic structure variations of molecules and polymers at the CG resolution. However, the performance of these models is limited by the ability to select reduced representations that preserve electronic structure information, which remains a challenge. We propose two methods for (i) identifying important electronically coupled atomic degrees of freedom and (ii) scoring the efficacy of CG representations used in conjunction with CG electronic predictions. The first method is a physically-motivated approach that incorporates nuclear vibrations and electronic structure derived from simple quantum chemical calculations. We complement this physically-motivated approach with a machine learning technique based on the marginal contribution of nuclear degrees of freedom to electronic prediction accuracy using an equivariant graph neural network. By integrating these two approaches, we can both identify critical electronically coupled atomic coordinates and score the efficacy of arbitrary CG representations for making electronic predictions. We leverage this capability to make a connection between optimized CG representations and the future potential for ``bottom-up" development of simplified model Hamiltonians incorporating non-linear vibrational modes. | Chun-I Wang; Charlie Maier; Nicholas Jackson | Theoretical and Computational Chemistry; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6449a175df78ec5015707a77/original/identifying-coarse-grained-representations-for-electronic-predictions.pdf |
6423ae5562fecd2a839bc59e | 10.26434/chemrxiv-2023-9tkg4 | Nickel-catalyzed exhaustive hydrodefluorination of perfluoroalkyl arenes | Perfluoroalkyl compounds are persistent environmental pollutants due to their strong C(sp3)−F bonds. Hydrodefluorination has emerged as a potential alternative disposal method for perfluoroalkyl compounds. Although the transformation of trifluoromethyl arenes into the corresponding methyl arenes has been studied by several research groups, hydrodefluorination reactions of longer perfluoroalkyl chains remain rare. Herein, we report exhaustive hydrodefluorination reactions of pentafluoroethyl arenes and longer-chain analogues using molecular nickel catalysis. Despite the cleavage of multiple C(sp3)−F bonds, the reaction already proceeds upon gentle heating (60 °C). A mechanistic investigation indicated that the reaction proceeds via benzylic hydrodefluorination reactions followed by homobenzylic ones. We reveal the multiple roles of the Ni catalyst, which include C−F bond cleavage, promotion of HF elimination, and hydrosilylation. | Ryohei Doi; Masashi Yasuda; Naoki Kajita; Kenta Koh; Sensuke Ogoshi | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Bond Activation; Transition Metal Complexes (Organomet.) | CC BY 4.0 | CHEMRXIV | 2023-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6423ae5562fecd2a839bc59e/original/nickel-catalyzed-exhaustive-hydrodefluorination-of-perfluoroalkyl-arenes.pdf |
678ad8dc6dde43c908fba038 | 10.26434/chemrxiv-2023-mbr7t-v4 | How THC Works: Structural Insights Explaining Ligand Affinity for, and Partial Agonism of, Cannabinoid Receptor 1 | CB1, a member of the G protein-coupled receptor class, is the putative protein target of THC, the psychoactive component of cannabis. To better identify new synthetic cannabinoids with increased activity, all cannabinoids with reported experimental binding to the CB1 receptor were modelled in silico to build a predictive model for CB1 affinity of small molecules. Computationally derived affinity is not sufficient in and of itself to predict binding, but coupled with the experimental evidence that ligands enter the receptor from the membrane rather than solvent, we provide a model that accurately describes the binding of these molecules by incorporating a correction factor for relative hydrophobicity. In addition, we propose a mechanism of action for partial CB1 agonists based on molecular dynamics simulations of THC homologues, modelling long time scale structural changes in the CB1 receptor. Together, the affinity model, and the mechanism of agonism/antagonism can allow for the computational prediction of both the effective behaviour and potency of novel cannabinoids, and several such predictions are made. | Farsheed Shahbazi-Raz; Daniel Meister; Azam Mohammadzadeh; John Trant | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678ad8dc6dde43c908fba038/original/how-thc-works-structural-insights-explaining-ligand-affinity-for-and-partial-agonism-of-cannabinoid-receptor-1.pdf |
668d3fd7c9c6a5c07ac37033 | 10.26434/chemrxiv-2024-6wk09 | ROSHAMBO: Open-Source Molecular Alignment and 3D Similarity Scoring | Efficient virtual screening techniques are critical in drug discovery for identifying potential drug candidates. We present an open-source package for molecular alignment and 3D similarity calculations optimized for large-scale virtual screening of small molecules. This work parallels widely used proprietary tools and offers an approach complementary to structure-based virtual screening. Our package employs the PAPER software for optimizing molecular alignments based on Gaussian volume overlaps. GPU acceleration is utilized to significantly reduce computational time and resource requirements. After obtaining the optimal alignments between the target and the query molecules, both shape and color (based on pharmacophore features) scores are computed to assess molecular similarity, with aligned molecules optionally being output in sdf format. The package was benchmarked using the DUDE-Z public datasets. Results demonstrated the package's near-state-of-the-art performance and robustness across multiple target classes, with speed that enables many routine ligand-based drug discovery workflows. As an open-source and freely available resource (github.com/molecularinformatics/roshambo) with both a convenient Python API and command line interface, our package also addresses the need for accessible and efficient virtual screening tools in drug discovery. | Rasha Atwi; Ye Wang; Simone Sciabola; Adam Antoszewski | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668d3fd7c9c6a5c07ac37033/original/roshambo-open-source-molecular-alignment-and-3d-similarity-scoring.pdf |
62e04636cf661270d7b615c1 | 10.26434/chemrxiv-2022-mvr06 | ARC-MOF: A Diverse Database of Metal-Organic Frameworks with DFT-Derived Partial Atomic Charges and Descriptors for Machine Learning | Metal-organic frameworks (MOFs) are a class of crystalline materials composed of metal nodes or clusters connected via semi-rigid organic linkers. Owing to their high surface area, porosity, and tunability, MOFs have received significant attention for numerous applications such as gas separation and storage. Atomistic simulations and data-driven methods (e.g., machine learning) have been successfully employed to screen large databases and successfully develop new experimentally synthesized and validated MOFs for CO2 capture. To enable data-driven materials discovery for any application, the first (and arguably most crucial) step is database curation. This work introduces the ab initio REPEAT charge MOF (ARC-MOF) database. This is a database of ~280,000 MOFs which have been either experimentally characterized or computationally generated, spanning all publicly available MOF databases. A key feature of ARC-MOF is that it contains DFT-derived electrostatic potential fitted partial atomic charges for each MOF. Additionally, ARC-MOF contains pre-computed descriptors for out-of-the-box machine learning applications. An in-depth analysis of the diversity of ARC-MOF with respect to the currently mapped design space of MOFs was performed – a critical, yet commonly overlooked aspect of previously reported MOF databases. Using this analysis, balanced subsets from ARC-MOF for various machine learning purposes have been identified. Other chemical and geometric diversity analyses are presented, with an analysis on the effect of charge assignment method on atomistic simulation of gas uptake in MOFs. | Jake Burner; Jun Luo; Andrew White; Adam Mirmiran; Ohmin Kwon; Peter G. Boyd; Stephen Maley; Marco Gibaldi; Scott Simrod; Victoria Ogden; Tom K. Woo | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e04636cf661270d7b615c1/original/arc-mof-a-diverse-database-of-metal-organic-frameworks-with-dft-derived-partial-atomic-charges-and-descriptors-for-machine-learning.pdf |
60c755b30f50db7f0d397f81 | 10.26434/chemrxiv.14151989.v1 | Rational Prediction of Distal Activity-Enhancing Mutations in Tryptophan Synthase | Allostery is a central mechanism for the regulation of multi-enzyme complexes. The mechanistic basis that drives allosteric regulation is poorly understood, but harbors key information for enzyme engineering. In the present study, we focus on the tryptophan synthase complex that is composed of TrpA and TrpB subunits, which allosterically activate each other. Specifically, we develop a rational approach for identifying key amino acid residues of TrpB distal from the active site. In particular, we predict positions crucial for shifting the inefficient conformational ensemble of the isolated TrpB to a productive ensemble through intra-subunit allosteric effects. The experimental validation of the new conformationally-driven TrpB design demonstrates its superior stand-alone activity in the absence of TrpA, comparable to those enhancements obtained after multiple rounds of experimental laboratory evolution. Our work evidences that the current challenge of distal active site prediction for enhanced function in computational enzyme design can be ultimately addressed. | Miguel ÁNgel Maria-Solano; Thomas Kinateder; Javier Iglesias-Fernández; Reinhard Sterner; Sílvia Osuna | Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755b30f50db7f0d397f81/original/rational-prediction-of-distal-activity-enhancing-mutations-in-tryptophan-synthase.pdf |
6470defbe64f843f41d1d13b | 10.26434/chemrxiv-2023-1plrm | Tailorable biofunctionalization of poly(acrylamide) hydrogels via firefly luciferin-bioinspired click ligation accelerates cell attachment, spreading and proliferation | Polyacrylamide (PAM) hydrogels are extensively used as extracellular matrix mimics to study specific cell-materials interactions. However, chemistries typically applied for biofunctionalization of PAM lack chemo-selectivity and control over ligand density, which undermine reproducibility of cellular behavior, which can lead to inconclusive experiments. In this work, we introduce firefly luciferin-inspired click ligation to enable controlled and tunable biofunctionalization of PAM hydrogels. A novel acrylamide-based co-monomer is synthesized and incorporated in PAM hydrogels using traditional protocols, which introduces cyanobenzothiazole (CBT) functional groups. CBT mediates biofunctionalization of PAM with N-Cys bearing biomolecules via luciferin click chemistry. Biofunctionalization takes place under mild conditions, with high efficiency within only a few minutes, and does not require light exposure. When compared to the current commercial gold standard for PAM biofunctionalization sulfo-SANPAH, hydrogels modified via luciferin click ligation show increased control in loading of cell-adhesive biochemical cues. This leads to increased cellular attachment, spreading and proliferation due to a more efficient, homogeneous, and functional biofunctionalization. Luciferin-inspired click ligation may become a new standard for reliable biofunctionalization of PAM hydrogels with increased control over the density and preserved function of the presented biological cues, thus allowing more robust platforms for 2D cell-materials interaction experimentation. | Alexis Wolfel; Minye Jin; Nuno Araújo-Gomes; Malin Becker; Jeroen Leijten; Liliana Moreira Teixeira; Julieta I. Paez | Materials Science; Polymer Science; Biocompatible Materials; Hydrogels; Polymerization (Polymers); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6470defbe64f843f41d1d13b/original/tailorable-biofunctionalization-of-poly-acrylamide-hydrogels-via-firefly-luciferin-bioinspired-click-ligation-accelerates-cell-attachment-spreading-and-proliferation.pdf |
60c73d4fbb8c1a81f63d971a | 10.26434/chemrxiv.5649775.v1 | The Molecular Origin of Enthalpy/Entropy Compensation in Biomolecular Recognition | Biomolecular recognition can be stubborn; changes in the structures of associating molecules, or the environments in which they associate, often yield compensating changes in enthalpies and entropies of binding, and no net change in affinities. This phenomenon—termed enthalpy/entropy (H/S) compensation—hinders efforts in biomolecular design, and its incidence—often a surprise to experimentalists—makes interactions between biomolecules difficult to predict. Although characterizing H/S compensation requires experimental care, it is unquestionably a real phenomenon that has, from an engineering perspective, useful physical origins. Studying H/S compensation can help illuminate the still-murky roles of water and dynamics in biomolecular recognition and self-assembly. This review summarizes known sources of H/S compensation (real and perceived) and lays out a conceptual framework for understanding and dissecting—and, perhaps, avoiding or exploiting—this phenomenon in biophysical systems. | Jerome M. Fox; Mengxia Zhao; Michael J. Fink; Kyungtae Kang; George M. Whitesides | Biophysical Chemistry; Statistical Mechanics; Structure; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2017-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d4fbb8c1a81f63d971a/original/the-molecular-origin-of-enthalpy-entropy-compensation-in-biomolecular-recognition.pdf |
63fe11b2937392db3d34de6f | 10.26434/chemrxiv-2023-vkq8q | Cumulative Neutral Loss Model for Fragment Deconvolution in Electrospray Ionization High-Resolution Mass Spectrometry Data | Fragment deconvolution is a crucial step during componentization of non-targeted analysis (NTA) high-resolution mass spectrometry (HRMS) data, aiming to filter out false positive (FP) signals that do not belong to the component. Moreover, inclusion of FP fragments could lead to, for example, wrong identification further down the workflow. Commonly used methods for deconvolution of fragment signals rely on the presence of a time domain (e.g., peak apex retention time difference and correlation analysis). However, when there is no or insufficient MS2 information in the time domain, these methods are unusable and only the mass domain remains. A probability based cumulative neutral loss (CNL) model for fragment deconvolution using the mass domain information was thus developed to allow deconvolution for such cases. The optimized model, with a mass tolerance of 0.005 Da and a CNL score threshold of -0.95, was able to achieve true positive rate (TPr) of 95.0%, a false discovery rate (FDr) of 25.6%, and a reduction rate of 39.9%. Additionally, the CNL model was extensively tested on real samples containing predominantly pesticides at different concentration levels and with matrix effects. Overall, the model was able to obtain a TPr above 95% with FD rates between 45% and 77% and reduction rates between 10% and 24%. Finally, the CNL model was compared with the retention time difference method and peak shape correlation analysis, showing that a combination of correlation analysis and the CNL model was the most effective for fragment deconvolution, obtaining a TPr of 93.1%, a FDr of 57.2%, and a reduction rate of 42.6%. | Denice van Herwerden; Jake O'Brien; Sascha Lege; Bob Pirok; Kevin Thomas; Saer Samanipour | Analytical Chemistry; Chemoinformatics; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2023-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63fe11b2937392db3d34de6f/original/cumulative-neutral-loss-model-for-fragment-deconvolution-in-electrospray-ionization-high-resolution-mass-spectrometry-data.pdf |
6493b19f853d501c004a4b82 | 10.26434/chemrxiv-2023-kn9w8 | Electronegativity equilibration based on symmetry | A simple rule is deduced, providing new insight into the role of symmetry in determining electronegativity equilibrium. A bell-shaped symmetric graph has been found that interrelates atomic stress and electronegativity in heteronuclear diatomic molecules. This model displays a perspective in which the electronegativity of bonded atoms is equilibrium and the stresses between atoms is equal. The uniqueness of this model is that it can calculate the electronegativity of atoms in different molecules. | weicheng zeng | Theoretical and Computational Chemistry; Inorganic Chemistry; Bonding; Theory - Inorganic; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6493b19f853d501c004a4b82/original/electronegativity-equilibration-based-on-symmetry.pdf |
60c754da842e650118db4232 | 10.26434/chemrxiv.12654512.v3 | Tracing Molecular Properties Throughout Evolution: A Chemoinformatic Approach. | <p>Evolution of metabolism is a longstanding yet unresolved question, and
several hypotheses were proposed to address this complex process from a
Darwinian point of view. Modern statistical bioinformatic approaches targeted to the comparative
analysis of genomes are being used to detect signatures of natural selection at
the gene and population level, as an attempt to understand the origin of
primordial metabolism and its expansion. These studies, however, are still mainly
centered on genes and the proteins they encode, somehow neglecting the small
organic chemicals that support life processes. In this work, we selected
steroids as an ancient family of metabolites
widely distributed in all eukaryotes and applied unsupervised machine learning techniques to reveal the traits that natural selection has
imprinted on molecular properties throughout the evolutionary process. Our
results clearly show that sterols, the primal steroids that first appeared,
have more conserved properties and that, from then on, more complex compounds
with increasingly diverse properties have emerged, suggesting that chemical diversification
parallels the expansion of biological complexity. In a wider context, these
findings highlight the worth of chemoinformatic approaches to a better understanding the evolution of
metabolism.</p> | Marcelo Otero; Silvina Sarno; Sofía Acebedo; Javier Alberto Ramirez | Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754da842e650118db4232/original/tracing-molecular-properties-throughout-evolution-a-chemoinformatic-approach.pdf |
6788d77efa469535b9413bbc | 10.26434/chemrxiv-2025-pb6d3 | Single atom substitutions in backbone aromatic groups alter membrane permeability and biological activity of cyclic peptides | Cyclic peptides hold significant potential as disruptors of challenging targets such as protein-protein interactions, but their poor membrane permeability often limits their use for intracellular targets. Inspired by nature, we explored the introduction of aromatic groups in the peptide backbone to address this limitation. Starting from model peptide Sanguinamide A, we synthesized a series of analogues in which the native thiazole moiety was replaced with various simple aromatic groups. This approach allowed us to systematically investigate how minimal changes in the nature of the aromatic group and the flexibility of the peptide backbone influence membrane permeability. Significant differences in permeability were observed among the analogues, and for those that were permeable, NMR spectroscopy revealed conformational changes in response to environment polarity. In addition to studying permeability, we assessed the impact of these chemical modifications on biological activity using a target-agnostic cell painting assay. While permeability generally correlated with biological activity, distinct differences in activity were observed depending on the specific aromatic group incorporated. These findings highlight the importance of backbone-embedded aromatic groups in modulating both membrane permeability and biological activity, offering valuable insights for the development of cyclic peptides as therapeutic agents. | Joseph Openy; Sabela Vega-Ces; Gulshan Amrahova; Emeline Mestdach; Celestine Chi; Benjamin Kissel; Peter 't Hart | Biological and Medicinal Chemistry; Biophysics; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6788d77efa469535b9413bbc/original/single-atom-substitutions-in-backbone-aromatic-groups-alter-membrane-permeability-and-biological-activity-of-cyclic-peptides.pdf |
65f7cde466c1381729352e74 | 10.26434/chemrxiv-2024-40nv9 | Supramolecular chemistry of an antiaromatic tetrapyrrole: zinc(II) norcorrole | Zinc norcorrole was prepared by metalation of freebase norcorrole in the presence of pyridine. Zinc norcorrole is isolated as its pyridine complex, which is square-pyramidal at zinc. The pi-conjugated norcorrole fragment is appreciably curved, as demonstrated by both X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, the latter of which shows characteristic ring current deshielding effects. Ligand exchange of pyridine with the bidentate ligand DABCO results in the (ZnNc)2•DABCO sandwich complex, which is also characterised by crystallography and NMR spectroscopy. The NMR resonances of the axial ligands in all of the complexes demonstrate that the ring current in zinc norcorrole is approximately 40 nA/T, which is comparable in magnitude to that in porphyrin. Analysis of the ligand-exchange processes on addition of DABCO to ZnNc•pyridine show that zinc norcorrole coordinates to axial nitrogen-containing ligands with approximately 10^3-fold higher binding constants than analogous porphyrins. | David Bradley; Ruoming Tian; Mohan Bhadbhade; Lauren Macreadie; Chowdhury Sarowar; Martin Peeks | Organic Chemistry; Inorganic Chemistry; Physical Organic Chemistry; Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2024-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f7cde466c1381729352e74/original/supramolecular-chemistry-of-an-antiaromatic-tetrapyrrole-zinc-ii-norcorrole.pdf |
637de8350058eb700761dcc6 | 10.26434/chemrxiv-2022-7zc11 | Discovery of 2-aminopyrimidines as potent agonists for
the bitter taste receptor TAS2R14
| The bitter taste receptor TAS2R14 is a G protein-coupled receptor that is found on the tongue as well as in the human airway smooth muscle and other extraoral tissues. Because its activation causes bronchodilatation, TAS2R14 is a potential target for the treatment of asthma or chronic obstructive pulmonary disease. Structural variations of flufenamic acid, a nonsteroidal anti-inflammatory drug, led us to 2-aminopyridines showing considerable efficacy and potency in an IP-One accumulation assay. In combination with a bioisosteric exchange of the carboxylic moiety by a tetrazole unit, a set of promising new TAS2R14 agonists was developed. The most potent ligand 28.1 (EC50 = 72 nM) revealed a six-fold higher potency than flufenamic acid and a maximum efficacy of 129%. Besides its unprecedented TAS2R14 activation, 28.1 revealed marked selectivity over a panel of 24 non-bitter taste human GPCRs. | Lukas Waterloo; Tara Pfeiffer; Harald Huebner; Fabrizio Fierro; Regine Brox; Stefan Löber; Dorothee Weikert; Masha Y. Niv; Peter Gmeiner | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637de8350058eb700761dcc6/original/discovery-of-2-aminopyrimidines-as-potent-agonists-for-the-bitter-taste-receptor-tas2r14.pdf |
60c74b4d702a9b3bc018b400 | 10.26434/chemrxiv.12316154.v1 | Helical Carbenium Ion: A Versatile Organic Photoredox Catalyst in Red-Light-Mediated Reactions | <div><p><a></a><a></a><a></a><a>Red light has the advantages of low energy, less health risk and high penetration depth through various media. Herein, </a>a <a>helical carbenium ion (</a><i>N,N’</i>-di-<i>n</i>-propyl-1,13-dimethoxyquinacridinium (<i><sup>n</sup></i>Pr-DMQA<sup>+</sup>) tetrafluoroborate) has been used as an organic photoredox catalyst for photoreductions and photooxidations in the presence of red light (λ<sub>max</sub> = 640 nm). It has catalyzed red-light-mediated dual transition-metal/photoredox-catalyzed C-H arylation and intermolecular atom transfer radical addition through oxidative quenching, affording products in 57-93% yields. Moreover, its potential in photooxidation catalysis has also been demonstrated by successful applications in red-light-induced aerobic oxidative hydroxylation of arylboronic acids and benzylic C(sp<sup>3</sup>)-H oxygenation through reductive quenching, delivering products in up to 92% yield. Thus, a versatile organic photoredox catalyst (helical carbenium ion)<b> </b>for red-light-mediated photoredox reactions has been developed.</p></div> | Liangyong Mei; Jose M Veleta; thomas Gianetti | Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b4d702a9b3bc018b400/original/helical-carbenium-ion-a-versatile-organic-photoredox-catalyst-in-red-light-mediated-reactions.pdf |
651817d1ade1178b246880d3 | 10.26434/chemrxiv-2023-mbh7p | Computational Screening of Photodynamics of
Transition-Metal Complexes | The design of photoactive compounds is challenging due to the complicated nature that the ensuing photodynamics can assume. The complexity of this problem increases with the size and flexibility of the system, and the challenge becomes especially difficult in the rational design of open-shell transition-metal complexes where many electronic states and nuclear degrees of freedom participate in the excited-state dynamics. The only alternative is then to screen larger numbers of compounds as is done in the present work using computer simulations for a class of near-infrared emitting vanadium(III) complexes. Starting from the mechanism of the known emitter VCl_3(ddpd) (ddpd = N,N'-di\-meth\-yl-N,N'-di\-py\-ri\-di\-ne-2-yl\-py\-ri\-di\-ne-2,6-diamine), we establish design principles including an increase in the ligand-field strength in the complex in order to achieve higher emission quantum yields. Based on these principles, we design a large set of complexes that are tested for larger ligand-field splitting in static quantum chemistry calculations. For the subset of complexes with increased ligand-field splitting, we then perform nonadiabatic dynamics simulations and identify two promising near-infrared emitter with potential similar or increased emission quantum yield compared to the VCl_3(ddpd) reference. An analysis of the mechanisms of all studied complexes reveals individual relaxation pathways for each compound, confirming the difficulty of the identifying useful rational design principles in these photoactive open-shell transition-metal complexes. | Nóra Kovács; Patrick Zobel | Theoretical and Computational Chemistry; Inorganic Chemistry; Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651817d1ade1178b246880d3/original/computational-screening-of-photodynamics-of-transition-metal-complexes.pdf |
67cb56cefa469535b96aa570 | 10.26434/chemrxiv-2025-wqzsz | Optimizing TEMPO-Functionalized Surfaces: Unraveling the Impact of Diazotization Conditions on Immobilization Efficiency | In this study, glassy carbon surfaces were modified via the electrochemical reduction of diazonium salts bearing a TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl) moiety. This work investigates the impact of diazotization conditions on the redox state of TEMPO and its subsequent immobilization efficiency on electrodes. Two diazotization methods were employed: one using nitrosonium tetrafluoroborate (NOBF₄) and the other using tert-butyl nitrite (tBuONO) in combination with boron trifluoride acetonitrile complex (BF₃-CH3CN). Cyclic voltammetry and electrochemical simulations revealed that the redox state of TEMPO is significantly influenced by the diazotization agents. NOBF₄ primarily oxidizes TEMPO to its oxoammonium form (TEMPO⁺), while the tBuONO/BF₃-CH3CN system leads to the formation of non-redox species alongside TEMPO⁺. The electrochemical grafting of these TEMPO-derivatized diazonium salts onto glassy carbon electrodes showed that the presence of TEMPO radicals during the electroreduction process hinders immobilization efficiency. This effect is attributed to the spontaneous reduction of diazonium salts by TEMPO radicals, which decreases the availability of diazonium species for surface grafting. The formation of non-redox species, which are regenerated after immobilization on the surface, appears to be a promising approach for achieving reproducible layers with higher surface concentrations. | Elie Bou Rahhal; Talia Bsaibess; Olivier Alévêque; Eric Levillain; Marylène Dias; Christelle Gautier | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study; Surface | CC BY 4.0 | CHEMRXIV | 2025-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cb56cefa469535b96aa570/original/optimizing-tempo-functionalized-surfaces-unraveling-the-impact-of-diazotization-conditions-on-immobilization-efficiency.pdf |
64c30107658ec5f7e54a901e | 10.26434/chemrxiv-2023-7z1s2 | Laboratory Kilogram-Scale Graphene Production from Coal | The flash Joule heating (FJH) method converts many carbon feedstocks into graphene in milliseconds to seconds using an electrical pulse. This opens an opportunity for processing low or negative value resources, such as coal and plastic waste, into high value graphene. Here, we demonstrate a lab-scale automation FJH system that allows the synthesis of 1.1 kg of turbostratic flash graphene from coal-based metallurgical coke (MC) in 1.5 h. The process is based on the automated conversion of 5.7 g of MC per batch using an electrical pulse width modulation system to conduct the bottom-up upcycle of MC into flash graphene. We then compare this method to two other scalable graphene synthesis techniques by both a life cycle assessment and a technoeconomic assessment. | Lucas Eddy; Duy Xuan Luong; Jacob Beckham; Kevin Wyss; Tyler Cooksey; Phelecia Scotland; Chi Hun Choi; Weiyin Chen; Paul Advincula; Zhiyong Zhang; Vladimir Mancevski; James Tour | Organic Chemistry; Materials Science; Carbon-based Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c30107658ec5f7e54a901e/original/laboratory-kilogram-scale-graphene-production-from-coal.pdf |
60c74304bb8c1a745c3da234 | 10.26434/chemrxiv.7889993.v3 | eMap: A Web Application for Identifying and Visualizing Electron or Hole Hopping Pathways in Proteins | <p>eMap is a web-based platform for identifying and visualizing electron or hole transfer pathways in proteins based on their crystal structures. The underlying model can be viewed as a coarse-grained version of the Pathways model, where each tunneling step between hopping sites represented by electron transfer active (ETA) moieties is described with one effective decay parameter that describes protein-mediated tunneling. ETA moieties include aromatic amino acid residue side chains and aromatic fragments of cofactors that are automatically detected, and, in addition, electron/hole residing sites that can be specified by the users. The software searches for the shortest paths connecting the user-specified electron/hole source to either all surface-exposed ETA residues or to the user-specified target. The identified pathways are ranked based on their length. The pathways are visualized in 2D as a graph, in which each node represents an ETA site, and in 3D using available protein visualization tools. Here, we present the capability and user interface of eMap 1.0, which is available at https://emap.bu.edu.</p> | Ruslan N. Tazhigulov; James R. Gayvert; Melissa Wei; Ksenia B. Bravaya | Bioinformatics and Computational Biology; Biophysics; Computational Chemistry and Modeling; Theory - Computational; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74304bb8c1a745c3da234/original/e-map-a-web-application-for-identifying-and-visualizing-electron-or-hole-hopping-pathways-in-proteins.pdf |
674dcdf15a82cea2faba94d5 | 10.26434/chemrxiv-2024-5nqfr | Deciphering the astrophotochemical inertness of H3+ at molecular level | The trihydrogen cation, H3+, is unique in the Universe. It serves as the primary proton reservoir, driving essential astrochemical reactions, and it functions as a thermostat for giant gas planets. H3+ has also remarkably low photodissociation rate, explained by its exceptionally high first electronic excitation energy (19.3 eV). Herein we reveal the key factors behind this high energy: (i) aromatic stabilization in its electronic ground state, (ii) antiaromatic destabilization in its first excited state, and (iii) a high nuclear-to-electronic charge ratio (+3 vs. -2). Through comparisons with analogous pi-conjugated carbocations, we find that ground state aromatic stabilization plus excited state antiaromatic destabilization raise the excitation energy of H3+ by 4.8 - 6.0 eV. Only with this increase can it fulfil its unique functions in space. | Josene Toldo; Jakob Staab; Eduard Matito; Cina Foroutan-Nejad; Henrik Ottosson | Theoretical and Computational Chemistry; Earth, Space, and Environmental Chemistry; Space Chemistry; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2024-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674dcdf15a82cea2faba94d5/original/deciphering-the-astrophotochemical-inertness-of-h3-at-molecular-level.pdf |
6467913aa32ceeff2de8c8f5 | 10.26434/chemrxiv-2023-crvs6 | Tetracene Dimers: A Platform for Intramolecular Down- and Up-conversion | Photon energy conversion can be accomplished in many different ways, including the two opposing manners, down-conversion (i.e., singlet fission, SF) and up-conversion (i.e., triplet-triplet annihilation up-conversion, TTA-UC). Both processes have the potential to help overcome the detailed balance limit of single-junction solar cells. Tetracene, in which the energies of the lowest singlet excited state and twice the triplet excited state are comparable, exhibits both down- and up-conversion. Here, we have designed meta-diethynylphenylene- and 1,3-diethynyladamantyl-linked tetracene dimers, which feature different electronic coupling, to characterize the interplay between intramolecular SF (intra-SF) and intramolecular TTA-UC (intra-TTA-UC) via steady-state and time-resolved absorption and fluorescence spectroscopy. Furthermore, we have used Pd-phthalocyanine as a sensitizer to enable intra-TTA-UC in the two dimers via indirect photoexcitation in the near-infrared part of the solar spectrum. The work is rounded off by temperature-dependent measurements, which outline key aspects of how thermal effects impact intra-SF and intra-TTA-UC in the different dimers. | Dirk Guldi; Yifan Bo; Yuxuan Hou; Dominik Thiel; Rene Weiss; Tim Clark; Michael Ferguson; Rik Tykwinski | Energy; Photovoltaics | CC BY 4.0 | CHEMRXIV | 2023-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6467913aa32ceeff2de8c8f5/original/tetracene-dimers-a-platform-for-intramolecular-down-and-up-conversion.pdf |
6760cd4381d2151a02fb5356 | 10.26434/chemrxiv-2024-9lpb9 | Digital Catalysis Platform (DigCat): A Gateway to Big Data and AI-Powered Innovations in Catalysis | The Digital Catalysis Platform (DigCat) is a pioneering integration of big data and AI tailored for catalysis materials research. It encompasses over 400,000 experimental performance data for electro-, thermo-, and photocatalysts, alongside more than 300,000 catalyst structures. DigCat provides dynamic data visualization, precise literature tracking, and an intelligent Q&A assistant, supported by advanced tools for on-the-cloud microkinetic modeling, machine learning force field training, and regression model development. Additionally, it features an AI-powered chatbot grounded in catalytic data and knowledge. As a pioneering digital catalysis platform and the world’s first publicly released full electrocatalysis experimental database, DigCat has made valuable contributions to advancing the field. Since its official launch in January 2024, the platform has been upgraded to Version 3.0 as of September 2024. Access DigCat at https://www.digcat.org. | Di Zhang; Hao Li | Catalysis; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2024-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6760cd4381d2151a02fb5356/original/digital-catalysis-platform-dig-cat-a-gateway-to-big-data-and-ai-powered-innovations-in-catalysis.pdf |
65d28a76e9ebbb4db9a68dc4 | 10.26434/chemrxiv-2024-t3fnt | Zn(II)-Driven Impact of Monomeric Transthyretin on Amyloid-beta Amyloidogenesis | Extracellular accumulation of amyloid-beta (Abeta) peptides in the brain plays a significant role in the development of Alzheimer's disease (AD). While the co-localization and interaction of proteins and metal ions with Abeta in extracellular milieu are established, their precise pathogenic associations remain unclear. Here we report the impact of Zn(II) on the anti-amyloidogenic properties of monomeric transthyretin (M-TTR), which coexists spatially with Abeta and Zn(II) in extracellular fluids. Our findings demonstrate the Zn(II)-promoted ternary complex formation involving M-TTR, Abeta40, and Zn(II) as well as M-TTR's proteolytic activity towards Abeta40. These interactions alter the inhibitory effect of M-TTR on Abeta40 amyloidogenesis, particularly affecting the primary nucleation process, and mitigate the cytotoxicity induced by Abeta40. This study unveils the variable activities of M-TTR towards Abeta40, driven by Zn(II), providing insights into how metal ions influence the entanglement of M-TTR in the Abeta-related pathology linked to AD. | Yelim Yi; Bokyung Kim; Young Ho Ko; Jin Hae Kim; Mi Hee Lim | Biological and Medicinal Chemistry; Inorganic Chemistry; Bioinorganic Chemistry; Biophysics; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d28a76e9ebbb4db9a68dc4/original/zn-ii-driven-impact-of-monomeric-transthyretin-on-amyloid-beta-amyloidogenesis.pdf |
60c7467b4c89199807ad2b59 | 10.26434/chemrxiv.11336087.v1 | Efficient CO2 Sequestration by a Solid-Gas Reaction Enabled by Mechanochemistry: The Case of L-Lysine | This study describes an efficient and solvent-free method for the regioselective production of L-lysine ammonium epsilon-carbamate by ball-milling L-lysine under an atmosphere of CO<sub>2</sub>. The regioselective formation of L-lysine ammonium epsilon-carbamate by this mechanochemical approach was confirmed by a complete analytical study, including <sup>1</sup>H-<sup>13</sup>C and <sup>1</sup>H-<sup>15</sup>N CP MAS NMR measurements as well as liquid NMR analysis, powder X-ray diffraction, thermal analysis, and elemental analysis. Time of milling, rotational speed, milling material, and liquid assistants were screened, while the reversibility of the process was assessed. This milling approach was compared with the syntheses in aqueous solution and in the solid-state without agitation. In addition to be regioselective, the synthesis by solvent-free mechanochemistry was found to be much faster than the other approaches while producing lot less waste. | Abdal-Azim Al-Terkawi; Frédéric Lamaty; Thomas-Xavier Métro | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7467b4c89199807ad2b59/original/efficient-co2-sequestration-by-a-solid-gas-reaction-enabled-by-mechanochemistry-the-case-of-l-lysine.pdf |
60c748c9469df41fe7f43aba | 10.26434/chemrxiv.11973132.v1 | Recycling Carbon: An Outreach Activity Designed to Introduce the General Public to Carbon Capture, Utilisation and Storage | Anthropogenic emissions of carbon dioxide are causing unmeasurable damage to our planet. As well as rapidly decreasing annual carbon emissions we need to remove already-emitted carbon dioxide from the atmosphere, so-called negative emissions. However, public opinion is important when deploying new carbon capture technology and prior research has shown that it is more likely to be accepted when local residents have been introduced prior. In this paper we describe a new outreach activity, Recycling Carbon, to introduce the general public to negative emissions technologies. Recycling Carbon was designed by researchers active in the development of carbon capture and utilisation and has proven very versatile, appealing to audiences of 5-75 year olds in a number of settings including classrooms, science fairs and as a public science lecture. Preliminary feedback, in the form of a before-activity and post-activity questionnaire, indicates that engagement with Recycling Carbon improves people’s understanding of negative emissions technology. Finally the paper discusses how engagement with Recycling Carbon is also an opportunity to discuss an individual’s carbon footprint. <br /> | Jennifer Rudd; Michael E. A. Warwick; Marco Taddei; Russell Wakeham | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748c9469df41fe7f43aba/original/recycling-carbon-an-outreach-activity-designed-to-introduce-the-general-public-to-carbon-capture-utilisation-and-storage.pdf |
6409066b0e6a36fabaf606fe | 10.26434/chemrxiv-2023-jdtd9-v2 | Nanometric chemical decomposition of infertile Himalayan soils from Uttarakhand | We present the nanometric chemical decomposition of Himalayan agricultural soils. The motivation to use this state-of-the-art material characterisation in the soil is to reduce the testing cost while increasing the efficiency of the characterisation. In India, a bulk volume of soil is still required for the characterisation of agricultural soil. The fertility of micronutrient contents and crop supply capacity vary greatly depending on soil types, crop types, ecology, and agroclimatic variability. Since total levels of micronutrients are rarely predictive of the availability of a nutrient to plants, knowledge of the differences in soil micronutrients that are available to plants is essential for the sensible management of micronutrient fertility and toxicity. In the state of Uttarakhand, low levels of micro-nutrients in the soil are frighteningly common, and this issue is made worse by the fact that many current cultivars of important crops are extremely vulnerable to low mineral levels. These baseline results are to be used to inform local farmers about the potential remedies, costs, and consequential benefits and durability. We intend not to present a generalized or generalized solution. Therefore, we limit our soil sample collections to five arc minutes (8.6 square kilometers) and document variations and heterogeneity in the chemical components of the soil. In this study, we used scanning electron microscopy to chemically deconstruct the barren Himalayan soils from Uttarakhand. Aluminium, carbon, oxygen, and silicon were identified as the primary elements that contributed more than 5% of the total weight and atomic percentage. Other elements include less than 4% of iron, titanium, nitrogen, sodium, magnesium, chloride, phosphorus, sulfur, potassium, and calcium. | KV Chinmaya; KP Sarbeena; Vinitha Johny; Sumantra Pal; Awnish Kumar; Gowravaram Mohan Rao; Siddharth Ghosh; Moumita Ghosh | Physical Chemistry; Nanoscience; Agriculture and Food Chemistry; Nanostructured Materials - Nanoscience; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6409066b0e6a36fabaf606fe/original/nanometric-chemical-decomposition-of-infertile-himalayan-soils-from-uttarakhand.pdf |
62d91954fe12e34247ace396 | 10.26434/chemrxiv-2022-98t71-v2 | Union Carbide Polymerization Catalysts: from Uncovering Active Site Structures to Designing Molecularly-Defined Analogs | The Union Carbide (UC) ethylene polymerization catalysts, based on chromocene dispersed on silica, show distinct features from the Phillips catalysts, but share the same heated debate regarding the structure of its active sites. Based on a combination of IR, EPR spectroscopies, labelling experiments, and DFT modelling, we identified monomeric surface-supported Cr(III) hydrides, (≡SiO)Cr(Cp)-H, as the active sites of the UC catalyst. These sites are formed in the presence of grafted and adsorbed chromocene as well as residual surface OH groups, only possible at high Cr loading, and involves a C-H activation of the Cp ring. These Cr-hydrides initiate polymerization, yielding Cr(III) alkyl species that insert ethylene through a Cossee-Arlman-type mechanism, as evidenced by spectroscopic studies. These insights inspired the design of a well-defined analogue, CpCr(CH(SiMe3)2)2 grafted on partially dehydroxylated silica, that shows similar spectroscopic and polymer structure as the UC catalyst, further supporting the proposed active site structure. | David Trummer; Anna Nobile; Pierre-Adrien Payard; Anton Ashuiev; Yuya Kakiuchi; Daniel Klose; Gunnar Jeschke; Christophe Copéret | Catalysis; Organometallic Chemistry; Polymer Science; Heterogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions; Polymerization (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d91954fe12e34247ace396/original/union-carbide-polymerization-catalysts-from-uncovering-active-site-structures-to-designing-molecularly-defined-analogs.pdf |
65cd6a5366c1381729ab0854 | 10.26434/chemrxiv-2024-p5t3l | CURATOR: Building Robust Machine Learning Potentials for Atomistic Simulations Autonomously with Batch Active Learning | To enable fast, resource efficient development and broad scale deployment of of high accuracy Machine-Learned Interatomic Potentials (MLIPs) with minimum expert involvement, we introduce CURATOR, an autonomous batch active learning workflow for constructing MLIPs. CURATOR integrates state of the art models, uncertainty quantification techniques, batch selection algorithms with user defined labeling and chemical-structure space exploration methods for data and compute efficient active learning. We also developed a novel efficient gradient computation method that calculates forces and stress based on the energy derivative with respect to accelerate CURATOR. Our evaluation across different chemical systems demonstrates that CURATOR considerably reduces the computational resources and time required to develop reliable MLIPs. In practical applications in novel complex materials and interfaces, CURATOR shows promising results, underscoring its potential in accelerating materials discovery. The flexibility and efficiency of CURATOR mark a significant advancement in the field of computational materials science, paving the way for more efficient and larger time-length scale atomistic simulations. | Xin Yang; Martin Hoffmann Petersen; Renata Sechi; William Sandholt Hansen; Sam Walton Norwood; Yogeshwaran Krishnan; Smobin Vincent; Jonas Busk; Francois Raymond J Cornet; Ole Winther; Juan Maria Garcia Lastra; Tejs Vegge; Heine Anton Hansen; Arghya Bhowmik | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cd6a5366c1381729ab0854/original/curator-building-robust-machine-learning-potentials-for-atomistic-simulations-autonomously-with-batch-active-learning.pdf |
667c71bd01103d79c53594f4 | 10.26434/chemrxiv-2024-dgtk3 | Synthesis, Characterization, and Catalytic CO2 Reduction Reactivity of Ruthenium CNC Pincer Complexes Containing Macrocyclic or Long Chain Wingtips | Ruthenium CNC pincer complexes, comprised of N-heterocyclic carbenes (NHCs) and a pyridyl ring, are highly active catalysts for carbon dioxide reduction. We hypothesized that the addition of long chain aliphatic groups with an olefin terminus as wingtips on these CNC pincers could be used to form macrocyclic catalysts by ring closing metathesis (RCM). We have synthesized three new ruthenium pincer catalysts, [(CNC)Ru(CH3CN)2Cl]OTf, containing a long chain olefin wingtip (4A-4C, where R = H, Me, OMe para to N on the pyridine ring) and performed RCM on 4B, followed by hydrogenation, to form a novel macrocyclic ruthenium catalyst, 6B. These four catalysts were tested for the photocatalytic reduction of CO2 in the presence (sensitized) and absence (self-sensitized) of an external photosensitizer. With a photosensitizer, these catalysts produced mostly CO (775 to 1210 TON) with smaller amounts of H2 also formed. The methyl substituted macrocyclic catalyst 6B showed a TON of 1185 for CO over 72 hours compared to a TON of 775 for CO for the acyclic catalyst 4B. The remote substituents at the para-position of the central pyridine ring significantly influence catalyst activity with R = OMe > H = Me. | Weerachai Silprakob; Jannatul Ferdous; Sanjit Das; Fengrui Qu; Jonah Jurss; Elizabeth Papish | Organic Chemistry; Inorganic Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667c71bd01103d79c53594f4/original/synthesis-characterization-and-catalytic-co2-reduction-reactivity-of-ruthenium-cnc-pincer-complexes-containing-macrocyclic-or-long-chain-wingtips.pdf |
60c755c4bdbb890217a3a8d3 | 10.26434/chemrxiv.14160404.v1 | Liquid Graphene Oxide Binder and Modified Glass Fiber Separator for Lithium Sulfur Battery with Highly Improved Cycling Performance | <p>Lithium sulfur (Li-S) batteries with high
theoretical energy density (~2.5 kWh kg<sup>-1</sup>) and high theoretical
gravimetric capacity (1672 mAh g<sup>-1</sup>) have drawn great attention as
they are promising candidates for large scale energy storage devices.
Unfortunately some technical obstacles hinder the practical application of Li-S
batteries such as formation of polysulfide intermediates between cathode and
anode as well as the insulating nature of sulfur cathode and other discharge
products. Glass fiber separators provide some cavities to withstand the
volume change of sulfur during cycling leading to long-term cycling stability. Here,
application of polar materials with novel liquid graphene oxide (L-GO) binder
rather than the standard polyvinylidene fluoride (PVDF) binder as effective
coatings on the glass fiber separator of the Li-S cell have been developed to
suppress the shuttle effect. The deposition of silicon dioxide (SiO<sub>2</sub>),
titanium dioxide (TiO<sub>2</sub>) and poly
(1,5-diaminoanthraquinone) (PDAAQ)
with L-GO binder on the glass fiber separator was investigated with<b> </b>polycarboxylate
functionalized graphene (PC-FGF/S)
cathode and Li metal anode. The cells with modified coatings and
L-GO as an efficient binder could accelerate conversion of long-chain
polysulfides to short-chain polysulfides and significantly
delayed the growth of lithium dendrites resulted the capacity retention of ~
1020, 1070 and 1190 mAh g<sup>-1</sup> for the cells with SiO<sub>2</sub>/L-GO,
TiO<sub>2</sub>/L-GO and PDAAQ/L-GO coated separators after 100 cycles. The
results demonstrate that ultrathin SiO<sub>2</sub>, TiO<sub>2</sub> and PDAAQ containing
coatings with L-GO binder on the glass fiber separator can drastically improve
the cyclability of the Li-S cells.</p> | Maryam Sadat Kiai | Nanostructured Materials - Nanoscience; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755c4bdbb890217a3a8d3/original/liquid-graphene-oxide-binder-and-modified-glass-fiber-separator-for-lithium-sulfur-battery-with-highly-improved-cycling-performance.pdf |
60c74cb4567dfe6248ec51d7 | 10.26434/chemrxiv.12118917.v2 | Optical Properties of Photodynamic Therapy Drugs in Different Environments: The Paradigmatic Case of Temoporfin | Computational tools have been used to study the photophysical and photochemical features of photosensitizers in photodynamic therapy (PDT) –a minimally invasive, less aggressive alternative for cancer treatment. PDT is mainly based by the activation of molecular oxygen through the action of a photoexcited sensitizer (photosensitizer). Temoporfin, widely known as mTHPC, is a second-generation photosensitizer, which produces the cytotoxic singlet oxygen when irradiated with visible light and hence destroys tumor cells. However, the bioavailability of the mostly hydrophobic photosensitizer, and hence its incorporation into the cells, is fundamental to achieve the desired effect on malignant tissues by PDT. In this study, we focus on the optical properties of the temoporfin chromophore in different environments –in <i>vacuo</i>, in solution, encapsulated in drug delivery agents, namely cyclodextrin, and interacting with a lipid bilayer. | busenur Aslanoglu; Ilya Yakavets; Vladimir Zorin; Henri-Pierre Lassalle; Francesca Ingrosso; Antonio Monari; Saron Catak | Biochemistry; Biophysics; Computational Chemistry and Modeling; Biophysical Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cb4567dfe6248ec51d7/original/optical-properties-of-photodynamic-therapy-drugs-in-different-environments-the-paradigmatic-case-of-temoporfin.pdf |
656096facf8b3c3cd704f116 | 10.26434/chemrxiv-2023-stbm1-v3 | Deciphering the Interplay Between Local and Global Dynamics of Anodic Metal Oxidation | The stark difference between global and local metal oxidation dynamics underscores the need for methodologies capable of performing precise sub-μm-scale and wide-field measurements. In this study, we present Reflective Microscopy as a tool developed to address this challenge, illustrated by the example of chronoamperometric Fe oxidation in NaCl solution. Analysis at a local scale of 10s of μm has revealed three distinct periods of Fe oxidation: the initial covering of the metal interface with a surface film, followed by the electrochemical conversion of the formed surface film, and finally, the in-depth oxidation of Fe. In addition, thermodynamic calculations and the quantitative analysis of changes in optical signal (light intensity), correlated with variations in refractive indexes, suggests the initial formation of maghemite, followed by its subsequent conversion to magnetite. The reactivity maps for all three periods are heterogeneous, which can be attributed to the preferential oxidation of certain crystallographic grains. Notably, at the global scale of 100s of μm, reactivity initiates at the electrode border and progresses towards its center, demonstrating a unique pattern that is independent of local metal structure. This finding underscores the significance of simultaneously employing sub-μm-precise, quantitative and wide-field measurements for a comprehensive description of metal oxidation processes. | Aleksei Makogon; Jean-Marc Noël; Frédéric Kanoufi; Viacheslav SHKIRSKIY | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study; Interfaces; Optics | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656096facf8b3c3cd704f116/original/deciphering-the-interplay-between-local-and-global-dynamics-of-anodic-metal-oxidation.pdf |
60c75290ee301cef9ec7ac15 | 10.26434/chemrxiv.13322768.v1 | Monolayer Nanosheets Formed by Liquid Exfoliation of Charge-as-Sisted Hydrogen-Bonded Frameworks | Hydrogen-bonded organic frameworks (HOFs) are a diverse and tunable class of materials, but their potential as free-standing two-dimensional nanomaterials has yet to be explored. Here we report the self-assembly of two layered hydrogen-bonded frameworks based on strong, charge-assisted hydrogen-bonding between carboxylate and amidinium groups. Ultrasound-assisted liquid exfoliation of both materials readily produces monolayer hydrogen-bonded organic nanosheets (HONs) with micron-sized lateral dimensions. The HONs show remarkable stability and maintain their extended crystallinity and monolayer structures even after being suspended in water at 80 °C for three days. These systems also exhibit efficient fluorescence quenching of an organic dye in organic solvents, superior to the quenching ability of the bulk frameworks. We anticipate that this approach will provide a route towards a diverse new family of molecular two-dimensional materials with great potential for use in separation, sensing, catalysis, delivery, and electronics materials applications. | Josh Nicks; Stephanie Boer; Nicholas White; jonathan Foster | Supramolecular Chemistry (Org.); Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75290ee301cef9ec7ac15/original/monolayer-nanosheets-formed-by-liquid-exfoliation-of-charge-as-sisted-hydrogen-bonded-frameworks.pdf |
613a615cb817b4154d1826b1 | 10.26434/chemrxiv-2021-f7kt8 | Photoredox Catalyzed Site-Selective Generation of Carbanions from C(sp3)-H bonds in Amines | The selective activation of sp3 carbon-hydrogen bonds in presence of multiple C¬-H bonds is challenging and remains of supreme importance in chemical research. Herein, we describe the activation of a C(sp3) H bond in α position to an amine via a carbanion intermediate. In the presence of several α amine sites, only one specific position is selectively activated. Applying this protocol, the proposed carbanion intermediate was effectively trapped with different electrophiles such as deuterium (D+), tritium (T+), or carbonyl compounds compiling over 50 examples. Further, this methodology was used to install deuterium or tritium in different drug derivatives (> 10 drugs) at a selected position in a late-stage functionalization. In addition, the protocol is suitable for a gram-scale synthesis and a detailed mechanistic investigation has been carried out to support our hypothesis. | Kathiravan Murugesan; Karsten Donabauer; Rok Narobe; Armin Bauer; Volker Derdau; Burkhard Koenig | Catalysis; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2021-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613a615cb817b4154d1826b1/original/photoredox-catalyzed-site-selective-generation-of-carbanions-from-c-sp3-h-bonds-in-amines.pdf |
60c753d60f50db5e93397c1d | 10.26434/chemrxiv.13560353.v1 | Application of the “EigenValue Analysis (EVANS)” Methodology to Build Quantitative Structure Pharmacokinetic Relationship Models | We present EigenValue ANalySis (EVANS), a QSPR methodology that considers 3D molecular information of enantiomeric ensembles of chiral molecules without the need to perform an alignment step. EVANS follows an intricate molecular modelling protocol that generates orthogonal eigenvalues from hybrid matrices of physicochemical properties and 3D structure; these eigenvalues are used as independent variables in QSPR analyses. The EVANS formalism has been presented and deployed to build quantitative structure pharmacokinetic relationship (QSPKR) models on a benchmark dataset for three critical PK parameters: steady-state volume of distribution (VDss), clearance (CL), and half-life (t1/2). Predictive QSPKR models were built by using the eigenvalues generated via the EVANS methodology in conjunction with multiple linear regression (MLR), random forest (RF), and support vector machine (SVM) algorithms, and it was observed that the EVANS QSPKR models sync with published work in the literature. Thus, we present the EVANS methodology as a first-line prediction tool to prioritise compounds in drug discovery and development. | Anish Gomatam; Blessy Joseph; Mushtaque S. Shaikh; Poonam Advani; Evans C. Coutinho | Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753d60f50db5e93397c1d/original/application-of-the-eigen-value-analysis-evans-methodology-to-build-quantitative-structure-pharmacokinetic-relationship-models.pdf |
63e587cc9da0bc6b33a61cb4 | 10.26434/chemrxiv-2023-hpp81 | Balancing on a Knife's Edge: Studies on the Synthesis of Pillar[6]arene Derivatives | Pillar[6]arenes are established as crucial building blocks in supramolecular chemistry, however they can be difficult to synthesize, particularly in the absence of large solubilizing substituents. In this work we explore variability in literature syntheses of pillar[6]arene derivatives, and suggest that the outcome is dependent on whether oligomeric intermediates stay in solution long enough for thermodynamically favourable macrocyclization to occur. We demonstrate that in a previously capricious BF3OEt2-mediated procedure, 5 mol% of a Brnsted acid can slow down the reaction to favour macrocycle formation. | Oscar Swirepik; Jordan Smith; Nicholas White | Organic Chemistry; Physical Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e587cc9da0bc6b33a61cb4/original/balancing-on-a-knife-s-edge-studies-on-the-synthesis-of-pillar-6-arene-derivatives.pdf |
62bab8dde84dd1169306de35 | 10.26434/chemrxiv-2022-dm6h1 | NH-bridged Dimeric Phosphazanes: Inorganic Molecular Switches based on Anion Responsive Bifurcated to Trifurcated Hydrogen Bond Transitions | Molecular machines and switches, supramolecular chemistry, and crystal engineering are vibrant areas of research. Organic chemists have devoted considerable efforts to develop a wide range of complex functional building blocks with enhanced properties and chemically responsive properties to advance these fields. However, the rational design of topologically versatile and chemically responsive building blocks in the main group arena is largely unexplored. Within this context, we have rationally designed a series of NH-bridged acyclic dimeric cyclodiphosphazanes species, [(μ-NH){PE(μ-NtBu)2PE(NHtBu)}2] (E= O and S), displaying bimodal bifurcated R21(8) and trifurcated R31(8,8) hydrogen bonding motifs. The reported species reversibly switch their topological arrangement in the presence of anions. Our results underscore these species as versatile building blocks for molecular machines and switches, as well as supramolecular chemistry and crystal engineering based on cyclophosphazane frameworks. | Gavin HUM; Si Jia Isabel Phang; How Chee Ong; Shina Quek; Felix Leon; Yi Xin Joycelyn Khoo; Chenfei Li; Jack K. Clegg; Jesus Diaz; mihaiela Stuparu; Felipe Garcia | Inorganic Chemistry; Main Group Chemistry (Inorg.); Sensors; Supramolecular Chemistry (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2022-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bab8dde84dd1169306de35/original/nh-bridged-dimeric-phosphazanes-inorganic-molecular-switches-based-on-anion-responsive-bifurcated-to-trifurcated-hydrogen-bond-transitions.pdf |
6182f31aad7f7cbb9f53f4a2 | 10.26434/chemrxiv-2021-4mw4j | A High Temperature Lithium Metal-Air Primary Battery Based on Solid Electrolytes and Molten Salt | Developing metal-oxygen batteries with a high specific energy (gravimetric energy density) is a significant challenge due to the highly reactive nature of active materials used as the negative electrode, such as Li, Al, or Mg. In addition, the metal-oxide discharge products are highly stable and passivating to many oxygen-reduction catalysts. Here we present an alterative way of utilizing the high specific energy lithium metal-oxygen reaction by combining both cation and anion transport in a single device, operated at 550°C. To do this, we combined a Li6.4La2.8Al0.2Zr1.4Ta0.6O12 (LLZO) cation solid electrolyte, yttria stabilized zirconia oxygen ion conductor, and KCl-LiCl eutectic salt as an interlayer between the two solid electrolytes. We find that the constructed battery shows an open circuit voltage consistent with the thermodynamic value predicted for the Li-O2 reaction at 550°C. Furthermore, we found that the cell could be discharged at 20 mA, showing no significant passivation of the reaction until all of the lithium metal was depleted. However, we were unable to re-deposit the lithium metal electrochemically, possibly due to parasitic reduction of the LLZO tube upon charging. This work presents a unique device which may inspire other high temperature electrochemical devices in the field. | Geoff McConohy; Dokyum Kim; Joon-Hyung Lee | Materials Science; Energy; Ceramics; Energy Storage | CC BY 4.0 | CHEMRXIV | 2021-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6182f31aad7f7cbb9f53f4a2/original/a-high-temperature-lithium-metal-air-primary-battery-based-on-solid-electrolytes-and-molten-salt.pdf |
6613ef45418a5379b064cc56 | 10.26434/chemrxiv-2024-glw4f | Assessing the Design Rules of Electrides | There are three heuristic criteria commonly used to identify electrides: an apparent valence of plus one, empty space in the crystal structure and the presence of a strongly electron-donating cation. We evoke and explore these criteria by mapping probable charges to a database of all known materials and isolating around around 4,000 compounds that are likely to exhibit an oxidation state of +1. Of these, we identify peaks in off-atom electron density by density functional theory and discuss the validity with which the design rules can be applied to these likely electrides. In doing so, we recover 4 experimentally confirmed electrides among 51 candidates identified as potential new electrides that were not considered previously. All results for each candidate are provided but perhaps of especial significance is the material Ba3AlO4 that has similar composition, components and chemistry to the stable and popular electride catalyst Ca12Al14O32. Overall, we find that the valence and void space rules are surprisingly useful but that there is a breadth of chemistry to electrides that can be severely restricted by considering only alkili and alkali earth metal compounds. | Zhikun Yao; Yanzhen Zhao; Wenjun Zhang; Lee Burton | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6613ef45418a5379b064cc56/original/assessing-the-design-rules-of-electrides.pdf |
67caaca981d2151a0274986c | 10.26434/chemrxiv-2025-gdx77-v2 | Recent advances in stimuli-responsive framework materials: understanding their response and searching for materials with targeted behavior | Although all molecular assemblies show some degree of flexibility, the past decade has shown that there is a higher propensity among framework materials to display large-scale dynamic behavior. Beyond the seminal discoveries of the important flexibility of metal–organic frameworks (MOFs), covalent organic frameworks (COFs), hybrogen-bonded organic frameworks (HOFs) or supramolecular organic frameworks (SOFs), and many other framework materials, the field has progressed rapidly: the number of known flexible materials is ever growing, and the diversity of the types of manifestation of this flexibility appears endless. In addition, the microscopic mechanism of their behavior has been studied using a growing combination of experimental characterization techniques, in situ and in operando measurements, as well as computational simulation methods.
In this Review, we present some of the significant advances in recent studies of stimuli-responsive framework materials. In particular, we highlight the novel responses that have been discovered in the past few years, the toolbox developed by researchers in the field to better understand the materials' behavior (both experimentally and computationally), and show some of the latest progress in the discovery of materials with targeted behavior, whether through de novo design or identification of known materials for new properties — similar to what is known in the field of drug discovery as repurposing. | François-Xavier Coudert | Physical Chemistry; Materials Science; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67caaca981d2151a0274986c/original/recent-advances-in-stimuli-responsive-framework-materials-understanding-their-response-and-searching-for-materials-with-targeted-behavior.pdf |
639aee4d81e4ba664a4e44f8 | 10.26434/chemrxiv-2022-dx58w | Challenges in the direct detection of chirality-induced spin selectivity: investigation of foldamer-based donor/acceptor dyads | Over the past two decades, the chirality-induced spin selectivity (CISS) effect was reported in several experiments disclosing a unique connection between chirality and electron spin. Recent theoretical works have highlighted time-resolved Electron Paramagnetic Resonance (trEPR) as a powerful tool to directly detect the spin polarisation resulting from CISS. Because of the absence of interfaces with conducting electrodes, such spectroscopic evidence could provide a clear understanding of how CISS works at the intramolecular level. Experimental results have demonstrated the potential of this approach for detecting a spin-polarised photoinduced electron transfer (ET) in hybrid systems comprising a CdSe quantum dot as an electron donor (D) connected by a chiral linker (χ) to a fullerene derivative as an electron acceptor (A). However, the study of the ET process in fully organic D-χ-A dyads holds tremendous potential for the unambiguous detection of CISS.
Here, we report a first attempt performed using novel D-χ-A dyads, comprising pyrene (D) and fullerene (A) connected by chiral saturated peptide bridges (χ) of different length and electric dipole moment. The dyads are investigated by an array of techniques, including cyclic voltammetry, optical spectroscopies, and trEPR. Despite the promising energy alignment of the electronic levels and the evidence of luminescence quenching, trEPR does not detect a significant ET highlighting the challenges of spectroscopic detection of CISS. However, the analysis allows the formulation of guidelines for the design of chiral organic model systems suitable to directly probe CISS-polarised ET. | Alberto Privitera; Davide Faccio; Demetra Giuri; Damiano Genovese; Francesco Tassinari; Liviana Mummolo; Mario Chiesa; Claudio Fontanesi; Enrico Salvadori; Andrea Cornia; Claudia Tomasini; Roberta Sessoli | Physical Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639aee4d81e4ba664a4e44f8/original/challenges-in-the-direct-detection-of-chirality-induced-spin-selectivity-investigation-of-foldamer-based-donor-acceptor-dyads.pdf |
60c74c2c567dfeb548ec50d2 | 10.26434/chemrxiv.12442868.v1 | Hydrophobicity Revisited: a Molecular Story | In a previous paper we have introduced a new hydrophobicity proclivity scale and justified its superior performance characteristics, particularly in the context of a scale for protein alignments, but also for its strong correlation with many other amino-acid physico-chemical properties. Within that paper, we calculated a corrected free energy of residue burial of each amino-acid in folded proteins from a linear regression of amino-acid free energy of transfer from water to n-Octanol (F&P octanol scale dGow, Y axis) and our Hydrophobicity Proclivity Scale<br />(HPS, X axis). In this present paper we pursue the latter general findings in more detail by considering the relationship of hydrophobicity and other physico-amino-<br />acid scales with the molecular geometry of amino-acids and secondary group structure/surface chemistry, with a concommitant discussion of the dimensions/geometry<br />of the caveties that amino-acids make in water. We identify a series of molecular physico-chemical properties that uniquely define the natural selection and geometry of the 20 natural amino-acids. We use the corrected free energy of amino-acid burials in proteins (Y axis) and a multiple linear regression to identify the AA molecular physico-chemical properties (X1, X2, ...) that explain the energetics of amino-<br />acid water contacts in an unfolded protein state to that of the folded protein state by modeling these two states as a solvent-solvent transfer, thus, providing a thermodynamical model for the initial stages of protein folding. Between our previous paper and the current paper we can greatly simplify and reduce the very large number of amino-acid scales in the literature to a small number of amino-acid property scales. Finally, we explore the numerical relationship between the structure of the genetic code and molecular physico-chemical properties of AA’s that in turn can be related directly to hydrophobicity. We validate and explain our novel models we describe herein with extensive data from the literature.<br /> | David Cavanaugh; Krishnan Chittur | Biochemistry; Bioengineering and Biotechnology; Bioinformatics and Computational Biology; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c2c567dfeb548ec50d2/original/hydrophobicity-revisited-a-molecular-story.pdf |
60c741aa842e657a0adb1f52 | 10.26434/chemrxiv.8100509.v1 | Insight into D6h Symmetry: Targeting Strong Axiality in Stable Dysprosium(III) Hexagonal Bipyramidal Single-Ion Magnets | Three dysprosium(III) single-molecule magnets (SMMs) with the rare hexagonal bipyramidal geometry have been isolated for the first time. Following a novel synthetic strategy where the strong uniaxial ligand field generated by the Ph<sub>3</sub>SiO<sup>-</sup> (Ph<sub>3</sub>SiO<sup>-</sup> = anion of triphenylsilanol) and the 2,4-di-<sup>t</sup>Bu-PhO<sup>-</sup> (2,4-di-<sup>t</sup>Bu-PhO<sup>-</sup> = anion of 2,4-di-tertbutylphenol) ligands combined with the weak equatorial field of the ligand L<sup>N6</sup>, leads to [Dy<sup>III</sup>(L<sup>N6</sup>)(2,4-di-<sup>t</sup>Bu-PhO)<sub>2</sub>](PF<sub>6</sub>) (<b>1</b>), [Dy<sup>III</sup>(L<sup>N6</sup>)(Ph<sub>3</sub>SiO)<sub>2</sub>](PF<sub>6</sub>) (<b>2</b>) and [Dy<sup>III</sup>(L<sup>N6</sup>)(Ph<sub>3</sub>SiO)<sub>2</sub>](BPh<sub>4</sub>) (<b>3</b>) hexagonal bipyramidal complexes with high anisotropy barriers of U<sub>eff</sub> = 973 K for <b>1</b>, U<sub>eff</sub> = 1080 K for <b>2</b> and U<sub>eff</sub> = 1124 K for <b>3 </b>under zero applied dc field. <i>Ab initio</i> calculations predict that the dominant magnetization reversal barrier of these complexes expands up to the 3rd Kramers doublet, thus revealing for the first time the exceptional uniaxial magnetic anisotropy that even the six equatorial donor atoms fail to negate, opening up the possibility to other higher-order symmetry SMMs. <br /> | Angelos Canaj; Sourav Dey; Emma Regincós Martí; Claire Wilson; Gopalan Rajaraman; Mark Murrie | Coordination Chemistry (Inorg.); Lanthanides and Actinides; Magnetism | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741aa842e657a0adb1f52/original/insight-into-d6h-symmetry-targeting-strong-axiality-in-stable-dysprosium-iii-hexagonal-bipyramidal-single-ion-magnets.pdf |
60c750df337d6c78c8e28423 | 10.26434/chemrxiv.12519485.v2 | Photoinduced Charge Transfer Dynamics in Carotenoid-Porphyrin-C60 Triad via the Linearized Semiclassical Nonequilibrium Fermi's Golden Rule | The nonequilibrium Fermi’s golden rule (NE-FGR) describes the time-dependent rate coefficient for electronic transitions, when the nuclear degrees of freedom start out in a <i>nonequilibrium</i> state. In this letter, the linearized semiclassical (LSC) approximation of the NE-FGR is used to calculate the photoinduced charge transfer rates in the carotenoid-porphyrin-C<sub>60</sub> molecular triad dissolved in explicit tetrahydrofuran. The initial nonequilibrium state corresponds to impulsive photoexcitation from the equilibrated ground-state to the ππ* state, and the porphyrin-to-C<sub>60</sub> and the carotenoid-to-C<sub>60</sub> charge transfer rates are calculated. Our results show that accounting for the nonequilibrium nature of the initial state significantly enhances the transition rate of the porphyrin-to-C<sub>60</sub> CT process. We also derive the instantaneous Marcus theory (IMT) from LSC NE-FGR, which casts the CT rate coefficients in terms of a Marcus-like expression, with explicitly time-dependent reorganization energy and reaction free energy. IMT is found to reproduce the CT rates in the system under consideration remarkably well. | Zhubin Hu; Zhengqing Tong; Margaret S. Cheung; Barry D. Dunietz; Eitan Geva; Xiang Sun | Theory - Computational; Photovoltaics; Chemical Kinetics; Photochemistry (Physical Chem.); Physical and Chemical Processes; Quantum Mechanics; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750df337d6c78c8e28423/original/photoinduced-charge-transfer-dynamics-in-carotenoid-porphyrin-c60-triad-via-the-linearized-semiclassical-nonequilibrium-fermi-s-golden-rule.pdf |
657fbd0f9138d23161e9c5eb | 10.26434/chemrxiv-2023-948wb | A Cationic Catechol Derivative Binds Anions in Competitive Aqueous Media | A simple dihydroxy isoquinolinium molecule (3+) was prepared by a modification of a literature procedure. Interestingly, during optimisation of the synthesis a small amount of the natural product pseudopalmatine was isolated, and characterised for the first time by X-ray crystallography. Compound 3+ contains a catechol motif and positive charge on the same scaffold and was found to be a potent anion receptor, binding sulfate strongly in 8:2 d6-acetone:D2O and 7:3 d6-acetone:D2O (K¬a > 104 and 2,100 M–1, respectively). Unsurprisingly, chloride binding was much weaker, even in the less polar solvent mixture 9:1 d6-acetone:D2O. The sulfate binding is remarkably strong for such a simple molecule, however anion binding studies were complicated by the tendency of the molecule to react with BPh4– or BF4– species during anion metathesis reactions. This gave two unusual zwitterions containing tetrahedral boronate centres, which were both characterised by X-ray crystallography. | Rosemary Goodwin; Nicholas White | Organic Chemistry; Inorganic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657fbd0f9138d23161e9c5eb/original/a-cationic-catechol-derivative-binds-anions-in-competitive-aqueous-media.pdf |
6631812991aefa6ce1d81c4d | 10.26434/chemrxiv-2023-g69tm-v2 | Chemically Accurate Singlet-Triplet Gaps of Arylcarbenes from Local Hybrid Density Functionals | Singlet-triplet (ST) gaps are key descriptors of carbenes, because their properties and reactivity are strongly spin-dependent. However, the theoretical prediction of ST gaps is challenging and generally thought to require elaborate correlated wavefunction methods or double-hybrid density functionals. By evaluating two recent test sets of arylcarbenes (AC12 and AC18), we show that local hybrid functionals based on the "common t" local mixing function (LMF) model achieve mean absolute errors below 1 kcal/mol at a computational cost only slightly higher than that of global hybrid functionals. An analysis of correlation contributions to the ST gaps suggests that the accuracy of the common t-LMF model is mainly due to an improved description of nondynamical correlation which, unlike exchange, is not additive in each spin-channel. Although spin-nonadditivity can be achieved using the local spin polarization alone, the using the "common", i.e., spin-unresolved, iso-orbital indicator t for constructing the LMF is found to be critical for consistent accuracy in ST gaps of arylcarbenes. The results support the view of LHs as vehicles to improve the description of nondynamical correlation rather than sophisticated exchange mixing approaches. | Robin Grotjahn; Justin Purnomo; Dayun Jin; Nicolas Lutfi; Filipp Furche | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6631812991aefa6ce1d81c4d/original/chemically-accurate-singlet-triplet-gaps-of-arylcarbenes-from-local-hybrid-density-functionals.pdf |
64b575b1ae3d1a7b0ddfbfcb | 10.26434/chemrxiv-2023-sdcdc | Energy Management and Economic Considerations of Intermittent Photovoltaic-Driven Electrochemical Ammonia Production | As the energy sector shifts from fossil fuels to renewable energy, there is a need for long-duration energy storage solutions to handle the intermittency of renewable electricity. Electrofuels, or fuels synthesized from excess electricity, are an emerging medium poised to meet long-duration energy storage requirements. Ammonia as an electrofuel is potentially ideal because ammonia has a relatively low liquefaction pressure, indicating that ammonia can be easily stored and transported. Here, we develop a framework to optimize the electrochemical production of ammonia powered by intermittent photovoltaic power. We also explore various buyback policies to understand the impact that policy has on the cost of intermittent ammonia and optimal sizing ratios. The optimal ratio of the photovoltaic to the electrolyzer is ~3.7 MW$_{PV}$/MW$_{ELEC}$ for an system that is completely powered by renewable photovoltaic power and operates intermittently. The optimal ratio of the photovoltaic to the electrolyzer is ~3.3 MW _PV/MW_Elec for a system that uses photovoltaics in conjunction with grid electricity and operates continuously. For the purchase price at the avoided cost of electricity, the optimal ratio of the solar panel to the electrolyzer increases to ~4 MW
_PV/MW_Elec for a system that can only sell to the grid and ~5 MW_PV/MW_Elect for a system that can buy and sell electricity to the grid at the avoided cost. Optimizing energy management by setting auxiliary battery size limits is essential to reduce ammonia cost, and the optimal battery size decreases as the buyback price of electricity increases. Finally, we find that systems connected to the grid and operating continuously have emissions comparable to the Haber-Bosch process because of the current emissions tied to the United States electricity generation. Thus, unless the grid is completely decarbonized, it is essential to create electro-fuels that rely minimally on grid electricity. | Sai Varanasi; Carlos Fernandez; Marta Hatzell | Chemical Engineering and Industrial Chemistry; Thermodynamics (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b575b1ae3d1a7b0ddfbfcb/original/energy-management-and-economic-considerations-of-intermittent-photovoltaic-driven-electrochemical-ammonia-production.pdf |
651a4253a69febde9e10b95f | 10.26434/chemrxiv-2023-k695d | Unraveling non-uniform strain-induced crystallization near a crack tip in natural rubber | Strain-induced crystallization (SIC) in natural rubber near crack tips significantly enhances crack growth resistance, but understanding the interplay between local strain field and crystallization remains challenging due to confined and heterogeneous characteristics. Using micro-scale digital image correlation and scanning wide-angle X-ray diffraction (with a narrow 10 µm square beam), this study maps local strain tensor properties and SIC in the vicinity of the crack tip and its peripheral zone (approximately 3 x 1 mm area). The analysis reveals a significant correlation between these properties, with the spatial distribution of the local principal strain axis influencing crystal orientation. Crucially, the maximum tensile component in the tensor of local principal strains predominantly dictates local crystallinity, irrespective of strain biaxiality. This finding paves the way for predicting crystallinity distribution using solely strain field data, offering valuable insights into the role of SIC in enhancing the crack growth resistance of natural rubber. | Kenji Urayama; Thanh-Tam Mai; Tomohiro Yasui; Ruito Tanaka; Hiroyasu Masunaga; Taizo Kabe; Katsuhiko Tsunoda; Shinichi Sakurai | Polymer Science; Biopolymers | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651a4253a69febde9e10b95f/original/unraveling-non-uniform-strain-induced-crystallization-near-a-crack-tip-in-natural-rubber.pdf |
60c754e0337d6cdadde28afb | 10.26434/chemrxiv.13813691.v1 | Improved Photodegradation of Anionic Dyes Using a Complex Graphitic Carbon Nitride and Iron-Based Metal-Organic Framework Material | <p>Introducing
heterostructure to graphitic carbon nitrides (g-C<sub>3</sub>N<sub>4</sub>) can
improve the activity of visible-light-driven catalysts for efficient treatment
of multiple toxic pollutants in water. Here we report for the first time that a
complex material can be constructed from an oxygen-doped g-C<sub>3</sub>N<sub>4</sub>
and MIL-53(Fe) metal-organic framework using a facile hydrothermal synthesis and
recycled polyethylene terephthalate from plastic waste. The novel multi-walled
nanotube structure of the O-g-C<sub>3</sub>N<sub>4</sub>/MIL-53(Fe) composite
which enables unique interfacial charge transfer at the heterojunction showed
an obvious enhancement in separation efficiency of the photochemical
electron-hole pairs. This resulted in narrow bandgap energy (2.30 eV compared
to 2.55 eV in O-g-C<sub>3</sub>N<sub>4</sub>), high photocurrent intensity
(0.17 mA cm<sup>-2 </sup>compared to 0.12 mA cm<sup>-2</sup> and 0.09 mA cm<sup>-2</sup>
in MIL-53(Fe) and O-g-C<sub>3</sub>N<sub>4</sub>, respectively), and excellent
catalytic performance in the photodegradation of anionic azo dyes (95% RR 195 and
99% RY 145 degraded after 4 h, and only a minor change in the efficiency
observed after four
consecutive tests). These
results demonstrate the development of new catalysts made from waste feedstocks
that show high stability, ease of fabrication and can operate in natural light
for environmental remediation.</p> | Huan Doan; Hoa Thi Nguyen; Valeska Ting; Shaoliang Guan; Jean-Charles Eloi; Simon R. Hall; Xuan Nui Pham | Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754e0337d6cdadde28afb/original/improved-photodegradation-of-anionic-dyes-using-a-complex-graphitic-carbon-nitride-and-iron-based-metal-organic-framework-material.pdf |
6374b55274b7b6c016001a5e | 10.26434/chemrxiv-2022-v5tw9 | Theory, implementation, and disappointing results for
two-photon absorption cross sections within the doubly electron-attached equation-of-motion coupled-cluster framework | The equation-of-motion coupled-cluster singles and doubles method with double electron attachment (EOM-DEA-CCSD) is capable of computing reliable energies, wave functions, and first-order properties of excited states in diradicals and polyenes that have significant doubly excited character with respect to the ground state without the need for including the computationally expensive triples excitations. Here, we extend the capabilities of the EOM-DEA-CCSD method to the calculations of a multiphoton property, two-photon absorption (2PA) cross sections. Closed-form expressions
for the 2PA cross sections are derived within the expectation-value approach using response wave functions. We analyze the performance of this novel implementation by comparing the EOM-DEA-CCSD energies
and 2PA cross sections with those computed using the CC3 quadratic response theory approach. As the benchmark system, we consider transitions to the states with doubly excited character in twisted ethene and in polyenes for which EOM-EE-CCSD (EOM-CCSD for
excitation energies) performs poorly. The EOM-DEA-CCSD 2PA cross sections are comparable with the CC3 results for twisted ethene; however, the discrepancies between the two methods are large for hexatriene. The observed trends are explained by configurational analysis of the 2PA channels. | Kaushik Nanda; Sahil Gulania; Anna Krylov | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6374b55274b7b6c016001a5e/original/theory-implementation-and-disappointing-results-for-two-photon-absorption-cross-sections-within-the-doubly-electron-attached-equation-of-motion-coupled-cluster-framework.pdf |
60c73e99f96a00b5ba285f59 | 10.26434/chemrxiv.6859940.v2 | Magnetic Structure of UO2 and NpO2 by First-Principle Methods | The magnetic structure of the actinide dioxides (AnO2) remains a subject of intense research and is key to the development of high-accuracy computational models. A low-temperature experimental investigation of the magnetic ground-state is complicated by thermal energy released from the radioactive decay of the actinide nuclei. To establish the magnetic groundstate, we have employed high-accuracy computational methods to systematically probe different magnetic structures. A transverse 1k antiferromagnetic ground-state with Fmmm (No. 69) crystal symmetry has been established for UO2, whereas a ferromagnetic (111) ground-state with R3 ̅m (No. 166) has been established for NpO2. This has a profound impact on future computational investigations. Band structure calculations have been performed to analyse these results. | James Pegg; Ashley E. Shields; Mark T. Storr; Andrew S. Wills; David Scanlon; Nora De Leeuw | Nuclear Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e99f96a00b5ba285f59/original/magnetic-structure-of-uo2-and-np-o2-by-first-principle-methods.pdf |
67bd83d26dde43c90861b16a | 10.26434/chemrxiv-2025-vf9l8 | Van der Waals-Enhanced Luminescence for CO2 detection in a Europium Metal-Organic Framework Composite | Effective CO₂ sensing is crucial for maintaining indoor air quality and human well-being. Porous metal-organic frameworks (MOF) have shown promise in gas sensing due to their unique structures. However, existing, luminescent Zr- and Zn-based MOFs for CO₂ detection face limitations such as broad emission bands, short lifetimes, and low quantum yields. This study introduces a novel europium-based MOF (Eu-MOF), the first lanthanide-based material for CO₂ sensing, showing a strong luminescent response to CO₂ presence with a detection limit of 3,109 ppm. This is the first direct correlation between CO₂ levels and optical response in a lanthanide-MOF. To improve sensor performance and durability, the Eu-MOF was embedded in a polydimethylsiloxane (PDMS) matrix, reducing water interference while maintaining CO₂ sensitivity. The findings highlight the potential of lanthanide-MOFs as a platform for developing sensitive and robust CO₂ sensors. | Jose Sanchez Costa; Estefania Fernandez-Bartolomé; Jorge Sangrador-Perez; Javier Urieta-Mora; Ana Martinez-Martinez; Raquel Utrera-Melero; Ruben Turo-Cortes; Carolina Sañudo; Roberta Poloni; David Fairen-Jimenez; Juan Cabanillas-Gonzalez; Nazario Martín | Materials Science; Composites; Hybrid Organic-Inorganic Materials; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bd83d26dde43c90861b16a/original/van-der-waals-enhanced-luminescence-for-co2-detection-in-a-europium-metal-organic-framework-composite.pdf |
60c74f41f96a0018e0287bed | 10.26434/chemrxiv.12871331.v1 | Colloidal HgTe Quantum Dot/Graphene Phototransistor with a Spectral Sensitivity Beyond 3 µm | Infrared light detection enables diverse technologies ranging from night vision to gas analysis. Emerging technologies such as low-cost cameras for self-driving cars require highly sensitive, low-cost photodetector cameras with spectral sensitivities up to wavelength of 10 um. For this purpose, colloidal quantum dot (QD) graphene phototransistors offer a viable alternative to traditional technologies owing to inexpensive synthesis and processing of QDs. However, the spectral range of these phototransistors have been thus far limited to 1.6 um. Here, we present HgTe QD/graphene phototransistors with spectral sensitivities up to 3 um, with specific detectivities of 6x10<sup>8</sup> Jones at a wavelength of 2.5 um and a temperature of 80 K. Even at kHz light modulation frequencies, specific detectivities exceed 10<sup>8</sup> Jones making them suitable for fast video imaging. The simple device architecture and QD film patterning in combination with a broad spectral sensitivity manifest an important step towards low-cost, multi-color infrared cameras.<br /> | Matthias Grotevent; Claudio U. Hail; Sergii Yakunin; Dominik Bachmann; Michel Calame; Dimos Poulikakos; Maksym
V. Kovalenko; Ivan Shorubalko | Nanostructured Materials - Materials | CC BY 4.0 | CHEMRXIV | 2020-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f41f96a0018e0287bed/original/colloidal-hg-te-quantum-dot-graphene-phototransistor-with-a-spectral-sensitivity-beyond-3-m.pdf |
670e7656cec5d6c1423a2c7b | 10.26434/chemrxiv-2024-24brt | A Single Atom Cu/TiO2 Photocatalyst for Advanced Redox Processes: Reactive Oxygen Species Generation Mechanisms | Single-atom catalysts (SACs) of copper dispersed in anatase TiO2 (Cu/TiO2) have attracted significant attention in various sustainable chemical processes, including water splitting, carbon monoxide oxidation, carbon dioxide reduction, chemical synthesis, and advanced oxidation processes for water treatment. Reactive oxygen species (ROS) are involved in these processes, but a mechanistic understanding of ROS generation on Cu/TiO2 SAC surfaces has not been established. Combining experimental investigation and computational simulation, this work provides unequivocal evidence for superoxide radical anion (O2•–) formation via reduction of the adsorbed oxygen by Cu+ and hydroxyl radical (•OH) production by oxidation of lattice oxygen within the bridging Cu-O-Ti structure on the SAC surface. The superior performance of the SAC has been demonstrated through its organic dye degradation, bactericidal activity, and biofilm disruption, indicating its wide applicability in water treatment and disinfection. The results and the methodologies will benefit the wide field of heterogeneous redox chemistry. | Naizhen Yu; Xu Zhang; Mita Dasog; Collins Nganou; Andrew Carrier; Dongchang Yang; Ken Oakes | Materials Science; Nanoscience; Catalysts; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670e7656cec5d6c1423a2c7b/original/a-single-atom-cu-ti-o2-photocatalyst-for-advanced-redox-processes-reactive-oxygen-species-generation-mechanisms.pdf |
66c85a27a4e53c4876571580 | 10.26434/chemrxiv-2024-ghsr7 | Formate Salt as a Bifunctional Reagent for Hydroxylation and Carbonylation Reactions Under Photochemically Driven Nickel Catalysis | In this study, we disclose for the first time that formate salt can be used as a bifunctional reagent for the synthesis of phenol derivatives and as a CO source for carbonylative cross-coupling processes using the COware gas reactor under activation free conditions. Key to this success is the in-situ synthesis of aryl formate via an unprecedented nickel/organophotocatalyst system under blue LED irradiation. This developed system demonstrated high applicability to various aryl iodide substrates for synthesizing phenol derivatives. Moreover, the generated CO could be utilized in a range of carbonylative C-heteroatom and C-C processes. Notably, commercially available H13COONa salt can serve as a bifunctional reagent for both synthesizing phenols and generating 13CO. | Yi Yang; JUNPING SU ; Timothe Guerin ; Martin Nielsen; Anis Tlili | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c85a27a4e53c4876571580/original/formate-salt-as-a-bifunctional-reagent-for-hydroxylation-and-carbonylation-reactions-under-photochemically-driven-nickel-catalysis.pdf |
6430d9660784a63aeebb4cb3 | 10.26434/chemrxiv-2023-kf54s | Catalyst Self-Assembly Accelerates Bimetallic Light-Driven Electrocatalytic H2 Evolution in Water | Hydrogen evolution is an important fuel-generating reaction that has been subject to mechanistic debate about the roles of monometallic and bimetallic pathways. In this study, molecular iridium catalysts that undergo photoelectrochemical dihydrogen evolution afford a rare opportunity to systematically understand the factors that promote bimetallic H–H coupling. Covalently tethered diiridium catalysts evolve H2 from neutral water faster than monometallic catalysts, even at lower overpotential. The origin of this improvement is noncovalent supramolecular self-assembly into “all-catalyst” nanoscale aggregates that efficiently harvest light and form H–H bonds. New monometallic catalysts containing long-chain alkane substituents leverage the self-assemly to evolve H2 from neutral water close to the expected maximum rate for a light-driven water splitting reaction and with activity even below 100 mV overpotential. Design parameters for holding multiple catalytic sites in close proximity and tuning catalyst microenvironment emerge from this work. | Isaac Cloward; Tianfei Liu; Jamie Rose; Annabell Bonn; Tamara Jurado; Matthew Chambers; Catherine Pitman; Marc ter Horst; Alexander Miller | Catalysis; Organometallic Chemistry; Energy; Electrocatalysis; Photocatalysis; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6430d9660784a63aeebb4cb3/original/catalyst-self-assembly-accelerates-bimetallic-light-driven-electrocatalytic-h2-evolution-in-water.pdf |
672a736f7be152b1d016a4d9 | 10.26434/chemrxiv-2024-0bp39-v2 | Multicomponent Syntheses Enable the Discovery of Novel Quisinostat-Derived Chemotypes as Histone Deacetylase Inhibitors | Epigenetic drug targets have become an important focus in drug discovery. One of the key mechanisms in epigenetics is the acetylation and deacetylation of histone proteins. In this study, we synthesized and evaluated novel histone deacetylase (HDAC) inhibitors derived from the clinical candidate quisinostat. A library of 16 compounds categorized in three novel chemotypes was rapidly generated using multicomponent reactions (MCRs), enabling efficient structure-activity relationship studies. The compounds were evaluated for their activity against Plasmodium falciparum, the main malaria parasite, and solid cancer cell lines. The antiplasmodial activity was assessed against P. falciparum strains 3D7 and Dd2, identifying compound 18b of the type C series as the most potent. It demonstrated low nanomolar IC50 values (IC50 (3D7) = 0.023 µM; IC50 (Dd2) = 0.047 µM) and high parasite selectivity (SIMRC-5/Pf3D7 > 2174). Docking studies suggested distinct binding modes of 18b with P. falciparum and human HDAC1. The in vitro anticancer activity was also evaluated in the Cal27 and HepG2 cell lines and compounds 9b, 9d, and 13f showed potent antiproliferative activity. Compound 9d significantly induced caspase 3/7-mediated apoptosis and caused hyperacetylation of histone H3 and α-tubulin, indicating robust cellular target engagement. Overall, in this work we have identified several promising HDAC inhibitors with antimalarial and anticancer activities, providing valuable leads for further drug development efforts aimed at creating derivatives with reduced cytotoxicity compared to quisinostat. | Daniel Stopper; Susanna Buntrock; Kathrin Tan; Lais Pessanha de Carvalho; Linda Schäker-Hübner; Jana Held; Matthias Kassack; Finn Kristian Hansen | Biological and Medicinal Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672a736f7be152b1d016a4d9/original/multicomponent-syntheses-enable-the-discovery-of-novel-quisinostat-derived-chemotypes-as-histone-deacetylase-inhibitors.pdf |
65fa1e6966c1381729592f1c | 10.26434/chemrxiv-2024-bvxjg-v2 | A New Topological Class of Interlocked and Interwoven Nanocarbons via Dynamic C-C Bond Formation | Topologically complex molecules are poised to play a crucial role in the future of materials science, providing control over entanglement at the smallest possible scale. Discovery of new topological constructs and robust strategies for their synthesis are central to expanding the field. Here a new topological class of molecules, named perplexanes, are identified that contain an unusual combination of interlocking and interweaving that defies traditional topological descriptors. Two nanocarbon perplexanes are rationally synthesized in high yield using reversible zirconocene coupling of alkynes. This dynamic C-C bond formation facilitates entanglement under thermodynamic control, enabling the use of simple precursors without the need for strong templating or preassembly. This provides a new toolkit for assembling topologically complex nanocarbons that should be generalizable to a wide range of other topologies. | Harrison M. Bergman; Angela Fan; Christopher G. Jones; August J. Rothenberger; Kunal K. Jha; Rex C. Handford; Hosea M. Nelson; Yi Liu; T. Don Tilley | Organic Chemistry; Organometallic Chemistry; Physical Organic Chemistry; Supramolecular Chemistry (Org.); Reaction (Organomet.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fa1e6966c1381729592f1c/original/a-new-topological-class-of-interlocked-and-interwoven-nanocarbons-via-dynamic-c-c-bond-formation.pdf |
63cf3566660694f4203bb1e2 | 10.26434/chemrxiv-2023-8ppnv | Assessment of Adsorbate π-backbonding in Copper(I) Metal-Organic Frameworks via Multinuclear NMR Spectroscopy and Density Functional Theory Calculations | We assess the binding of C2H4 to the coordinately unsaturated copper(I) sites of the metal-organic frameworks Cu(I)-ZrTpmC* and Cu(I)-MFU-4l via 13C solid-state nuclear magnetic resonance spectroscopy, density functional theory (DFT), and natural localized molecular orbital (NLMO) analysis. Using these methods, forward-donation and back-donation contributions between C2H4 and the exposed Cu(I) are delineated and high-binding enthalpies are contextualized as a function of electronic changes upon site modification and adsorption. With the infrastructure for DFT and solid-state 13C NMR becoming more routine for scientists, we envision these results will support the study of exposed electron-rich metal sites in a variety of chemical applications. | Lena M. Funke; Romit Chakraborty; Kurtis M. Carsch; Martin Head-Gordon; Jeffrey R. Long; Jeffrey A. Reimer | Theoretical and Computational Chemistry; Analytical Chemistry; Nanoscience; Analytical Chemistry - General; Nanostructured Materials - Nanoscience; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63cf3566660694f4203bb1e2/original/assessment-of-adsorbate-backbonding-in-copper-i-metal-organic-frameworks-via-multinuclear-nmr-spectroscopy-and-density-functional-theory-calculations.pdf |
63730d1577ffe7b333ee3629 | 10.26434/chemrxiv-2022-s8skg | Rapid Access to 2-Substituted Bicyclo[1.1.1]pentanes | The replacement of aryl rings with C(sp3)-rich structures has garnered significant interest in drug discovery due to the potential for improved pharmacokinetic properties upon substitution. In particular, 1,3-difunctionalized bicyclo[1.1.1]pentanes (BCPs) have been widely adopted as bioisosteres for para-substituted arene rings, appearing in a number of lead pharmaceutical candidates. Due to their medicinal importance, multiple methods have been developed to efficiently synthesize these 1,3-difunctionalized BCPs. However, despite the pharmaceutical value of 2-substituted BCPs as replacements for ortho- or meta-substituted arene rings, general and rapid syntheses of these scaffolds remain elusive. Current approaches to 2-substituted BCPs rely on installation of the bridge substituent prior to BCP core construction, leading to lengthy step counts and often non-modular sequences. While challenging, direct functionalization of the strong bridge BCP C–H bonds would offer a more streamlined pathway to diverse 2-substituted BCPs. Here we report a generalizable synthetic linchpin strategy for bridge functionalization via radical C–H abstraction of the BCP core. Through mild generation of a strong hydrogen atom abstractor, we rapidly synthesize novel 2-substituted BCP synthetic linchpins in one pot. These synthetic linchpins then serve as common precursors to complex 2-substituted BCPs, allowing one step access to a number of previously inaccessible electrophile and nucleophile fragments at the 2-position via two new metallaphotoredox protocols. Altogether, this platform enables the expedient synthesis of four pharmaceutical analogs, all of which show similar or improved properties compared to their aryl-containing equivalents, demonstrating the potential of these 2-substituted BCPs in drug development. | David W. C. MacMillan; Olivia L. Garry; Michael Heilmann; Jingjia Chen; Yufan Liang; Xiaheng Zhang; Xiaoshen Ma; Charles S. Yeung; David Jonathan Bennett | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63730d1577ffe7b333ee3629/original/rapid-access-to-2-substituted-bicyclo-1-1-1-pentanes.pdf |
65e74eb69138d23161b9b225 | 10.26434/chemrxiv-2023-rcvdn-v2 | Complexation and Disproportionation of Group 4 Metal (Alkoxy) Halides with Phosphine Oxides | Group 4 Lewis acids are well-known catalysts and precursors for (non-aqueous) sol-gel chemistry. Titanium, zirconium and hafnium halides, and alkoxy halides are precursors for the controlled synthesis of nanocrystals, often in the presence of Lewis base. Here, we investigate the interaction of Lewis bases with the tetrahalides (MX4 X = Cl, Br) and metal alkoxy halides (MXx(OR)4-x, x = 1-3, R = OiPr, OtBu). The tetrahalides yield the expected Lewis acid-base adducts MX4L2 (L = tetrahydrofuran or phosphine oxide). The mixed alkoxy halides react with Lewis bases in a more complex way. 31P NMR spectroscopy reveals that excess of phosphine oxide yields predominantly the complexation product, while a (sub)stoichiometric amount of phosphine oxide causes disproportionation of the MXx(OR)4-x species into MXx+1(OR)3-x and MXx-1(OR)5-x. The combination of complexation and disproportionation yields an atypical Job plot. In the case of zirconium isopropoxy chlorides, we fitted the concentration of all observed species and extracted thermodynamic descriptors from the Job plot. The complexation equilibrium constant decreases in the series: ZrCl3(OiPr) > ZrCl2(OiPr)2 >> ZrCl(OiPr)3, while the disproportionation equilibrium constant follows the opposite trend. Using calculations at the DFT level of theory, we show that disproportionation is driven by the more energetically favorable Lewis acid-base complex formed with the more acidic species. We also gain more insight into the isomerism of the complexes. The disproportionation reaction turns out to be a general phenomenon, for titanium, zirconium and hafnium, for chlorides and bromides, and for iso-propoxides and tert-butoxides. | Carlotta Seno; Rohan Pokratath; Dietger Van den Eynden; Ajmal Roshan Unniram Parambil; Evert Dhaene; Alessandro Prescimone; Jonathan De Roo | Theoretical and Computational Chemistry; Inorganic Chemistry; Nanoscience; Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e74eb69138d23161b9b225/original/complexation-and-disproportionation-of-group-4-metal-alkoxy-halides-with-phosphine-oxides.pdf |
66d23cd520ac769e5f664dcd | 10.26434/chemrxiv-2024-gkt49 | Selective Reduction of Esters to Aldehydes Using Fiddler Crab-Type Boranes | The partial reduction of esters to aldehydes is a fundamentally important transformation for the synthesis of numerous fine chemicals and consumer goods. However, despite the many efforts, limitations have persisted, such as competing overreduction, low reproducibility, use of exigent reaction conditions and hazardous chemicals. Here, we report a novel catalyst family with a unique steric design which promotes the catalytic partial reduction of esters with unprecedented, near-perfect selectivity and efficiency. This metal-free catalytic method is ready to be placed at the disposal of chemists to provide valuable aldehyde intermediates and products and shows promise for streamlining synthetic methods in academic and industrial settings. | Ádám Dudás; Ádám Gyömöre; Bence Balázs Mészáros; Stefánia Gondár; Renáta Adamik; Dániel Fegyverneki; Dávid Papp; Konrad Bernhard Otte; Sergio Ayala; János Daru; József Répási; Tibor Soós | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d23cd520ac769e5f664dcd/original/selective-reduction-of-esters-to-aldehydes-using-fiddler-crab-type-boranes.pdf |
654e54fddbd7c8b54b04ed70 | 10.26434/chemrxiv-2023-xt020 | Simultaneous control of crystallite size and interlayer spacing of MoS2 to achieve pseudocapacitive lithium intercalation | The functional properties of molybdenum disulfide (MoS2) are highly dependent on its structure. Here, we present a one-pot hydrothermal synthesis approach allowing to simultaneous control MoS2 structure over several length scales. Lowering the pH of the hydrothermal precursor solution leads to smaller crystallite sizes of the pristine MoS2 formed. Moreover, the addition of alkyldiamines to the same precursor solution leads to their physical confinement between the forming MoS2 layers without the formation of covalent bonds, yielding interlayer-expanded MoS2. Controlling alkyldiamine precursor concentration can vary the number of confined structural pillars in interlayer-expanded MoS2. Electrochemical lithium intercalation is tested as a function of MoS2 structural properties. It is revealed that both smaller crystallite sizes and expanded interlayer-spacing lead to an increasingly pseudocapacitive lithium intercalation signature. The number of lithium that is reversibly stored in interlayer-expanded MoS2 is increased to almost 1.5 per formula unit. The results provide a facile synthesis approach to simultaneously control MoS2 crystallite size and d-spacing, which may be of interest for applications beyond lithium intercalation, such as multivalent ion intercalation or electrocatalytic hydrogen evolution. | Jaehoon Choi; Hyein Moon; Simon Fleischmann | Energy; Energy Storage; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654e54fddbd7c8b54b04ed70/original/simultaneous-control-of-crystallite-size-and-interlayer-spacing-of-mo-s2-to-achieve-pseudocapacitive-lithium-intercalation.pdf |
640095f79789de3dd9c9b921 | 10.26434/chemrxiv-2023-gq2h0 | Disequilibrating azoarenes by visible-light sensitization under confinement | The process of vision begins with the absorption of light by retinal, which triggers isomerization around a
double bond and, consequently, a large conformational change in the surrounding protein opsin. However,
certain organisms evolved different visual systems; for example, deep-sea fishes employ chlorophyll-like
antennas capable of capturing red light and sensitizing the nearby retinal molecule via an energy-transfer
process. Similar to retinal, most synthetic photochromic molecules, such as azobenzenes and
spiropyrans, switch by double-bond isomerization. However, this reaction typically requires shortwavelength
(ultraviolet) light, which severely limits the applicability of these molecules. Here, we introduce
DisEquilibration by Sensitization under Confinement (DESC) – a supramolecular approach to switch various
azoarenes from the E isomer to the metastable Z isomer using visible light of desired color, including red. DESC
relies on a combination of a coordination cage and a photosensitizer (PS), which act together to bind and
selectively sensitize E-azoarenes. After switching to the Z isomer, the azoarene loses its affinity to—and is
expelled from—the cage, which can convert additional copies of E into Z. In this way, the cage⋅PS complex
acts as a light-driven supramolecular machine, converting photon energy into chemical energy in the form of
out-of-equilibrium photostationary states, including ones that cannot be accessed via direct photoexcitation. | Julius Gemen; Jonathan R. Church; Tero-Petri Ruoko; Nikita Durandin; Michał J. Białek; Maren Weissenfels; Moran Feller; Miri Kazes; Veniamin A. Borin; Magdalena Odaybat; Rishir Kalepu; Yael Diskin-Posner; Dan Oron; Matthew J. Fuchter; Arri Priimagi; Igor Schapiro; Rafal Klajn | Organic Chemistry; Catalysis; Nanoscience; Photochemistry (Org.); Supramolecular Chemistry (Org.); Photocatalysis | CC BY 4.0 | CHEMRXIV | 2023-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640095f79789de3dd9c9b921/original/disequilibrating-azoarenes-by-visible-light-sensitization-under-confinement.pdf |
651770b1006594091225365b | 10.26434/chemrxiv-2023-nmf04 | Extended voltage imaging in cardiomyocytes with a triplet state quencher-stabilized silicon rhodamine | Voltage imaging of cardiac electrophysiology with voltage-sensitive dyes has long been a powerful complement to traditional methods like patch-clamp electrophysiology. Chemically synthesized voltage sensitive fluorophores offer flexibility for imaging in sensitive samples like human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs), since they do not require genetic transformation of the sample. One serious concern for any fluorescent voltage indicator, whether chemically synthesized or genetically encoded, is phototoxicity. We have been exploring self-healing fluorophores that use triplet state quenchers (TSQs) as a means to reduce the already low phototoxicity of VoltageFluor dyes developed in our lab. We previously showed that conjugation of the TSQ cyclooctatetraene (COT) to a fluorescein based VoltageFluor dye substantially reduced phototoxicity. Here, we show that this approach can be applied to far-red Silicon rhodamine dyes. COT-conjugated Si-rhodamines show improved photostability and reduced phototoxicity in hiPSC-CMs compared to the unmodified dye. This enables imaging of hiPSC-CMs for up to 30 minutes with continuous illumination. We show that this effect is mediated by a combination of reduced singlet oxygen production and lower loading in the cellular membrane. We discuss future applications and avenues of improvement for TSQ-stabilized VoltageFluor dyes. | Kayli Martinez; Nels Gerstner; Samantha Yang; Evan Miller | Biological and Medicinal Chemistry; Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651770b1006594091225365b/original/extended-voltage-imaging-in-cardiomyocytes-with-a-triplet-state-quencher-stabilized-silicon-rhodamine.pdf |
60c744a4702a9bb1d218a88f | 10.26434/chemrxiv.9873689.v1 | Bioinspired Simultaneous Changes in Fluorescence Color, Brightness and Shape of Hydrogels Enabled by AIEgens | Development of
stimuli-responsive materials with complex practical functions is significant
for achieving bioinspired artificial intelligence. It is challenging to
fabricate stimuli-responsive hydrogels showing simultaneous changes in
fluorescence color, brightness and shape in response to one stimulus.
Herein a bilayer hydrogel strategy was designed by utilizing an
aggregation-induced emission luminogen (AIEgen) tetra-(4-pyridylphenyl)ethylene
(TPE-4Py) to fabricate hydrogels with the above capabilities. Bilayer hydrogel
actuators with ionomer of poly(acrylamide-r-sodium 4-styrenesulfonate) (PAS) as
matrix of both active and passive layers and TPE-4Py as the core function
element in the active layer were prepared. At acidic pH, the protonation of
TPE-4Py led to fluorescence color and brightness changes of the actuators and
the electrostatic interactions between the protonated TPE-4Py and
benzenesulfonate groups of PAS chains in the active layer caused the actuators
to deform. The proposed TPE-4Py/PAS-based bilayer hydrogel actuators with such
responsiveness to stimulus provide pregnant insights in the design of intelligent
systems and are highly attractive material candidates in fields of 3D/4D
printing, soft robots and smart wearable
devices. | Zhao Li; Xiaofan Ji; Junyi Gong; Yubing Hu; Wenjie Wu; Xinnan Wang; Hui-Qing Peng; Ryan Tsz Kin Kwok; Jacky W. Y. Lam; Ben Zhong Tang | Polyelectrolytes - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744a4702a9bb1d218a88f/original/bioinspired-simultaneous-changes-in-fluorescence-color-brightness-and-shape-of-hydrogels-enabled-by-ai-egens.pdf |
60c74b60842e659a0edb3136 | 10.26434/chemrxiv.12278066.v2 | Repurposing of FDA Approved Drugs for the Identification of Potential Inhibitors of SARS-CoV-2 Main Protease | <p>COVID-19, responsible for several deaths, demands a cumulative effort of scientists worldwide to curb the pandemic. The main protease, responsible for the cleavage of the polyprotein and formation of replication complex in virus, is considered as a promising target for the development of potential inhibitors to treat the novel coronavirus. The effectiveness of FDA approved drugs targeting the main protease in previous SARS-COV (s) reported earlier indicates the chances of success for the repurposing of FDA drugs against SARS-COV-2. Therefore, in this study, molecular docking and virtual screening of FDA approved drugs, primarily of three categories: antiviral, antimalarial, and peptide, are carried out to investigate their inhibitory potential against the main protease. Virtual screening has identified 53 FDA drugs on the basis of their binding energies (< -7.0 kcal/mol), out of which the top two drugs Velpatasvir (-9.1 kcal/mol) and Glecaprevir (-9.0 kcal/mol) seem to have great promise. These drugs have a stronger affinity to the SARS-CoV-2 main protease than the crystal bound inhibitor α-ketoamide 13B (-6.7 kcal/mol) or Indinavir (-7.5 kcal/mol) that has been proposed in a recent study as one of the best drugs for SARS-CoV-2. The <i>in-silico</i> efficacies of the screened drugs could be instructive for further biochemical and structural investigation for repurposing. The molecular dynamics studies on the shortlisted drugs are underway. </p> | Abhik Kumar Ray; Parth Sarthi Sen Gupta; Saroj Kumar Panda; Satyaranjan Biswal; Malay Kumar Rana | Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b60842e659a0edb3136/original/repurposing-of-fda-approved-drugs-for-the-identification-of-potential-inhibitors-of-sars-co-v-2-main-protease.pdf |
60c751fd702a9b0cef18c03f | 10.26434/chemrxiv.13173278.v1 | Design of a Small-Scale Supercritical Water Oxidation Reactor. Part II: Numerical Modeling and Validation | <p>The experimental
data from the laboratory-scale supercritical water oxidation reactor was
leveraged to validate the CFD approach allowing for efficient and accurate
modeling of the process. The reactor operating on ethanol as a pilot fuel was
modeled using CFD with global oxidation mechanism. Fluid properties were
determined using polynomial fit approximations, which yielded excellent
agreement with NIST data over a range of temperatures at an isobaric pressure
of 25 MPa. The model predicts the fluid temperature within 30°C of measured
values for different inlet fuel concentrations. The ethanol decomposition of ~99%
occurs within 20% of the reactor length at T~600 °C. The analysis of Damkohler
(<i>Da</i>) and Reynolds (<i>Re</i>) numbers shows that the reactor operates in
a distributed reaction region, owing to the excellent combustion stability of the
inverted gravity reactor configuration. The modeling approach can aid the design
of future more complex SCWO reactors and process optimization. </p> | Anmol L. Purohit; John Misquith; Stuart Moore; Brian Pinkard; John Kramlich; Per G. Reinhall; Igor V. Novosselov | Process Control; Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751fd702a9b0cef18c03f/original/design-of-a-small-scale-supercritical-water-oxidation-reactor-part-ii-numerical-modeling-and-validation.pdf |
62a183678f92d9272d4abc01 | 10.26434/chemrxiv-2022-zqmbv | Experimental observation of the resonant doorways to the anion chemistry: the dynamic role of the dipole-bound Feshbach resonances in the dissociative electron attachment | Anion chemical dynamics of autodetachment and fragmentation mediated by the dipole-bound state (DBS) have been thoroughly investigated in a state-specific way for the first time by employing the picosecond time-resolved or the nanosecond frequency-resolved spectroscopy combined with the cryogenically cooled ion trap and velocity-map imaging techniques. For the ortho-, meta-, or para-iodophenoxide anion (o-, m-, or p-IPhO-), the C-I bond rupture giving the anionic iodide (I-) fragment occurs via the nonadiabatic transition from the DBS to the nearby valence-bound states (VBS) of the anion where the vibronic coupling into the S1 (π-sigma*) state (which is repulsive along the C-I bond extension coordinate) should be largely responsible. The dynamic details are governed by the isomer-specific nature of the potential energy surfaces in the vicinity of the DBS-VBS curve crossings, as manifested in the huge different chemical reactivity of o-, m-, or p-IPhO-. It is confirmed here that the C-I bond dissociation is mediated by DBS resonances, providing the foremost evidence that the metastable DBS plays the essential role as the doorway into the anion chemistry especially of the dissociative electron attachment (DEA). The fragmentation channel is dominant when it is mediated by the DBS resonances located below the electron-affinity (EA) threshold, whereas it is kinetically adjusted by the competitive autodetachment process when the DBS resonances lying above EA convey the electron to the valence orbitals. The product yield of the C-I bond cleavage is strongly mode-dependent as the rate of the concomitant autodetachment is much influenced by the characteristics of the individual vibrational modes, paving a new way of the reaction control of the anion chemistry. | Do Hyung Kang; Jinwoo Kim; Han Jun Eun; Sang Kyu Kim | Physical Chemistry; Chemical Kinetics; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2022-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a183678f92d9272d4abc01/original/experimental-observation-of-the-resonant-doorways-to-the-anion-chemistry-the-dynamic-role-of-the-dipole-bound-feshbach-resonances-in-the-dissociative-electron-attachment.pdf |
659b969f9138d231616eb0e0 | 10.26434/chemrxiv-2024-tkv7w-v2 | Sulfoxide-mediated Cys-Trp-selective bioconjugation that enables protein labeling and peptide heterodimerization | A method was developed that enables the magnesium chloride (MgCl2)-activated S-acetamidomethyl cysteine sulfoxide (Cys(Acm)(O)) to induce the sp2(C−H) sulfenylation of the indole ring of Trp residues. The reaction operates under mild acidic conditions using acetic acid or an ionic liquid in a highly Trp-selective manner to give the Trp-sulfenylated products. Other than Trp, all other proteinogenic amino acids are unreactive to the sulfenylation conditions. We demonstrated the successful application of this reaction to a variety of peptides, including lysozyme protein. Furthermore, we achieved the Trp-modification of a monoclonal antibody (trastuzumab®) by a MgCl2-mediated reaction in an acidic ionic liquid. The resulting modified antibody exhibited antibody performance comparable to the parent protein. The presence of an amide moiety in the Acm group contributes to the difference in chemical behavior between S-Acm and S-p-methoxybenzyl (MBzl)-protected cysteine sulfoxide. This is because the S-Acm sulfoxide is converted to S-chlorocysteine responsible for Trp-sulfenylation under less acidic conditions than those required for the reaction of S-MBzl sulfoxide. Based on this rationale, we prepared a linker possessing S-Acm and S-MBzl oxide moieties and subjected the linker to hetero dimerization of DNA-binding Myc and Max peptides containing a Trp handle. The one-pot/stepwise Cys-Trp conjugation between the linker and DNA-binding peptides allowed the generation of a heterodimeric Myc/Max DNA binder. | Daishiro Kobayashi; Masaya Deda; Junya Hayashi; Kota Hidaka; Yutaka Kohmura; Takaaki Tsunematsu; Kohei Nishino; Harunori Yoshikawa; Kento Ohkawachi; Kiyomi Nigorikawa; Tetsuro Yoshimaru; Naozumi Ishimaru; Wataru Nomura; Toyomasa Katagiri; Hidetaka Kosako; Akira Otaka | Organic Chemistry; Bioorganic Chemistry | CC BY 4.0 | CHEMRXIV | 2024-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659b969f9138d231616eb0e0/original/sulfoxide-mediated-cys-trp-selective-bioconjugation-that-enables-protein-labeling-and-peptide-heterodimerization.pdf |
64b954beb605c6803b110bce | 10.26434/chemrxiv-2023-zzdvd | Multi-type Electronic Interactions in Precursor Solutions of Molecular Doped P3HT Polymer | Spin casting of molecular doped polymer solution mixtures is one of the commonly used methods to obtain conductive organic semiconductor films. In spin-casted films, electronic interaction among the dopant and polymer is one of the crucial factors that dictate the doping efficiency. Here, we investigate excitonic couplings using ultrafast two-dimensional electronic spectroscopy to examine the different types of electronic interaction in ion pairs of the prototype F4TCNQ doped P3HT polymer system in precursor solution mixture for spin-casting. Off-diagonal peaks in 2D spectra clearly establish the excitonic coupling between P3HT+ and F4TCNQ− ions in solution. The observed excitonic coupling is the direct manifestation of Coulombic interaction amongst the ion-pair. The excited state lifetime of F4TCNQ− in ion-pairs shows biexponential decay: 30 fs and 200 fs, which hints towards the presence of heterogeneous population with different interaction strengths. To examine the nature of these different types of interactions in solution mixture, we study the system using molecular dynamics simulations on a fully solvated model employing the generalized Amber force field. We retrieve three dominant interaction modes of F4TCNQ anions with P3HT: side-chain, π-stack and slipped stack. To quantify these interactions, we complement our studies with electronic structure calculations, which reveal the excitonic coupling strengths of: ∼75 cm−1 for side-chain, ∼150 cm−1 for π-π-stack, and ∼69 cm−1 for slipped stack. These various interaction modes provide information on the key geometries of the seed structures in precursor solution mixtures, which may determine the final structures in spin-casted films. The insights gained from our study may guide new strategies to control and ultimately tune the Coulomb interactions in polymer-dopant solutions. | Vandana Tiwari; Xin Li; Zheng Li; Ian Jacobs; Hong-Guang Duan; Henning Sirringhaus; R. J. Dwayne Miller; Ajay Jha | Physical Chemistry; Materials Science; Polymer Science; Conducting polymers; Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b954beb605c6803b110bce/original/multi-type-electronic-interactions-in-precursor-solutions-of-molecular-doped-p3ht-polymer.pdf |
648c34bc4f8b1884b7619630 | 10.26434/chemrxiv-2023-fz0lz | Empowering extra fuel supply in E. coli by electron bifurcation for robust H2, ATP and succinate production
| Microbial production of hydrogen (future ideal fuel and important gas for industries) under anoxic conditions has limited ATP availability and low efficiency. We engineered E. coli K12 to acquire a flavin-based electron bifurcation (FBEB) system, a bioenergetic route typically found in strict anaerobes, which uses NADH to generate low potential reduced ferredoxin and high potential butyryl-CoA. The oxygen-tolerant FBEB-E. coli showed higher H2 and succinate production (2-4 folds), lower cellular reduction potentials, greater accumulation of cellular reductants and various metabolites, including ATP (up to a 7-fold increase). It could better tolerate prolonged and recycled usage of the engineered cell for H2 and succinate production than the native strain. FBEB-E. coli could also use various substrates such as formate, D-glucose and food waste for H2 and succinate production. This is a promising pathway to sustainable H2 and succinate production. This work also demonstrates that E. coli with an extra electron bifurcation system is a robust synthetic biology host. | Pattarawan Intasian; Chalermroj Sutthaphirom; Asweena Binlaeh; Jittima Phonbuppha; Juthamas Jaroensuk; Somjai Teanphonkrang ; Thamonwan Woraruthai; Charndanai Tirapanampai; Warunya Onchan; Albert Schulte; Wolfgang Buckel; Nopphon Weeranoppanant; Thanyaporn Wongnate; Jeerus Sucharitakul; Pimchai Chaiyen | Biological and Medicinal Chemistry; Catalysis; Energy | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648c34bc4f8b1884b7619630/original/empowering-extra-fuel-supply-in-e-coli-by-electron-bifurcation-for-robust-h2-atp-and-succinate-production.pdf |
64782ed44f8b1884b7a25f97 | 10.26434/chemrxiv-2023-4bq69-v2 | A Porous Crystalline Nitrone-Linked Covalent Organic Framework | Herein, we report the synthesis of a nitrone-linked covalent organic framework, COF-115, by combining N, N', N', N'''-(ethene-1,1,2,2-tetrayltetrakis(benzene-4,1-diyl))tetrakis(hydroxylamine) and terephthaladehyde via a polycondensation reaction. The formation of the nitrone functionality was confirmed by solid-state 13C multi cross-polarization magic angle spinning NMR spectroscopy of the 13C-isotope-labeled COF-115 and Fourier-transform infrared spectroscopy. The permanent porosity of COF-115 was evaluated through low-pressure N2, CO2, and H2 sorption experiments. Water vapor and carbon dioxide sorption analysis of COF-115 and the isoreticular imine-linked COF indicated a superior potential of N-oxide-based porous materials for atmospheric water harvesting and CO2 capture applications. Density functional theory calculations provided valuable insights into the difference between the adsorption properties of these COFs. Lastly, photoinduced rearrangement of COF-115 to the associated amide-linked material was successfully demonstrated. | Daria Kurandina; Banruo Huang; Wentao Xu; Nikita Hanikel; Andrea Darù; Gautam D. Stroscio; Kaiyu Wang ; Laura Gagliardi; F. Dean Toste; Omar M. Yaghi | Organic Chemistry; Materials Science; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-06-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64782ed44f8b1884b7a25f97/original/a-porous-crystalline-nitrone-linked-covalent-organic-framework.pdf |
Subsets and Splits
No saved queries yet
Save your SQL queries to embed, download, and access them later. Queries will appear here once saved.