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6344ad08e665bd4f3e261b5b | 10.26434/chemrxiv-2022-hcvn0-v2 | Research progress of electrospray ion source principle | The theory of ion source is of great significance to the design and development of ion source, the slow development of this restricts the design and development of ion source, which makes the ion source meet many bottlenecks from laboratory to commercialization. By introducing ion evaporation model (IEM), charged residue model (CRM), chain ejection theory, Zhu yixin's experiment and theory, ion migrate and transport, the paper summarizes the recent research progress in this field, and looks forward to the development of this kind research. | jiehong luo | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6344ad08e665bd4f3e261b5b/original/research-progress-of-electrospray-ion-source-principle.pdf |
6705170351558a15ef7eac9a | 10.26434/chemrxiv-2024-kcvpz | SLIC-SABRE at microtesla fields enables high levels of nuclear spin polarization without magnetic shielding | Employing nuclear spin hyperpolarization to enhance NMR sensitivity opens new horizons for metabolic studies and chemical reaction monitoring. Among the hyperpolarization techniques, Signal Amplification by Reversible Exchange (SABRE) is prominent for its ability to transfer spin order from parahydrogen to target nuclei, especially 13C and 15N, without the chemical modification of the substrate under study. Despite its power, existing implementations of SABRE require expensive equipment like radiofrequency (RF) hardware and magnetic shielding. This paper demonstrates the SLIC-SABRE method at low magnetic fields as a low-cost and efficient technique for achieving high 15N polarization using a simple setup, consisting only of a small set of magnetic coils driven by a desktop PC sound card. The method yields up to 17% polarization across various SABRE-active molecules, outperforming the conventional SABRE-SHEATH approach and significantly enhancing the accessibility of hyperpolarization techniques. | Vitaly Kozinenko; Alexey Kiryutin; Alexandra Yurkovskaya | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6705170351558a15ef7eac9a/original/slic-sabre-at-microtesla-fields-enables-high-levels-of-nuclear-spin-polarization-without-magnetic-shielding.pdf |
64f7217f79853bbd78258440 | 10.26434/chemrxiv-2023-ltr9v-v2 | DiffSeqMol: A Non-Autoregressive Diffusion-Based Approach for Molecular Sequence Generation and Optimization | The application of deep generative models for molecular discovery has witnessed a significant surge in recent years. Currently, the field of molecular generation and molecular optimization is predominantly governed by autoregressive models regardless of how molecular data is represented. However, an emerging paradigm in the generation domain is diffusion models, which treat data non-autoregressively and has achieved significant breakthroughs in areas such as image generation. The potential and capability of diffusion models in molecular generation and optimization tasks remain largely unexplored. In order to investigate the potential applicability of diffusion models in the domain of molecular exploration, we proposed DiffSeqMol, a molecular sequence generation model, underpinned by diffusion process. DiffSeqMol distinguishes itself from traditional autoregressive methods by its capacity to draw samples from random noise and direct generating the entire molecule. Through experiment evaluations, we demonstrated that DiffSeqMol can achieve, even surpass, the performance of established state-of-the-art models on unconditional generation tasks and molecular optimization tasks. | Zixu Wang; yangyang chen; Xiucai Ye | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f7217f79853bbd78258440/original/diff-seq-mol-a-non-autoregressive-diffusion-based-approach-for-molecular-sequence-generation-and-optimization.pdf |
6650a26691aefa6ce1e3576e | 10.26434/chemrxiv-2024-q1pfb | Possibilities and limits of DNA-enabled programmable 2D self-assembly | Programmable self-assembly provides a promising avenue to improve upon traditional synthesis and create multi-component materials with emergent properties and arbitrary nanoscale complexity. However, its most successful realizations utilizing DNA often use complicated arduous procedures that result in low yields. Here, we employ coarse-grained molecular dynamics to uncover the ranges of temperatures and misbinding strengths needed for successful one-pot self-assembly of generic, two-dimensional (2D), and distinguishable blocks. Analysis of the energies associated with a single-stranded DNA interacting with all other sequences within a mixture revealed that the success of DNA-based assembly is primarily determined by the strongest misbinding a given sequence can encounter with a sequence highly similar to its reverse complement. This enabled us to design optimized sequence ensembles with acceptably weak and consequently rare misbinding. An estimate is provided for the maximum size of, and complexity of sequences needed to synthesize self-assembled structures with high accuracy and yield, with potential relevance for DNA-functionalized low-dimensional materials for electronics and energy storage. | Nicholas Tjahjono; Evgeni Penev; Boris Yakobson | Theoretical and Computational Chemistry; Materials Science; Nanoscience | CC BY 4.0 | CHEMRXIV | 2024-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6650a26691aefa6ce1e3576e/original/possibilities-and-limits-of-dna-enabled-programmable-2d-self-assembly.pdf |
60c74aaa842e655cb4db2f99 | 10.26434/chemrxiv.12170424.v2 | Not One, But Five: Virtual Screening-Driven Drug Discovery of SARS-CoV2 Enzyme Inhibitors Targeting Viral Attachment, Replication and Post-Translational Infection Mechanisms | The novel coronavirus SARS-CoV2, the causative agent of the worldwide pandemic disease COVID-19, emerged in December 2019 forcing lockdown of communities in many countries. The absence of specific drugs and vaccines, the rapid transmission of the virus, and the increasing number of deaths worldwide have necessitated the need to discover substances that can be tapped for drug development. With the aid of bioinformatics and computational modelling, ninety seven secondary metabolites from fungi previously reported to exhibit antiviral properties were docked onto SARS-CoV2 enzymes involved in viral attachment, replication and post-translational mechanisms followed by <i>in silico</i> ADMET prediction (absorption, distribution, metabolism, excretion and toxicity) of the hit compounds. Thus, two fumiquinazoline alkaloids quinadoline B (<b>19</b>), scedapin C (<b>15</b>), and the polyketide isochaetochromin D1 (<b>8</b>) exhibited high binding affinities depending on the target protein. The compounds were active against the cysteine proteases, papain-like protease (PLpro) and chymotrypsin-like protease (3CLpro) which are involved in post-translational modifications, RNA-directed RNA polymerase (RdRp) which is essential in viral replication, non-structural protein 15 (nsp15) which is involved in evasion of host immunity, and the spike protein which is responsible for binding to GRP78. Quinadoline B (<b>19</b>) was predicted to confer favorable ADMET values, high gastrointestinal absorptive probability and poor blood-brain barrier crossing capacities. | Mark Tristan J. Quimque; Kin Israel Notarte; Rey Arturo T. Fernandez; Mark Andrew O. Mendoza; Rhenz Alfred D. Liman; Justin Allen K. Lim; Luis Agustin E. Pilapil; Jehiel Karsten H. Ong; Adriel M. Pastrana; Allan Patrick Macabeo | Bioorganic Chemistry; Natural Products; Organic Compounds and Functional Groups; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74aaa842e655cb4db2f99/original/not-one-but-five-virtual-screening-driven-drug-discovery-of-sars-co-v2-enzyme-inhibitors-targeting-viral-attachment-replication-and-post-translational-infection-mechanisms.pdf |
67d56fac81d2151a027bbcba | 10.26434/chemrxiv-2025-1z8v9-v2 | Theory of Field-Dependent NMR Shifts in Paramagnetic Molecules | NMR chemical shifts depend on the applied magnetic flux density, and this becomes more and more important as stronger and stronger magnetic fields are becoming available. Herein, we develop a theory of the field dependence of NMR shifts of paramagnetic molecules in solution. Our derivation leads to two distinct approaches: a finite field approach that describes the shift up to infinite order in the applied field B0 but requires numerical integration for the orientational average, and a 2nd order approach that is valid up to 2nd order in B0. In this latter approach, the orientational average can be performed analytically and the field dependence cleanly separates into two additive terms: the well-known “indirect” field dependence due to incomplete averaging in solution and the “direct” field dependence due to the nonlinear response to the external field. In analogy to the diamagnetic case, the direct field dependence depends on a fourth-order tensor τ whose elements are fourth derivatives of the electronic Helmholtz free energy. Generalizing the Van den Heuvel–Soncini equation, we provide analytical sum-over-states equations for these higher-order derivatives. Using the NiSAL-HDPT complex as an example, we demonstrate the applicability of the 2nd order approach at room temperature and the highest commercially available field strength and show that it agrees well with the field dependence measured experimentally. | Lucas Lang; Letizia Fiorucci; Giacomo Parigi; Claudio Luchinat; Enrico Ravera | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2025-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d56fac81d2151a027bbcba/original/theory-of-field-dependent-nmr-shifts-in-paramagnetic-molecules.pdf |
62834c3b59f0d64cfa933e98 | 10.26434/chemrxiv-2022-bdbc0 | Simultaneous Estimation of Gas Adsorption Equilibria and Kinetics of Individual Shaped Adsorbents | Shaped adsorbents are typically employed in several gas separation and sensing applications. The performance of these adsorbents is dictated by two key factors, their adsorption equilibrium capacity and kinetics. Often, adsorption equilibrium and textural properties are reported for materials. Adsorption kinetics, despite its impact on performance in a given application, are seldom presented due to the challenges associated with measuring them. Therefore, robust and practical experimental approaches -- preferably using small quantities of material -- to characterize both the adsorption equilibrium and kinetics for shaped adsorbents is necessary. The overarching goal of this work is to develop an approach to characterize the adsorption properties of shaped adsorbents with less than 100 mg of sample. To this aim, we have developed an experimental dynamic sorption setup, complemented with mathematical models, to describe the mass transport in the system. We embed these models into a derivative-free optimizer to predict model parameters for adsorption equilibrium and kinetics. We evaluate the performance of our approach using three adsorbents. Further, we test the robustness of our mathematical framework using a digital twin. We show that framework can rapidly and quantitatively characterize adsorption properties at a milligram scale, making it suited for screening of novel porous materials. | Hassan Azzan; Ashwin Kumar Rajagopalan; Anouk L'Hermitte; Ronny Pini; Camille Petit | Chemical Engineering and Industrial Chemistry; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62834c3b59f0d64cfa933e98/original/simultaneous-estimation-of-gas-adsorption-equilibria-and-kinetics-of-individual-shaped-adsorbents.pdf |
65cd3a7166c1381729a8c68e | 10.26434/chemrxiv-2024-ndt2d-v2 | Labelling and composition of contraband electronic cigarettes: Analysis of products from Australia | Background: The sale of nicotine-containing electronic cigarettes (e-cigarettes) is prescription only in Australia, regulated under the TGO110. Australian e-cigarette users, however, are purchasing e-cigarette products outside of the intended pathways. Methods: The labelling of e-cigarette packaging (N=388 boxes) and the chemical composition of disposable e-cigarettes and pods (N=428) were analysed for adherence to the current Australian regulations. These samples were obtained from over-the-counter retailers in NSW. Results: Following the announcement of the prescription only model for nicotine-containing e-cigarettes in Australia in mid 2021 there was a clear shift in the labelling of products. Any mention of the word ‘nicotine’ was removed from e-cigarette packaging by early 2022 and nicotine warnings were replaced with generic underage sale warnings. Despite this labelling the vast majority (98.8%) of devices analysed contained nicotine, most (89%) at high concentration (>30 mg/mL) and 4.2% contained at least one chemical prohibited by the TGO110. Conclusions: Manufacturers have removed any mention of nicotine from the original e-cigarette packaging to circumvent regulations and continue their sale. The packaging of e-cigarette products in Australia is generally not indicative of their contents, particularly nicotine, and most did not display required warnings. Ingredients with associated health risks, prohibited in legal vapes by the TGO110, were found in samples. Consequently, the risks of e-cigarette use cannot be appropriately identified from the information supplied on the packaging or device. | Caitlin Jenkins; Fraser Powrie; Jody Morgan; Celine Kelso | Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cd3a7166c1381729a8c68e/original/labelling-and-composition-of-contraband-electronic-cigarettes-analysis-of-products-from-australia.pdf |
60c74583702a9b60de18aa17 | 10.26434/chemrxiv.10052348.v1 | Improved Deep-Red Phosphorescence in Cyclometalated Iridium Complexes via Ancillary Ligand Modification | In this work, we describe bis-cyclometalated iridium complexes with efficient deep-red luminescence. Two different cyclometalating (C^N) ligands‒1-phenylisoquinoline (piq) and 2-(2- pyridyl)benzothiophene (btp)‒are used with six strong π-donating ancillary ligands (L^X) to furnish a suite of 10 new complexes with the general formula Ir(C^N)2(L^X). Improvements in deep-red photoluminescence quantum yields were accomplished by the incorporation of sterically encumbering substituents onto the ancillary ligand, which can enhance the radiative rate constant (kr) and/or reduce the non-radiative rate constant (knr). Five of the complexes were characterized by X-ray crystallography, and all of them were investigated by in-depth spectroscopic and electrochemical measurements.<br /> | Evanta Kabir; Steven Sittel; Boi-Lien Nguyen; Thomas Teets | Coordination Chemistry (Inorg.); Organometallic Compounds; Coordination Chemistry (Organomet.); Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74583702a9b60de18aa17/original/improved-deep-red-phosphorescence-in-cyclometalated-iridium-complexes-via-ancillary-ligand-modification.pdf |
64bd8aa5b605c6803b3bce5f | 10.26434/chemrxiv-2023-twmn8 | QSPR AND ARTIFICIAL NEURAL NETWORK PREDICTIONS OF HYPERGOLIC IGNITION DELAYS FOR ENERGETIC IONIC LIQUIDS | Due to their negligible volatility, energetic ionic liquids are being considered as next generation hypergolic fuels for replacing toxic monomethylhydrazine. One design challenge for energetic ionic liquids is to maintain their ignition delays as close to that of monomethylhydrazine. The ignition process of ionic liquids with an oxidizer, such as nitric acid, is a complex process and, to date, there are no theoretical methods for predicting the ignition delay. The present work examines two correlation methods, Quantitative Structure Property Relationship (QSPR) and Artificial Neural Networks (ANNs), for their ability to predict this quantity. A set of five descriptors were chosen from a pool of more than 160 to establish these correlations. A good QSPR correlation was obtained using these descriptors. We then trained an artificial neural network and examined the predictive ability of the network using an extensive 5-fold cross validation process with the same set of descriptors. A number of data normalization techniques were examined for network training and validation. The results show that ANNs exhibit excellent prediction capabilities for this application. | Debasis Sengupta; Maciej Z. Pindera; J. Vernon Cole; Ghanshyam L. Vaghjiani | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64bd8aa5b605c6803b3bce5f/original/qspr-and-artificial-neural-network-predictions-of-hypergolic-ignition-delays-for-energetic-ionic-liquids.pdf |
60c7457ebb8c1aa0e63da6d2 | 10.26434/chemrxiv.10042907.v1 | Synthesis of 3-Azidopropyl-Functionalized GalNAc-β-(1→4)-Gal Natural Disaccharide | Oligosaccharides such as the GalNAc-β-(1→4)-Gal disaccharide are involved in host-pathogen interactions and their synthesis is a continuing challenge for organic chemists. Only a few reports have discussed the synthesis of functionalized GalNAc-β-(1→4)-Gal for its further conjugation and applications in glycobiology. The synthetic route described here is taking advantage of (1) a simple and affordable GlcNAc donor which is epimerized to the more expensive GalNAc donor and (2) a 1,6-anhydro-galactose acceptor exalting the reactivity at the 4-position of galactose. The allyloxycarbonyl (Alloc) protecting group used at the 2-position of the GalNAc residue was important (1) for a successful epimerization of the GlcNAc residue into the corresponding GalNAc donor but also (2) for the stereoselective β-glycosylation through anchimeric assistance. The key disaccharide intermediate was further transformed to a trichloroacetimidate donor which could then be glycosylated with any alcohol. The example chosen here is the 3-azidopropyl aglycon for the design of multivalent glycoclusters.<br /> | Sebastien Vidal; Dominique Lafont; Shuai Wang | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7457ebb8c1aa0e63da6d2/original/synthesis-of-3-azidopropyl-functionalized-gal-n-ac-1-4-gal-natural-disaccharide.pdf |
678d5dea6dde43c90838b2f2 | 10.26434/chemrxiv-2024-4rh6c-v2 | Predicting Liquid-Liquid Phase Separation of Submicron Proxies for Atmospheric Secondary Aerosol | Liquid–liquid phase separation (LLPS) of atmospheric aerosols can significantly impact climate, air quality, and human health. However, their complex composition, small size, and history-dependent properties result in great uncertainty in the modeling of aerosol phase state and atmospheric processes. Herein, using cryogenic transmission electron microscopy (cryo-TEM), we examined model submicron aerosols composed of organic compounds and ammonium sulfate, and established a parameterization for the separation relative humidity (SRH) that accounts for chemical composition, particle size, and equilibration time. We evaluated different variables that describe chemical composition: O/C ratio, partition coefficient, solubility, molar mass, and polarizability. The O/C ratio fits the SRH of micrometer droplets best, and by using a scaling factor to translate the micrometer SRH parameterization to submicron aerosols, we incorporate the effects of size and equilibration time. The measured scaling factor for the submicron mean SRH (30nm – 1𝜇m, 20 min equilibration times) is 0.80, the factor becomes 1 with equilibration time over 1 hour, and is equal to 0, meaning that SRH is absent, when the aerosol dry diameter is smaller than 30 nm. Our parameterization will aid in universal SRH modeling, potentially leading to more accurate predictions of aerosol mass, optical properties, hygroscopicity, and heterogeneous chemistry. | Qishen Huang; Kiran Pitta; Andreas Zuend; Miriam Freedman | Physical Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science; Microscopy | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678d5dea6dde43c90838b2f2/original/predicting-liquid-liquid-phase-separation-of-submicron-proxies-for-atmospheric-secondary-aerosol.pdf |
675c5e887be152b1d0df4a74 | 10.26434/chemrxiv-2024-vrnfz | Precision design for polymethacrylate recycling: a radical ring-opening polymerization approach with systematic degradable thionolactone-centered triads | A recycling by design challenge for methacrylate-rich polymers, with applications such as coatings, casts, protective materials and pharmaceutical formulations, is the precise systematic incorporation of (bio)degradable thioester bonds to achieve intrinsic (bio)degradability upon environmental disposal. Unfortunately the most efficient (degradable) thionolactone dibenzo[c,e]oxepine-5(7h)-thione (DOT) is incompatible with methacrylate derivatives, implying the absence of MMA-DOT-MMA formation in poly(methyl methacrylate (PMMA) backbones. As shown in the present work, DOT can be encapsulated through a fast radical ring-opening polymerization (rROP) in a symmetric triad, by utilizing methyl acrylate (MA) or N-phenyl maleimide (PhMal) as an auxiliary comonomer. The intriguing formation of MA-DOT-MA and PhMal-DOT-PhMal triads is realized, and demonstrated to be compatible with MMA addition. This enables the controlled formation of MMAx-(MA-DOT-MA)-MMAy and MMAx-(PhMal-DOT-PhMal)-MMAy, hence, for the first time the well-defined inclusion of degradable moieties in PMMA backbones with low DOT amounts. Validated Coupled Matrix-based Monte Carlo (CMMC) simulations are utilized to design the synthesis conditions by playing with the initial comonomer and solvent amounts. Specifically, these simulations identified unconventional synthesis conditions, resulting in a 2 times shift in the peak average molar mass for the MMA/DOT/PhMal degradable polymer (number average molar mass Mn of 60,000 g.mol-1) and a 25 times lower Mn for the degraded oligomers (2,000-2,500 g.mol-1 within the target range). The model-based insights have been experimentally confirmed, opening the pathway to regulated (bio)degradability for polymethacrylates under industrially relevant radical polymerization conditions. | Bastien Luzel; Ignatii Efimov; Mariya Edeleva; Noémie Gil; Catherine Lefay; Didier Gigmes; Paul Van Steenberge; Dagmar D'hooge; Yohann Guillaneuf | Polymer Science; Polymer chains; Polymerization (Polymers) | CC BY 4.0 | CHEMRXIV | 2024-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675c5e887be152b1d0df4a74/original/precision-design-for-polymethacrylate-recycling-a-radical-ring-opening-polymerization-approach-with-systematic-degradable-thionolactone-centered-triads.pdf |
60c74c1f702a9bbb2518b5cb | 10.26434/chemrxiv.8248250.v3 | A Spatially Orthogonal Hierarchically Porous Acid-Base Catalyst for Cascade and Antagonistic Reactions | <p>Complex
organic molecules are of great importance to academic and industrial chemistry
and typically synthesised from smaller building blocks by multistep reactions.
The ability to perform multiple (distinct) transformations in a single reactor would greatly reduce the number
of manipulations required for chemical manufacturing, and hence the development
of multifunctional catalysts for such one-pot
reactions is highly desirable. Here we report the synthesis of a hierarchically
porous framework, in which the macropores are selectively functionalised with a
sulfated zirconia solid acid coating, while the mesopores are selectively
functionalised with MgO solid base nanoparticles. Active site compartmentalisation and substrate channelling protects base catalysed triacylglyceride transesterification from poisoning by free fatty acid impurities (even at 50
mol%), and promotes the efficient two-step cascade deacetylation-Knoevenagel condensation of dimethyl acetals to cyanoates.<br /></p> | Mark Isaacs; christopher parlett; neil robinson; Lee Durndell; Jinesh Manayil; Simon Beaumont; Shan Jiang; Nicole Hondow; Alexander Lamb; Michael Johns; Karen Wilson; Adam Lee | Nanostructured Materials - Materials; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Acid Catalysis; Base Catalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c1f702a9bbb2518b5cb/original/a-spatially-orthogonal-hierarchically-porous-acid-base-catalyst-for-cascade-and-antagonistic-reactions.pdf |
63086b56d147b26db4b92adb | 10.26434/chemrxiv-2022-zmr80 | E-Z Isomerization in Guanidine: Second-order Saddle Dynamics, Non-statisticality, and Time-frequency Analysis | Our recent work on the E-Z isomerization reaction of guanidine using ab initio chemical dynamics simulations [Rashmi et al, Regul. Chaotic Dyn. 2021, 26, 119] emphasized the role of second-order saddle (SOS) in the isomerization reaction; however could not unequivocally establish the non-statistical nature of the dynamics followed in the reaction. In the present study, we performed thousands on-the-fly trajectories using forces computed at the MNDO level to investigate the influence of second-order saddle in the E-Z isomerization reaction of guanidine and the role of intramolecular vibrational energy redistribution (IVR) on the reaction dynamics. The simulations reveal that while majority of the trajectories follow the traditional transition state pathways, 15% of the trajectories follow the SOS path. The dynamics was found to be highly non-statistical with the survival probabilities of the reactants showing large deviations from those obtained within the RRKM assumptions. In addition, a detailed analysis of the dynamics using time-dependent frequencies and the frequency ratio spaces reveal the existence of multiple resonance junctions that indicate the existence of regular dynamics and long-lived quasi-periodic trajectories in the phase space associated with non-RRKM behavior. | Richa Rashmi; Pankaj Kumar Yadav; Aniruddha Seal; Manikandan Paranjothy; Upakarasamy Lourderaj | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63086b56d147b26db4b92adb/original/e-z-isomerization-in-guanidine-second-order-saddle-dynamics-non-statisticality-and-time-frequency-analysis.pdf |
66f28509cec5d6c1420a7c6b | 10.26434/chemrxiv-2024-2x1kq | Reaction Mechanism of 2-Amido-2-Aminoacetic Acid Formation From Iminoacetic Acid and Amide - A Comparative DFT Study | A reaction mechanism for the reaction of iminoacetic acid with formamide, resulting in 2-amido-2-aminoacetic acid is proposed. The role of the Zn(II) - catalyst is elucidated. Two possible reaction pathways were calculated by means of DFT. Furthermore, a competing side reaction, yielding N-(1,1- dihodroxy-2-iminoethyl)amide was simulated. ETS-NOCV, IRI and CDA analysis was employed on various important molecular states. A reasonable mechanism for the main reaction was found, where the rate determining step is energetically more favorable than the rate determining step of the side reaction. Furthermore, this reaction mechanism explains the importance of the transition metal. | Georg Dazinger | Theoretical and Computational Chemistry; Organometallic Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f28509cec5d6c1420a7c6b/original/reaction-mechanism-of-2-amido-2-aminoacetic-acid-formation-from-iminoacetic-acid-and-amide-a-comparative-dft-study.pdf |
618dca35b039f235bea16095 | 10.26434/chemrxiv-2021-zfzp1-v2 | Searching Building Blocks with Large Excited-State Gaps in Five-memebered Heterocyclic Rings by Aromaticity Strategy | Organic molecules with large gap between the excited singlet/triplet states can be applied in hot exciton emission and singlet fission to beat the spin statistics limit in optoelectronic devices. Herein, a novel strategy is proposed for achieving large triplet-triplet gap (E(T1T2)) and singlet-triplet gap (E(S1T1)) by manipulating the aromaticity of the low-lying excited states. Partially conjugated five-membered heterocyclic rings are found to naturally have low E(T1) owing to high aromaticity obeying Baird’s Rule. Utilizing such ring (pyrazoline) as a bridge and selecting various donor and acceptor moieties, numbers of derivatives have been theoretically designed with tunable emission colors, significantly large E(T1T2) and E(S1T1), and satisfying E(T2)>E(S1)≥2E(T1). The ultrafast spectroscopy and sensitization measurements for one of them with blue fluorescence (named TPA-DBPrz) confirm the calculated prediction. This work opens a new avenue and provides molecular units to develop high-efficiency optoelectronic materials. | Qi Sun | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618dca35b039f235bea16095/original/searching-building-blocks-with-large-excited-state-gaps-in-five-memebered-heterocyclic-rings-by-aromaticity-strategy.pdf |
60c7453c842e657be3db25cf | 10.26434/chemrxiv.9991937.v1 | Tropoelastin-Inspired, Non-Ionic, Self-Coacervating Polyesters as Strong Underwater Adhesives | Inspired from the one-component self-coacervation of tropoelastin and mussel foot protein-3s, we created the first non-ionic, single component coacervates that can coacervate in a all ranges of pH (acidic to basic) and wide range of ionic strengths with degradability, rapid curing and strong underwater adhesion. In contrast to the complex coacervates, these ‘charge-free’ coacervates are potential candidates as tissue adhesives and sealants, adhesives for sensor attachment to wet skin, and as sprayable adhesives. Their potential use in the clinic arises from their enhanced stability to changes in external conditions, cytocompatibility, biodegradability and modular nature in incorporating various functional groups and crosslinkers. | Amal Narayanan; Joshua Menefee; Qianhui Liu; Ali Dhinojwala; Abraham Joy | Aggregates and Assemblies; Biodegradable Materials; Coating Materials; Nanostructured Materials - Materials; Polyelectrolytes - Materials; Hydrogels; Organic Polymers; Polyelectrolytes - Polymers; Nanostructured Materials - Nanoscience; Interfaces; Photochemistry (Physical Chem.); Self-Assembly; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7453c842e657be3db25cf/original/tropoelastin-inspired-non-ionic-self-coacervating-polyesters-as-strong-underwater-adhesives.pdf |
60c74435f96a0012fc286957 | 10.26434/chemrxiv.9745388.v1 | An Epoxide Intermediate in Glycosidase Catalysis | <div>Retaining glycoside hydrolases cleave their substrates through stereochemical retention at the anomeric position. Typically, this involves two-step mechanisms using either an enzymatic nucleophile via a covalent glycosyl enzyme intermediate, or neighboring group participation by a substrate-borne 2-acetamido neighboring group via an oxazoline intermediate; no enzymatic mechanism with participation of the sugar 2-hydroxyl has been reported. Here, we detail structural, computational and kinetic evidence for neighboring group participation by a mannose 2-hydroxyl in glycoside hydrolase family 99 endo-α-1,2-mannanases. We present a series of crystallographic snapshots of key species along the reaction coordinate: a Michaelis complex with a tetrasaccharide substrate; complexes with intermediate mimics, β-1,2-aziridine and β-1,2-epoxide; and a product complex. The 1,2-epoxide intermediate mimic displayed hydrolytic and transfer reactivity analogous to that expected for the 1,2-anhydro sugar intermediate supporting its catalytic equivalence. Quantum mechanics/molecular mechanics modelling of the reaction coordinate predicted a reaction pathway through a 1,2-anhydro sugar via a transition state in an unprecedented flattened, envelope (<i>E</i><sub>3</sub>) conformation. Kinetic isotope effects for anomeric-<sup>2</sup>H and anomeric-<sup>13</sup>C support an oxocarbenium ion-like transition state and that for C2-<sup>18</sup>O (1.052 ± 0.006) directly implicates nucleophilic participation by the C2-hydroxyl. Collectively, these data substantiate this unprecedented and long-imagined enzymatic mechanism.</div><div><br /></div> | Lukasz F. Sobala; Gaetano Speciale; Sha Zhu; Lluís Raich; Natalia Sannikova; Andrew J. Thompson; ZALIHE HAKKI; Dan Lu; Saeideh Shamsi Kazem Abadi; Andrew
R. Lewis; Victor Rojas-Cervellera; Ganeko Bernardo-Seisdedos; Yongmin Zhang; Oscar Millet; Jesús Jiménez-Barbero; Andrew J. Bennett; Matthieu Sollogoub; Carme Rovira; Gideon J. Davies; Spencer Williams | Biochemistry; Chemical Biology; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74435f96a0012fc286957/original/an-epoxide-intermediate-in-glycosidase-catalysis.pdf |
60c74b224c89192fa4ad33a6 | 10.26434/chemrxiv.12294146.v1 | Electronic Couplings in the Reduced State Lie at the Origin of Color Changes of Ommochromes | In the colorful world of pigments and dyes, the chemical reduction of chromophores usually leads to bleaching because of π-conjugation interruption. Yet, the natural phenoxazinone-based ommochrome pigment called xanthommatin displays a bathochromic (i.e. red) shift upon two-electron reduction to its corresponding phenoxazine, whose electronic origins are not completely disclosed. In this study, we investigated, at quantum chemical level, a series of phenoxazinone/phenoxazine pairs that was previously explored by UV-Vis spectroscopy (Schäfer and Geyer, 1972), and which displays different hypsochromic and bathochromic shifts upon reduction. Density Functional Theory (DFT) and Time-Dependent DFT (TDDFT) have been applied to compute their optical properties in order to find a rational explanation of the observed photophysical behavior. Based on our results, we propose that the electro-accepting power of auxochromes and their conjugation facilitate intramolecular charge-transfers across the phenoxazine bridge by lowering unoccupied molecular orbitals via electronic and geometric couplings, leading ultimately to bathochromy. Our findings therefore suggest new potential ways to adjust the color-changing ability of phenoxazinones in technological contexts. Overall, this model extends our mechanistic understanding of the many biological functions of ommochromes in invertebrates, from tunable color changes to antiradical behaviors.<br /> | Florent Figon; Jérôme Casas; Ilaria Ciofini; Carlo Adamo | Chemical Biology; Computational Chemistry and Modeling; Quantum Computing | CC BY NC 4.0 | CHEMRXIV | 2020-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b224c89192fa4ad33a6/original/electronic-couplings-in-the-reduced-state-lie-at-the-origin-of-color-changes-of-ommochromes.pdf |
635c5c7518a8cc76c355d8e5 | 10.26434/chemrxiv-2022-lqms7-v3 | Cycling Performance and Mechanistic Insights of Ferricyanide Electrolytes in Alkaline Redox Flow Batteries | Ferrocyanide, such as K4[Fe(CN)6], is one of the most popular cathode electrolyte (catholyte) materials in redox flow batteries. However, its chemical stability in alkaline redox flow batteries has been debated. Mechanistic understandings at the molecular level are necessary to elucidate the cycling stability of K4[Fe(CN)6] and its oxidized state (K3[Fe(CN)6]) based electrolytes and guide their proper use in flow batteries for energy storage. Herein, we presented a suite of battery tests and spectroscopic studies to understand the chemical stability of K4[Fe(CN)6] and its charged state, K3[Fe(CN)6], at a variety of conditions. In a strong alkaline solution (pH 14), it was found that the balanced K4[Fe(CN)6]/K3[Fe(CN)6] half-cell experienced a fast capacity decay under dark conditions. Our studies revealed the chemical reduction of K3[Fe(CN)6] by a graphite electrode leads to the charge imbalance in the half-cell cycling and is the major cause of the observed capacity decay. In addition, at pH 14, K3[Fe(CN)6] undergoes a slow CN‒/OH‒ exchange reaction. The dissociated CN‒ ligand can chemically reduce K3[Fe(CN)6] to K4[Fe(CN)6], and it is converted to cyanate (OCN‒) and further, decompose into CO32‒ and NH3. Ultimately, the irreversible chemical conversion of CN‒ to OCN‒ leads to the irreversible decomposition of K4/K3[Fe(CN)6] at pH 14. | Maowei Hu; Abigail Wang; Tianbiao Liu; Jian Luo | Materials Science; Inorganic Chemistry; Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635c5c7518a8cc76c355d8e5/original/cycling-performance-and-mechanistic-insights-of-ferricyanide-electrolytes-in-alkaline-redox-flow-batteries.pdf |
65f71d849138d23161a74a24 | 10.26434/chemrxiv-2024-tfk5v | The competing reaction mechanisms of peptide bond formation in water revealed by deep potential molecular dynamics and path sampling | The formation of an amide bond is an essential step in the synthesis of materials and drugs, and in the assembly of amino-acids to form peptides. The mechanism of this reaction has been studied extensively, in particular to understand how it can be catalyzed, but a representation capable of explaining all the experimental data is still lacking. Numerical simulation should provide the necessary molecular description, but the solvent involvement poses a number of challenges. Here, we combine the efficiency and accuracy of neural network potential-based reactive molecular dynamics with the extensive and unbiased exploration of reaction pathways provided by transition path sampling. Using microsecond-scale simulations at the density functional theory level, we show that this method reveals the presence of two competing distinct mechanisms for peptide bond formation between alanine esters in aqueous solution. We describe how both reaction pathways, via a general base catalysis mechanism and via direct cleavage of the tetrahedral intermediate respectively, change with pH. This result contrasts with the conventional mechanism involving a single pathway in which only the barrier heights are affected by pH. We show that this new proposal involving two competing mechanisms is consistent with the experimental data, and we discuss the implications for peptide bond formation under prebiotic conditions and in the ribosome. Our work shows that integrating deep potential molecular dynamics with path sampling provides a powerful approach for exploring complex chemical mechanisms. | Rolf David; Iñaki Tuñón; Damien Laage | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f71d849138d23161a74a24/original/the-competing-reaction-mechanisms-of-peptide-bond-formation-in-water-revealed-by-deep-potential-molecular-dynamics-and-path-sampling.pdf |
60c7436d337d6c062be26bb4 | 10.26434/chemrxiv.8869406.v2 | Constructing Spin-Adiabatic States for the Modeling of Spin-Crossing Reactions I. A Shared-Orbital Implementation | In the modeling of spin-crossing reactions, it has become popular to directly explore the spin-adiabatic surfaces. Specifically, through constructing spin-adiabatic states from a two-state Hamiltonian (with spin-orbit coupling matrix elements) at each geometry, one can readily employ advanced geometry optimization algorithms to acquire a “transition state" structure, where the spin crossing occurs. In this work, we report the implementation of a fully variational spin-adiabatic approach based on Kohn-Sham density functional theory spin states (sharing the same set of molecular orbitals) and the Breit-Pauli one-electron spin-orbit operator. For three model spin-crossing reactions [predissociation of N2O, singlet-triplet conversion in CH2, and CO association to Fe(CO)4], the spin-crossing points were easily obtained. Our results also indicated the Breit-Pauli one-electron spin-orbit coupling can vary significantly along the reaction pathway on the spin-adiabatic energy surface. On the other hand, due to the restriction that low-spin and high-spin states share the same set of molecular orbitals, the acquired spin-adiabatic energy surface shows a cusp (i.e. a first-order discontinuity) at the crossing point, which prevents the use of standard geometry optimization algorithms to pinpoint the crossing point. An extension with this restriction removed is being developed to achieve the smoothness of spin-adiabatic surfaces. | Yunwen Tao; Zheng Pei; Nicole Bellonzi; Yuezhi Mao; zhu zou; Wanzhen Liang; Zhibo Yang; Yihan Shao | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7436d337d6c062be26bb4/original/constructing-spin-adiabatic-states-for-the-modeling-of-spin-crossing-reactions-i-a-shared-orbital-implementation.pdf |
62712a0e11b14625c739a1d5 | 10.26434/chemrxiv-2022-vmwn0 | Solvent Dependence on Cooperative Vibrational Strong Coupling and Cavity Catalysis | Strong light-matter coupling offers a unique way to control chemical reactions at the molecular level. Here, we try to compare the solvent effect on a solvolysis process under cooperative vibrational strong coupling (VSC). Two solvents, ethyl acetate and cyclopentanone are chosen to study cavity catalysis by coupling the C=O stretching band of the reactant and the solvent molecules to a Fabry-Perot cavity mode. Interestingly, both the solvent system catalyze the chemical reaction under cooperative VSC conditions. However, the resonance effect on catalysis is observed at different temperatures for the two solvent systems, which is further confirmed by thermodynamic studies. Cavity detuning and other control experiments suggest that cooperative VSC of the solvent plays a crucial role in modifying the transition state energy of the reaction. These findings, along with other observations, cement the concept of polaritonic chemistry. | Jaibir Singh; Jyoti Lather; Jino GEORGE | Physical Chemistry; Catalysis; Photocatalysis; Chemical Kinetics; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62712a0e11b14625c739a1d5/original/solvent-dependence-on-cooperative-vibrational-strong-coupling-and-cavity-catalysis.pdf |
60c74e639abda24bb5f8d622 | 10.26434/chemrxiv.12746609.v1 | Self-Organization of Alpha Helical Proteins in Bioinspired Membranes and Vesicles | <p><b>ABSTRACT</b></p><p>A fundamental understanding of protein-protein and protein-lipid interactions under various conditions can reveal the energy pathways in photosynthetic bacterial membranes. In this study, we examine the role of key factors such as bilayer curvature, the concentration, helical separation and hydrophobic mismatch of proteins on their self-organization in bilayers. We also develop an understanding of the physical factors underlying the aggregation of proteins. We determine the impact of bilayer curvature by comparing the aggregation of proteins in membranes and vesicles. We identify a threshold helical separation below which small, stable aggregates are observed. Large, unstable protein aggregates are observed above the threshold separation. We examine the effect of the deformations incurred by the proteins via their concentration, and show the aggregation of the proteins to arise from their deformation-induced displacement. We demonstrate the negative hydrophobic mismatch condition to favor a higher degree of protein aggregation. We adopt the Molecular Dynamics simulation technique along with a coarse-grained force field to capture the behavior spanning extensive spatiotemporal scales. Our results can guide experimental studies of bioinspired materials with structure-function properties mimicking those of photosynthetic bacterial membranes, or assist in understanding the organization of inclusions in polymeric matrices.</p> | Akash Banerjee; Zachary Finkel; Meenakshi Dutt | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e639abda24bb5f8d622/original/self-organization-of-alpha-helical-proteins-in-bioinspired-membranes-and-vesicles.pdf |
663bc28621291e5d1dc9eea6 | 10.26434/chemrxiv-2024-9dtb7 | Size Onset of Metallic Behavior in Neutral Aluminum Clusters | The excited state lifetimes of neutral (Al)n clusters up to ~1 nm in diameter in size, where n ≤ 43, are systematically measured with femtosecond time-resolved mass spectrometry. The onset of metallic behavior is identified as a distinct change in the relaxation behavior initiated with single ultraviolet (400 nm) photon excitation. The experimentally measured excited state lifetimes gradually decrease with size for small molecular scale clusters (n < 10) before becoming indistinguishable for larger clusters (n > 9), where the measurements are comparable to electron-lattice relaxation time of bulk Al (~300 fs). Particularly intense, or magic, Aln clusters do not exhibit any significant excited state lifetime behavior. Time-dependent density functional theory quantify the excited state properties and are presented to show that dynamics are strongly tied to the excited state charge carrier distributions and overlap, rather than detailed changes related to changes in the cluster’s electronic and geometric structure. The consistency in excited state lifetimes for clusters larger than n = 9 is attributed to the hybridization of the s- and p- orbitals as well as increasing delocalization. Al3 exhibits unique temporal delay in its transient behavior that is attributed to a transition from triangular ground state to linear structure upon excitation. | Chase Rottener; Carter Jarman; Shaun Sutton; Scott Sayres | Physical Chemistry; Nanoscience; Clusters; Photochemistry (Physical Chem.); Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663bc28621291e5d1dc9eea6/original/size-onset-of-metallic-behavior-in-neutral-aluminum-clusters.pdf |
62a307c6ae34b5f63b9831a4 | 10.26434/chemrxiv-2022-tvrt8 | Cationic Gold(II) Complexes: Experimental and Theoretical Study | Gold(II) complexes are rare and their application for catalysis of chemical transformations is unexplored. The reason is their easy oxidation or reduction to the more stable gold(III) or gold(I) complexes, respectively. We explored the thermodynamics of the formation of the [(L)AuIIX]+ complexes (L = ligand, X = halogen) from their gold(III) precursors and investigated the stability and the spectral properties in the IR and VIS range of the formed gold(II) complexes in the gas phase. The results show that the best ancillary ligands L for stabilizing gaseous [(L)AuIIX]+ complexes are bidentate and tridentate ligands with nitrogen donor atoms. The electronic structure and spectral properties of the investigated gold(II) complexes were correlated with the quantum chemical calculations. The results show that the molecular and electronic structure of the gold(II) complexes as well as their spectroscopic properties are very similar to the analogous stable copper(II) complexes. | Jaya Mehara; Adarsh Koovakattil Surendran; Teun van Wieringen; Deeksha Setia; Cina Foroutan-Nejad; Michal Straka; Lubomir Rulisek; Jana Roithova | Inorganic Chemistry; Bonding; Coordination Chemistry (Inorg.); Transition Metal Complexes (Inorg.) | CC BY 4.0 | CHEMRXIV | 2022-06-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a307c6ae34b5f63b9831a4/original/cationic-gold-ii-complexes-experimental-and-theoretical-study.pdf |
6415c6a32bfb3dc251f945a7 | 10.26434/chemrxiv-2023-jdn03 | Boosting Circularly Polarized Luminescence from Alkyl-Locked Axial Chirality Scaffold by Restriction of Molecular Motions | Boosting the circularly polarized luminescence of small organic molecules has been a stubborn challenge because of weak structure rigidity and dynamic molecular motions. To investigate and eliminate these factors, here, we carried out the struc-ture-property relationship studies on a newly-developed axial chiral scaffold of bidibenzo[b,d]furan. The molecular rigidity was finely tuned by gradually reducing the alkyl-chain length. The environmental factors were considered in solution, crystal, and polymer matrix at different temperatures. As a result, a significant amplification of the dissymmetry factor glum from 10-4 to 10-1 with a 146-fold magnification was achieved, corresponding to the situation from (R)-4C in solution to (R)-1C in polymer film at room temperature. A synergistic strategy of increasing the intramolecular rigidity and enhancing the inter-molecular interaction to restrict the molecular motions was thus proposed to improve circularly polarized luminescence. The though-out demonstrated relationship will be of great importance for the development of high-performance small organic chiroptical systems in the future. | Wenbin Huang; Kang Zhou; Engui Zhao; Zikai He | Physical Chemistry; Organic Chemistry; Materials Science; Organic Compounds and Functional Groups; Dyes and Chromophores; Optics | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6415c6a32bfb3dc251f945a7/original/boosting-circularly-polarized-luminescence-from-alkyl-locked-axial-chirality-scaffold-by-restriction-of-molecular-motions.pdf |
6164d107aa918dcf2927d962 | 10.26434/chemrxiv-2021-zvq4t | Development of an N-Terminal BRD4 Bromodomain-Targeted Degrader | Targeted protein degradation is a powerful induced-proximity tool to control cellular concentrations of native proteins using small molecules. However, the design of selectivity in protein degradation remains challenging. In the case of Bromodomain and Extra-Terminal (BET) family proteins, BRD4 has emerged as the primary therapeutic target over other family members BRD2, 3 and T, but strategies to selectively degrade BRD4 rely on the use of pan-BET inhibitors optimized for BRD4:E3 protein-ubiquitin ligase (E3) ternary complex formation. Here, we report a potent and selective inhibitor for the first bromodomain of BRD4, iBRD4-BD1 (IC50 = 12 nM, 23-6200-fold intra-BET selectivity). We further use this novel inhibitor to develop dBRD4-BD1 that induces selective degradation of BRD4 at a DC50 of 280 nM. The design of BRD4 selectivity up-front enables the study of BRD4 biology in the absence of wider BET-inhibition, simplifies design of future BRD4-selective degraders as new E3 recruiting ligands are discovered, and provides a tool to design additional heterobifunctional BRD4-selective probes. | Anand Divakaran; Huda Zahid; Wenwei Lin; Taosheng Chen; Dan Harki; william pomerantz | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6164d107aa918dcf2927d962/original/development-of-an-n-terminal-brd4-bromodomain-targeted-degrader.pdf |
60c74d85842e655304db34b6 | 10.26434/chemrxiv.12630539.v1 | A Combination of Ivermectin and Doxycycline Possibly Blocks the Viral Entry and Modulate the Innate Immune Response in COVID-19 Patients | <p></p><p>The current outbreak of the
corona virus disease 2019 (COVID-19), has affected almost entire world and
become pandemic now. Currently, there is neither any FDA approved drugs nor any
vaccines available to control it. Very recently in Bangladesh, a group of
doctors reported astounding success in treating patients suffering from
COVID-19 with two commonly used drugs, Ivermectin and Doxycycline. In the
current study we have explored the possible mechanism by which these drugs
might have worked for the positive response in the COVID-19 patients. To
explore the mechanism we have used molecular docking and molecular dynamics simulation
approach. Effectiveness of Ivermectin and doxycycline were evaluated against Main
Protease (Mpro), Spike (S) protein, Nucleocapsid (N), RNA-dependent RNA
polymerase (RdRp, NSP12), ADP Ribose Phosphatase (NSP3), Endoribonuclease
(NSP15) and methyltransferase (NSP10-NSP16 complex) of SARS-CoV-2 as well as human
angiotensin converting enzyme 2 (ACE2) receptor. Our study shows that both
Ivermectin and doxycycline have significantly bind with SARS-CoV-2 proteins but
Ivermectin was better binding than doxycycline. Ivermectin showed a perfect binding
site to the Spike-RBD and ACE2 interacting region indicating that it might be
interfering in the interaction of spike with ACE2 and preventing the viral entry
in to the host cells. Ivermectin also exhibited significant binding affinity
with different SARS-CoV-2 structural and non-structural proteins (NSPs) which
have diverse functions in virus life cycle. Significant binding of Ivermectin with
RdRp indicate its role in the inhibition of the viral replication and
ultimately impeding the multiplication of the virus. Ivermectin also possess
significant binding affinity with NSP3, NSP10, NSP15 and NSP16 which helps
virus in escaping from host immune system. Molecular dynamics simulation study
shows that binding of the Ivermectin with Mpro, Spike, NSP3, NSP16 and ACE2 was
quiet stable. Thus, our docking and simulation studies reveal that combination
of Ivermectin and doxycycline might be executing the effect by inhibition of viral
entry and enhance viral load clearance by targeting various viral functional
proteins.</p><p></p> | Dharmendra Kumar Maurya | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d85842e655304db34b6/original/a-combination-of-ivermectin-and-doxycycline-possibly-blocks-the-viral-entry-and-modulate-the-innate-immune-response-in-covid-19-patients.pdf |
63bbe84ba5c354823a8c1f54 | 10.26434/chemrxiv-2023-zddx7 | Optimization of General Molecular Properties in the Equilibrium Geometry Using Quantum Alchemy: An Inverse Molecular Design Approach | Inverse molecular design allows optimization of molecules in chemical space and is promising for accelerating the development of functional molecules and materials. To design realistic molecules, it is necessary to consider geometric stability during optimization. In this work, we introduce an inverse design method that optimizes molecular properties by changing the chemical composition in the equilibrium geometry. The optimization algorithm of our recently developed molecular design method has been modified to allow molecular design for general properties at a small computational cost. The proposed method is applicable to large chemical space based on quantum alchemy without empirical data. We demonstrate the applicability of the present method in the optimization of the electric dipole moment and atomization energy in chemical spaces for (BF, CO), (N2, CO), and BN-doped benzene derivatives. Moreover, we also investigate and discuss the applicability of quantum alchemy to the electric dipole moment. | Takafumi Shiraogawa; Jun-ya Hasegawa | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bbe84ba5c354823a8c1f54/original/optimization-of-general-molecular-properties-in-the-equilibrium-geometry-using-quantum-alchemy-an-inverse-molecular-design-approach.pdf |
65e19018e9ebbb4db9a32c62 | 10.26434/chemrxiv-2024-fqpp4 | How Surface Defects Shape the Excitons and Photoluminescence of Ultrasmall CdSe Quantum Dots | Ultrasmall CdSe quantum dots (QDs) with diameters up to 2 nm show broad photoluminescence (PL) spectra presumably due to emission from band-edge excitons and defect states. However, the origin of the defect emission and the effect of defects on the band-edge excitons is not fully understood. Based on spin-orbit density functional theory and screened configuration interaction singles and in comparison with previous PL measurements, we show that two different kinds of defects, Cd-dimer and Se defects, are likely to contribute to the defect PL. Further, we observe that these defects lead to a localization of the molecular orbitals (MOs) involved in the band-edge excitons creating large electric dipoles in the MOs. In the excitonic states, these dipoles cause multiexponential PL decay from the band-edge states with a highly anisotropic polarization of the emission. The polarization is found to be very sensitive with respect to the exact composition of the surface. | Torben Steenbock; Emilia Drescher; Tobias Dittmann; Gabriel Bester | Materials Science; Nanoscience; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e19018e9ebbb4db9a32c62/original/how-surface-defects-shape-the-excitons-and-photoluminescence-of-ultrasmall-cd-se-quantum-dots.pdf |
666c2ae8c9c6a5c07a762dc5 | 10.26434/chemrxiv-2024-mr7bz | On the Interplay Between Force, Temperature, and Electric Fields in the Rupture Process of Mechanophores | The use of oriented external electric fields (OEEFs) shows promise as an alternative method for catalyzing chemical reactions. The ability to target a specific bond by aligning it with a bond-weakening electric field may be beneficial in mechanochemical reactions, which use mechanical force to selectively rupture specific bonds. Previous computational studies have focused primarily on a static description of molecules in OEEFs, while the crucial influence of thermal oscillations on the stability of the molecules has been neglected. Here, we performed ab initio molecular dynamics (AIMD) simulations based on density functional theory (DFT) to investigate the behaviour of a model mechanophore under the simultaneous influence of thermal and electric field effects. We examine and compare the changes to the bond and its thermal oscillations in strong OEEFs at various temperatures, without and with mechanical stretching forces applied to the molecule. We show that the change in bond length caused by an electric field is largely independent of the temperature, both without and with applied mechanical force. The amplitude of the thermal oscillation increases with increasing field strength and with increasing temperature, but at low temperatures, the application of mechanical force leads to an additional increase in amplitude. Our research shows that methods for applying mechanical force and OEEFs can be safely combined and included in an AIMD simulation at both low and high temperatures, allowing researchers to computationally investigate mechanochemical reactions in realistic application scenarios. | Tarek Scheele; Tim Neudecker | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666c2ae8c9c6a5c07a762dc5/original/on-the-interplay-between-force-temperature-and-electric-fields-in-the-rupture-process-of-mechanophores.pdf |
672996b65a82cea2fa0eaf21 | 10.26434/chemrxiv-2024-857hp | An Oxidation-Resistant High Entropy Alloy for Aqueous Aluminum-Battery Chemistries | Aqueous Aluminum (Al)-metal batteries are impractical due to a passivating Al2O3 layer on Al-metal that impedes Al3+ diffusion. To overcome this challenge, an oxide interface that is thin enough to allow facile Al3+ transport, while also passivating the highly reactive Al-metal/water interface is needed. Here, we report an Al-based high entropy alloy that satisfies these conflicting requirements. First-principles calculations indicate that Al atoms in the solid-solution give up electrons to neighboring elements, thermodynamically suppressing the alloy’s tendency to oxidize. Besides this, we find that the alloy’s oxidation is kinetically sluggish compared to Al. Owing to these reasons, the alloy-water interface is permeable to Al3+ with a low overpotential that remains stable. Taking advantage of this, we demonstrate a high-performing aqueous Al – Selenium (Se) conversion chemistry battery. | Apurva Anjan; Adwitiya Rao; Rohit Manoj; Varad Mahajani; Kevin Bhimani; Xue Yao; Jonathan D. Poplwasky; Chandra Veer Singh; Nikhil Koratkar | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672996b65a82cea2fa0eaf21/original/an-oxidation-resistant-high-entropy-alloy-for-aqueous-aluminum-battery-chemistries.pdf |
60c74d61567dfe9460ec532a | 10.26434/chemrxiv.12605309.v1 | Homochirality Is Originated from Handedness of Helices | Homochirality is a common feature of amino acids and carbohydrates, whose origin is still unknown. For example, 19 of 20 natural amino acids are L-chiral but deoxyribose sugars in DNA are always D-chiral. Meanwhile, right-handed helices are ubiquitous in nature. Are these two phenomena intrinsically correlated? Here, we propose that homochirality of amino acids and nucleotide sugars is originated from the handedness of helices. We show that right-handed 3<sub>10-</sub>helix and alpha-helix favor the L-chiral form for amino acids, but for deoxyribose sugars right-handed helices prefer the D-chiral form instead. Our analyses unveil that there exist strong cooperativity effects dominated by electrostatic interactions. This work not only resolves the mystery of homochirality by providing a unified explanation for the origin of homochirality in proteins and DNA using helical secondary structures as the root cause, but also ratifies the Principle of Chirality Hierarchy, where chirality of a higher hierarchy dictates that of lower ones. Possible applications of the present work to asymmetric synthesis and macromolecular assembly are discussed. | Shubin Liu | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d61567dfe9460ec532a/original/homochirality-is-originated-from-handedness-of-helices.pdf |
670852dd51558a15efbbae16 | 10.26434/chemrxiv-2024-0djqt-v3 | The global threat from the irreversible accumulation of trifluoroacetic acid (TFA) | Trifluoroacetic acid (TFA) is a persistent and mobile substance that has been increasing in concentrations within diverse environmental media, including rain, soils, human serum, plants, plant-based foods, and drinking water. Currently, TFA concentrations are orders of magnitude higher than those of other per- and polyfluoroalkyl substances (PFAS). This accumulation is due to many PFAS having TFA as a transformation product, including several fluorinated gases (F-gases), pesticides, pharmaceuticals and industrial chemicals, in addition to direct release of industrially produced TFA. Due to TFA’s extreme persistence and ongoing emissions, concentrations are increasing irreversibly. What remains less clear is the thresholds where irreversible effects on local or global scales occur. There are indications from mammalian toxicity studies that TFA is toxic to reproduction and that it exhibits liver toxicity. Ecotoxicity data are scarce, with most data for aquatic systems; fewer data are available for terrestrial plants, where TFA bioaccumulates most readily. Collectively, these trends imply that TFA meets the criteria of a planetary boundary threat for novel entities because of increasing planetary-scale exposure, where potential, irreversible disruptive impacts on vital earth system processes could occur. The rational response to this is to instigate binding actions to reduce emissions of TFA and its many precursors. | Hans Peter H. Arp; Andrea Gredelj; Juliane Glüge; Martin Scheringer; Ian T. Cousins | Earth, Space, and Environmental Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670852dd51558a15efbbae16/original/the-global-threat-from-the-irreversible-accumulation-of-trifluoroacetic-acid-tfa.pdf |
60c7490df96a00403d287190 | 10.26434/chemrxiv.12017118.v1 | Synthesis and Spectral Properties of Gem-Dimethyl Chlorin Photosensitizers | Chlorins that bear a gem-dimethyl group, which attributes their resistance to oxidation, are of interest for applications in photomedicine. Herein, we present the synthesis and the photophysical properties of two geminal-dimethyl chlorins (dihydroporphyrins) and their free base counterparts that act as efficient singlet oxygen generators and thus exhibit potential for use in photodynamic therapy (PDT) as anticancer or antimicrobial agents upon further derivatization. A complete characterization of their spectral and photophysical properties is accompanied by density functional calculations (DFT) as well as time dependent (TD) DFT to investigate the features of the frontier molecular orbitals. To demonstrate the potential of these compounds, standard palladium mediated reaction yielded a porphyrin-chlorin dyad in moderate yield. | zoi melissari; harry sample; Brendan Twamley; René M. Williams; Mathias O.. Senge | Bioorganic Chemistry; Photochemistry (Org.); Physical Organic Chemistry; Drug Discovery and Drug Delivery Systems; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.); Crystallography; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7490df96a00403d287190/original/synthesis-and-spectral-properties-of-gem-dimethyl-chlorin-photosensitizers.pdf |
61fba470eb6d16a3b1e87c21 | 10.26434/chemrxiv-2022-c5xgb | Accurate, Affordable, and Generalisable Machine Learning Simulations of Transition Metal X-ray Absorption Spectra using the XANESNET Deep Neural Network | The affordable, accurate, and reliable prediction of spectroscopic observables plays a key role in the analysis of increasingly-complex experiments. In this Article, we develop and deploy a deep neural network (DNN) – XANESNET – for predicting the lineshape of first-row transition metal K-edge X-ray absorption near-edge structure (XANES) spectra. XANESNET predicts the spectral intensities using only information about the local coordination geometry ofthe transition metal complexes encoded in a feature vector of weighted atom-centred symmetry functions (wACSF). We address in detail the calibration of the feature vector for the particularities of the problem at hand, and we explore the individual feature importances to reveal the physical insight that XANESNET obtains at the Fe K-edge. XANESNET relies on only a few judiciously-selected features – radial information on the first and second coordination shells suffices, along with angular information sufficient to separate satisfactorily key coordination geometries. The feature importance is found to reflect the XANES spectral window under consideration and is consistent with the expected underlying physics. We subsequently apply XANESNET at nine first-row transition metal (Ti–Zn) K-edges. It can be optimised in as little as a minute, predicts instantaneously, and provides K-edge XANES spectra with an average accuracy of ca. ± 2–4% in which the positions of prominent peaks are matched with a > 90% hit rate to sub-eV (ca.0.8 eV) error. | Conor Rankine; Thomas Penfold | Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry; Theory - Computational; Machine Learning; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2022-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61fba470eb6d16a3b1e87c21/original/accurate-affordable-and-generalisable-machine-learning-simulations-of-transition-metal-x-ray-absorption-spectra-using-the-xanesnet-deep-neural-network.pdf |
66badffdc9c6a5c07a0eed93 | 10.26434/chemrxiv-2024-4nm88-v2 | Chemoproteomics-Enabled De Novo Discovery of Metallothionein Degraders Facilitates Probing Its Role in Cancer | Proteolysis targeting chimeras (PROTACs) represent powerful tools to modulate the activity of classically “undruggable” proteins, but their application has been limited to known ligands and a few select protein classes. Herein, we present our chemoproteomic strategy for de novo discovery of PROTAC degraders. Using comparative PROTAC versus ligand global proteomics analyses, we rapidly identify proteins selectively downregulated by “untargeted” PROTAC probes containing an E3 ligase recruiter and various cysteine-reactive protein-of-interest (POI) ligands. In this manuscript, we showcase our approach by identifying a first-in-class acrylamide- and VHL-based PROTAC for metallothionein 2A (MT2A) – a small, cysteine-rich, metal-binding protein implicated in heavy metal detoxification, zinc homeostasis, and cellular metastasis. Notably, isoform-specific MT overexpression has been shown to augment cellular migration and invasion across several cancer cell lines, though precise mechanisms are unknown due to insufficient tools to study MTs. We show that optimized PROTAC AA-BR-157 covalently binds conserved C44, degrades overexpressed MT2A with nanomolar potency, and reduces migration and invasion of triple negative breast cancer MDA-MB-231 cells. We further demonstrate a time-dependent increase in intracellular zinc levels following MT2A degradation as well as downregulation of protein diaphanous homolog 3 (DIAPH3), a positive regulator of actin and cell motility. Super-resolution imaging of MDA-MB-231 cells shows that downregulation of MT2A and DIAPH3 inhibits cell polarization and thereby migration, suggesting that MT2A regulates motility via DIAPH3-dependent cytoskeletal remodeling. In summary, our strategy enables the discovery of PROTACs for novel disease-related targets and lays the groundwork for expansion of the druggable proteome. | Brittney Racioppo; Dany Pechalrieu; Daniel Abegg; Brendan Dwyer; Neal Ramseier; Ying Hu; Alexander Adibekian | Biological and Medicinal Chemistry; Analytical Chemistry; Mass Spectrometry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66badffdc9c6a5c07a0eed93/original/chemoproteomics-enabled-de-novo-discovery-of-metallothionein-degraders-facilitates-probing-its-role-in-cancer.pdf |
6450d3736ee8e6b5ed74631e | 10.26434/chemrxiv-2023-q988s | Model-based evaluation of piston reactor to produce hydrogen from methane via catalytic SMR and ATR routes
| Piston reactor technology can enable process intensification for electrical and mechanical power conversion to chemical products. Previous work has investigated hydrogen production via partial oxidation of methane (POM) in piston reactors; however, other routes remain unexplored. This work aims to theoretically evaluate if catalytic steam methane reforming (SMR) and methane autothermal reforming (ATR) constitute promising routes for hydrogen production using piston reactor technology for typical parameters and conditions encountered in automotive internal combustion engines (ICE). Specifically, the aim is to use reactor modeling and consider process design aspects in the early stages of investigation to provide direction and justify the next research and development stages involving experimentation, while eliminating infeasible options from the further expensive analysis. The piston reactor is first modeled using a zero-dimensional thermodynamic single-zone piston model coupled with available steady-state kinetic models for these routes. This model-based analysis shows that the highly endothermic SMR reaction is not feasible at ICE conditions, leading to its elimination from further assessments and studies. Thermal coupling of an endothermic reaction with a side-exothermic reaction is a potential solution to drive thermodynamically limited endothermic reaction routes in the piston reactor. The reactor modeling revealed that operation become feasible by coupling SMR with POM in ATR-type scenarios and achieves process intensification compared to steady-state ATR reactors through a significantly higher hydrogen production per catalyst (287-fold increase) and similar methane conversion between 89% and 97% at significantly lowered intake feed temperature (reduced by 283 K). The implementation of ATR piston reactors into grey and blue hydrogen production process designs is explored to understand overall performance and economy of scale effects. The process design studies reveal that the piston reactor-based processes offer savings of approx. 20% in hydrogen production costs compared to conventional ATR processes considering identical plant sizes and natural gas prices. The hydrogen production study highlights the value of the implemented approach for quickly identifying promising directions for further detailed experimental and modeling studies during early-stage exploration. | Aya Abousrafa; Mary Katebah; Patrick Linke; Mamoun Al-Rawashdeh; Timothy Jacobs | Chemical Engineering and Industrial Chemistry; Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6450d3736ee8e6b5ed74631e/original/model-based-evaluation-of-piston-reactor-to-produce-hydrogen-from-methane-via-catalytic-smr-and-atr-routes.pdf |
60c74b93337d6c7a45e27ad3 | 10.26434/chemrxiv.12355526.v1 | Surface-Only Spectroscopy for Diffusion-Limited Systems Using Ultra-Low Temperature DNP MAS NMR at 16.4 T | Conventional dynamic-nuclear-polarization (DNP) technique at T ~100 K can enhance sensitivity of magic-angle spinning (MAS) NMR over 100-fold for standard samples containing urea/proline at high-field conditions, B0= 9.4–16.4 T. In the scene of real applications, however, the achievable enhancement is often much lower than for urea/proline due to faster 1H relaxation (T1H) promoted by molecular-segmental fluctuations and methyl-group rotations active even at low temperatures, hindering an efficient polarization diffusion within the system. Here, we show at 16.4 T that ultra-low temperature (T≪100 K) provides a general way to improve the DNP efficiency for such diffusion-limited systems as we demonstrate on microcrystalline sample of a tripeptide N-f-MLF-OH. In a further step, the hyperpolarization localized at the crystal surface enabled “surface-only” spectroscopy eliminating background signals from the crystal core. The surface-only data, rather than the currently popular surface-enhanced data, should prove to be useful in many applications in biological and material sciences. | Yoh Matsuki; Tomoaki Sugishita; Toshimichi Fujiwara | Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b93337d6c7a45e27ad3/original/surface-only-spectroscopy-for-diffusion-limited-systems-using-ultra-low-temperature-dnp-mas-nmr-at-16-4-t.pdf |
60c752599abda2e855f8ddd2 | 10.26434/chemrxiv.13286723.v1 | Resolving the Equal Number Density Puzzle: Molecular Picture from Simulations of LiCl(aq) and NaCl(aq) | The change in number densities of aqueous solutions of alkali chlorides should be qualitatively predictable. Typically, as cations get bigger the number density of the solution decreases. However, aqueous solutions of lithium and sodium chloride exhibit at ambient conditions practically identical number densities at equal molalities despite different ionic sizes. Here, we provide an atomistic interpretation of this experimentally observed anomalous behavior using molecular dynamics simulations. The obtained results show that rigidity of the Li<sup>+</sup> first and second solvation shells and associated compromised hydrogen bonding result in practically equal average water densities in the local hydration regions for Li+ and Na+ despite different sizes of the cations. In addition, in more distant regions from the cations, the water densities of these two solutions also coincide. These findings thus provide an atomistic interpretation for matching number densities of LiCl and NaCl solutions. In contrast, the number density differences between NaCl and KCl solutions, as well as between LiCl and KCl solutions behave in a regular fashion with lower number densities of solutions observed for larger cations. | Man Nguyen Thi Hong; Ondrej Tichacek; Hector Martinez-Seara; Philip E. Mason; Pavel Jungwirth | Solvates; Computational Chemistry and Modeling; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752599abda2e855f8ddd2/original/resolving-the-equal-number-density-puzzle-molecular-picture-from-simulations-of-li-cl-aq-and-na-cl-aq.pdf |
60c73eda469df44911f4296c | 10.26434/chemrxiv.7137827.v1 | A Simple and Practical Method for Incorporating Augmented Reality into the Classroom and Laboratory | This manuscript provides two demonstrations of how Augmented Reality (AR), which is the projection of virtual information onto a real-world object, can be applied in the classroom and in the laboratory. Using only a smart phone and the free HP Reveal app, content rich AR notecards were prepared. The physical notecards are based on Organic Chemistry I reactions and show only a reagent and substrate. Upon interacting with the HP Reveal app, an AR video projection shows the product of the reaction as well as a real-time, hand-drawn curved-arrow mechanism of how the product is formed. Thirty AR notecards based on common Organic Chemistry I reactions and mechanisms are provided in the Supporting Information and are available for widespread use. In addition, the HP Reveal app was used to create AR video projections onto laboratory instrumentation so that a virtual expert can guide the user during the equipment setup and operation. | Kyle Plunkett | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73eda469df44911f4296c/original/a-simple-and-practical-method-for-incorporating-augmented-reality-into-the-classroom-and-laboratory.pdf |
60c75401567dfe9598ec5fec | 10.26434/chemrxiv.13262681.v2 | Excited State Dynamics of 7-Deazaguanosine and Guanosine 5’ Monophosphate | <p>Minor
structural modifications to the DNA and RNA nucleobases have a significant
effect on their excited state dynamics and electronic relaxation pathways.<b> </b>In this study, the excited state
dynamics of 7-deazaguanosine and guanosine 5’-monophosphate are investigated in
aqueous and in a mixture of methanol and water using femtosecond broadband
transient absorption spectroscopy following excitation at 267 nm. The transient
spectra are collected using photon densities that ensure no parasitic
multiphoton-induced signal from solvated electrons. The data can be fit satisfactorily
using a two- or three-component kinetic model. By analyzing the results from
steady-state, time-resolved, computational calculations, and the methanol-water
mixture, the following general relaxation mechanism is proposed for both
molecules, L<sub>b</sub> ®
L<sub>a</sub> ®
<sup>1</sup>ps*(ICT) ®
S<sub>0</sub>, where the <sup>1</sup>ps*(ICT) stands for an intramolecular charge transfer excited
singlet state with significant ps*
character. In general, longer lifetimes for internal conversion are obtained
for 7-deazaguanosine compared to guanosine 5’-monophosphate. Internal
conversion of the <sup>1</sup>ps*(ICT)
state to the ground state occurs on a similar time scale of a few picoseconds
in both molecules. Collectively, the results demonstrate that substitution of a
single nitrogen for a methine (C-H) group at position seven of the guanine
moiety stabilizes the <sup>1</sup>pp* L<sub>b</sub> and L<sub>a</sub> states and alter the
topology of their potential energy surfaces in such a way that the relaxation
dynamics in 7-deazaguanosine are slowed down compared to those in guanosine
5’-monophosphate but not for the internal conversion of <sup>1</sup>ps*(ICT) state to the ground state.</p> | Sarah E. Krul; Sean J. Hoehn; Karl Feierabend; Carlos Crespo-Hernández | Biophysical Chemistry; Photochemistry (Physical Chem.); Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75401567dfe9598ec5fec/original/excited-state-dynamics-of-7-deazaguanosine-and-guanosine-5-monophosphate.pdf |
674e132b7be152b1d0b67c91 | 10.26434/chemrxiv-2024-rnh83 | Ammonia Adsorption at High Temperature and Pressure using Sodium Containing Aluminosilicates: Selectivity over Nitrogen and Multicycle Working Capacities | Separating NH3 from N2 and H2 using adsorption onto porous materials at elevated pressures and temperatures has been proposed as a promising alternative to optimize the Haber-Bosch (HB) synthesis process. However, experimental data on NH3 adsorption at high pressure are scarce and necessary to properly evaluate NH3 adsorption as a possible and viable separation option. Using commercial Na-LTA, Na-X, and Na-Y zeolites (Si/Al 1.00, 1.26, 2.79, respectively), we evaluated the NH3 equilibrium adsorption up to 15 bar and temperatures of 323, 373, 423, and 473 K. N2 adsorption isotherms were measured at 323 and 473 K. All the zeolite samples were activated at 673 K to ensure complete dehydration. At 36 bar total pressure and 473 K, ideal adsorbed solution theory (IAST) predicts selectivity for NH3 over N2 of 265, 234, and 211 for Na-LTA, Na-X, and Na-Y, respectively. Separation factors based on IAST and kinetic selectivity are estimated as 128, 39, and 46, respectively. The enhanced selectivity of Na-LTA is attributed to diffusion limitations for N2 stemming from its narrower pore size. NH3 working capacities through 5-cycle PSA tests at 473 K directly correlate with the Si/Al ratio, with Na-Y zeolite achieving the highest working capacity at 2.50 mmol cm-3. However, VSA tests with desorption via dynamic vacuum for 10 min yielded a working capacity of up to 8.83 mmol cm-3 for Na-X. Gibbs ensemble Monte Carlo simulations are carried out to investigate the adsorption of NH3, N2, and their mixture in Na-LTA. Analysis of the simulation trajectories indicates that the NH3 molecules bind strongly to the Na+ cations and displace nitrogen in mixtures. | Cristian Aristizabal-Gonzalez; Juan Carlos Munoz-Senmache; Prerna Prerna; J. Ilja Siepmann; Michael Tsapatsis; Arturo Hernandez-Maldonado | Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Thermodynamics (Chem. Eng.); Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674e132b7be152b1d0b67c91/original/ammonia-adsorption-at-high-temperature-and-pressure-using-sodium-containing-aluminosilicates-selectivity-over-nitrogen-and-multicycle-working-capacities.pdf |
60c7491cbb8c1aecee3dadbf | 10.26434/chemrxiv.12015651.v1 | Iron Catalyzed Formal [3+2] Cycloaddition of Tetrahydroisoquinoline Affording Amide-bearing Dihydropyrrolo[2,1-a]isoquinolines | <p>We have developed an iron(III) chloride hexahydrate catalyzed formal [3+2] cycloaddition of tetrahydroisoquinolines with amide group-bearing Morita-Baylis-Hillman (MBH) carbonates. A range of highly functionalized dihydropyrrolo[2,1-<i>a</i>]isoquinolines could be prepared through SN2’/oxidation/ electrocyclization/aromatization cascade (32-62% yield).</p><p><br /></p> | Si-Wei Liu; Dan-Dan Ma; Xin-Xin Zhu; Cheng-Dan Luo; Hui-Lin Tan; Xiao-Li Ju; Xue Tan; Xiao-Hui Tang; Jie Huang; Jia Wang; Xian-Xun Wang; Hai-Lei Cui | Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2020-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7491cbb8c1aecee3dadbf/original/iron-catalyzed-formal-3-2-cycloaddition-of-tetrahydroisoquinoline-affording-amide-bearing-dihydropyrrolo-2-1-a-isoquinolines.pdf |
6528d31045aaa5fdbbe85421 | 10.26434/chemrxiv-2023-v2tx2-v2 | Polyelectrolyte Complex Hydrogel Scaffoldings
Enable Extrusion-based 3D Bioprinting of Low-Viscosity Bioinks | We generate self-assembled biocompatible scaffolds with excellent structural integrity based on complex-forming block polyelectrolytes that enable extrusion-based 3D bioprinting of large constructs from low-viscosity bioinks. Despite remarkable progress of biofabrication techniques in tissue engineering, the development of extrudable bioinks that perform optimally at physiological temperatures remains a major challenge. Most biopolymer and photocurable precursor solutions exhibit low viscosities at 37 °C, resulting in undesirable flows and loss of form prior to chemical crosslinking. Temperature-sensitive bioinks, such as gelatin methacryloyl (GelMA), can be deposited near their gelling point, but suffer from suboptimal temperature-induced pre-gelation, poor cell viability emerging from long holding times in the cooled cartridges, inefficient temperature transfer from the print bed, and discontinuous layer-by-layer fabrication. Here, we demonstrate that block polyelectrolyte additives serve as effective viscosity enhancers when added to non-extrudable precursor solutions. Rapid, electrostatic self-assembly of block polyelectrolytes into either jammed micelles or interconnected networks provides hydrogel scaffoldings that form nearly instantly, lend initial structural robustness upon deposition, and enhance shear and tensile strength of the cured bioinks. Moreover, our approach enables continuous extrusion without the need of chemical crosslinking between individual layers, paving the way for fast biomanufacturing of human-scale tissue constructs with improved inter-layer bonding. | Tobias Gockler; Defu Li; Alisa Grimm; Felix Mecklenburg; Michael Grün; Ute Schepers; Samanvaya Srivastava | Materials Science; Polymer Science; Biopolymers; Hydrogels; Polyelectrolytes - Polymers; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6528d31045aaa5fdbbe85421/original/polyelectrolyte-complex-hydrogel-scaffoldings-enable-extrusion-based-3d-bioprinting-of-low-viscosity-bioinks.pdf |
621d31c257a9d25c436ea885 | 10.26434/chemrxiv-2022-08jm9-v2 | Machine learned calibrations to high-throughput molecular excited state calculations | Understanding the excited state properties of molecules provides insights into how they interact with light. These interactions can be exploited to design compounds for photochemical applications, including enhanced spectral conversion of light to increase the efficiency of photovoltaic cells. While chemical discovery is time- and resource-intensive experimentally, computational chemistry can be used to screen large-scale databases for molecules of interest in a procedure known as high-throughput virtual screening. The first step usually involves a high-speed but low-accuracy method to screen large numbers of molecules (potentially millions) so only the best candidates are evaluated with expensive methods. However, use of a coarse first-pass screening method can potentially result in high false positive or false negative rates. Therefore, this study uses machine learning to calibrate a high-throughput technique (xTB-sTDA) against a higher accuracy one (TD-DFT). Testing the calibration model shows a ~6-fold decrease in error in-domain and a ~3-fold decrease out-of-domain. The resulting mean absolute error of ~0.14 eV is in line with previous work in machine learning calibrations and out-performs previous work in linear calibration of xTB-sTDA. We then apply the calibration model to screen a 250k molecule database and map inaccuracies of xTB-sTDA in chemical space. We also show generalizability of the workflow by calibrating against a higher-level technique (CC2), yielding a similarly low error. Overall, this work demonstrates machine learning can be used to develop a both cheap and accurate method for large-scale excited state screening, enabling accelerated molecular discovery across a variety of disciplines. | Shomik Verma; Miguel Rivera; David O. Scanlon; Aron Walsh | Theoretical and Computational Chemistry; Materials Science; Energy; Dyes and Chromophores; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2022-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621d31c257a9d25c436ea885/original/machine-learned-calibrations-to-high-throughput-molecular-excited-state-calculations.pdf |
673b94d9f9980725cfa1abbf | 10.26434/chemrxiv-2024-qfbz7 | Exploring the interaction of key factors in Collaborative problem-solving: Evidence from German and Chinese Students | As a key part of 21st-century skills, collaborative problem-solving (CPS) skills have been recognized as critical to both academic achievement and professional success. This paper explores the multifaceted influences on CPS skills among ninth-grade students in Germany and tenth-grade students in China within the context of chemistry education. Methodologically, a chemical assessment tool, CPS-C, was developed based on the CPS framework of PISA 2015, and various factors including cognitive ability, prior knowledge, motivation, mental load, stress, and CPS were measured. Results revealed significant differences between German and Chinese students across these factors, highlighting cultural and educational difference. Structural equation modeling (SEM) analysis demonstrated the intricate relationships between these factors and CPS performance, underscoring the importance of prior knowledge, cognitive ability, and motivation in enhancing CPS skills while revealing the detrimental effects of stress on performance. Additionally, CPS skills in chemistry exhibited positive correlations with academic performance in Biology, Physics, and Mathematics, indicating the transferability of CPS skills across disciplines. Overall, this study contributes to our understanding of CPS in diverse cultural and educational contexts, offering insights for educators and policymakers to design effective instructional strategies for fostering CPS skills in chemistry education. | Yike Ying; Ruediger Tiemann | Chemical Education | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673b94d9f9980725cfa1abbf/original/exploring-the-interaction-of-key-factors-in-collaborative-problem-solving-evidence-from-german-and-chinese-students.pdf |
60c753d3bdbb896669a3a515 | 10.26434/chemrxiv.13554677.v1 | LignoPhot: Photoactive Hybrid lignin/Bi4O5Br2/BiOBr Composite for Complex Pollutants Removal | Valorization of lignin is still an open question and lignin has therefore remained an underutilized biomaterial. This situation is even more pronounced for hydrolysis lignin, which is characterized by a highly condensed and excessively cross-linked structure. We report on photoactive lignin/Bi<sub>4</sub>O<sub>5</sub>Br<sub>2</sub>/BiOBr bio-inorganic composites consisting of a lignin substrate that is coated by Bi<sub>4</sub>O<sub>5</sub>Br<sub>2</sub>/BiOBr nanosheet photocatalysts. The structure of the hybrid material was investigated by means of X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), transmission electron microscopy including energy dispersive X-ray (EDX) spectroscopy, and solid state <sup>1</sup>H−<sup>13</sup>C nuclear magnetic resonance spectroscopy (<sup>1</sup>H−<sup>13</sup>C NMR). The material contains 18.9% of Bi<sub>4</sub>O<sub>5</sub>Br<sub>2</sub>/BiOBr and was found to be effective for the photocatalytic degradation of cationic methylene blue (MB) and zwitterionic rhodamine B (RhB) dyes under irradiation with 405 nm light. Lignin/Bi<sub>4</sub>O<sub>5</sub>Br<sub>2</sub>/BiOBr was able to decrease the dye concentration from 80 mg·L<sup>–1</sup> to 12.3 mg·L<sup>–1</sup> for RhB (85%) and from 80 mg·L<sup>–1</sup> to 4.4 mg·L<sup>–1</sup> for MB (95%). Complementary to the dye degradation, the lignin as a main component of the composite, was found to be efficient and rapid biosorbent for metal ions in aqueous solutions. The highest adsorption capacity was found after 2 hours of phases contact and reached 0.45 mmol·g<sup>–1 </sup>for Ni(II) ions (neutral media). The low cost, simplicity of the synthesis, good stability and ability to simultaneously photooxidize organic dyes and to adsorb metal ions, make the developed photoactive lignin/Bi<sub>4</sub>O<sub>5</sub>Br<sub>2</sub>/BiOBr composite a prospective material for textile wastewaters remediation | Tetyana Budnyak; Joy Onwumere; Ievgen V. Pylypchuk; Aleksander Jaworski; Jianhong Chen; Anna Rokicińska; Mikael E. Lindström; Piotr Kustrowski; olena Sevastyanova; Adam Slabon | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753d3bdbb896669a3a515/original/ligno-phot-photoactive-hybrid-lignin-bi4o5br2-bi-o-br-composite-for-complex-pollutants-removal.pdf |
61004dd50321149eb0b83f12 | 10.26434/chemrxiv-2021-h5451-v2 | The zwitterion isomer of orthosilicic acid and its role in neutral pH dimerization from density functional theory. | Using density functional theory, the plausible existence of the zwitterion isomer of orthosilicic acid is proposed to account for some of the properties of silica in water. Explicit hydration and explicit addition of salt are used in modeling the zwitterion and the dimerization reaction. Paths between orthosilicic acid, the zwitterion and the autoionization products are presented. The pK for the formation of the aqueous zwitterion species is calculated to be 7.78 in dilute silica solutions and the activation energy for the dimerization reaction ranges from 59.8 kJ/mol to 70.7 kJ/mol depending on salt concentration. | Mihali Felipe | Theoretical and Computational Chemistry; Earth, Space, and Environmental Chemistry; Geochemistry; Hydrology and Water Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61004dd50321149eb0b83f12/original/the-zwitterion-isomer-of-orthosilicic-acid-and-its-role-in-neutral-p-h-dimerization-from-density-functional-theory.pdf |
65d4e2e7e9ebbb4db9ce0051 | 10.26434/chemrxiv-2024-685qb | Aquamarine: Quantum-Mechanical Exploration of Conformers and Solvent Effects in Large Drug-like Molecules | We here introduce the Aquamarine (AQM) dataset, an extensive quantum-mechanical (QM) dataset that contains the structural and electronic information of 59,783 low-and high-energy conformers of 1,653 molecules with a total number of atoms ranging from 2 to 92 (mean:50.9), and containing up to 54 (mean:28.2) non-hydrogen atoms. To gain insights into the solvent effects as well as collective dispersion interactions for drug-like molecules, we have performed QM calculations supplemented with a treatment of many-body dispersion (MBD) interactions of structures and properties in the gas phase and implicit water. Thus, AQM contains over 40 global (molecular) and local (atom-in-a-molecule) physicochemical properties (including ground-state and response properties) per conformer computed at the tightly converged PBE0+MBD level of theory for gas-phase molecules, whereas PBE0+MBD with the modified Poisson-Boltzmann (MPB) model of water was used for solvated molecules. By addressing both molecule-solvent and dispersion interactions, AQM dataset can serve as a challenging benchmark for state-of-the-art machine learning methods for property modeling and \textit{de novo} generation of large (solvated) molecules with pharmaceutical and biological relevance. | Leonardo Rafael Medrano Sandonas; Dries Van Rompaey; Alessio Fallani; Mathias Hilfiker; David Hahn; Laura Perez-Benito; Jonas Verhoeven; Gary Tresadern; Joerg Kurt Wegner; Hugo Ceulemans; Alexandre Tkatchenko | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Machine Learning; Physical and Chemical Properties | CC BY 4.0 | CHEMRXIV | 2024-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d4e2e7e9ebbb4db9ce0051/original/aquamarine-quantum-mechanical-exploration-of-conformers-and-solvent-effects-in-large-drug-like-molecules.pdf |
64c40896ce23211b20b7771f | 10.26434/chemrxiv-2023-vdtk0 | Comparing the Structures and Photophysical Properties of Two Charge Transfer Co-crystals | In the search for molecular materials for next-generation optoelectronic devices, organic co-crystals have emerged as a promising class of semiconductors for their unique photophysical properties. This paper presents a joint experimental-theoretical study of ground and excited state charge transfer (CT) interactions in two CT co-crystals. Reported herein is a novel CT co-crystal Npe:TCNQ, formed from 4-(1-naphthylvinyl) pyridine (Npe) and 7,7,8,8-tetracyanoquinodimethane (TCNQ) molecules via molecular self-assembly. The electronic structure and photophysical properties of Npe:TCNQ are compared with those of the co-crystal composed of Npe and 1,2,4,5-tetracyanobenzene (TCNB) molecules, Npe:TCNB, reported here with a higher-symmetry (monoclinic) crystal structure than previously published. Npe:TCNB and Npe:TCNQ dimer clusters are used as theoretical model systems for the co-crystals and their electronic structure is compared to that of the extended solids via periodic boundary conditions density functional theory (PBC DFT). UV-Vis absorption spectra of the dimers are computed with time-dependent density functional theory (TD-DFT) and compared to experimental UV-Vis diffuse reflectance spectra. Both Npe:TCNB and Npe:TCNQ are found to exhibit neutral character in the S0 state and ionic character in the S1 state. The degree of CT in the S0 state of Npe:TCNB is found to be slightly smaller than that of Npe:TCNQ, as predicted from differences in electron affinities of the acceptors. Furthermore, the degree of CT in the S1 state of Npe:TCNB is found to be slightly higher than that of Npe:TCNQ, aligning with predictions employing a recently developed orbital similarity metric. | Laura McCaslin; Ali Abou Taka; Joseph E. Reynolds III; Neil C. Cole-Filipiak; Mohana Shivanna; Christine J. Yu; Patrick Feng; Mark D. Allendorf; Krupa Ramasesha; Vitalie Stavila | Physical Chemistry; Materials Science; Optical Materials; Photochemistry (Physical Chem.); Materials Chemistry; Crystallography | CC BY 4.0 | CHEMRXIV | 2023-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c40896ce23211b20b7771f/original/comparing-the-structures-and-photophysical-properties-of-two-charge-transfer-co-crystals.pdf |
65bf7a3b66c1381729f07b2c | 10.26434/chemrxiv-2023-xdj5w-v4 | Boosting the biodegradation and bioactivity of PBS-DLS copolymers via incorporation of PEG | Biodegradable polymers play a crucial role in the development of materials for biomedical applications. This study investigates the enzymatic biodegradation, bioactivity, and cytotoxicity of poly(butylene succinate-dilinoleic succinate) (PBS-DLS) copolymers modified with poly(ethylene glycol) (PEG). Two copolymer variations with different segmental compositions (70 wt% and 60 wt% of hard segments) were synthesized. After modifying the copolymers with PEG, the presence of a lipase catalyst accelerated degradation after 20 days, evidenced by reduced residual content. Gel permeation chromatography analysis showed up to 40% decrease in molecular weight, while gravimetric analysis indicated a mass loss of up to 10% during enzymatic degradation. Morphological examination revealed that the enzymatic breakdown, facilitated by hydrolase activity (boosted by the presence of PEG), resulted in surface erosion, holes, cracks and changes in spherulitic morphology. It highlights the tunable degradation pathways of these copolymers. Bioactivity studies demonstrated the formation of biomimetic calcium/phosphate (Ca/P) crystals, with varying stoichiometry based on segmental composition. Copolymers with higher crystallinity (70 wt% hard segments) favored tricalcium phosphate-like crystal formation, while those with lower crystallinity (60 wt% hard segments) were more susceptible to hydroxyapatite precipitation. In vitro cytotoxicity tests using mice fibroblasts exhibited excellent cell viability and attachment for all copolymers. These findings highlight the significance of these copolymers in developing biodegradable materials for medical applications. The ability to control degradation through PEG modification, along with their bioactivity and cell compatibility, positions them as promising candidates for diverse biomedical applications. | Moein Zarei; Beata Michalkiewicz; Miroslawa El Fray | Materials Science; Polymer Science; Biocompatible Materials; Biodegradable Materials; Materials Processing | CC BY 4.0 | CHEMRXIV | 2024-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bf7a3b66c1381729f07b2c/original/boosting-the-biodegradation-and-bioactivity-of-pbs-dls-copolymers-via-incorporation-of-peg.pdf |
6290a441f89e5df2a0e7cc4a | 10.26434/chemrxiv-2022-26s1t-v3 | Advances in nano- and microscale NMR spectroscopy using diamond quantum sensors | Quantum technologies have seen a rapid developmental surge over the last couple of years. Though often overshadowed by quantum computation, quantum sensors show tremendous potential for widespread applications in chemistry and biology. One system stands out in particular: the nitrogen-vacancy (NV) center in diamond, an atomic-sized sensor allowing the detection of nuclear magnetic resonance (NMR) signals at unprecedented length scales down to a single proton. In this article, we review the fundamentals of NV center-based quantum sensing and its distinct impact on nano- to microscale NMR spectroscopy. Furthermore, we highlight and discuss possible future applications of this novel technology ranging from energy research, material science, or single-cell biology, but also associated challenges of these rapidly developing NMR sensors. | Robin D. Allert; Karl D. Briegel; Dominik B. Bucher | Physical Chemistry; Optics; Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2022-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6290a441f89e5df2a0e7cc4a/original/advances-in-nano-and-microscale-nmr-spectroscopy-using-diamond-quantum-sensors.pdf |
60c757aa337d6c175fe29068 | 10.26434/chemrxiv.14438861.v1 | Identification of the FDA-Approved Drug Pyrvinium as a Novel Inhibitor of PD-1/PD-L1 Interaction | <p>Immune checkpoint blockade involving inhibition of the PD-1/PD-L1 interaction has provided unprecedented clinical benefits in treating a variety of tumors. To date, a total of six antibodies that bind to either PD-1 or PD-L1 protein and in turn inhibit the PD-1/PD-L1 interaction have received clinical approvals. Despite being highly effective, these expensive large biotherapeutics possess several inherent pharmacokinetic limitations that can be successfully overcome through the use of low-molecular-weight inhibitors. One such promising approach involves small-molecule induced dimerization and sequestration of PD-L1, leading to effective PD-1/PD-L1 inhibition. Herein, we present discovery of such potential bioactive PD-L1 dimerizers through a structure- and ligand-based screening of a focused library of approved and investigational drugs worldwide. The most promising compound Pyrvinium, an FDA-approved anthelmintic drug, showed IC<sub>50</sub> value of ~29.66 µM. It is noteworthy that Pyrvinium, being an approved drug, may prove especially suitable as a good starting point for further medicinal chemistry efforts, leading to design and development of even more potent structural analogs as selective PD-1/PD-L1 inhibitors. Furthermore, the adopted integrated virtual screening protocol may prove useful in screening other larger databases of lead- and drug-like molecules for hit identification in the domain of small-molecule PD-1/PD-L1 inhibitors.<br /></p> | Elena Fattakhova; Jeremy Hofer; Juliette DiFlumeri; Madison Cobb; Timothy Dando; Zachary Romisher; Justin Wellington; Michael Oravic; Madison Radnoff; Sachin Patil | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757aa337d6c175fe29068/original/identification-of-the-fda-approved-drug-pyrvinium-as-a-novel-inhibitor-of-pd-1-pd-l1-interaction.pdf |
67adb8456dde43c908b11ae2 | 10.26434/chemrxiv-2025-1s2mm | Predict Before You Precipitate: Learning Templating Effects in HOI Antimony and Bismuth Halides | Hybrid organic-inorganic (HOI) antimony and bismuth halides exhibit diverse structural features and have been studied intensely for their promising electronic and optical properties. There are well-explored structure-property relations for these materials. However, a thorough understanding of synthesis routes and templating effects is lacking, turning their targeted synthesis into an open challenge. In this study, we assemble a literature data set of established HOI material candidates and train an explainable machine learning (ML) classification model to explore the templating effects in more detail. With a classification accuracy upwards of 70%, our model is effective in predicting HOI structure types based on the reactants and points out several structural and electrostatic design features for the organic cation that influence the inorganic substructure most strongly. We further demonstrate the validity of our classifier on 9 newly synthesized members of this materials class and propose incremental learning routes to expand the model in future research. | Jakob Blahusch; Konstantin S. Jakob; Johannes T. Margraf; Karsten Reuter; Bettina V. Lotsch | Theoretical and Computational Chemistry; Inorganic Chemistry; Machine Learning; Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67adb8456dde43c908b11ae2/original/predict-before-you-precipitate-learning-templating-effects-in-hoi-antimony-and-bismuth-halides.pdf |
60c7591b567dfe4654ec6981 | 10.26434/chemrxiv.14645217.v1 | 501Y.V2 Spike Protein Resists the Antibody in Atomistic Simulations | <div>
<p><a>SARS-CoV-2 Spike (S) protein is a
major biological target for COVID-19 vaccine design. Unfortunately, recent
reports indicated that Spike (S) protein mutations can lead to antibody
resistance. </a>However, understanding the process is limited, especially at the
atomic scale. The structural change of S protein and neutralizing antibody fragment
(FAb) complexes was thus probed using molecular dynamics (MD) simulations. In
particular, backbone RMSD of the 501Y.V2 complex was significantly larger than
that of the WT implying a large structural change of the mutation system. Moreover,
the mean of
, CCS, and SASA are almost the same when compared
two complexes, but the distribution of these values are absolutely different. Furthermore,
the free energy landscape of the complexes was significantly changed when the 501Y.V2
variant was induced. The binding pose between S protein and FAb was thus
altered. The FAb-binding affinity to S protein was thus reduced due to
revealing over steered-MD (SMD) simulations. The observation is in good
agreement with the respective experiment that the 501Y.V2 SARS-CoV-2 variant
can escape from neutralizing antibody (NAb).</p>
</div> | Son Tung Ngo | Biophysics; Computational Chemistry and Modeling; Theory - Computational; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7591b567dfe4654ec6981/original/501y-v2-spike-protein-resists-the-antibody-in-atomistic-simulations.pdf |
64edacc9dd1a73847fbfd769 | 10.26434/chemrxiv-2023-nsbtp | Describing the SAXS Profile of Unilamellar Liposomes via Beating Waves | Unilamellar liposomes are spherical vesicles that can transport and deliver drugs. Here, we present a straightforward mathematical model that describes the features of small-angle X-ray scattering (SAXS) from unilamellar liposomes. | Laura Baraldi; Serena Rosa Alfarano ; Flavia Sousa; Raffaele Mezzenga ; Barbara Rothen-Rutishaser; Alke Fink; Sandor Balog | Nanoscience; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64edacc9dd1a73847fbfd769/original/describing-the-saxs-profile-of-unilamellar-liposomes-via-beating-waves.pdf |
619e4b16836f656a557bd40b | 10.26434/chemrxiv-2021-hdx4p | Updated Prediction of Aggregators and Assay Interfering Substructures in Food Compounds | Positive outcomes in biochemical and biological assays of food compounds may appear due to the well-described capacity of some compounds to form colloidal aggregates that adsorb proteins, resulting in their denaturation and loss of function. This phenomenon can lead to wrongly ascribing mechanisms of biological action for these compounds (false positives), as the effect is non-specific and promiscuous. Similar false positives can show up due to chemical (photo)reactivity, redox cycling, metal chelation, interferences with the assay technology, membrane disruption, etc., which are more frequently observed when the tested molecule has some definite interfering substructures. Although discarding false positives can be achieved experimentally, it would be very useful to have in advance a prognostic value for possible aggregation and/or interference, based only in the chemical structure of the compound tested, in order to be aware of possible issues, help in prioritization of compounds to test, design of appropriate assays, etc. Previously, we applied cheminformatic tools derived from the drug discovery field to identify putative aggregators and interfering substructures in a database of food compounds, the FooDB, comprising 26457 molecules at that time. Here we provide an updated account of that analysis based on a current, much-expanded version of the FooDB, comprising a total of 70855 compounds. In addition, we also apply a novel machine learning model (the SCAM Detective) to predict aggregators with 46%-53% increased accuracies over previous models. In this way, we expect to provide the researchers in the mode of action of food compounds with a much improved, robust, and widened set of putative aggregators and interfering substructures of food compounds. | Andres Sanchez-Ruiz; Gonzalo Colmenarejo | Theoretical and Computational Chemistry; Agriculture and Food Chemistry; Food; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619e4b16836f656a557bd40b/original/updated-prediction-of-aggregators-and-assay-interfering-substructures-in-food-compounds.pdf |
621f904250b6211f93e6ae5e | 10.26434/chemrxiv-2022-xlttk | Recycling of Carbon Fiber Reinforced Polymers in a Subcritical Acetic Acid Solution | A novel single-stage solvolysis process is demonstrated for recycling carbon fibers from an epoxy-based composite material using 50 wt% acetic acid solution under subcritical conditions. The process yields 100% recovery efficiency for fibers in less than 30 min at 300 °C. Qualitative SEM / EDS analysis of the fibers reveals that the recovered fibers are entirely free of resin, while the carbon fiber surfaces were not damaged. SEM images and gravimetric measurements of the composites treated at lower temperatures and short residence times show an initial increase in mass of the CFRP samples, suggesting a two-step process, consisting of initial composite swelling due to uptake of solvent, followed by depolymerization and chemical decomposition of the polymer. FTIR and GC-MS analyses confirm resin decomposition and production of aromatic and aliphatic compounds, which could potentially be recovered for re-use. | Shreyas Shetty; Brian Pinkard ; Igor Novosselov | Physical Chemistry; Materials Science; Polymer Science; Carbon-based Materials; Composites; Materials Processing | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621f904250b6211f93e6ae5e/original/recycling-of-carbon-fiber-reinforced-polymers-in-a-subcritical-acetic-acid-solution.pdf |
6147fea018be8567dc286453 | 10.26434/chemrxiv-2021-jnskt-v3 | Optical Nature of Non-Substituted Triphenylmethyl Cation: Crystalline State Emission, Thermochromism, and Phosphorescence | Since the discovery of the triphenylmethyl (trityl) cation 120 years ago, a variety of aromatic cations having various colors and luminescence properties have been rigorously studied. Many, differently substituted trityl cations have been synthesized and their optical properties have been elucidated. However, the optical properties of the parent, non-substituted and highly reactive trityl cation, which was observed to be very weakly luminescent, have not been subjected to detailed investigation. In the effort described herein, we explored the optical nature of non-substituted trityl hexafluorophosphate (PF6) in the crystalline state. Trityl PF6 was found to exist as two crystal polymorphs including a yellow (Y) and an orange (O) form. Moreover, we observed that these crystalline forms display crystalline-state emission with different colors. The results of X-ray crystallographic analysis showed that the two polymorphs have totally different molecular packing arrangements. Furthermore, an investigation of their optical properties revealed that the O-crystal undergoes a distinct color change to yellow upon cooling as a consequence of a change in the nature of the charge transfer interaction between the cation and PF6 anion, and that both the Y and O crystal exhibit phosphorescence. | Tomohiko Nishiuchi; Hikaru Sotome; Risa Fukuuchi; Kenji Kamada; Hiroshi Miyasaka ; Takashi Kubo | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6147fea018be8567dc286453/original/optical-nature-of-non-substituted-triphenylmethyl-cation-crystalline-state-emission-thermochromism-and-phosphorescence.pdf |
675a9725f9980725cfd0160b | 10.26434/chemrxiv-2024-kz26k | Quantum Coulombic Interactions Mediate Free Radical Control in Radical SAM Viperin/RSAD2 | There are thousands of radical S-adenosylmethionine (rSAM) enzymes capable of catalyzing over 80 distinct reactions, yet their use in biotechnological applications is limited, primarily due to a lack of understanding of how these enzymes control highly reactive radical intermediates. Here, we show that little-known quantum Coulombic interactions are, in part, responsible for free radical control in Viperin/RSAD2, one of the few radical SAM enzymes expressed in humans. Using molecular dynamics and high-level multi-state broken-symmetry quantum mechanical/molecular mechanics calculations, we elucidated the mechanistic details of the catalysis, identifying a key step characterized by the formation of an unprecedented metastable deprotonated ribose radical intermediate. This intermediate is thermodynamically stabilized by spin-charge exchange-correlation interactions—a quantum Coulombic effect. The magnitude of this stabilization is such that the radical displays acidity two to six pKa units lower than that of closed-shell ribose. Given the omnipresence of negative charges in biological systems, these interactions potentially represent a universal mechanism for stabilizing and controlling highly reactive radical intermediates across radical enzymes, opening new avenues for enzymatic engineering and biotechnological applications. | M. Hossein Khalilian; Gino DiLabio | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675a9725f9980725cfd0160b/original/quantum-coulombic-interactions-mediate-free-radical-control-in-radical-sam-viperin-rsad2.pdf |
667aab1901103d79c516c406 | 10.26434/chemrxiv-2024-prpb7 | Enhancing Nanozyme-Based Colorimetric Assays by Optimizing Substrate Composition | Nanozymes, while promising alternatives to natural peroxidases in colorimetric assays, are often hindered by lower catalytic efficiencies. While various strategies exist to enhance signal intensity in nanozyme-based assays, substrate optimization remains largely underexplored. The vast majority of studies rely on standard sodium acetate buffers or commercially-sourced substrates optimized for horseradish peroxidase, neglecting the unique catalytic properties of different nanozymes. This work presents a systematic optimization of 3,3',5,5'-tetramethylbenzidine (TMB)-based substrate compositions for four common nanozymes: iron oxide, LaNiO3, Mn-doped CeO2, and platinum nanoparticles. Our findings reveal that while sodium acetate buffer is suitable for LaNiO3, alternative buffers significantly enhance signal intensity (41-68%) for the other nanozymes. Further optimization of ionic strength, organic co-solvent type and concentration, and TMB/H2O2 concentrations yielded improvements in signal intensity, analytical sensitivity, and assay time. This study also identifies common pitfalls encountered during substrate optimization and proposes potential solutions. We posit that substrate composition should be a standard optimization step in the development of nanozyme-based assays, and the use of commercially-sourced substrates with undisclosed compositions should be avoided. | Pavel Khramtsov; Rishat Valeev; Marina Eremina; Mikhail Rayev | Biological and Medicinal Chemistry; Analytical Chemistry; Nanoscience; Nanocatalysis - Catalysts & Materials | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667aab1901103d79c516c406/original/enhancing-nanozyme-based-colorimetric-assays-by-optimizing-substrate-composition.pdf |
60c73fdf0f50db723c395867 | 10.26434/chemrxiv.7504697.v1 | Combining Polarizable Embedding with the Frenkel Exciton Model: Applications to Absorption Spectra with Overlapping Solute-Solvent Bands | Modeling of spectral properties of extended chemical systems, such as the case of a solute in a solvent, is often performed based on so-called hybrid models in which only part of the complete system is given a quantum chemical description. The remaining part of the system is represented by an embedding potential treating the environment either by a discrete or continuum model. In order to successfully make use of minimally sized quantum chemical regions, the<br />embedding potential should represent the environment as authentic as possible. Here, the importance of exactly such an accurate description of the embedding potential is investigated by comparing the performance of the Polarizable Embedding scheme against larger sized full quantum mechanical calculations. Our main conclusion is that as long as the solute and solvent do not overlap in their absorption spectra, the Polarizable Embedding approach shows results consistent with full quantum chemical calculations. For partly overlapping absorption spectra the Polarizable Embedding approach can furthermore successfully be expanded within a Frenkel exciton approach based on only economical monomeric quantum chemical calculations. Thus, by extending the Polarizable Embedding scheme to the exciton picture it is possible to cover computations of the whole absorption spectrum and<br />still reduce the computational cost compared to costly cluster calculations.<br /> | Julie Stendevad; Jacob Kongsted; Casper Steinmann | Photochemistry (Physical Chem.); Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2019-01-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fdf0f50db723c395867/original/combining-polarizable-embedding-with-the-frenkel-exciton-model-applications-to-absorption-spectra-with-overlapping-solute-solvent-bands.pdf |
66238ad521291e5d1d3d8b8f | 10.26434/chemrxiv-2024-2ll7z | Mass spectrometry imaging with trapped ion mobility spectrometry (TIMS) facilitates spatially resolved chondroitin, dermatan and hyaluronan glycosaminoglycan (GAG) oligosaccharide analysis in situ. | The spatial analysis of glycosaminoglycans (GAGs) by type and sulphation state is currently unobtainable. Here, we describe a mass spectrometry imaging (MSI) approach which enables the detection, identification, localisation and profiling of GAG oligosaccharides directly from retinal tissue. With in situ treatment of tissues with relevant chondroitinase enzymes, we liberate and spatially resolve chondroitin, dermatan and hyaluronan disaccharides through to hexasaccharides directly from tissue sections. We demonstrate, through the use of trapped ion mobility spectrometry (TIMS), that it is possible to both separate and semi-quantify isomeric GAG oligosaccharide ions across histologically relevant regions. Hence, we describe the first step towards the spatially resolved analysis of multiple GAGs and their oligosaccharide sulphation state(s) in tissues. | Anthony Devlin; Felicia Green; Zoltan Takats | Analytical Chemistry; Biochemical Analysis; Imaging; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66238ad521291e5d1d3d8b8f/original/mass-spectrometry-imaging-with-trapped-ion-mobility-spectrometry-tims-facilitates-spatially-resolved-chondroitin-dermatan-and-hyaluronan-glycosaminoglycan-gag-oligosaccharide-analysis-in-situ.pdf |
651caf94bda59ceb9ad14eb8 | 10.26434/chemrxiv-2023-v7ksw | Carboxylic Acid-Catalyzed Controlled Ring-Opening Polymerization of Sarcosine N-Carboxyanhydride: Fast Kinetics, Ultra-High Molecular Weight, and Mechanistic Insights | The rapid and controlled synthesis of high molecular weight (MW) polysarcosine (pSar), a potential polyethylene glycol (PEG) alternative, via the ring-opening polymerization (ROP) of N-carboxyanhydride (NCA) is rare and challenging. Here, we report carboxylic acid-catalyzed well-controlled ROP of Sar-NCA, which accelerates the polymerization rate up to 50 times, and enables the robust synthesis of pSar with unprecedented high molecular weight (MW) up to 586 kDa (DP ~ 8200) and exceptionally narrow dispersity (Ð) below 1.02. Density functional theory (DFT) calculations combined with mechanistic experiments identify the carbamic acid as dormant species before generating the secondary amine for chain propagation, and elucidate the role of carboxylic acid as a bifunctional catalyst that significantly facilitates proton transfer processes and avoids charge separation. High MW pSar demonstrates improved thermal and mechanical properties over low MW pSar. This work provides a simple yet highly efficient approach to ultra-high MW pSar and generates new fundamental understandings useful not only for the ROP of Sar-NCA but also other NCAs. | Shuo Wang; Ming-Yuan Lu; Si-Kang Wan; Chun-Yan Lyu; Zi-You Tian; Kai Liu; Hua Lu | Theoretical and Computational Chemistry; Organic Chemistry; Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651caf94bda59ceb9ad14eb8/original/carboxylic-acid-catalyzed-controlled-ring-opening-polymerization-of-sarcosine-n-carboxyanhydride-fast-kinetics-ultra-high-molecular-weight-and-mechanistic-insights.pdf |
60c74b12bb8c1a2ae03db12f | 10.26434/chemrxiv.12179037.v2 | Multi-Targeting of Functional Cysteines in Multiple Conserved SARS-CoV-2 Domains by Clinically Safe Zn-ejectors | <div><div><div><p>We present a near-term treatment strategy to tackle pandemic outbreaks of coronaviruses with no specific drugs/vaccines by combining evolutionary and physical principles to identify conserved viral domains containing druggable Zn-sites that can be targeted by clinically safe Zn-ejecting compounds. By applying this strategy to SARS-CoV-2 polyprotein-1ab, we predicted multiple labile Zn-sites in papain-like cysteine protease (PLpro), nsp10 transcription factor, and nsp13 helicase. These are attractive drug targets because they are highly conserved among coronaviruses and play vital structural/catalytic roles in viral proteins indispensable for viral replication. We show that five Zn-ejectors can release Zn2+ from PLpro and nsp10, and clinically-safe disulfiram and ebselen can not only covalently bind to the Zn-bound/catalytic cysteines in both proteins, but also inhibit PLpro protease activity. We propose combining disulfiram/ebselen with broad-spectrum antivirals/drugs to target different conserved domains acting at various stages of the virus life cycle to synergistically inhibit SARS-CoV-2 replication and reduce the emergence of drug resistance.</p></div></div></div> | Karen Sargsyan; Chien-Chu Lin; Ting Chen; Cédric Grauffel; Yi-Ping Chen; Wei-Zeng Yang; Hanna S. Yuan; Carmay Lim | Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b12bb8c1a2ae03db12f/original/multi-targeting-of-functional-cysteines-in-multiple-conserved-sars-co-v-2-domains-by-clinically-safe-zn-ejectors.pdf |
6306eb96d858fb1bfa5b5f5a | 10.26434/chemrxiv-2022-7tnzg-v2 | Quantitative Dynamics of the Paradigmatic SN2 reaction OH− + CH3F on a Chemically Accurate Full-Dimensional Potential Energy Surface | The bimolecular reaction between OH− and CH3F is not just a prototypical SN2 process but also has three other product channels. Here, we develop an accurate full-dimensional potential energy surface (PES) based on 191 193 points calculated at the level CCSD(T)-F12a/aug-cc-pVTZ. A detailed dynamics and mechanism analysis were carried out on this PES by using the quasi-classical trajectory approach. It is verified that the trajectories do not follow the minimum energy path (MEP) but directly dissociate to F− and CH3OH. In addition, a new transition state for proton exchange and a new product complex CH2F−‧‧‧H2O for proton abstraction were discovered. The trajectories avoid the transition state or this complex, instead dissociate to H2O and CH2F− directly through the ridge regions of the MEP before the transition state. These non-MEP dynamics become more pronounced at high collision energies. Detailed dynamics simulations provide new insights into the atomic-level mechanisms of the title reaction thanks to the new chemically accurate PES with the aid of the machine learning. | Jie Qin; Yang Liu; Jun Li | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6306eb96d858fb1bfa5b5f5a/original/quantitative-dynamics-of-the-paradigmatic-sn2-reaction-oh-ch3f-on-a-chemically-accurate-full-dimensional-potential-energy-surface.pdf |
60c758bfbb8c1a02b73dcab8 | 10.26434/chemrxiv.14594568.v1 | A Switchable Sensor for Cu2+ and Zn2+ Based on Xanthene Moietymaking a Path for a Complex Molecular Encryption System Based on Color and Fluorescent Change | <p>Colorimetric and fluorescent detection methods for metal analytes has
become a powerful tool for qualitative and quantitative analysis in the last
decade due to their immediate output, cost-effectiveness,
specificity/selectivity, zero interference, high detection limit, and application
in practical samples. Sensing Cu<sup>2+</sup>, Ni<sup>2+,</sup> or Zn<sup>2+</sup>
like analytes gained a lot of attention due to their significance in
biological, medical, and environmental purposes. To account for this purpose,
we synthesized and designed a colorimetric, fluorescent off-on, and reversible
chemosensor <b>EYM</b> having xanthene as a
signaling moiety and 4-carbamoyl-3-Butenoic
acid as a receptor moiety. The <b>EYM</b>
probe is then screened with Al<sup>3+</sup>, V<sup>3+</sup>, Na<sup>+</sup>, K<sup>+</sup>, Fe<sup>3+</sup>,
Mg<sup>2+</sup>, Ca<sup>2+</sup>, Fe<sup>2+</sup>, Co<sup>2+</sup>, Zn<sup>2+</sup>,
Cd<sup>2+</sup>, Hg<sup>2+</sup>, Mn<sup>2+</sup>, Co<sup>3+</sup>, Pb<sup>2+</sup>,
Cu<sup>2+</sup>, Pd<sup>2+</sup>, and V<sup>4+</sup><sup> </sup>in DMSO: H<sub>2</sub>O (4:1) solvent system
where <b>EYM</b> shows absorbance change
specifically for Cu<sup>2+</sup> at 541nm changing from colorless to dark pink.
The detection limit and association constant of the <b>EYM</b> probe for Cu<sup>2+</sup> is 78.5nM and (6.013-5.947)´10<sup>9</sup> M<sup>-1,</sup> respectively.
The coordination of Cu<sup>2+</sup> with <b>EYM</b>
is in (1:2: Ligand: Metal) stoichiometric ratio. The immediate saturation time
(~2 sec) and low detection limit (78.5nM) of the EYH probe give competitiveness
over other sensors in practical applicability in real-life samples detection of
Cu<sup>2+</sup>. Not only this, the <b>EYM</b>
sensor can switch from mono to bi to tri-functional sensor for Cu<sup>2+</sup>,
Ni<sup>2+,</sup> and Zn<sup>2+</sup> with the stimuli of water in the DMSO
solvent. The <b>EYM</b> shows specific
abnormal fluorescent enhancement in contact with Zn<sup>2+</sup> in DMSO
solvent. The detection limit for Zn<sup>2+</sup> is 79nM same as Cu<sup>2+</sup>
in a colorimetric assay. Switchable sensing is utilized to make complex
molecular LOGIC GATE operations, including password-protected molecular
encryption systems.</p> | Amar Raj; Ankur Gupta | Supramolecular Chemistry (Org.); Analytical Chemistry - General; Chemoinformatics; Spectroscopy (Anal. Chem.); Sensors | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758bfbb8c1a02b73dcab8/original/a-switchable-sensor-for-cu2-and-zn2-based-on-xanthene-moietymaking-a-path-for-a-complex-molecular-encryption-system-based-on-color-and-fluorescent-change.pdf |
624fa8b302f70175dadb0401 | 10.26434/chemrxiv-2022-zwbkk | Tripeptide-assisted gold nanocluster formation for sensing Fe3+ and Cu2+ | Over the past decade, various fluorescent gold nanoclusters (AuNCs) have been studied for their potential as metal ion sensors. Due to the importance of the surface ligand in stabilizing nanocluster and sensing target metal ions, there is a great need of further investigations into possible surface ligands to develop selective and sensitive sensors. In this study, we designed very simple tripeptides to form fluorescent AuNCs by taking advantage of the reduction capability of tyrosine under alkaline conditions. In addition to studying the role of tyrosine in forming AuNC, we also investigated the role of tyrosine in sensing metal ions. Two tripeptides, tyrosine-cysteine-tyrosine (YCY) and serine-cysteine-tyrosine (SCY), were prepared and used for the formation of AuNCs. We obtained AuNCs with blue and red fluorescence from YCY peptides and AuNCs with blue fluorescence from SCY peptides. We found that the fluorescence of blue fluorescence-emitting YCY- and SCY-AuNCs is selectively quenched with Fe3+ and Cu2+, while the fluorescence of the red fluorescence-emitting YCY-AuNC is stable with 13 different metal ions. We have observed that the number of tyrosine residues affects the response of sensors. In the presence of different metal ions, different aggregation propensities were observed from DLS measurement. These results suggest the chelation between the peptide on the AuNC surface and the target ions results in aggregation and causes fluorescence quenching. Our study has shown that very simple and short peptides can be designed rationally for the formation of fluorescent AuNCs and utilized as the surface ligand for the metal ion sensing. | Jonghae Youn; Peiyuan Kang; Justin Crowe; Caleb Thornsbury; Peter Kim; Zhenpeng Qin; Jiyong Lee | Nanoscience; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624fa8b302f70175dadb0401/original/tripeptide-assisted-gold-nanocluster-formation-for-sensing-fe3-and-cu2.pdf |
679cc03781d2151a02ac6a8d | 10.26434/chemrxiv-2024-tqf0x-v3 | Bayesian Illumination: Inference and Quality-Diversity Accelerate Generative Molecular Models | In recent years, there have been considerable academic and industrial research efforts to develop novel generative models for high-performing, small molecules. Traditional, rules-based algorithms such as genetic algorithms [Jensen, Chem. Sci., 2019, 12, 3567-3572] have, however, been shown to rival deep learning approaches in terms of both efficiency and potency. In previous work, we showed that the addition of a quality-diversity archive to a genetic algorithm resolves stagnation issues and substantially increases search efficiency [Verhellen, Chem. Sci., 2020, 42, 11485-11491]. In this work, we expand on these insights and leverage the availability of bespoke kernels for small molecules [Griffiths, Adv. Neural. Inf. Process. Syst., 2024, 36] to integrate Bayesian optimisation into the quality-diversity process. This novel generative model, which we call Bayesian Illumination, produces a larger diversity of high-performing molecules than standard quality-diversity optimisation methods. In addition, we show that Bayesian Illumination further improves search efficiency com- pared to previous generative models for small molecules, including deep learning approaches, genetic algorithms, and standard quality-diversity methods. | Jonas Verhellen | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Drug Discovery and Drug Delivery Systems; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679cc03781d2151a02ac6a8d/original/bayesian-illumination-inference-and-quality-diversity-accelerate-generative-molecular-models.pdf |
61d4054b7284d0115e025a47 | 10.26434/chemrxiv-2022-1b6sv | Unusual milk oligosaccharides and the biosynthetic pathways | Free oligosaccharides are abundant macronutrients in milk and involved in prebiotic functions and antiadhesive binding of pathogenic bacteria to colonocytes. Despite the importance of these oligosaccharides, structural determination of oligosaccharides is challenging, and milk oligosaccharide biosynthetic pathways remain unclear. Oligosaccharide structures are conventionally determined using a combination of chemical reactions, exoglycosidase digestion, nuclear magnetic resonance spectroscopy, and mass spectrometry. Most reported free oligosaccharides are highly abundant and have lactose at the reducing end, and current oligosaccharide biosynthetic pathways in human milk are proposed based on these oligosaccharides. In this study, a new mass spectrometry technique, which can identify linkages, anomericities, and stereoisomers, was applied to determine the structures of free oligosaccharides in human, bovine, and caprine milk. Oligosaccharides that do not follow the current biosynthetic pathways and are not synthesized by any discovered enzymes were found, indicating the existence of undiscovered biosynthetic pathways and enzymes. New biosynthetic pathways were proposed. | Wei-Chien Weng; Hun-En Liao; Shih-Pei Huang; Shang-Ting Tsai; Hsu-Chen Hsu; Chia-Yen Liew; Veeranjaneyulu Gannedi; Shang-Cheng Hung; Chi-Kung Ni | Analytical Chemistry; Biochemical Analysis | CC BY NC 4.0 | CHEMRXIV | 2022-01-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d4054b7284d0115e025a47/original/unusual-milk-oligosaccharides-and-the-biosynthetic-pathways.pdf |
642046f862fecd2a83761ff7 | 10.26434/chemrxiv-2023-9trxb | In Vivo Metabolic Imaging of [1-13C]Pyruvate-d3 Hyperpolarized By Reversible Exchange With Parahydrogen | Metabolic magnetic resonance imaging (MRI) using hyperpolarized (HP) pyruvate has shown promise as a non-invasive technique for diagnosing, staging, and monitoring response to treatment in cancer and other diseases. The clinically established method for producing HP pyruvate is dynamic nuclear polarization; however, it is rather expensive and slow. Here, we demonstrate fast (6 min), low-cost production of HP [1-13C]pyruvate-d3 in aqueous solution using Signal Amplification By Reversible Exchange (SABRE), and in vivo metabolic MRI. The injected solution was sterile, non-toxic, pH neutral and contained ≈30 mM [1-13C]pyruvate-d3 polarized to ≈11% (residual 250 mM methanol and 20 µM catalyst). It was obtained by rapid solvent evaporation and metal filtering. The procedure was well tolerated by all four mice studied here. This achievement is a significant step of making HP MRI available to a wider community. Fast, low-cost, and high-throughput parahydrogen-hyperpolarization has become a viable alternative for metabolic MRI of living organisms. | Henri de Maissin; Philipp Groß; Obaid Mohiuddin; Moritz Weigt; Luca Nagel; Marvin Herzog; Zirun Wang; Robert Willing; Wilfried Reichardt; Martin Pichotka; Lisa Heß; Thomas Reinheckel; Henning Jessen; Robert Zeiser; Michael Bock; Dominik von Elverfeldt; Maxim Zaitsev; Sergey Korchak; Stefan Glöggler; Jan-Bernd Hövener; Eduard Chekmenev; Franz Schilling; Stephan Knecht; Andreas Benjamin Schmidt | Physical Chemistry; Organic Chemistry; Analytical Chemistry; Imaging; Spectroscopy (Anal. Chem.); Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2023-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642046f862fecd2a83761ff7/original/in-vivo-metabolic-imaging-of-1-13c-pyruvate-d3-hyperpolarized-by-reversible-exchange-with-parahydrogen.pdf |
6181f07181c4fc4724eaf295 | 10.26434/chemrxiv-2021-kwjg1 | Internal and external catalysis in boronic ester networks | In dynamic materials, the reversible condensation between boronic acids and diols provides adaptability, self-healing ability, and responsiveness to small molecules and pH. Recent work has shown that the thermodynamics and kinetics of bond exchange determine the mechanical properties of dynamic polymer networks. However, prior studies have focused on how structural and environmental factors influence boronic acid–diol binding affinity, and design rules for tuning the kinetics of this dynamic bond are lacking. In this work, we investigate the effects of diol (or polyol) structure and salt additives on the rate of bond exchange, binding affinity, and the mechanical properties of the corresponding polymer networks. To better mimic the environment of polymer networks in our small-molecule model systems, we incorporated proximal amide groups, which are used to conjugate diols to polymers, and included salts commonly found in buffers. Using one-dimensional selective exchange spectroscopy (1D EXSY), we find that both proximal amides and buffering anions induce significant rate acceleration consistent with internal and external catalysis, respectively. This rate acceleration is reflected in the stress relaxation of gels formed using PEG modified with different alcohols, and in the presence of salts containing acetate or phosphate. These findings contribute to the fundamental understanding of the boronic ester dynamic bond and offer new molecular strategies to tune the macromolecular properties of dynamic materials. | Boyeong Kang; Julia Kalow | Organic Chemistry; Materials Science; Polymer Science; Physical Organic Chemistry; Hydrogels | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6181f07181c4fc4724eaf295/original/internal-and-external-catalysis-in-boronic-ester-networks.pdf |
6772d0346dde43c908cf8cc1 | 10.26434/chemrxiv-2024-x4dt6 | A perspective on the reaction mechanisms of CO2 electrolysis | In this work we analyze the current state of CO2 electrolysis and give our best analysis of what we believe is the most dominant mechanism for all predominant products in CO2 electrolysis. We draw on both computational and experimental literature to develop conclusions for C1 and C2 products. From this, we develop a set of self-consistent mechanistic rules. As the volume of literature on the mechanism towards C3 products is substantially smaller than on C1 and C2 products, these rules help us in evaluating mechanistic routes towards C3 products. While these mechanistic routes are speculative, it does give us a point of reference that can be modified in the future based on further developments in the field. | Brian Seger; Georg Kastlunger; Alexander Bagger; Soren Scott | Catalysis; Electrocatalysis | CC BY NC 4.0 | CHEMRXIV | 2024-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6772d0346dde43c908cf8cc1/original/a-perspective-on-the-reaction-mechanisms-of-co2-electrolysis.pdf |
677ec6d16dde43c908c010f2 | 10.26434/chemrxiv-2025-xt8vg | The Hexaphenyl-1,2-Diphosphonium Dication [Ph3P–PPh3]2+ | The oxidation of triphenylphosphine by perfluorinated phenaziniumF aluminate in difluorobenzene affords the hexaaryl-1,2-di¬phosphonium dialuminate 1. Dication 12+ is isoelectronic with elusive hexaphenylethane, where instead the formation of a mixture of the trityl radical and Gomberg’s dimer is favored. Quantum-chemical calculations in combination with Raman/IR spectroscopies rationalize the stability of the P–P bonded dimer in 12+ and suggest, akin to the halogens, facile homolytic as well as heterolytic scission. Thus, 12+ serves as a surrogate of both the triphenylphosphorandiylium dication (Ph3P2+) and the triphenylphosphine radical monocation (Ph3P•+). Treating 1 with dimethylaminopyridine (DMAP) replaces triphenylphosphine under heterolytic P–P bond scission. Qualifying as a superoxidant (E vs. Fc/Fc+ = +1.44 V), 1 oxidizes trimethylphosphine. Based on halide abstraction experiments (−BF4, −PF6, −SbCl6, −SbF6) as well as the deoxygenation of triethylphosphine oxide, triflate anions as well as toluic acid, 1 also features Lewis superacidity. The controlled hydrolysis affords Hendrickson’s reagent, which itself finds broad use as dehydration agent. Formally homolytic P–P bond scis¬sion is induced by diphenyldisulfide (PhSSPh), dihydrogen, and the triple bond in acetonitrile. The irradiation by light cleaves the P–P bond homolytically and generates transient triphenylphosphine radical cations, which engage in H-atom abstraction as well as CH phosphoranylation. | Fabian Dankert; Simon P. Muhm; Chandan Nandi; Sergi Danés; Sneha Mullassery; Petra Herbeck-Engel; Bernd Morgenstern; Robert Weiss; Pedro Salvador Sedano; Dominik Munz | Organic Chemistry; Inorganic Chemistry; Organic Synthesis and Reactions; Frustrated Lewis Pairs; Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677ec6d16dde43c908c010f2/original/the-hexaphenyl-1-2-diphosphonium-dication-ph3p-p-ph3-2.pdf |
6731e222f9980725cfd28c19 | 10.26434/chemrxiv-2024-trrzk | An atomically precise Pt17 nanocluster: their electronic structure and high activity for a hydrogen evolution reaction | Pt nanoclusters (Pt NCs) approximately 1 nm in size show potential as catalysts owing to their large specific surface areas and unique electronic structures, which are influenced by quantum size effects. However, synthesizing Pt NCs with atomic precision under ambient conditions remains challenging, with [Pt17(CO)12(PPh3)8]z (z = 1+ or 2+; CO = carbon monoxide; PPh3 = triphenylphosphine) being the only current example of such a NC. It exhibits extraordinary stability, and its electronic structure and catalytic utility in a range of reactions are topics of widespread interest. In this study, we reveal its electronic structure and explore its catalytic activity in the hydrogen evolution reaction (HER). Our findings revealed that [Pt17(CO)12(PPh3)8]z possesses a discrete electronic structure, with the HOMO and LUMO primarily constituted by the s, p, and d orbitals of Pt; that a Pt17 NC-supported carbon-black catalyst (Pt17/CB) achieves 3.59-times the HER mass activity of a commercially available Pt/CB catalyst; and that the optimal electronic structure of the surface Pt atoms in Pt17/CB significantly enhances its HER activity. These insights underscore the potential of leveraging atomically precise Pt NCs in the design and development of highly active electrocatalysts for water splitting. | Kazutaka Oiwa; Kaoru Ikeda; Ryuki Kurosaki; Kotaro Sato; Naoki Nishi; Haruna Tachibana; Md. Ahsanul Haque; Tokuhisa Kawawaki; Kenji Iida; Yuichi Negishi | Catalysis; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2024-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6731e222f9980725cfd28c19/original/an-atomically-precise-pt17-nanocluster-their-electronic-structure-and-high-activity-for-a-hydrogen-evolution-reaction.pdf |
636d60ba33f7336563e2757f | 10.26434/chemrxiv-2022-6p7rr | Silole-Analog MK-3 Dyes with a Large Bathochromic Shift for Organic Solar Cells | Substituting the middle thiophene ring in the MK-3 dye with a silole ring, the B3LYP calculations have shown that the absorption wavelengths of the new dyes, Me2Si-MK-3 and F2Si-MK-3, are bathochromically shifted by about 100 nm from 436 nm (MK-3). This large red shift is due mainly to a higher HOMO energy level in the Me2Si-MK-3 dye (-5.19 eV) with respect to the MK-3 dye (-5.30 eV) but to a lower LUMO energy level in the F2Si-MK-3 dye (-3.41 eV) compared to the MK-3 dye (-3.09 eV). These results suggest a wide range of alternatives in altering absorption wavelengths in the design of organic dyes for solar cells. Additionally, the calculations have shown the absorption intensities of the proposed new dyes are higher than that of the MK-3 dye. A pragmatic technique is developed to accurately describe the photon excitation of dye molecules by considering higher energy molecular orbital involvement. All three set of data, the HOMO-LUMO gap, the TD-B3LYP, and the calibrated TD-B3LYP, show the consistent red shifts for the new dye molecules with respect to the MK-3 dye. | George Hudson; Lichang Wang | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636d60ba33f7336563e2757f/original/silole-analog-mk-3-dyes-with-a-large-bathochromic-shift-for-organic-solar-cells.pdf |
6456ce481ca6101a45e5a2b6 | 10.26434/chemrxiv-2023-c8gpf | Coherent Dynamic Nuclear Polarization using Chirped Pulses | This paper presents a study of coherent dynamic nuclear polarization (DNP) using frequency swept
pulses at 94 GHz which optimize the polarization transfer efficiency. Accordingly, an enhancement ℇ∼496
was observed using 10mM trityl-OX063 as the polarizing agent in a standard d8-glycerol:D2O:H2O :: 6:3:1
glassing matrix at 70K. At present this is the largest DNP enhancement reported at this microwave
frequency and temperature. Furthermore, the frequency swept pulses enhance the nuclear magnetic
resonance (NMR) signal and reduce the recycle delay, accelerating the NMR signal acquisition. | Yifan Quan; Manoj V. H. Subramanya; Yifu Ouyang; Michael Mardini; Thierry Dubroca; Stephen Hill; Robert G. Griffin | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6456ce481ca6101a45e5a2b6/original/coherent-dynamic-nuclear-polarization-using-chirped-pulses.pdf |
62fbf8c5bde0862cc463bc33 | 10.26434/chemrxiv-2022-p4wtd | A stable α-lactam reagent for bioconjugation and proteomic profiling | Electrophilic groups are one of the key pillars of contemporary chemical biology and medicinal chemistry, constituting the anchor point for the design of targeted covalent inhibitors, the identification of novel therapeutic targets, and the development of a wide diversity of bioconjugation and proteomic profiling techniques. Naturally, there is great interest in the discovery of new types of biologically relevant electrophiles with potent action and broad applicability. For instance, the group of 3-membered N-heterocyclic compounds - such as aziridines, azirines, and oxaziridines – combine unique electronic properties and structural strain to trigger their respective potential and applicability as covalent tools. The α-lactams are also members of this group of compounds, but, until this point, their utility within the field has been unexplored. Here, we demonstrate an α-lactam reagent that can be efficiently employed in the framework of bioconjugation and proteomic profiling. We have designed and synthesised a stable α-lactam, AM2, that is compatible with aqueous buffers, and have extensively characterised its properties and reactivity. In simple settings, AM2 was e.g. found to be reactive towards both thiols and amines, with the former reacting significantly faster. We further demonstrated that AM2 undergoes conjugation to free cysteine residues in peptides suggesting applications for bioconjugation. Interestingly, liver carboxylesterase 1 (CES1), a serine hydrolase with key roles in both endo- and xenobiotic metabolism, was found as a highly selective covalent target for AM2 in HepG2 liver cancer cells. All in all, our study constitutes the starting point for the further development of α-lactam-based electrophilic probes and exploration of their use in covalent chemical biology. | Alejandro Mahía; Anders Kiib; Marija Nisavic; Johan Palmfeldt; Thomas Poulsen | Biological and Medicinal Chemistry; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fbf8c5bde0862cc463bc33/original/a-stable-lactam-reagent-for-bioconjugation-and-proteomic-profiling.pdf |
64f092df79853bbd78cbbeaa | 10.26434/chemrxiv-2022-0dnsz-v2 | Topochemical Fluorination of LaBaInO4 to LaBaInO3F2, their Optical Characterization and Photocatalytic Activities for Hydrogen Evolution | We report on a non-oxidative topochemical route for the synthesis of a novel indate-based oxyfluoride, LaBaInO3F2, using a low-temperature reaction of Ruddlesden–Popper-type LaBaInO4 with polyvinylidene difluoride as a fluorinating agent. The reaction involves the replacement of oxide ions with fluoride ions as well as the insertion of fluoride ions at interstitial sites. From the characterization via powder X-ray diffraction (PXRD) and Rietveld analysis as well as automated electron diffraction tomography (ADT) it is deduced that the fluorination results in a symmetry lowering from I4/mmm (139) to monoclinic C2/c (15) with an expansion perpendicular to the perovskite layers and a strong tilting of the octahedra in the ab plane. Disorder of the anions on the apical and the interstitial sites seems to be favored. The most stable configuration for the anion ordering is estimated based on an evaluation of bond distances from the ADT measurements via bond valence sums (BVSs). The observed disordering of the anions in the oxyfluoride results in changes of the optical properties and thus shows that the topochemical anion modification can present a viable route to alter optical properties. Partial densities of states (PDOSs) obtained from ab initio density functional theory (DFT) calculations reveal a bandgap modification upon fluoride-ion introduction which originates from the presence of the oxide anions on the interstitial sites. The photocatalytic performance of the oxide and oxyfluoride shows that both of the materials are photocatalytically active for hydrogen (H2) evolution. | Shama Perween; Kerstin Wissel; Zsolt Dallos; Morten Weiss; Yuji Ikeda; Sami Vasala; Sabine Strobel; Peter Schuetzenduebe; Pascal M. Jeschenko; Ute Kolb; Roland Marschall; Blazej Grabowski; Pieter Glatzel | Materials Science; Catalysis; Heterogeneous Catalysis; Photocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f092df79853bbd78cbbeaa/original/topochemical-fluorination-of-la-ba-in-o4-to-la-ba-in-o3f2-their-optical-characterization-and-photocatalytic-activities-for-hydrogen-evolution.pdf |
60d487fb461f56068c4898fa | 10.26434/chemrxiv-2021-v2vd7 | Nitrogen K-edge X-ray absorption Spectra of
Ammonium and Ammonia in Water Solution:
Assessing the Performance of Polarizable
Embedding Coupled Cluster Methods | As X-ray absorption measurements of solutes in liquid environment become increasingly accessible, there is a strong need for reliable theoretical methods to assist in the interpretation of the experimental data.
Coupled cluster (CC) methods, considered among the most accurate tools in electronic structure theory to obtain molecular properties and spectra, have been extensively
developed over the last decade to simulate X-ray absorption in the gas phase. Their performance for solvated species, on the other hand, has remained so far largely unexplored.
Here, we investigate the current state of the art of CC modeling of N K-edge X-ray absorption of aqueous ammonia and ammonium, based on various levels of QM/MM. Both the level of CC calculations and polarizable embedding are scrutinized. The results are compared to existing experimental data as well as simulations based on transition-potential density functional theory results. | Peter Reinholdt; Marta L. Vidal; Jacob Kongsted; Marcella Iannuzzi; Sonia Coriani; Michael Odelius | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2021-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d487fb461f56068c4898fa/original/nitrogen-k-edge-x-ray-absorption-spectra-of-ammonium-and-ammonia-in-water-solution-assessing-the-performance-of-polarizable-embedding-coupled-cluster-methods.pdf |
653fd7d648dad23120b68311 | 10.26434/chemrxiv-2023-pr52z | Synthesis of thioxanthone 10,10-dioxides and sulfone-fluoresceins via Pd-catalyzed sulfonylative homocoupling | Our report describes the facile and scalable preparation of 9H-thioxanthen-9-one 10,10-dioxides via Pd-catalyzed sulfonylative homocoupling of the appropriately substituted benzophenones. This transformation provides a straightforward entry to previously unreported sulfone-fluoresceins and -fluorones. Several examples of these red-fluorescent dyes have been prepared, characterized and evaluated as live-cell permeant labels compatible with super-resolution fluorescence microscopy with 775 nm stimulated emission depletion. | Gergely Knorr; Mariano L. Bossi; Alexey N. Butkevich; Stefan W. Hell | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2023-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653fd7d648dad23120b68311/original/synthesis-of-thioxanthone-10-10-dioxides-and-sulfone-fluoresceins-via-pd-catalyzed-sulfonylative-homocoupling.pdf |
668a94e501103d79c548317d | 10.26434/chemrxiv-2024-2442r | Clustering of the Membrane Protein by Molecular Self-assembly Downregulates Signaling Pathway for Cancer Cell Inhibition | This work reports a cyclic peptide appended self-assembled scaffold that recognizes the membrane protein EGFR and arrests the EGFR signaling by assembly induced aggregation through multivalent interactions. Being incubating with cells, the oligomers of PAD-1 first recognize overexpressed EGFR on cancer cell membrane for arresting EGFR, which then initiate cellular uptake through endocytosis. The accumulation of PAD-1 and EGFR in the lysosome results in the formation of nanofibers, leading to lysosomal membrane permeabilization (LMP). These processes disrupt the homeostatic of EGFR and inhibit the downstream signaling transduction of EGFR for cancer cell survive. Moreover, LMP induced the releasing of protein aggregates could generate endoplasmic reticulum (ER) stress, resulting in cancer cell death selectively. In vivo studies indicate the efficient anti-tumor efficiency of PAD-1 in tumor bearing mice. As a first example, this work provides an alternative strategy for controlling protein behavior for tuning cellular events in living cells. | Ying Li; Liangbo Hu; Jing Wang; huaimin wang | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668a94e501103d79c548317d/original/clustering-of-the-membrane-protein-by-molecular-self-assembly-downregulates-signaling-pathway-for-cancer-cell-inhibition.pdf |
60c7426a0f50db334c395ccf | 10.26434/chemrxiv.8244719.v1 | Layered Manganese Bismuth Tellurides with GeBi4Te7– and GeBi6Te10–type Structures: Towards Multifunctional Materials | <p>The crystal structures of new layered manganese bismuth tellurides with the compositions Mn0.85(3)Bi4.10(2)Te7 and Mn0.73(4)Bi6.18(2)Te10 were determined by single-crystal X-ray diffraction, including the use of microfocused synchrotron radiation. These analyses reveal that the layered structures deviate from the idealized stoichiometry of the 12<i>P</i>-GeBi4Te7 (space group <i>P</i>3<i>m</i>1) and 51<i>R</i>-GeBi6Te10 (space group <i>R</i>3<i>m</i>) structure types they adopt. Modified compositions Mn1–<i>x</i>Bi4+2<i>x</i>/3Te7 (<i>x </i>= 0.15 – 0.2) and Mn1–<i>x</i>Bi6+2<i>x</i>/3Te10 (<i>x </i>= 0.19 – 0.26) assume cation vacancies and lead to homogenous bulk samples as confirmed by Rietveld refinements. Electron diffraction patterns exhibit no diffuse streaks that would indicate stacking disorder. The alternating quintuple-layer [M2Te3] and septuple-layer [M3Te4] slabs (M = mixed occupied by Bi and Mn) with 1:1 sequence (12<i>P </i>stacking) in Mn0.85Bi4.10Te7 and 2:1 sequence (51<i>R </i>stacking) in Mn0.81Bi6.13Te10 were also observed in HRTEM images. Temperature-dependent powder diffraction and differential scanning calorimetry show that the compounds are high temperature phases, which are metastable at ambient temperature. Magnetization measurements are in accordance with a MnII oxidation state and point at predominantly ferromagnetic coupling in both compounds. The thermoelectric figures of merit of n-type conducting Mn0.85Bi4.10Te7 and Mn0.81Bi6.13Te10 reach <i>zT </i>= 0.25 at 375 °C and <i>zT </i>= 0.28 at 325 °C, respectively. Although the compounds are metastable, compact ingots exhibit still up to 80% of the main phases after thermoelectric measurements up to 400 °C.</p> | Daniel Souchay; Markus Nentwig; Daniel Günther; Simon Keilholz; Johannes de Boor; Alexander Zeugner; Anna Isaeva; Michael Ruck; Anja U. B. Wolter; Bernd Büchner; Oliver Oeckler | Magnetism; Solid State Chemistry; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7426a0f50db334c395ccf/original/layered-manganese-bismuth-tellurides-with-ge-bi4te7-and-ge-bi6te10-type-structures-towards-multifunctional-materials.pdf |
64794c37e64f843f412dbf7d | 10.26434/chemrxiv-2023-2fc3w | Lipid Landscapes: Vibrational Spectroscopy for Decoding Membrane Complexity | Cell membranes are incredibly complex environments containing hundreds of components. Despite substantial advances in the past decade, fundamental questions related to lipid-lipid interactions and heterogeneity persist. This review explores the complexity of lipid membranes, showcasing recent advances in vibrational spectroscopy to characterize the structure, dynamics, and interactions at the membrane interface. We include an overview of modern techniques such as surface-enhanced infrared spectroscopy (SEIRAS) as a steady-state technique with single-bilayer sensitivity, two-dimensional sum-frequency generation (2D SFG) spectroscopy, and two-dimensional infrared (2D IR) spectroscopy to measure time-evolving structures and dynamics with femtosecond time resolution. Furthermore, we discuss the potential of multiscale MD simulations, focusing on recently developed simulation algorithms which have emerged as a powerful approach to interpret complex spectra. We highlight persistent challenges in accurately sampling heterogeneous ensembles in multicomponent membranes. Overall, this review provides an up-to-date comprehensive overview of the powerful combination of vibrational spectroscopy and simulations to illuminate lipid-lipid, lipid-protein, and lipid-water interactions in the intricate conformational landscape of cell membranes. | Xiaobing Chen; Ziareena Al-Mualem; Carlos Baiz | Physical Chemistry; Biophysical Chemistry; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64794c37e64f843f412dbf7d/original/lipid-landscapes-vibrational-spectroscopy-for-decoding-membrane-complexity.pdf |
641614772bfb3dc251fbff47 | 10.26434/chemrxiv-2023-cdqc6 | Modulating Enzyme’s Activity and Specificity through Pre-Installed Posttranslational Modifications (PTMs) on Substrate: The Role of PTM-induced Substrate-Assisted Stimulation | Understanding the underlying principles for crosstalk involving posttranslational modifications (PTMs) is of fundamental importance. In this article, we review some of previous results which indicated that pre-installed PTMs on nucleosome substrates (or nucleosome peptides) may stimulate the activity and change the specificity of histone modifying enzymes for the next PTMs. Discussions are also made on the results showing that ubiquitin (Ub) within the M1-diUb substrate could remodel the active site of OTULIN, a human deubiquitinase (DUB), and stimulate its activity. We term such stimulation effects as PTM-induced substrate-assisted stimulation (PTM-induced SAS) and propose that it could be one of the general strategies in PTM crosstalk and may provide a unique way to relay signals. It is suggested that although PTM-induced SAS seems to offer an attractive mechanism, detailed studies are still necessary to fully understand how the stimulations are created and translated into the increased activities and how widely it may occur in biological systems. | Hong Guo; Ping Qian | Catalysis; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641614772bfb3dc251fbff47/original/modulating-enzyme-s-activity-and-specificity-through-pre-installed-posttranslational-modifications-pt-ms-on-substrate-the-role-of-ptm-induced-substrate-assisted-stimulation.pdf |
65315e0d87198ede07cb645a | 10.26434/chemrxiv-2023-g7n49 | 77PD-Quinone: Synthesis, Coho Salmon Toxicity Assessment, and Comparison with the Commercial Antidegradant 77PD | There is a growing interest in assessing the toxicity of para-phenylenediamine-based rubber additives and their quinone transformation products. A technique for the multi-gram scale synthesis of 2,5-diaminoquinones was developed to prepare 2,5-bis((5-methylhexan-2-yl)amino)cyclohexa-2,5-diene-1,4-dione (77PD-quinone) for toxicity assessment. The toxicities of N,N'-bis(5-methyl-2-hexanyl)-1,4-benzenediamine (77PD) and 77PD-quinone were evaluated in coho salmon. Juvenile coho salmon were exposed to a geometric series of five test concentrations of 77PD or 77PD-quinone, a negative control (dilution water), and a solvent control (100 µL/L dimethylformamide) for 96 hours under flow-through conditions. 77PD was found to be toxic to coho salmon with a 96 hour LC50 value of 24 µg/L active ingredient (a.i.), and the NOEC was 13 µg a.i./L. No mortality was observed for 77PD-quinone at the highest attainable dose level, 226 µg a.i./L, at which signs of test water saturation were observed. | Judicaël Chapelet; Malik Al-Afyouni; Joshua Tyhurst; Jonathan Penney; Christina Roselli; Senthilkumar Kuppusamy; Timothy Ross; Ling Zhang; Sean Gallagher; John Aufderheide; Daniel Brougher | Organic Chemistry; Earth, Space, and Environmental Chemistry; Organic Synthesis and Reactions; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65315e0d87198ede07cb645a/original/77pd-quinone-synthesis-coho-salmon-toxicity-assessment-and-comparison-with-the-commercial-antidegradant-77pd.pdf |
66335a18418a5379b03cd9ae | 10.26434/chemrxiv-2024-d8rpg | Fueling from the Electrochemistry of Halide Solid Electrolytes | Unveiling the electrochemistry of solid-state Li2ZrCl6 halide electrolyte, we reveal its dual function as both an ion conductor and a supplementary electron source/sink. This groundbreaking discovery leads to a remarkable long-term enhancement of the specific capacity of industry-relevant heavily loaded LiFePO4 electrodes by several tens of percent, while significantly amplifying that of Si-based or anode-less full cells through effective compensation for side reactions. We show that these effects can potentially be tuned by adjusting the initial xLiCl-ZrCl4 composition of the solid electrolyte (SE), which may thus become a new and mighty parameter for balancing the two electrodes. | Branimir Stamenkovic; Ying Shirley Meng; Philippe Moreau; Joel GAUBICHER | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66335a18418a5379b03cd9ae/original/fueling-from-the-electrochemistry-of-halide-solid-electrolytes.pdf |
65c49d5be9ebbb4db9e954a9 | 10.26434/chemrxiv-2024-tcxvq | Degradation Benefits Polymerization: Photo-Generated Self-Degradable Organo-Catalyst for Higher-Efficiency ATRP and Pure Polymers | In the realm of polymer-based 3D photo printing, challenges arise from the side effects, notably the persistent presence of photocatalyst residues and metal contamination. These impurities pose significant risks in various applications, including electronics, biological tissues, and medical implants. At the same time, spatial-/time-/light-controlled 3D photo printing has been hindered by low-efficiency polymerization concerning both initiation and monomer conversion. To address these criti-cal issues, a pioneering concept, “degradation-inhibited quench,” is introduced and implemented within photopolymeriza-tion to solve the problems mentioned above. This innovative approach aims to produce pure polymers via higher-efficiency Atom Transfer Radical Polymerization (ATRP) with a unique class of diketopyrrolopyrrole (DPP) derivatives as organo-photocatalysts at an extremely low concentration (as low as 50ppm). Through this approach, pure polymers with ultra-high molecular weight (UHMW) have been successfully synthesized. For instance, poly(methyl methacrylate) (PMMA) achieved a monomer conversion of > 50%, a molecular weight of 2.1 million, and a dispersity of 1.38 after 12 h additional dark reaction. Notably, this novel photopolymerization method demonstrates applicability across a broad spectrum of monomers, with or without solvents, including acrylate, acrylic, styrene, and acrylonitrile. Mechanism insights revealed that the production of UHMW PMMA stemmed from the degradation of intermediate complex DPP•+/Br-, which originated from the photo initiation. This degradation inhibited the oxidative quenching of active propagating chain radicals, thereby significantly extending their lifespan. This groundbreaking concept embraces the potential for further development of highly effective organo-photocatalysts and reactive systems specifically tailored for 3D photopolymerization. Moreover, this novel spatial-/time-/light-controlled polymerization approach does not require any additional purification, offering energy and cost-saving manufacturing technology. | Yan Luo; Lingpu Jia; Yanghong Xu; Enmin Hu; Meekyung Song; Xiaofeng Zhu; Young Soo Kang; Yun Huang; Long Yang | Organic Chemistry; Catalysis; Polymer Science; Organic Polymers; Organocatalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c49d5be9ebbb4db9e954a9/original/degradation-benefits-polymerization-photo-generated-self-degradable-organo-catalyst-for-higher-efficiency-atrp-and-pure-polymers.pdf |
60c7517cbb8c1a02f63dbce3 | 10.26434/chemrxiv.13173701.v1 | Delocalized Metal-Oxygen π-Redox Is the Origin of Anomalous Non-Hysteretic Capacity in Li-Ion and Na-Ion Cathode Materials | The anomalous capacity of Li-excess cathode materials has ignited a vigorous debate over the nature of the underlying redox mechanism, which promises to substantially increase the energy density of rechargeable batteries. Unfortunately, nearly all materials exhibiting this anomalous capacity suffer from irreversible structural changes and voltage hysteresis. Non-hysteretic excess capacity has been demonstrated in Na<sub>2</sub>Mn<sub>3</sub>O<sub>7</sub> and Li<sub>2</sub>IrO<sub>3</sub>, making these materials key to understanding the electronic, chemical and structural properties that are necessary to achieve reversible excess capacity. Here, we use high-fidelity random-phase-approximation (RPA) electronic structure calculations and group theory to derive the first fully consistent mechanism of non-hysteretic oxidation beyond the transition metal limit, explaining the electrochemical and structural evolution of the Na<sub>2</sub>Mn<sub>3</sub>O<sub>7</sub> and Li<sub>2</sub>IrO<sub>3</sub> model materials. We show that the source of anomalous non-hysteretic capacity is a network of pi-bonded metal-d and O-p orbitals, whose activity is enabled by a unique resistance to transition metal migration. The pi-network forms a collective, delocalized redox center. We show that the voltage, accessible capacity, and structural evolution upon oxidation are collective properties of the pi-network rather than that of any local bonding environment. Our results establish the first rigorous framework linking anomalous capacity to transition metal chemistry and long-range structure, laying the groundwork for engineering materials that exhibit truly reversible capacity exceeding that of transition metal redox. | Daniil Kitchaev; Julija Vinckeviciute; Anton Van der Ven | Electrochemistry; Solid State Chemistry; Theory - Inorganic; Computational Chemistry and Modeling; Theory - Computational; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7517cbb8c1a02f63dbce3/original/delocalized-metal-oxygen-redox-is-the-origin-of-anomalous-non-hysteretic-capacity-in-li-ion-and-na-ion-cathode-materials.pdf |
63dc36cefcfb27a31f5b72a6 | 10.26434/chemrxiv-2022-nz2w8-v3 | Compactness Matters: Improving Bayesian Optimization Efficiency of Materials Formulations through Invariant Search Spaces | Would you rather search for a line inside a cube or a point inside a square? Physics-based simulations and wet-lab experiments often have symmetries (degeneracies) that allow reducing problem dimensionality or search space, but constraining these degeneracies is often unsupported or difficult to implement in many optimization packages, requiring additional time and expertise. So, are the possible improvements in efficiency worth the cost of implementation? We demonstrate that the compactness of a search space (to what extent and how degenerate solutions and non-solutions are removed) affects Bayesian optimization search efficiency. Here, we use the Adaptive Experimentation (Ax) Platform by Meta and a physics-based particle packing simulation with eight or nine tunable parameters, depending on the search space compactness. These parameters represent three truncated log-normal distributions of particle sizes which exhibit compositional-invariance and permutation-invariance characteristic of formulation problems (e.g., chemical formulas, composite materials, alloys). We assess a total of four search space types which range from none up to both constraint types imposed simultaneously. In general, the removal of degeneracy through problem reformulation (as seen by the optimizers surrogate model) improves optimization efficiency. We recommend that optimization practitioners in the physical sciences carefully consider the trade-off between implementation cost and search efficiency before running expensive optimization campaigns. | Sterling Baird; Jason R. Hall; Taylor D. Sparks | Materials Science; Chemical Engineering and Industrial Chemistry; Composites; Materials Processing; Process Control | CC BY 4.0 | CHEMRXIV | 2023-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63dc36cefcfb27a31f5b72a6/original/compactness-matters-improving-bayesian-optimization-efficiency-of-materials-formulations-through-invariant-search-spaces.pdf |
60c73dd3702a9b6aa2189c34 | 10.26434/chemrxiv.5410924.v3 | Bond-length distributions for ions bonded to oxygen: Results for the lanthanides and actinides and discussion of the f-block contraction | Bond-length distributions have been examined for eighty-four configurations of the lanthanide ions and twenty-two configurations of the actinide ions bonded to oxygen. The lanthanide contraction for the trivalent lanthanide ions bonded to O<sup>2-</sup> is shown to vary as a function of coordination number and to diminish in scale with increasing coordination number. | Olivier Charles Gagné | Solid State Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2017-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd3702a9b6aa2189c34/original/bond-length-distributions-for-ions-bonded-to-oxygen-results-for-the-lanthanides-and-actinides-and-discussion-of-the-f-block-contraction.pdf |
64350ff8a41dec1a56de1970 | 10.26434/chemrxiv-2023-tfxr4 | Unexpected Electrophiles in the Atmosphere - Anhydride Nucleophile Reactions and Uptake to Biomass Burning Emissions | Biomass burning is a significant contributor to atmospheric pollution, its emissions have been found to have adverse impacts on climate and human health. Largely, these impacts are dictated by how the composition of the emissions changes once emitted into the atmosphere. Recently, anhydrides have been identified as a significant fraction of biomass burning emissions, however, little is known about their atmospheric evolution, or their interactions within the burn plume. Without this understanding, it is challenging to predict the impact of anhydrides on biomass burning emissions, and by extension, their influence on climate and health. In this study, we investigate anhydrides as potentially unrecognized electrophiles in the atmosphere. Firstly, by exploring their reactivity towards important biomass burning emitted nucleophiles, and secondly, by measuring their uptake on the emissions themselves. Our results show that phthalic and maleic anhydride can react with a wide range of nucleophiles, including hydroxy and amino-containing compounds, such as levoglucosan or aniline. Additionally, using a coated-wall flow tube setup, we demonstrate that anhydrides reactively uptake to biomass burning films and influence their composition. The anhydride nucleophile reaction was found to be irreversible, proceeding without sunlight or free radicals and indicating it may occur during the day or night time. Furthermore, the reaction products were found to be water-stable and contain functional groups which enhance their mass and likely contribute to the formation of secondary organic aerosol, with knock-on climate effects. Overall, our study sheds light on the fundamental chemistry of anhydrides and their potential impacts in the atmosphere. | Max Loebel Roson; Maya Abou-Ghanem; Erica Kim; Shuang Wu; Dylan Long; Sarah Styler; Ran Zhao | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64350ff8a41dec1a56de1970/original/unexpected-electrophiles-in-the-atmosphere-anhydride-nucleophile-reactions-and-uptake-to-biomass-burning-emissions.pdf |
60c750859abda2456bf8da5a | 10.26434/chemrxiv.12400715.v2 | SAMPL7 TrimerTrip Host-Guest Binding Affinities from Extensive Alchemical and End-Point Free Energy Calculations | <p></p><p> The prediction of host-guest binding
affinities with computational modelling is still a challenging task. In the 7<sup>th</sup>
statistical assessment of the modeling of proteins and ligands (SAMPL)
challenge, a new host named TrimerTrip was synthesized and the thermodynamic
parameters of 16 structurally diverse guests binding to the host were
characterized. In the TrimerTrip-guest challenge, only structures of the host
and the guests are provided, which indicates that the predictions of both the
binding poses and the binding affinities are under assessment. In this work,
starting from the binding poses obtained from our previous enhanced sampling
simulations in the configurational space, we perform extensive alchemical and
end-point free energy calculations to calculate the host-guest binding
affinities retrospectively. The alchemical predictions with two widely accepted
charge schemes (i.e. AM1-BCC and RESP) are in good agreement with the
experimental reference, while the end-point estimates perform poorly in
reproducing the experimental binding affinities. Aside from the absolute value
of the binding affinity, the rank of binding free energies is also crucial in
drug design. Surprisingly, the end-point MM/PBSA method seems very powerful in
reproducing the experimental rank of binding affinities. Although the length of
our simulations is long and the intermediate spacing is dense, the convergence
behavior is not very good, which may arise from the flexibility of the host
molecule. Enhanced sampling techniques in the configurational space may be
required to obtain fully converged sampling. Further, as the length of sampling
in alchemical free energy calculations already achieves several hundred ns,
performing direct simulations of the binding/unbinding event in the physical
space could be more useful and insightful. More details about the binding
pathway and mechanism could be obtained in this way. The nonequilibrium method
could also be a nice choice if one insists to use the alchemical method, as the
intermediate sampling is avoided to some extent. </p><p></p> | Zhe Huai; Huaiyu Yang; Xiao Li; Zhaoxi Sun | Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry; Biophysical Chemistry; Physical and Chemical Processes; Statistical Mechanics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750859abda2456bf8da5a/original/sampl7-trimer-trip-host-guest-binding-affinities-from-extensive-alchemical-and-end-point-free-energy-calculations.pdf |
66e1629212ff75c3a103e36c | 10.26434/chemrxiv-2024-jwkc5 | Tracking Dendrites and Solid Electrolyte Interphase Formation with Dynamic Nuclear Polarization - NMR Spectroscopy | Polymer-ceramic composite electrolytes enable safe implementation of Li metal batteries with potentially transformative energy density. Nevertheless, the formation of Li-dendrites and its complex interplay with the Li-metal solid electrolyte interphase (SEI) remain a substantial obstacle which is poorly understood. Here we tackle this issue by a combination of solid-state NMR spectroscopy and Overhauser dynamic nuclear polarization (DNP) which boosts NMR interfacial sensitivity through polarization transfer from the metal conduction electrons. We achieve unprecedented molecular-level insight into dendrites formation and propagation within the composites and determine the composition and properties of their SEI. We find that the dendrite’s quantity and growth path depend on the ceramic content and correlated with battery’s lifetime. We show that the enhancement of Li resonances in the SEI occurs through Li/Li+ charge transfer in Overhauser DNP, allowing us to correlate DNP enhancements and Li transport and directly determine the SEI lithium permeability. These findings have promising implications for SEI design and dendrites management which are essential for the realization of Li metal batteries. | Ayan Maity; Asya Svirinovsky Arbeli; Yehuda Buganim; Chen Oppenheim; Michal Leskes | Physical Chemistry; Materials Science; Energy; Nanostructured Materials - Materials; Energy Storage; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e1629212ff75c3a103e36c/original/tracking-dendrites-and-solid-electrolyte-interphase-formation-with-dynamic-nuclear-polarization-nmr-spectroscopy.pdf |
6723ba66f9980725cfb53954 | 10.26434/chemrxiv-2024-d5x48 | A short scalable route to bis-morpholine spiroacetals and oxazepane analogues: useful 3D-scaffolds for compound library assembly | sp3-Rich molecular scaffolds incorporating nitrogen heterocycles represent important starting points for the assembly of compound screening libraries and drug discovery. Herein, we report a four-step synthesis of a conformationally well-defined sp3-rich scaffold, incorporating two morpholine rings embedded within a spiroacetal framework. The synthesis involves the intermediacy of a 2-chloromethyl-substituted morpholine, accessed from readily available starting materials, namely aminoalcohols and epichlorohydrin. Base-mediated dehydrochlorination affords an exocyclic enol ether, from which the second morpholine ring is constructed in two steps. Scaffold synthesis is high-yielding and can be performed on large scale. The methodology allows ready substitution of one –or both– of the morpholine rings for 1,4-oxazepanes and the generation of 6,7- and 7,7-spiroacetal analogues, which are virtually unexplored in drug discovery. Substituted 6,6-systems can also be prepared, and in some instances, undergo acid-mediated anomerization to deliver the scaffolds in high diastereoselectivity. The two amine functionalities embedded in the 6,6- and 6,7-spiroacetal scaffolds were sequentially functionalized, allowing the generation of a diverse physical compound library. These library compounds occupy a similar chemical space to small-molecule drugs that have been approved for clinical application by the Food and Drug Administration yet are structurally dissimilar, and may therefore act upon novel targets, representing attractive starting materials for drug discovery. | Daniel Kovari; Louise Male; Kimberley Roper; Christian Mang; Oliver Kunz; Liam Cox | Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2024-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6723ba66f9980725cfb53954/original/a-short-scalable-route-to-bis-morpholine-spiroacetals-and-oxazepane-analogues-useful-3d-scaffolds-for-compound-library-assembly.pdf |
66144a4721291e5d1d6905e8 | 10.26434/chemrxiv-2024-p7p42 | Solid-Phase Synthesis of Diverse Macrocycles By Regiospecific 2-Pyridone Formation: Scope and Applications | This study introduces a novel solid-phase macrocyclization method generating 2-pyridone rings. This method relies on the intramolecular condensation between secondary and tertiary dimethoxy-propionic amide (DMPA) units. This selective reaction leads to the formation of a single, well-defined regioisomer. The method demonstrates remarkable efficiency in producing diverse peptidic and non-peptidic bioactive targets, paving the way for the development of innovative macrocycle libraries featuring the 2-pyridone unit. | Skander Abboud; Thomas Kodadek | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66144a4721291e5d1d6905e8/original/solid-phase-synthesis-of-diverse-macrocycles-by-regiospecific-2-pyridone-formation-scope-and-applications.pdf |
6391e4ab0fd99260313d58f2 | 10.26434/chemrxiv-2022-j6lxx | Dimerization/elimination of β-styrylmalonates under action of TiCl4 | A new type of dimerization of dimethyl (β-styryl)malonates in the presence of TiCl4 accompanied by elimination of a methanol molecule was discovered. Selective methods for the synthesis of substituted trimethyl 4-hydroxy-[1,1´-biaryl]-3,3,5(2H)-tricarboxylates and trimethyl 7-hydroxy-9,10-dihydro-5,9-methanobenzo[8]annulene-6,8,8(5H)-tricarboxylates were developed. The regularities of the occurring processes were determined and a similar reaction of β-styrylmalonate with benzylidenemalonate in the presence of TiCl4 was performed in the scope of the suggested mechanism. | Denis Borisov; Grigory Chermashentsev; Konstantin Potapov; Roman Novikov; Yury Tomilov | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6391e4ab0fd99260313d58f2/original/dimerization-elimination-of-styrylmalonates-under-action-of-ti-cl4.pdf |
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