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636fbfc5fbfd38d985dbf1bb | 10.26434/chemrxiv-2022-0wb98 | Selecting the Regularization Parameter in the Distribution of Relaxation Times | Electrochemical impedance spectroscopy (EIS) is a characterization technique used widely in electrochemistry. Obtaining EIS data is simple when modern electrochemical workstations are used; however, analyzing EIS spectra is still a considerable quandary. The distribution of relaxation times (DRT) has emerged as a solution to this challenge. Nevertheless, DRT deconvolution underlies an ill-posed optimization problem, which is often solved by ridge regression (RR). RR’s accuracy strongly depends on the choice of the regularization level as encapsulated in the parameter λ. In this article, five cross-validation methods (i.e., generalized cross-validation, modified generalized cross-validation, robust generalized cross-validation, re-im cross-validation, and k-fold cross-validation) and the L-curve method are studied for the selection of λ. A hierarchical Bayesian DRT (hyper-λ) deconvolution method is also analyzed, whereby λ_0, a parameter analogous to λ, is obtained through cross-validation. The analysis of synthetic data suggests that the values of λ selected by generalized and modified generalized cross-validation are the most accurate among the methods studied. Furthermore, synthetic EIS spectra show that the hyper-λ approach outperforms optimal RR when λ_0 is obtained by generalized and modified generalized cross-validation. This research is expected to foster additional research on the central topic of regularization level selection for DRT analysis. This article not only explores various cross-validation methods, but also provides, through pyDRTtools, an implementation that may serve as a starting point for future research. | Adeleke Maradesa; Baptiste Py; Ting Hei Wan; Mohammed B. Effat; Francesco Ciucci | Materials Science; Energy; Energy Storage; Fuels - Energy Science; Fuel Cells | CC BY 4.0 | CHEMRXIV | 2022-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636fbfc5fbfd38d985dbf1bb/original/selecting-the-regularization-parameter-in-the-distribution-of-relaxation-times.pdf |
672c29745a82cea2fa5487bb | 10.26434/chemrxiv-2024-0q839 | Accuracy of One-Electron Technique for Estimating LUMO Energies of Triphenylamine Derivatives | Accurate estimations of HOMO, LUMO, and HOMO-LUMO energy gaps of organic small molecules (OSMs) are critical to understand experimental observations and assist in rational design of new OSMs in many OSM-based technologies. Recently, a one-electron technique was used to estimate LUMO energies of cyclopenta-fused polycyclic aromatic hydrocarbons and found the technique improves the accuracy of predictions of LUMO and HOMO-LUMO gap. In this work, we evaluated the accuracy of this technique in predicting the LUMO and HOMO-LUMO energy gaps of 4-vinyl-N,N-di(p-tolyl)aniline (MTPA) and its six derivatives from ten functionals: B3LYP, B3PW91, HSEH1PBE, MPW91PW91, CAM-B3LYP, wB97XD, BPV86, PBE, TPSS, and HCTC. This study shows that the accuracies of predictions using the one-electron technique are improved significantly for the results from wB97XD and CAM-B3LYP functionals, while the accuracy of predictions does not improve much for the results from B3LYP, B3PW91, and MOPW1PW91. The accuracy of predictions from BPV86, PBE, TPSS, and HCTC decreases upon using the one-electron technique. | Benjamin Parks; Grant Kelly; Pamela Ubaldo; Peshala Jayamaha; Lichang Wang | Physical Chemistry; Materials Science; Photosensitizers; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672c29745a82cea2fa5487bb/original/accuracy-of-one-electron-technique-for-estimating-lumo-energies-of-triphenylamine-derivatives.pdf |
634d358f4a187610dce6c909 | 10.26434/chemrxiv-2022-t41rx | Optimal bond-constraint topology for molecular
dynamics simulations of cholesterol | We recently observed artificial temperature gradients in molecular dynamics (MD) simulations of phase separating ternary lipid mixtures using the Martini 2 force field. We traced this artifact to insufficiently converged bond length constraints with typical time steps and default settings for the linear constraint solver (LINCS). Here, we systematically optimize the constraint scaffold of cholesterol. With massive virtual sites in an equimomental arrangement, we accelerate bond constraint convergence while preserving the original cholesterol force field and dynamics. The optimized model does not induce nonphysical temperature gradients even at relaxed LINCS settings and is at least as fast as the original model at the strict LINCS settings required for proper thermal sampling. Furthermore, we provide a python script to diagnose possible problems with constraint convergence also for other molecules and force fields. Equimomental constraint topology optimization can also be used to boost constraint convergence in atomistic MD simulations of molecular systems. | Balázs Fábián; Sebastian Thallmair; Gerhard Hummer | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634d358f4a187610dce6c909/original/optimal-bond-constraint-topology-for-molecular-dynamics-simulations-of-cholesterol.pdf |
60c754544c89195617ad44c2 | 10.26434/chemrxiv.13644218.v1 | A General Strategy for C(sp3)–H Functionalization with Nucleophiles Using Methyl Radical as a Hydrogen Atom Abstractor | We have developed a photocatalytic method that employs widely available, low-cost nucleophiles and a readily accessible HAT precursor for C(sp<sup>3</sup>)–H fluorination, chlorination, etherification, thioetherification, azidation, and carbon–carbon bond formation. Mechanistic studies are consistent with methyl radical-mediated HAT and linear free-energy relationships suggest that radical oxidation influences site-selectivity. Furthermore, this approach was highly effective for the construction of multi-halogenated scaffolds and the late-stage functionalization of several bioactive molecules and pharmaceuticals with tunable regioselectivity. | Isabelle Leibler; Makeda A. Tekle-Smith; Abigail Doyle | Organic Synthesis and Reactions; Physical Organic Chemistry; Photocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754544c89195617ad44c2/original/a-general-strategy-for-c-sp3-h-functionalization-with-nucleophiles-using-methyl-radical-as-a-hydrogen-atom-abstractor.pdf |
62307058835f771e2102df7b | 10.26434/chemrxiv-2022-nx4n1 | Weak Dewar bond modulates protonated azaindole photodynamics | Recent experimental work revealed that the lifetime of the S3 state of protonated 7-azaindole is about ten times slower than that of protonated 6-azaindole. We simulated the nonradiative decay pathways of these molecules using trajectory surface hopping dynamics after photoexcitation into S3 to elucidate the reason for this difference. Both isomers mainly follow a common pp* relaxation pathway involving multiple state crossings while coming down from S3 to S1 in the subpicosecond time scale. However, the simulations reveal that the excited-state topographies are such that while the 6-isomer can easily access the region of nonadiabatic transitions, the internal conversion of the 7-isomer is delayed by a pre-Dewar bond formation with a boat conformation. | Ritam Mansour; Saikat Mukherjee; Max Pinheiro Jr; Jennifer A. Noble; Christophe Jouvet; Mario BARBATTI | Theoretical and Computational Chemistry; Physical Chemistry; Photochemistry (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62307058835f771e2102df7b/original/weak-dewar-bond-modulates-protonated-azaindole-photodynamics.pdf |
66f33511cec5d6c142186da9 | 10.26434/chemrxiv-2024-cmvd4 | Simple, Enantiocontrolled Azetidine Library Synthesis via Strain Release Functionalization of 1-Azabicyclobutanes | A simple, modular, programmable approach to access complex stereopure azetidines through strain-release functionalization is disclosed. The synthetic methods developed enable parallel synthesis of stereodefined azetidines that would be otherwise laborious to produce. Given the privileged nature of these structures, a set of ste-reoprobes for use in activity-based protein profiling was prepared and evaluated, revealing proteins in human can-cer cells with were liganded with clear stereo- and chemo-selectivity | Michael Bielecki; Molhm Nassir; Hayden A. Sharma; Nathanyal J. Truax; Nicholas Raheja; Ty M. Thompson; Tamara El-Hayek Ewing; Bruno Melillo; Benjamin F. Cravatt; Phil S. Baran | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Biochemistry; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2024-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f33511cec5d6c142186da9/original/simple-enantiocontrolled-azetidine-library-synthesis-via-strain-release-functionalization-of-1-azabicyclobutanes.pdf |
627fb53944bdd5da106317b8 | 10.26434/chemrxiv-2022-b2rln | Switching Between Hydrogenation and Olefin Transposition Catalysis via NH Cooperativity in Mn(I) pincer complexes | While Mn-catalyzed (de)hydrogenation of carbonyl derivatives have been well established, the reactivity of Mn hydrides with olefins remains very rare. Herein we report the first Mn(I) pincer complex that effectively promotes site-controlled transposition of olefins. This new reactivity is shown to emerge once the N-H functionality within Mn/NH bifunctional complex is suppressed by alkylation. While detrimental for carbonyl (de)hydrogenation, such a masking of the cooperative NH functionality allows for the highly efficient conversion of a wide range of allylarenes to higher-value 1-propenybenzenes in near-quantitative yield with excellent stereoselectivities. The reactivity towards a single positional isomerization was also retained for longer-chain alkenes resulting in the highly regioselective formation of 2-alkenes, which are less thermodynamically stable compared to other possible isomerization products. The detailed mechanistic analysis of reaction between activated Mn catalyst and olefins points to catalysis operating via a metal alkyl mechanism - one of the three conventional transposition mechanisms previously unknown in Mn complexes. | Wenjun Yang; Manuela Weber; Ivan Chernyshov; Evgeny Pidko; Georgy Filonenko | Catalysis; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2022-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627fb53944bdd5da106317b8/original/switching-between-hydrogenation-and-olefin-transposition-catalysis-via-nh-cooperativity-in-mn-i-pincer-complexes.pdf |
60c74d6f337d6c1a4fe27dc0 | 10.26434/chemrxiv.12619064.v1 | Engineering Micromechanics of Soft Porous Crystals for Negative Gas Adsorption | Framework materials at the molecular level, such as metal-organic frameworks (MOF), were recently found to exhibit exotic and counterintuitive micromechanical properties. Stimulated by host-guest interactions, these so-called soft porous crystals can display counterintuitive adsorption phenomena such as negative gas adsorption (NGA). NGA materials are bistable frameworks where the occurrence of a metastable overloaded state leads to pressure amplification upon a sudden framework contraction. How can we control activation barriers and energetics via functionalization of the molecular building blocks that dictate the frameworks’
30 mechanical response? In this work we tune the elastic and inelastic properties of building blocks at the
31 molecular level and analyze the mechanical response of the resulting frameworks. From a set of 11 frameworks, we demonstrate that widening of the backbone increases elasticity, while elongation of the building blocks results in a decrease in critical yield stress of buckling. We further functionalize the backbone
by incorporation of sp3 hybridized carbon atoms to soften the molecular building blocks, or stiffen them with
sp2 and sp carbons. Computational modeling shows how these modifications of the building blocks tune the
36 activation barriers within the energy landscape of the guest-free bistable frameworks. Only frameworks with
free energy barriers in the range of 800 to 1100 kJ mol–1 37 per unit cell, and moderate yield stress of 0.6 to
38 1.2 nN for single ligand buckling, exhibit adsorption-induced contraction and negative gas adsorption. Advanced experimental in situ methodologies give detailed insights into the structural transitions and the adsorption behavior. The new framework DUT-160 shows the highest magnitude of NGA ever observed for nitrogen adsorption at 77 K. Our computational and experimental analysis of the energetics and mechanical response functions of porous frameworks is an important step towards tuning activation barriers in dynamic framework materials and provides critical design principles for molecular building blocks leading to pressure amplifying materials<br /> | Simon Krause; Jack D. Evans; Volodymyr Bon; Irena Senkovska; Sebastian Ehrling; Paul Iacomi; Daniel D. Többens; Dirk Wallacher; Manfred S. Weiss; Bin Zheng; Pascal G. Yot; Guillaume Maurin; Philip L. Llewellyn; François-Xavier Coudert; Stefan Kaskel | Coordination Chemistry (Inorg.); Solid State Chemistry; Supramolecular Chemistry (Inorg.); Computational Chemistry and Modeling; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d6f337d6c1a4fe27dc0/original/engineering-micromechanics-of-soft-porous-crystals-for-negative-gas-adsorption.pdf |
60c73e15bdbb89ab9ba37d83 | 10.26434/chemrxiv.6406886.v1 | The Effect of Tacticity and Side Chain Structure on the Coil Dimensions of Polyolefins | <pre>The key to the discovery of materials with targeted properties lies in the understanding of structure-property relationships. In this work, we evaluate the relationship between the polymer structure and their coil dimensions, and explore new polymers based on these relations. Coil dimensions are important features of polymers which affect their performance in various applications, including drug delivery, waste-water treatment, and engine oils. Coil dimensions of the polyolefins are dependent on the number, size, and stereo orientation of side chains along the backbone. Thus, controlling these attributes allows us to tailor the coil dimensions of polyolefins. In the proposed scheme, we calculate the radius of gyration (<i>R<sub>g</sub></i>) of polyolefin chains using molecular dynamics simulations and validate against experimental results. Simulated annealing is implemented to ensure the capture of different configurations. This model affords the ability to quantify the effect tacticity has on the coil dimensions of polyolefins. The results show the suppression of tacticity effects when the polymer chains transition to bottlebrush structures, demonstrating that the side chain steric hindrance plays an important role in the rigidity of the chain backbone. Further, the model is used to evaluate the compositional effects by determining the rigidity of propylene and 1-hexene copolymers. Combining our model with virtual high-throughput screening techniques, we evaluated the coiling behavior of hundreds of new polymers. Using the screening results, we established correlations between the structure of the side chain and the coil dimensions of polymers.</pre><pre>The supplementary material accompanying this paper includes the library of 275 polymers and their corresponding <i>K<sub>s</sub></i> values.<br /></pre> | Mohammad Atif Faiz Afzal; Jarod M. Younker; George Rodriguez | Oligomers; Organic Polymers; Polymer chains; Computational Chemistry and Modeling; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2018-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e15bdbb89ab9ba37d83/original/the-effect-of-tacticity-and-side-chain-structure-on-the-coil-dimensions-of-polyolefins.pdf |
66833d9201103d79c5b32edc | 10.26434/chemrxiv-2024-hzzd5 | Organophotoredox Pd-Catalyzed C–H Arylation at Room Temperature using Diaryliodonium Salts | Direct functionalization of C–H bonds is the most expeditious strategy to build complexity into organic molecules. Unfortunately, most Pd-catalyzed C–H arylation strategies require high temperatures or stoichiometric oxidants. The creation of metallaphotoredox C–H arylation in 2011 forged a new pathway to achieve arylation at room temperature. Since this discovery, most reports still use explosive diazonium salts as aryl radical precursors. Alternatively, a single report uses bench-stable diaryliodonium salts, albeit with an Ir-based pho-tocatalyst. Herein, we develop an organophotoredox manifold that enables Pd-catalyzed C–H arylation of numerous N-aryl amide sub-strates including the preparation of unsymmetrical m-terphenyl products. The results we present are expected to revitalize the use of dia-ryliodonium salts to achieve room temperature arylations of wide-ranging C–H bond classes. | Christopher Bennett; Nicholas McDonald; Erik Romero | Organic Chemistry; Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66833d9201103d79c5b32edc/original/organophotoredox-pd-catalyzed-c-h-arylation-at-room-temperature-using-diaryliodonium-salts.pdf |
60c754030f50dba931397c61 | 10.26434/chemrxiv.12709538.v2 | Antibody Screening Results for Anti-Nucleocapsid Antibodies Towards the Development of a SARS-CoV-2 Nucleocapsid Protein Antigen Detecting Lateral Flow Assay | <p></p><p>The global COVID-19 pandemic has created an urgent
demand for large numbers of inexpensive, accurate, rapid, point-of-care
diagnostic tests. Analyte-based assays are suitably inexpensive and can be rapidly
mass-produced, but for sufficiently accurate performance they require highly
optimized antibodies and assay conditions. We used an automated liquid handling
system, customized to handle arrays of lateral flow immunoassay (LFA) tests in
a high-throughput screen, to identify anti-nucleocapsid antibodies that will
perform optimally in an LFA. We tested 1021 anti-nucleocapsid antibody pairs as
LFA capture and detection reagents with the goal of highlighting pairs that
have the greatest affinity for unique epitopes of the nucleocapsid protein of
SARS-CoV-2 within the LFA format. In contrast to traditional antibody screening
methods (e.g., ELISA, bio-layer interferometry), the method described here
integrates real-time reaction kinetics with transport in, and immobilization
directly onto, nitrocellulose. We have identified several candidate antibody
pairs that are suitable for further development of an LFA for SARS-CoV-2.</p><p></p> | David Cate; Helen Hsieh; Veronika Glukhova; Joshua D Bishop; H Gleda Hermansky; Brianda Barrios-Lopez; Ben D Grant; Caitlin E Anderson; Ethan Spencer; Samantha Kuhn; Ryan Gallagher; Rafael Rivera; Crissa Bennett; Sam A Byrnes; John T Connelly; Puneet K Dewan; David S. Boyle; Bernhard H Weigl; Kevin P Nichols | Biochemical Analysis | CC BY 4.0 | CHEMRXIV | 2021-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754030f50dba931397c61/original/antibody-screening-results-for-anti-nucleocapsid-antibodies-towards-the-development-of-a-sars-co-v-2-nucleocapsid-protein-antigen-detecting-lateral-flow-assay.pdf |
60c74f6c842e654e33db37fc | 10.26434/chemrxiv.12901304.v1 | Organocatalyzed Fluoride Metathesis | A new organocatalyzed fluoride metathesis reaction between fluoroarenes and carbonyl derivatives is reported. The reaction exchanges fluoride (F–) and alternate nucleophiles (OAc–, CO2R–, SR–, Cl–, CN–, NCS–). The approach provides a conceptually novel route to manipulate the fluorine content of organic molecules. By combining fluorination and defluorination steps into a single catalytic cycle, a byproduct free and 100% atom-efficient reaction can be achieved. | Mark Crimmin; Daniel Mulryan; Andrew J. P. White | Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f6c842e654e33db37fc/original/organocatalyzed-fluoride-metathesis.pdf |
63af138fa2da4bc38c15b8d3 | 10.26434/chemrxiv-2022-q0djp-v2 | Adaptation of Chiral GC into existing undergraduate labs to improve student appreciation of stereochemistry | The critical role of stereochemistry in life, medicine, and industry mandates that stereochemistry is well represented in undergraduate lab curricula. This has primarily been achieved via experiments in the enantiomeric resolution of asymmetric acids and bases followed by polarimetric analysis, NMR analysis using chiral shift reagents, and NMR, GC, and HPLC analysis of diastereomeric derivatives of the chiral molecules. Despite the increasing prevalence of the utility of GCs and LCs fitted with chiral columns in academia and the chemical industry, they have seen limited involvement in undergraduate training. To achieve the stereochemical laboratory requirements without sacrificing existing lab techniques, we have modified two standard laboratory experiments to include chiral GC analysis as follows: (1) The extraction of carvone from spearmint leaves and caraway seeds via steam distillation or other extraction methods is a lab widely used to demonstrate stereochemistry. However, the analysis of the products from the extraction is often limited to thin-layer chromatograms that confirm the presence of carvone and shows that the enantiomers have similar polarity. By including a GC method using a β-DEX™ 225 column in this lab, students were able to compare retention times of the spearmint and caraway extracts with those in a racemic mixture, then predict whether they are R or S by comparing with an injection of a pure R-carvone sample. (2) The reduction of aldehydes and ketones is another common experiment done in most institutions. Sodium borohydride reduction of acetophenone produced a racemic mixture which was observed as two retention times on the chromatogram. Reduction using the two enantiomers of commercially available CBS catalysts provided relatively enantiopure alcohols. Students could predict which enantiomers resulted from each enantiomer of the CBS catalyst by comparing it with a commercially obtained enantiopure alcohol. They also used chromatographic data to calculate the enantiomeric excess from their reactions. The experiments also teach students other essential techniques like inert-atmosphere techniques, thin-layer chromatography, the use of multivendor software for analysis, and the effect of reaction conditions on product yield and stereochemistry | Nicholas Griffin; Marshall Ritchie; Tyler Lynn; Kate Dear; Tyler Deutsch; Leigha Dillard; Barnabas Otoo | Chemical Education; Chemical Education - General | CC BY 4.0 | CHEMRXIV | 2023-01-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63af138fa2da4bc38c15b8d3/original/adaptation-of-chiral-gc-into-existing-undergraduate-labs-to-improve-student-appreciation-of-stereochemistry.pdf |
60c75032469df4438ff44815 | 10.26434/chemrxiv.13005344.v1 | Ordered LiNi0.5Mn1.5O4 Cathode in Bis(fluorosulfonyl)imide-Based Ionic Liquid Electrolyte: Importance of the Cathode-Electrolyte Interphase | <div><div><div><p>The high voltage (4.7 V vs. Li+ /Li) spinel lithium nickel manganese oxide (LiNi0.5 Mn1.5 O4 , LNMO) is a promising candidate for the next-generation of lithium ion batteries due to its high energy density, low cost and environmental impact. However, poor cycling performance at high cutoff potentials limits its commercialization. Herein, hollow structured LNMO is synergistically paired with an ionic liquid electrolyte, 1M lithium bis(fluorosulfonyl)imide (LiFSI) in N-propyl-N-methylpyrrolidinium bis(fluorosulfonyl)imide (Pyr1,3 FSI) to achieve stable cycling performance and improved rate capability. The optimized cathode-electrolyte system exhibits extended cycling performance (>85% capacity retention after 300 cycles) and high rate performance (106.2mAhg–1 at 5C) even at an elevated temperature of 65 ◦C. X-ray photoelectron spectroscopy and spatially resolved x-ray fluorescence analyses confirm the formation of a robust, LiF-rich cathode electrolyte interphase. This study presents a comprehensive design strategy to improve the electrochemical performance of high-voltage cathode materials.</p></div></div></div> | Hyeon Jeong Lee; Zachary Brown; Ying Zhao; Jack Fawdon; Weixin Song; Ji Hoon Lee; Mauro Pasta | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75032469df4438ff44815/original/ordered-li-ni0-5mn1-5o4-cathode-in-bis-fluorosulfonyl-imide-based-ionic-liquid-electrolyte-importance-of-the-cathode-electrolyte-interphase.pdf |
60c75009337d6c9c41e2821c | 10.26434/chemrxiv.12982217.v1 | Insight into the Scope and Mechanism for Transmetallation of Hydrocarbyl Ligands on Complexes Relevant to C-H Activation | <div><div><div><p>We report the transmetallation of hydrocarbyl fragments (Me, Bn, Ph) from a variety of organo-metallic complexes relevant to C-H activation (Ir, Rh, W, Mo) to Pt(II) electrophiles. The scope of suitable hydrocarbyl donors is remarkable in that three different classes of organometallics with widely varying reactivity all undergo the same general reaction with Pt(II) electrophiles. A competitive substituent effect experiment reveals faster transmetallation of more electron rich hydrocarbyl groups. A sterochemical probe reveals that transmetallation to Hg(II) proceeds with retention of stereochemistry. This study suggests that transmetallation could provide a viable path for catalytic function- alization of stable complexes resulting from C-H bond activation and other processes.</p></div></div></div> | Natalie Chan; Joseph
J. Gair; Michael Roy; Yehao Qiu; Duo-Sheng Wang; Landon J. Durak; Liwei Chen; Alexander S. Filatov; Jared C. Lewis | Catalysis; Kinetics and Mechanism - Organometallic Reactions; Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75009337d6c9c41e2821c/original/insight-into-the-scope-and-mechanism-for-transmetallation-of-hydrocarbyl-ligands-on-complexes-relevant-to-c-h-activation.pdf |
6144a11aa7b249f19c2e2bf2 | 10.26434/chemrxiv-2021-v8qzs | Probing Molecular Chirality of Ground and
Electronically Excited States in the UV-vis and
X-ray Regimes: An EOM-CCSD Study | We present several strategies for computing electronic circular dichroism (CD) spectra across different frequency ranges at the equation-of-motion coupled-cluster singles
and doubles level of theory. CD spectra of both ground and electronically excited states are discussed. For selected cases, the approach is compared with coupled-cluster linear
response results as well as time-dependent density functional theory. The extension of the theory to include the effect of spin-orbit coupling is presented and illustrated by
calculations of X-ray CD spectra at the L edge. | Josefine Andersen; Kaushik D. Nanda; Anna I. Krylov; Sonia Coriani | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6144a11aa7b249f19c2e2bf2/original/probing-molecular-chirality-of-ground-and-electronically-excited-states-in-the-uv-vis-and-x-ray-regimes-an-eom-ccsd-study.pdf |
6570ea7c29a13c4d47ce600d | 10.26434/chemrxiv-2023-6dhn7 | Phage display against two-dimensional metal-organic nanosheets as a new route to highly selective biomolecular recognition surfaces | Peptides are important biomarkers for a range of diseases, however distinguishing different amino-acid sequences using artificial receptors remains a major challenge in biomedical sensing. Here we present a new approach to creating highly selective recognition surfaces using phage display biopanning against metal-organic nanosheets (MONs) and demonstrate their use as the next-generation of biomolecular recognition surfaces. Three MONs (ZIF-7, ZIF-7-NH2 and Hf-BTB-NH2) were chosen as initial targets to demonstrate how simple synthetic modifications can enhance selectivity towards specific amino acid sequences. Each MON system was added to a solution containing every possible combination of 7-residue peptides attached to bacteriophage hosts and the highest affinity binding peptides for each system was identified via successive biopanning rounds. In each case only a single peptide sequence was isolated (YNYRNLL – ZIF-7, NNWWAPA – ZIF-7-NH2 and FTVRDLS – Hf-BTB-NH2). This indicates that these MONs are highly selective, which is attributed to their 2D nanosheet structure. Zeta potential and contact angle measurements were conducted on each MON and combined with calculated properties for the peptide sequences and binding studies to provide insights into the relative importance of electrostatic, hydrophobic and co-ordination bonding interactions. A quartz crystal microbalance (QCM) was used to model phage binding and the Hf-BTB-NH2 MON coated QCM produced a 5-fold higher signal for FTVRDLS functionalised phage compared to phage with generic peptide sequences. Further studies focusing on Hf-BTB-NH2 confirmed that the VRDL sequence was highly conserved, and on-target binding exhibited equilibrium dissociation constants that are comparable to natural recognition materials. Surface plasmon resonance (SPR) studies indicated a 4600-fold higher equilibrium dissociation constant (KD) for FTVRDLS compared to those obtained for off-target sequences, comparable to those of antibodies (KD = 4 x10-10). We anticipate that the highly tunable nature of MONs will enhance our understanding of binding interactions and enable molecular recognition of biomedically important peptides. | Amelia C. Wood; Edwin C. Johnson; Ram R. R. Prasad; Mark V. Sullivan; Nicholas W. Turner; Steven P. Armes; Sarah S. Staniland; Jonathan A. Foster | Biological and Medicinal Chemistry; Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Coordination Chemistry (Inorg.); Chemical Biology | CC BY 4.0 | CHEMRXIV | 2023-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6570ea7c29a13c4d47ce600d/original/phage-display-against-two-dimensional-metal-organic-nanosheets-as-a-new-route-to-highly-selective-biomolecular-recognition-surfaces.pdf |
67533ef6085116a133988d14 | 10.26434/chemrxiv-2024-4qn97 | Exploring the Atomic-Scale Interactions at the Interface of Reducible Oxide and Ruthenium Nanocatalyst in Ammonia Decomposition | Reconstructing interfaces at the atomic level through interactions between precious metal catalysts and highly stable oxides opens new possibilities for enhancing inherent catalytic properties. Here, we investigate the interactions between metal oxide particles and Ru nanoparticles formed through the pyrolysis of metal-organic frameworks (MOFs) composed of oxide clusters with varying reducibility, accompanied by Ru precursor ions in an oxygen-suppressed, high-temperature environment. This study utilizes the ammonia decomposition reaction as a probe to examine these interactions. Despite having an ideal size of 2.3 nm for ammonia decomposition, Ru nanoparticles interacting strongly with reducible CeO2 nanoparticles exhibit relatively low conversion rates. Post-catalysis, X-ray absorption spectroscopy (XAS) analysis reveals changes at the interface between CeO2 and Ru particles, shedding light on the correlation between the electron occupancy of Ru nanoparticles and their catalytic activity for ammonia decomposition. | Mansu Kim; Jian Liu; Jonghwan Park; Sohui Kim; Kunmo Koo; Vinayak P. Dravid; Dongmok Whang; Joseph T. Hupp | Materials Science; Catalysts | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67533ef6085116a133988d14/original/exploring-the-atomic-scale-interactions-at-the-interface-of-reducible-oxide-and-ruthenium-nanocatalyst-in-ammonia-decomposition.pdf |
6170964045f1ee16e8344643 | 10.26434/chemrxiv-2021-85xnl | Understanding the Origins of Changing the Product Specificity Properties of Arginine Methyltransferase PRMT7 by E181→D and E181→D/Q329→A Mutations: A QM/MM Study | Arginine methylations can regulate important biological processes and affect many cellular activities, and the enzymes that catalyze the methylations are protein arginine methyltransferases (PRMTs). The biological consequences of arginine methylations depend on the methylation states of arginine that are determined by the PRMT’s product specificity. Although the product specificity is a very important property, it is still unknown concerning why different PRMTs may generate different methylation states for the target arginine residues on protein substrates. PRMT7 is the only known member of Type III PRMT that produces mono-methylarginine (MMA) product. Interestingly, its E181D and E181D/Q329A mutants can catalyze, respectively, the formation of asymmetrically di-methylated arginine (ω-NG, NG-dimethylarginine or ADMA) and symmetrically di-methylated arginine (ω-NG, N'G-dimethylarginine or SDMA). The exact reasons for such product specificity modification as a result of the mutations have been unclear. Here QM/MM molecular dynamics (MD) and potential of mean force (PMF) free-energy simulations are performed for the E181D and E181D/Q329A mutants to understand the catalytic mechanism and the origin of their different product specificities from that of the wild-type PRMT7 as well as between E181D and E181D/Q329A. The simulations show that while the free energy barriers of E181D and E181D/Q329A for the first methylation are higher than that of the wild type, E181D and E181D/Q329A have the ability to add the second methyl group to the target mono-methyl arginine and generate ADMA and SDMA, respectively. The free energy barriers for E181D and E181D/Q329A to produce ADMA and SDMA, respectively, are considerably lower than the corresponding barriers involving the wild-type enzyme. Moreover, the computational study identifies some important structural, electronic and dynamic features that lead to the different product specificities and activities of the wild-type PRMT7, E181D and E181D/Q329A. These factors may play important roles in controlling the activity and product specificity of other PRMTs as well. | Wan-Sheng Ren; Adua Rahman; Kai-Bin Jiang; Hao Deng; Yuan-Yuan Zhao; Wei-Jie Zhang; Kedian Liu; Ping Qian; Hong Guo | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6170964045f1ee16e8344643/original/understanding-the-origins-of-changing-the-product-specificity-properties-of-arginine-methyltransferase-prmt7-by-e181-d-and-e181-d-q329-a-mutations-a-qm-mm-study.pdf |
672ba1127be152b1d036bfee | 10.26434/chemrxiv-2024-zq975 | Accurate Free Energy Calculation via
Multiscale Simulations Driven by Hybrid
Machine Learning and Molecular Mechanics
Potentials | Our study focused on the implementation and testing of machine learning interatomic potentials (MLIPs) into the AMBER software suite. This implementation enables us to perform a novel type of molecular dynamics simulation utilizing the hybrid machine learning/molecular mechanics (ML/MM) potentials. To underpin the capabilities of ML/MM simulations, we first validated our implementation at a fundamental physical level by confirming energy and momentum conservation laws. The successful validation indicates that our implementation is able to produce adequate and physically interpretable samplings. Building upon this, for the first time to the best of our knowledge, we proposed an ML/MM-compatible thermodynamic integration (TI) protocol to tackle real-world challenges, such as solvation free energy calculation. Our results demonstrate that this computational protocol can predict hydration free energies with an accuracy of less than 1.00 kcal/mol compared to experimental data, paving the way for the use of ML/MM in multiscale simulations to addressing future drug design problems. Moreover, by applying ML/MM in molecular dynamics simulations of protein-ligand complexes, we demonstrated that the adequate samplings enable us to accurately reproduce experimental binding free energies. Thus, our implementation can offer new insights into biomolecular systems using the ML/MM "microscope". Last, we demonstrated that our implementation can achieve nanosecond timescale simulations daily after significant effort being put to improve the code performance. In a conclusion, we have successfully implemented ML/MM potential to AMBER software package after overcoming limitations in current multi-scale simulations including low computational efficiency. We have advanced TI theory allowing us to accurately predict free energies with ML/MM potentials. | Xujian Wang; Junmei Wang; Xiongwu Wu; Bernard Brooks | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672ba1127be152b1d036bfee/original/accurate-free-energy-calculation-via-multiscale-simulations-driven-by-hybrid-machine-learning-and-molecular-mechanics-potentials.pdf |
65c4b37266c1381729357802 | 10.26434/chemrxiv-2024-thvq5 | Breaking Cycles: Saponification-Enhanced NMR Fingerprint Matching for the Identification and Stereochemical evaluation of cyclic lipodepsipeptides from natural sources | We previously described NMR based fingerprint matching using peptide backbone (CHα) resonances as a fast and reliable way to perform structural dereplication of Pseudomonas cyclic lipodepsipeptides (CLiPs). In addition, its combination with total synthesis of a small library of CLiPs was shown to afford unambiguous determination of the stereochemistry, further opening these compounds for structure-activity relationship studies and three-dimensional structure determination. However, the need to include on-resin macrocycle formation in the synthetic workflow results in considerable burden and limits universal applicability to CLiPs. Here we show that this drawback can be removed by first converting the native CLiP of interest into its linearized analogue via controlled hydrolysis of the depsi bond through saponification. By avoiding the macrocycle formation altogether, the required synthesis effort is strongly reduced as it now only requires production of linear peptide analogues. The NMR fingerprints of the linear peptide analogues display a sufficiently distinctive chemical shift fingerprint to act as effective discriminators. The approach is developed using viscosin group CLiPs and subsequently demonstrated on putisolvin, leading to a structural revision, and tanniamide, a newly isolated compound defining a new group in the Pseudomonas CLiP portfolio. These examples demonstrate the effectiveness of the saponification- enhanced approach that broadens applicability of NMR fingerprint matching for the determination of the stereochemistry of CLiPs. | Penthip Muangkaew; Durga Prasad; Vic De roo; Yentl Verleysen; René De Mot; Monica Höfte; Annemieke Madder; Niels Geudens; José Martins | Organic Chemistry; Earth, Space, and Environmental Chemistry; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c4b37266c1381729357802/original/breaking-cycles-saponification-enhanced-nmr-fingerprint-matching-for-the-identification-and-stereochemical-evaluation-of-cyclic-lipodepsipeptides-from-natural-sources.pdf |
60c74293bdbb892564a384fd | 10.26434/chemrxiv.8312375.v1 | Blinded Prediction of Protein-Ligand Binding Affinity Using Amber Thermodynamic Integration for the 2018 D3R Grand Challenge 4 | <p>In the framework of the 2018 Drug Design Data Resource (D3R)
grand challenge 4, blinded predictions on relative binding free energy were
performed for a set of 39 ligands of the Cathepsin S. We leveraged the GPU-accelerated
thermodynamic integration (GTI) of Amber 18 to advance our computational
prediction. When our entry was compared to experimental results, good
correlation was observed (Kendall’s τ: 0.62, Spearman’s ρ: 0.80 and Pearson’s R:
0.82), with the highest correlation to experiment among all submissions. We designing a parallelized transformation map that placed ligands into
several groups based on common alchemical substructures; TI transformations were
carried out for each ligand to the relevant substructure, and between
substructures. Our calculations were all conducted using the linear potential
scaling scheme in Amber TI because we believe the softcore potential/dual
topology approach implemented in current Amber TI is highly fault-prone. The
issue was illustrated by using two examples in which typical preparation for
the dual topology approach of Amber TI fails. Overall, the high accuracy of our
prediction is a result of recent advances in force fields (ff14SB and GAFF), as
well as rapid calculation of ensemble averages enabled by the GPU
implementation of Amber. The success in a blinded prediction strongly suggests
that alchemical free energy calculation in Amber is a promising tool for future
commercial drug design.</p> | Junjie Zou; Chuan Tian; Carlos Simmerling | Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74293bdbb892564a384fd/original/blinded-prediction-of-protein-ligand-binding-affinity-using-amber-thermodynamic-integration-for-the-2018-d3r-grand-challenge-4.pdf |
60c7476e469df45e7df43804 | 10.26434/chemrxiv.9917399.v2 | Development and Comparison of Formula Assignment Algorithms for Ultrahigh-Resolution Mass Spectra of Natural Organic MatterDevelopment and Comparison of Formula Assignment Algorithms for Ultrahigh-resolution Mass Spectra of Natural Organic Matter | Increasing number of application of ultrahigh-resolution mass spectrometry (UHR-MS) to natural organic matter (NOM) characterization requires an efficient and accurate formula assignment from a number of mass data. Herein, we newly developed two automated batch codes (namely TRFu and FuJHA) and assessed their formula assignment accuracy together with frequently used open access algorithms (i.e., Formularity and WHOI). Overall assignment accuracy for 8,719 NOM-like emerging chemicals with known molecular formulae (mass range from 68 Da to 1,000 Da) was highest (94%) for TRFu. TRFu also showed the highest formula assignment rate (98.6%) for totally 76,880 UHR-MS peaks from 35 types of NOM (e.g., aquatic, soil/sediment, biochar). Therefore, as a reliable and practically feasible tool, the automated batch TRFu (freely available at ChemRxiv, DOI:10.26434/chemrxiv.9917399) can precisely characterize UHR-MS spectra of various NOM and could be extended to non-target screening of NOM-like emerging chemicals in natural and engineered environments including drinking water sources and wastewater effluents.<br /> | Qing-Long Fu; Manabu Fujii; Thomas Riedel | Environmental Science; Geochemistry; Soil Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7476e469df45e7df43804/original/development-and-comparison-of-formula-assignment-algorithms-for-ultrahigh-resolution-mass-spectra-of-natural-organic-matter-development-and-comparison-of-formula-assignment-algorithms-for-ultrahigh-resolution-mass-spectra-of-natural-organic-matter.pdf |
66ba12a25101a2ffa81768a5 | 10.26434/chemrxiv-2024-x4fdr-v2 | Selection for Photocatalytic Function through Darwinian Evolution of Synthetic Self-Replicators | The onset of Darwinian evolution represents a key step in the transition of chemical systems into living ones. Here, we show the emergence of Darwinian evolution in two systems of self-replicating molecules, where natural selection favors replicator mutants best capable of catalyzing the production of the precursors required for their own replication. Such selection for protometabolic activity was observed in a system where trimer and hexamer replicators compete for common resources, as well as in a system of different hexamer replicator mutants. An out-of-equilibrium replication-destruction regime was implemented in a flow reactor, where replication from continuously supplied dithiol building blocks needs to keep up with “destruction” by outflow. Selection occurred based on the ability of the mutants to activate a cofactor that photocatalytically produces singlet oxygen which, in turn, enhances the rate by which dithiol building blocks are converted into disulfide-based replicator precursors. Selection was based on a functional trait (catalytic activity) opening up Darwinian evolution as a tool for catalyst development. This work functionally integrates self-replication with protometabolism and Darwinian evolution and marks a further advance in the de-novo synthesis of life. | Kai Liu; Omer Markovitch; Chris van Ewijk; Yari Katar Knelissen; Armin Kiani; Marcel Eleveld; Wouter H. Roos; Sijbren Otto | Organic Chemistry; Catalysis; Supramolecular Chemistry (Org.); Photocatalysis | CC BY NC 4.0 | CHEMRXIV | 2024-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ba12a25101a2ffa81768a5/original/selection-for-photocatalytic-function-through-darwinian-evolution-of-synthetic-self-replicators.pdf |
6648a92a21291e5d1d9f8357 | 10.26434/chemrxiv-2024-sq8nh | Ab initio Accuracy Neural Network Potential for Drug-like Molecules | The advent of machine learning (ML) in computational chemistry heralds a transformative approach to one of the quintessential challenges in computer-aided drug design (CADD): the accurate and cost-effective calculation of atomic interactions. By leveraging a neural network (NN) potential, we address this balance and push the boundaries of the NN potential's representational capacity. Our work details the development of a robust general-purpose NN potential, architected on the framework of DPA-2, a deep learning potential with attention, which demonstrates remarkable fidelity in replicating the interatomic potential energy surface for drug-like molecules comprising eight critical chemical elements: H, C, N, O, F, S, Cl, and P. We employed state-of-the-art molecular dynamic techniques, including temperature acceleration and enhanced sampling, to construct a comprehensive dataset to ensure exhaustive coverage of relevant configurational spaces. Our rigorous testing protocols, including torsion scanning, global minimum searches, and high-temperature MD simulations across various organic molecules, have culminated in an NN model that achieves chemical precision commensurate with the highly regarded DFT model, while significantly outstripping the accuracy of prevalent semi-empirical methods. This study presents a leap forward in the predictive modelling of molecular interactions, offering extensive applications in drug development and beyond. | Manyi Yang; Duo Zhang; Xinyan Wang; Lingfeng Zhang; Tong Zhu; Han Wang | Theoretical and Computational Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6648a92a21291e5d1d9f8357/original/ab-initio-accuracy-neural-network-potential-for-drug-like-molecules.pdf |
60c757ecbdbb891443a3accd | 10.26434/chemrxiv.14481375.v1 | Substitution Effects on a New Pyridylbenzimidazole Acceptor for Thermally Activated Delayed Fluorescence and Their Use in Organic Light-Emitting Diodes | <p>In this work we introduce a new acceptor for use in thermally activated delayed fluorescence (TADF) emitters, pyridylbenzimidazole, which when coupled with phenoxazine, allows efficient TADF occurs. <i>N</i>-functionalization of the benzimidazole using methyl, phenyl and <i>tert</i>-butyl groups permits colour tuning and adjustment of the optoelectronic properties and suppression of aggregation-caused quenching (ACQ) with minimal impact on the TADF mechanism. Good photoluminescence quantum yields, F<sub>PL</sub>, (49% - 68%) in mCP-doped films are reported for the emitters. The functionalized derivatives support a higher doping of 7 wt% before a fall-off in F<sub>PL</sub> is observed, in contrast with the parent compound, which undergoes ACQ at doping concentrations greater than 1 wt%. We find complex conformational dynamics, reflected in the time-resolved decay profile. D<i>E</i><sub>ST</sub> is modulated by N-substituents of the benzimidazole and ranges of between 0.22 eV and 0.32 eV in doped films. Density Functional Theory (DFT) calculations suggest the importance of intermediate triplet excited states to enhance the RISC rate. Vacuum-deposited organic light-emitting diodes (OLEDs), prepared using three of the four analogs show maximum external quantum efficiencies, EQE<sub>max</sub>, of 23.9%, 22.2% and 18.6% for <b>BIm(Me)PyPXZ</b>, <b>BIm(Ph)PyPXZ</b> and <b>BImPyPXZ</b>, respectively, with a correlated and modest efficiency roll-off at 100 cd m<sup>-2</sup> of 19% 13%, and 24% of the EQE<sub>max</sub>, respectively; higher maximum luminance values of 21,000 cd m<sup>-2</sup> and 18,000 cd m<sup>-2 </sup>are also obtained for <b>BIm(Ph)PyPXZ</b> and <b>BIm(Me)PyPXZ</b>, respectively, compared to 8,000 cd m<sup>-2</sup> for <b>BImPyPXZ</b>.</p> | David Hall; P Rajamalli; Eimantas Duda; Subeesh Madayanad Suresh; Francesco Rodella; Sergey Bagnich; Cameron Carpenter-Warren; David Cordes; Alexandra Slawin; Peter Strohriegl; David Beljonne; Anna Köhler; Yoann Olivier; Eli Zysman-Colman | Organic Compounds and Functional Groups; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757ecbdbb891443a3accd/original/substitution-effects-on-a-new-pyridylbenzimidazole-acceptor-for-thermally-activated-delayed-fluorescence-and-their-use-in-organic-light-emitting-diodes.pdf |
61ce4cdb5b23d409b30f476b | 10.26434/chemrxiv-2021-zp9z3 | Origin of the Bright Photoluminescence of Thiolate-protected Gold Nanoclusters: Confined Structural Water Molecules as Real Emitters | The availability of a range of excited states has enriched zero-, one- and two- dimensional quantum nanomaterials with interesting luminescence properties, in particular for noble metal nanoclusters (NCs) as typical examples. But, the elucidation and origin of optoelectronic properties remains elusive. In this report, using widely used Au(I)-alkanethiolate complex (Au(I)-SRs, R = -(CH2)12H) with AIE characteristics as a model system, by judiciously manipulating the delicate surface ligand interactions at the nanoscale interface, together with a careful spectral investigations and an isotope diagnostic experiment of heavy water (D2O), we evidenced that the structural water molecules (SWs) confined in the nanoscale interface or space are real emitter centers for photoluminescence (PL) of metal NCs and the aggregate of Au(I)-SRs complexes, instead of well-organized metal core dominated by quantum confinement mechanics. Interestingly, the aggregation of Au(I)-SRs generated dual fluorescence-phosphorescence emission and the photoluminescence intensity was independent on the degree of aggregation but showed strong dependency on the content and state of structural water molecules (SWs) confined in the aggregates. SWs are different from traditional hydrogen bonded water molecules, wherein, due to interfacial adsorption or spatial confinement, the p orbitals of two O atoms in SWs can form a weak electron interaction through spatial overlapping, which concomitantly constructs a group of interfacial states with π bond characteristics, consequently providing some alternative channels (or pathways) to the radiation and/or non-radiation relaxation of electrons. Our results provide completely new insights to understand the fascinating properties (including photoluminescence, catalysis and chirality, etc.) of other low-dimension quantum dots and even for aggregation-induced emission luminophores (AIEgens). This also answers the century old debate on whether and how water molecules emit bright color. | Bo Peng; kun zhang | Physical Chemistry; Nanoscience; Interfaces; Photochemistry (Physical Chem.); Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ce4cdb5b23d409b30f476b/original/origin-of-the-bright-photoluminescence-of-thiolate-protected-gold-nanoclusters-confined-structural-water-molecules-as-real-emitters.pdf |
675aed39f9980725cfd82977 | 10.26434/chemrxiv-2024-qs8d7-v2 | Relaxation optimized heteronuclear experiments for extending the size limit of RNA nuclear magnetic resonance | The application of NMR to large RNAs has been limited by the inability to perform heteronuclear correlation experiments essential for resolving overlapping 1H NMR signals, determining inter-proton distance restraints and inter-helical orientations for structure calcula-tions, and evaluating conformational dynamics. Approaches exploiting 1H-13C correlations that are routinely applied to proteins and small RNAs of ~60 nucleotides or fewer are impractical for larger RNAs due to rapid dipolar relaxation of protons by their attached car-bons. Here we report a 2H-enhanced, 1H-15N correlation approach that enables atom-specific NMR characterization of much larger RNAs. Purine H8 transverse relaxation rates are reduced ~20-fold with ribose perdeuteration, enabling efficient magnetization transfer via two-bond 1H-15N couplings. We focus on H8-N9 correlation spectra which benefit from favorable N9 chemical shift anisotropy. Chemical shift assignment is enabled by retention of protons at the C1′ position, which allow measurement of two-bond H1′-N9 and through-space H1′-H8 correlations with only a minor effect on H8 relaxation. The approach is demonstrated for the 232 nucleotide HIV-1 Rev response element, where chemical shift assignments, 15N-edited nuclear Overhauser effects, and 1H-15N residual dipolar couplings are readily obtained from sensitive, high-resolution spectra. Heteronuclear correlated NMR methods that have been essential for the study of proteins can now be extended to RNAs of at least 78 kDa. | Aarsh Shah; Heer Patel; Arjun Kanjarpane; Michael Summers; Jan Marchant | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675aed39f9980725cfd82977/original/relaxation-optimized-heteronuclear-experiments-for-extending-the-size-limit-of-rna-nuclear-magnetic-resonance.pdf |
60c74e680f50db59d03971fb | 10.26434/chemrxiv.12751154.v1 | H2 Evolution from H2O via O–H Oxidative Addition Across a 9,10-Diboraanthracene | The boron-centered water reactivity of the boroauride complex
([Au(B2P2)][K(18-c-6)]; (B2P2, 9,10-bis(2-(diisopropylphosphino)-
phenyl)-9,10-dihydroboranthrene) and its corresponding twoelectron oxidized complex, Au(B2P2)Cl, are presented. The
tolerance of Au(B2P2)Cl towards H2O was demonstrated and
subsequent hydroxide/chloride exchange was acheived in the
presence of H2O and triethylamine to afford Au(B2P2)OH.
Au(B2P2)]Cl and [Au(B2P2)]OH are poor Lewis acids as judged by the
Gutmann-Becket method, with [Au(B2P2)]OH displaying facile
hydroxide exchange between B atoms of the DBA ring as evidenced
by variable temperature 31P NMR and low temperature 1H and 11B
NMR. The reaction of the reduced boroauride complex [Au(B2P2)]–
with 1 equivalent of H2O produces a hydride/hydroxide product,
[Au(B2P2)(H)(OH)]–, that, upon addition of a second equivalent of
H2O, rapidly evolves H2 to yield the dihydroxide compound,
[Au(B2P2)(OH)2]–. [Au(B2P2)]Cl can be regenerated from
[Au(B2P2)(OH)2]– via HCl·Et2O, providing a synthetic cycle for H2
evolution from H2O enabled by O–H oxidative addition at a
diboraanthracene unit. | Jordan W. Taylor; William Harman | Coordination Chemistry (Inorg.); Main Group Chemistry (Inorg.); Main Group Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e680f50db59d03971fb/original/h2-evolution-from-h2o-via-o-h-oxidative-addition-across-a-9-10-diboraanthracene.pdf |
60c744ff469df42de0f43429 | 10.26434/chemrxiv.9761633.v1 | Fc-Binding Antibody-Recruiting Molecules for Cancer Therapy: Exploiting Endogenous IgG Without antigen–Fab Interactions | <div><div><div><p>Small molecules emulating the effector functions of antibodies have potential clinical benefits because of their low immunogenicity. Antibody-recruiting molecules (ARMs) are bispecific molecules designed to redirect endogenous antibodies to targets. However, endogenous antibodies show intra/inter-patient differences regarding their concentrations and affinities, limiting the potential of ARMs. We sought to address this issue using a Fc-binding peptide instead of an antigen for antibody redirection. Fc-binding ARM (Fc-ARM) targeting folate receptor-α (FR-α) expressed on cancer cells, formed a ternary complex of Fc-ARM, FR-α, and antibody on cancer cells. The ability of this ternary complex to activate natural killer cells was positively correlated with its Fc affinity, and did not require the Fab region. Fc-ARM hitchhiked on pooled human IgG to enhance its blood retention, and suppressed tumor growth in a mouse xenograft model of human cancer. Thus, Fc-ARM has the potential to be employed as a less immunogenic alternative to therapeutic antibodies.</p></div></div></div> | Koichi Sasaki; Minori Harada; Yoshiki Miyashita; Hiroshi Tagawa; Akihiro Kishimura; Takeshi Mori; Yoshiki Katayama | Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744ff469df42de0f43429/original/fc-binding-antibody-recruiting-molecules-for-cancer-therapy-exploiting-endogenous-ig-g-without-antigen-fab-interactions.pdf |
60c742f0337d6c4515e26b0a | 10.26434/chemrxiv.8346107.v2 | Synthesis and Mechanism of Action of Group a Streptogramin Antibiotics That Overcome Resistance | <div>
<div>
<p>Natural products serve as chemical blueprints for the majority of classes of antibiotics in our clinical arsenal. The evolutionary process by which these molecules arise is inherently accompanied by the co-evolution of resistance mechanisms that shorten the clinical lifetime of any given class.
Virginiamycin acetyltransferases (Vats) are resistance proteins that provide protection against
streptogramins, potent Gram-positive antibiotics that inhibit the bacterial ribosome. Due to the
challenge of selectively modifying the chemically complex, 23-membered macrocyclic scaffold of
group A streptogramins, analogs that overcome Vat resistance have not been previously accessible. Here we report the design, synthesis, and antibacterial evaluation of group A streptogramin antibiotics
with unprecedented structural variability. Using cryo-electron microscopy and forcefield-based
refinement, we characterize the binding of eight analogs to the bacterial ribosome at high resolution
(2.4-2.8 Å), revealing new binding interactions that extend into the peptidyl tRNA binding site and
towards synergistic binders that occupy the nascent peptide exit tunnel. Two of these analogs have excellent activity against a streptogramin-resistant strain of S. aureus expressing VatA and exhibit
decreased acetylation rates in vitro. Our results demonstrate that the combination of rational design
and modular chemical synthesis can revitalize classes of antibiotics that are limited by naturally arising resistance mechanisms.</p></div></div> | Qi Li; Jenna Pellegrino; D. John Lee; Arthur Tran; Ruoxi Wang; Jesslyn Park; Kaijie Ji; David Chow; Na Zhang; Axel Brilot; Justin Biel; Gydo van Zundert; Ken Borrelli; Dean Shinabarger; Cindy Wolfe; Beverly Murray; Matthew Jacobson; James Fraser; Ian Seiple | Natural Products; Biochemistry; Biophysics; Chemical Biology; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742f0337d6c4515e26b0a/original/synthesis-and-mechanism-of-action-of-group-a-streptogramin-antibiotics-that-overcome-resistance.pdf |
668479005101a2ffa8340ee9 | 10.26434/chemrxiv-2024-8plw8 | Removal of Cationic and Anionic Dyes from Textile Waste Effluent using a Magnetic Nanocomposite made of Activated Carbon and Magnesium-Doped Bismuth Ferrite | The (BiMgFeO4/activated carbon) composite has been developed deploying glycine as fuel in a self-combustion process. It was employed to remove methyl green (MG), a cationic dye, and methyl orange (MO), an anionic dye, from aqueous solutions. It was characterized by specific surface area measurement (BET), scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and X-ray diffraction (XRD). FTIR spectra showed three bands located around 548.18 cm-1, 973. cm-1, and 1577.01 cm-1 attributed to the stretching vibrations of Bi-O, Fe-O, Mg-O, and O-H, respectively. The SEM images revealed a highly porous and irregular structure beneficial for the effective diffusion of dye molecules. The sample contains a notable proportion of holes with different sizes of pores. The microcavities observed on the adsorbent surface were conducive to good diffusion of the dye molecules. The composite's mesoporous structure was deduced by BET analysis, which allowed us to determine the material's specific surface area of 20.289 m2/g and its pore diameter of 7.54 nm. X-ray diffraction showed peaks attributed to Fe3O4, MgO, and Bi2O3 (confirming the presence of BiMgFeO4 ferrite) and other peaks attributed to dehydrated hemicellulose and carbon/graphite (confirming the use of activated carbon). The various experimental parameters affecting the performance of this reaction, such as temperature, contact time, initial dye concentration, and adsorbent mass, were studied. The composite's pH zero charge point (pHPZC) was found to be 8.77. The equilibrium isotherms were described using the Freundlich and Langmuir adsorption models. The equilibrium time was a function of the starting dye concentration in the adsorption tests. Adsorption equilibrium for (BiMgFeO4/activated carbon) was formed after 120 min, according to adsorption kinetic analysis. Moreover, the results revealed that pseudo-second-order kinetics could correctly characterize the adsorption of MO and MG on the composite. Adsorption isotherms confirmed that the adsorption process of both dyes onto the (BiMgFeO4/activated carbon) composite was successful. The Langmuir model appears to be best suited to the adsorption of MO and MG on the(BiMgFeO4/activated carbon), with a maximum adsorption capacity of 196.078 mg.g-1 and 192.307 mg.g-1 respectively, at 298 K. The adsorption of the two dyes was spontaneous and exothermic, in line with the thermodynamic parameters associated with the sorbent/adsorbate system. The determination of the isosteric heat of adsorption revealed that physisorption takes place with weak intermolecular interactions between the two dyes and the composite surface. | Sabrine Saad; Assia Hassen; Amel Ben Slimane | Earth, Space, and Environmental Chemistry; Environmental Science; Hydrology and Water Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668479005101a2ffa8340ee9/original/removal-of-cationic-and-anionic-dyes-from-textile-waste-effluent-using-a-magnetic-nanocomposite-made-of-activated-carbon-and-magnesium-doped-bismuth-ferrite.pdf |
623dfab82c50103b30887df7 | 10.26434/chemrxiv-2022-ght05 | Cobalt-Catalyzed Tandem Deamination, Decarboxylation, and Dehomologation of Primary Amines to Carboxylic Acids in Water | Selective transformation of carboxylic acids through oxidative deamination of primary amines is a catalytically challenging and useful transformation. Herein, we present a simple protocol for the transformation of primary amines to carboxylic acids with the readily accessible, cheap cobalt catalyst in the presence of an oxidant, exhibiting good functional group tolerance. While the deamination reaction of benzylamine derivatives proceeds smoothly to provide the corresponding carboxylic acids, the same with substituted 2-arylethylamines under the reaction conditions resulted in the expulsion of carbon dioxide and leads to the formation of the dehomologation product, i.e., carboxylic acids having one carbon atom less. Experimental studies, including control experiments and kinetic studies, were undertaken to shed light on the mechanism. | Arup Mukherjee; Deep Chowdhury | Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623dfab82c50103b30887df7/original/cobalt-catalyzed-tandem-deamination-decarboxylation-and-dehomologation-of-primary-amines-to-carboxylic-acids-in-water.pdf |
6762aba781d2151a021a58fa | 10.26434/chemrxiv-2024-b4x63 | Bioprocess Optimization of Lobster Waste Treatment Using Lactococcus lactis and Lactobacillus paracasei for N-polysaccharide Extraction | This study focuses on optimizing microbial processes for producing nitrogenous polysaccharides, specifically chitin and chitosan, from crustacean waste using response surface methodology. Lactococcus lactis and Lactobacillus paracasei were employed as microbial strains to assess the effects of key process variables: temperature, time, and substrate concentration, on the degrees of demineralization (DD%) and deproteinization (DP%). The results showed that L. lactis achieved a DD% of 80.61% and a DP% of 41.16%, while L. paracasei demonstrated superior performance with a DD% of 88.87% and a DP% of 55.96%. Fourier-transform infrared (FTIR) spectroscopy confirmed the presence of functional groups characteristic of commercially available chitosan, underscoring the potential of these microbial strains in sustainable chitin/chitosan production. Despite these promising results, the limited proteolytic activities of both strains highlighted the need to incorporate protease-producing microorganisms or adopt a secondary deproteinization step to improve purity. This study emphasizes the potential of green chemistry approaches in enhancing chitin/chitosan extraction, paving the way for sustainable waste management and resource recovery within the seafood industry. | Oseweuba Valentine Okoro; Elza Khalid; Andrew Amenaghawon; Lei Nie; Keikhosro Karimi; Philippe Claeys; Armin Shavandi | Agriculture and Food Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6762aba781d2151a021a58fa/original/bioprocess-optimization-of-lobster-waste-treatment-using-lactococcus-lactis-and-lactobacillus-paracasei-for-n-polysaccharide-extraction.pdf |
659dc178e9ebbb4db9ce2e39 | 10.26434/chemrxiv-2024-5vrcc | A review of mathematical modeling of bone remodeling from a systems biology perspective | Bone remodeling is an essential physiological process in the adult skeleton. Due to the complex nature of this process, many mathematical models of bone remodeling have been developed. Each of these models has unique features, but they have underlying patterns. In this review, the authors highlight the important aspects frequently found in mathematical models for bone remodeling and discuss how and why these aspects are included when considering the physiology of the bone basic multicellular unit, which is the term used for the collection of cells responsible for bone remodeling. The review also emphasizes the view of bone remodeling from a systems biology perspective. Understanding the systemic mechanisms involved in remodeling will help provide information on bone pathology associated with aging, endocrine disorders, cancers, and inflammatory conditions and enhance systems pharmacology. Furthermore, some features of the bone remodeling cycle and interactions with other organ systems that have not yet been modeled mathematically are discussed as promising future directions in the field. | Carley V. Cook; Ariel M. Lighty; Brenda J. Smith; Ashlee N. Ford Versypt | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Engineering and Industrial Chemistry; Bioengineering and Biotechnology; Bioinformatics and Computational Biology; Biophysics | CC BY 4.0 | CHEMRXIV | 2024-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659dc178e9ebbb4db9ce2e39/original/a-review-of-mathematical-modeling-of-bone-remodeling-from-a-systems-biology-perspective.pdf |
651169b8b927619fe7c81910 | 10.26434/chemrxiv-2023-4813l-v2 | Revisiting the Bonding Evolution Theory: A Fresh Perspective on the Ammonia Pyramidal Inversion and Bond Dissociations in Ethane and Borazane | This work offers a comprehensive and fresh perspective on the bonding evolution theory (BET) framework, originally proposed by Silvi and collaborators [J. Phys. Chem. A, 1997, 101, 7277–7282]. By underscoring Thom’s foundational work, we identify the parametric function characterizing bonding events along a reaction pathway through a three-step sequence to establish such association rigorously, namely: (a) computing the determinant of the Hessian matrix at all potentially degenerate critical points, (b) computing the relative distance between these points, and (c) assigning the unfolding based on these computations and considering the maximum number of critical points for each unfolding. In-depth examination of the ammonia inversion and the dissociation of ethane and ammonia borane molecules yields a striking discovery: no elliptic umbilic flag is detected along the reactive coordinate for any of the systems, contradicting previous reports. Our findings indicate that the core mechanisms of these chemical reactions can be understood using only two folds, the simplest polynomial of Thom's theory, leading to considerable simplification. In contrast to previous reports, no signatures of the elliptic umbilic unfolding were detected in any of the systems examined. This finding dramatically simplifies the topological rationalization of electron rearrangements within the BET framework, opening new approaches for investigating complex reactions. | Leandro Ayarde Henríquez; Cristian Guerra; Mario Duque-Noreña; Eduardo Chamorro | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2023-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651169b8b927619fe7c81910/original/revisiting-the-bonding-evolution-theory-a-fresh-perspective-on-the-ammonia-pyramidal-inversion-and-bond-dissociations-in-ethane-and-borazane.pdf |
6666da4b409abc0345122e0d | 10.26434/chemrxiv-2024-40z1t | Laser spectroscopic characterization of supersonic jet cooled 2,6-diazaindole (26DAI) | In this article, we present the laser spectroscopic investigation of a nitrogen rich indole derivative, 2,6-diazaindole (26DAI) in the gas phase for the first time. Laser induced fluorescence (LIF) and two-color resonant two-photon ionization (2C-R2PI) spectroscopies were carried out to understand the role of N-insertion on the electronic excitation of indole derivatives. The band origin for S1←S0 electronic transition was observed at 33915 cm-1, which was red shifted by 713 cm-1 and 1317 cm-1 from that of 7-azaindole and indole, respectively. The single vibronic level fluorescence (SVLF) spectroscopy of the molecule depicted a large Franck-Condon activity till 2500 cm-1 for ground state vibrational modes. The experimental vibrational frequencies from the SVLF spectrum were compared to Franck-Condon simulated frequencies at two different level of theories. The more accurate results were found at B3LYP-D4/def2-TZVPP, than the more energy demanding MP2/cc-pVDZ level. Fluorescence-dip infrared (FDIR) spectrum was recorded to determine the N-H stretching frequency of the molecule in the ground state, which was observed at 3524 cm-1. The photoionization efficiency spectroscopy was performed to measure the ionization energy of the molecule as 71866 cm-1, which is significantly higher as compared to 7-azaindole and indole. Thus, the above study suggests that the N-rich biomolecules appear to have a considerably lower risk of photodamage. The current investigation can shed light on to the nature’s way of stabilizing bio-relevant molecules with a possible N-insertion mechanism. | Bhavika Kalal; Simran Baweja; Surajit Maity | Physical Chemistry; Biophysical Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6666da4b409abc0345122e0d/original/laser-spectroscopic-characterization-of-supersonic-jet-cooled-2-6-diazaindole-26dai.pdf |
61aa38576d4e8f3bdba8aead | 10.26434/chemrxiv-2021-18x0d | HyFactor: Hydrogen-count labelled graph-based defactorization Autoencoder | Graph-based architectures are becoming increasingly popular as a tool for structure generation. Here, we introduce a novel open-source architecture HyFactor which is inspired by previously reported DEFactor architecture and based on the hydrogen labeled graphs. Since the original DEFactor code was not available, its new implementation (ReFactor) was prepared in this work for the benchmarking purpose. HyFactor demonstrates its high performance on the ZINC 250K MOSES and ChEMBL data set and in molecular generation tasks, it is considerably more effective than ReFactor. The code of HyFactor and all models obtained in this study are publicly available from our GitHub repository: https://github.com/Laboratoire-de-Chemoinformatique/hyfactor | Tagir Akhmetshin; Arkadii Lin; Daniyar Mazitov ; Evgenii Ziaikin ; Timur Madzhidov; Alexandre Varnek | Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61aa38576d4e8f3bdba8aead/original/hy-factor-hydrogen-count-labelled-graph-based-defactorization-autoencoder.pdf |
66e39131cec5d6c142e900c0 | 10.26434/chemrxiv-2024-m59d9 | Norm-conserving 5f-in-core Pseudopotentials and Gaussian Basis Sets Optimized for Tri- and Tetra-Valent Actinides (An = Pa-Lr) | Relativistic pseudopotentials and basis sets are the workhorse for modeling heavy elements of lanthanides and actinides. The norm-conserving Goedecker, Teter, and Hutter (GTH) pseudopotential is advantageous for modeling lanthanides and actinides compounds and condensed systems because of its transferability and accuracy. In this work, we develop a set of well-benchmarked GTH-type 5f-in-core pseudopotentials with scalar-relativistic effects, together with associated Gaussian basis sets for the most commonly encountered trivalent and tetravalent actinides (An(III), An(IV); An = Pa-Lr). The 5f-in-core GTH pseudopotentials are constructed by placing 5f-subconfiguration 5fn open shells of An(III) and 5fn-1 of An(IV) (n = 2-14) into the atomic core in the core-valence separation. The different performances of 5f-in-core GTH pseudopotentials for trivalent and tetravalent actinides are further analyzed from the chemical bonding features of actinides. The formalism of 5f-in-core GTH pseudopotentials circumvent the computational difficulty arising from 5fx open valence shell. The optimized 5f-in-core GTH PPs and Gaussian basis sets can be used to accelerate the costly first-principles modeling of structure-complicated actinide compounds and condensed-phase actinide systems. | Jun-Bo Lu; Yang-Yang Zhang; Jian-Biao Liu; Jun Li | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e39131cec5d6c142e900c0/original/norm-conserving-5f-in-core-pseudopotentials-and-gaussian-basis-sets-optimized-for-tri-and-tetra-valent-actinides-an-pa-lr.pdf |
668b468f5101a2ffa8b8b4fe | 10.26434/chemrxiv-2024-j1s1c | Methylammonium Tetrafluoroborate Additive for Spontaneous Heterointerface Modulation in a Narrow-Bandgap FAPbI3 Photoabsorber for Perovskite Solar Cells | Over the past decade, the photovoltaic (PV) performance of perovskite solar cells (PSCs) has been considerably improved with the development of perovskite photoabsorbers. Among these, formamidinium-lead-iodide (FAPbI3) is a promising photoabsorber owing to its narrow bandgap and is mainly used in n–i–p-structured PSCs. The property modulation of FAPbI3 photoabsorbers while retaining their narrow bandgap is imperative for further development of PSCs. Molecular tetrafluoroborate anion (BF4−)-based materials can be used as additives in perovskite layers to prevent bandgap widening, while facilitating perovskite crystal growth; thus, they are suitable for FAPbI3 photoabsorbers in principle. However, BF4−-based additives for narrow-bandgap FAPbI3 photoabsorbers have not been developed. This is presumably because of the higher temperatures required for FAPbI3 formation than that for other wide-bandgap perovskites, which likely changes the effects of BF4-based additives from those for wide-bandgap perovskites. In this study, we verified the applicability of methylammonium tetrafluoroborate (MABF4) as an additive in narrow-bandgap FAPbI3 photoabsorbers for improving their PV performance primarily via the spontaneous modulation of the heterointerfaces between FAPbI3 and carrier-transport materials, rather than through crystal growth facilitation. At the interface of the hole-transport material and FAPbI3, MABF4 addition effectively eliminates the surface defects in all FAPbI3 components, even in the absence of BF4− anions over the heated FAPbI3 surface, suggesting a defect-suppression mechanism, which differs from that observed in conventional ones. Moreover, at the interface of FAPbI3 and the TiO2 electron-transport material, the BF4−-derived species, which likely includes decomposed BF4− anions owing to the high-temperature heating, spontaneously segregates upon deposition, thereby modulating the heterointerface. Furthermore, in addition to the carrier mobility ratio in FAPbI3 (e−:h+ ≈ 7:3), time-resolved microwave conductivity measurement revealed that BF4 addition eliminates carrier traps at the heterointerfaces. Our findings provide insights into the promising FAPbI3-based PSCs, offering a valuable tool for their further development. | Daisuke Kubota; Ryuzi Katoh; Hiroyuki Kanda; Hiroyuki Yaguchi; Takurou N. Murakami; Naoyuki Nishimura | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668b468f5101a2ffa8b8b4fe/original/methylammonium-tetrafluoroborate-additive-for-spontaneous-heterointerface-modulation-in-a-narrow-bandgap-fa-pb-i3-photoabsorber-for-perovskite-solar-cells.pdf |
671cf3771fb27ce124a9ce01 | 10.26434/chemrxiv-2024-lcgb6 | Quick-and-Easy Validation of Protein–Ligand Binding Models Using Fragment-Based Semi-Empirical Quantum Chemistry | Electronic structure calculations in enzymes converge very slowly with respect to the size of the model region that is described using quantum mechanics (QM), requiring hundreds of atoms to obtain converged results and exhibiting substantial sensitivity (at least in smaller models) to which amino acids are included in the QM region. As such, there is considerable interest in developing automated procedures to construct a QM model region based on well-defined criteria. However, testing such procedures is burdensome due to the cost of large-scale electronic structure calculations. Here, we show that semi-empirical methods can be used as alternatives to density functional theory (DFT) to assess convergence in sequences of models generated by various automated protocols. The cost of these convergence tests is reduced even further by means of a many-body expansion. We use this approach to examine convergence (with respect to model size) of protein–ligand binding energies. Fragment-based semi-empirical calculations afford well-converged interaction energies in a tiny fraction of the cost required for DFT calculations. Two-body interactions between the ligand and single-residue amino acid fragments provide affords a low-cost way to construct a "QM-informed" enzyme model of reduced size, furnishing an automatable active-site model-building procedure. This provides a streamlined, user-friendly approach for constructing ligand binding-site models that requires neither a priori information nor manual adjustments. Extension to model-building for thermochemical calculations should be straightforward. | Paige Bowling; Dustin Broderick; John Herbert | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Bioengineering and Biotechnology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2024-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671cf3771fb27ce124a9ce01/original/quick-and-easy-validation-of-protein-ligand-binding-models-using-fragment-based-semi-empirical-quantum-chemistry.pdf |
65aad795e9ebbb4db98b69e8 | 10.26434/chemrxiv-2023-gtl30-v2 | A Scalable Synthesis of Adjuvanting Antigen Depots Based on Met-al-Organic Frameworks | Vaccines have saved countless lives by preventing and even irradicating infectious diseases. Commonly used subunit vaccines comprising one or multiple recombinant proteins isolated from a pathogen demonstrate a better safety profile than live or attenuated vaccines. However, the immunogenicity of these vaccines is weak, and therefore, subunit vaccines require a series of doses to achieve sufficient immunity against the pathogen. Here, we show that the biomimetic mineralization of the inert model antigen, ovalbumin (OVA), in zeolitic imidazolate framework-8 (ZIF-8) significantly improves the humoral immune response over three bolus doses of OVA (OVA 3×). Encapsulation of OVA in ZIF-8 (OVA@ZIF) demonstrated higher serum antibody titers against OVA than OVA 3×. OVA@ZIF vaccinated mice displayed higher populations of germinal center (GC) B cells and IgG1+ GC B cells as opposed to OVA 3×, indicative of class-switching recombination. We show that the mechanism of this phenomenon is at least partly owed to the metalloimmunological effects of the zinc metal as well as the sustained release of OVA from the ZIF-8 composite. The system acts as an antigen reservoir for antigen-presenting cells to traffic into the draining lymph node, enhancing the humoral response. Lastly, our model system OVA@ZIF is produced quickly at the gram scale in a laboratory setting, sufficient for up to 20,000 vaccine doses. | Ryanne N. Ehrman; Olivia R. Brohlin; Yalini H. Wijesundara; Sneha Kumari; Orikeda Trashi; Thomas S. Howlett; Ikeda Trashi; Fabian C Herbert; Arun Raja; Shailendra Koirala; Nancy Tran; Noora M. Al-Kharji; Wendy Tang; Milinda C. Senarathna; Laurel M. Hagge; Ronald A. Smaldone; Jeremiah Gassensmith | Biological and Medicinal Chemistry; Bioengineering and Biotechnology; Drug Discovery and Drug Delivery Systems; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65aad795e9ebbb4db98b69e8/original/a-scalable-synthesis-of-adjuvanting-antigen-depots-based-on-met-al-organic-frameworks.pdf |
6616187e91aefa6ce13a17de | 10.26434/chemrxiv-2024-qqgqk | Molecular Docking and Molecular Dynamics Simulation to Predict Inhibitors Against HIV Envelope 1 Protein | HIV (human immunodeficiency virus) is a virus that attacks the immune system, which serves as the body’s defense mechanism. If untreated, HIV can lead to AIDS (acquired immunodeficiency syndrome), which raises risk for a host of problems, especially infections and cancers. According to data from 2022, there are 39 million people worldwide afflicted with HIV. HIV remains a leading cause of death globally, although AIDS-related deaths have declined due to ART (antiretroviral therapy). There are two main types of HIV viruses: HIV-1 and HIV-2. HIV-1 is more prevalent worldwide, while HIV-2 is less pathogenic and found predominantly in Africa. Although not fully understood, the key differences between HIV-1 and HIV-2 viruses, lie in the mechanism of retroviral pathogenesis. HIV-1 is comprised of a protein called the envelope protein, which is required for entry of the virus into the host cell. In our work, we have used computational strategies like molecular docking and molecular dynamics simulations to predict inhibitors that can bind to the envelope protein, thus inhibiting viral entry into the host cell. Based on our studies, we have proposed five chemical compounds that bind strongly to the viral envelope protein. These chemical compounds bind specifically to the Phe43 cavity on the envelope protein. The Phe43 cavity is a promising target for drug therapy. We have also introduced virtual reality (VR) technology to visualize and modify the protein-ligand complexes. Our current work will not only help in developing novel therapeutics against HIV, but also pave way for many potential new treatments, thus helping combat the global burden of this disease. | Mustafa Arif; Gaurav Sharma | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6616187e91aefa6ce13a17de/original/molecular-docking-and-molecular-dynamics-simulation-to-predict-inhibitors-against-hiv-envelope-1-protein.pdf |
667ba7f8c9c6a5c07a682267 | 10.26434/chemrxiv-2024-jn35r | Towards a universal method for middle-down analysis of antibodies via proton transfer charge reduction – Orbitrap mass spectrometry | Modern mass spectrometry technology allows for extensive sequencing of the ~25 kDa subunits of monoclonal antibodies (mAbs) produced by IdeS proteolysis followed by disulfide bond reduction, an approach known as middle-down mass spectrometry (MD MS). However, the spectral congestion of tandem mass spectra of large polypeptides dramatically complicates fragment ion assignment. Here, we report the development and benchmark of an MD MS strategy based on the combination of different ion fragmentation techniques with proton transfer charge reduction (PTCR) to simplify the gas-phase sequencing of mAb subunits. Applied on the liquid chromatography time scale using an Orbitrap Tribrid mass spectrometer, PTCR produces easy-to-interpret mass spectra with limited ion signal overlap. We demonstrate that the accurate estimation of the number of charges submitted to the Orbitrap mass analyzer after PTCR allows for the detection of charge-reduced product ions over a wide mass-over-charge (m/z) window with low parts per million m/z accuracy. Therefore, PTCR-based MD MS analysis increases not only sequence coverage, number of uniquely identified fragments and number of assigned complementary ion pairs, but also the general confidence in the assignment of subunit fragments. This data acquisition method can be readily applied to any class of mAbs without an apparent need for optimization, and benefits from the high resolving power of the Orbitrap mass analyzer to return sequence coverage of individual subunits exceeding 80% in a single run, and >90% when just two experiments are combined. | Ryan Oates; Linda Lieu; Jake Kline; Christopher Mullen; Kristina Srzentić; Romain Huguet; Graeme McAlister; Jingjing Huang; David Bergen; Rafael Melani; Vlad Zabrouskov; Kenneth Durbin; John Syka; Luca Fornelli | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667ba7f8c9c6a5c07a682267/original/towards-a-universal-method-for-middle-down-analysis-of-antibodies-via-proton-transfer-charge-reduction-orbitrap-mass-spectrometry.pdf |
6268d38def2ade1fa03ed12b | 10.26434/chemrxiv-2022-3dsm2-v2 | Glycidyl Silanes Enable Regioselective Hydrosilylation of Internal Propargyl Alcohols and Direct Transformation into Activated Silanes for Further Chemical Transformation | Herein, we develop glycidyl silanes to facilitate highly regioselective hydrosilylation of internal propargyl alcohols, the products of which can in turn be converted to synthetically useful fluorosilanes for further chemical transfor-mations under mild conditions. Structure–selectivity studies and density functional theory calculations are consistent with high regioselectivity arising from a critical intermolecular hydrogen bond between the glycidyl and propargylic hydroxy groups. A broad substrate scope illustrates the generality of this reaction to form beta-E silylalkenes. Treatment of the beta-E silylalkenes with a fluoride salt induces simultaneous removal of the glycidyl group and activation of the silane under mild conditions. The fluorosilane products can be converted into vinyl arene and ketone derivatives via Hiyama coupling and Tamao–Fleming oxidation reactions, respectively. The discovery that glycidyl silane improves hydrosilylation regioselectivity and is compatible with expedient silylalkene derivatization may prove applicable to a variety of similar alkyne hydrofunctionalization reactions. | Akihiro Sugawara; Soya Koremura; Yusuke Sasano; Haruhisa Kikuchi | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6268d38def2ade1fa03ed12b/original/glycidyl-silanes-enable-regioselective-hydrosilylation-of-internal-propargyl-alcohols-and-direct-transformation-into-activated-silanes-for-further-chemical-transformation.pdf |
6703286d51558a15ef4d4911 | 10.26434/chemrxiv-2024-d03h6 | Structural and Functional Analysis of SAM-Dependent N-Methyltransferases Involved in Ovoselenol and Ovothiol Biosynthesis | Thio/selenoimidazole N-pi-methyltransferases are an emerging family of enzymes responsible for catalyzing the final enzymatic step in the biosynthesis of ovothiol and ovoselenol, S/Se-containing histidine-derived antioxidants. These unique enzymes are widespread among prokaryotes yet bear only marginal sequence similarity to other known methyltransferases. Likewise, little is known about the structural determinants of their reactivities. Here we report the first ligand-bound X-ray crystal structures of this family, including OvsM from the ovoselenol pathway as well as a member of a previously unknown clade of standalone ovothiol-biosynthetic N-pi-methyltransferases, which we have designated OvoM. Unlike previously reported ovothiol methyltransferases, which are fused as a C-terminal domain to the sulfoxide synthase OvoA, OvoMs are discrete enzymes and function independently. Comparative structural analyses of OvsM and OvoM reveal several conserved, ligand-induced tertiary and secondary structure changes, and suggest that similar conformational changes may apply to dual-domain OvoA enzymes. Mutagenesis experiments support a model in which the rearrangement of OvoA’s two domains facilitates substrate recognition through interaction with a key Tyr residue located within the domain linker. Furthermore, biochemical experiments highlight the essential role of an active site Asp residue, which likely functions as a catalytic base in the SN2-like nucleophilic substitution reaction catalyzed by these enzymes. | Kendra Ireland; Chase Kayrouz; Marissa Abbott; Mohammad Seyedsayamdost; Katherine Davis | Biological and Medicinal Chemistry; Catalysis; Biochemistry; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6703286d51558a15ef4d4911/original/structural-and-functional-analysis-of-sam-dependent-n-methyltransferases-involved-in-ovoselenol-and-ovothiol-biosynthesis.pdf |
6291410e6209e0c55c544b3d | 10.26434/chemrxiv-2022-m2m48 | The composite method of symmetry adapted
perturbation theory | In symmetry-adapted perturbation theory (SAPT), accurate calculations on non-covalent interaction for large complexes with more than 50 atoms are impractical using a large basis set. The more efficient with a smaller basis set, however, usually results in poor prediction in terms of dispersion and overall energies. In this study, we propose a composite method with a baseline calculated at SAPT2/aug-cc-pVTZ with dispersion term corrected at SAPT2+ level with a smaller basis set at the canonical limit using extrapolation techniques. Two point and three point extrapolation schemes are discussed, and we showed that our composite methods perform better than the previously ranked silver standard and can even compete with gold standard with the computational cost in between the latter and former's.
| Zhongwei Li; Zhihao Deng; Chang Liu; Yingsheng Zhang | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6291410e6209e0c55c544b3d/original/the-composite-method-of-symmetry-adapted-perturbation-theory.pdf |
65afa2e666c138172914459d | 10.26434/chemrxiv-2024-dz0kj | Guest-host Chemistry with Phenothiazine-substituted Amides. | Guest-host interactions between a 3-(10-phenothiazinyl)propanamide) functionalized dipropylenetriamine pincer (host) and simple amides of malonic acid and analogs (guests) have been investigated, and the system has been transferred to a generation 5 3-(10-phenothiazinyl)propanamide) substituted polypropylene imine dendrimer. The association constants in chloroform solution have been determined by NMR on the model system and are in the region 103 to 104 M-1. | Jørn Bolstad Christensen; Rasmus Lewinsky | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2024-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65afa2e666c138172914459d/original/guest-host-chemistry-with-phenothiazine-substituted-amides.pdf |
675479ab7be152b1d0409bff | 10.26434/chemrxiv-2024-ggqsc | Application of proline-2′-deoxymugineic acid as potential fertilizer to alleviate zinc deficiency in paddy soils | Zinc (Zn) deficiency affects around 50% of rice paddy soils worldwide. This leads to reduced production and poor nutritional composition of food with detrimental consequences to human health. In this work we show that proline-2′-deoxymugineic acid (PDMA), a new synthetic organic ligand, forms strong and stable complexes with zinc(II) in paddy soil conditions and therefore can be used as a novel zinc(II)-fertiliser. To demonstrate this, we determined ZnII-binding properties of PDMA and potential competition with other metal ions, identifying the paddy soil conditions where PDMA application is more effective to increase ZnII-complexation. Our results indicate that PDMA is a strong ZnII-chelator in paddy soil and the most favorable conditions for the effective application of PDMA as ZnII-fertilizer is providing PDMA in flooded soil at pH from 7 to 9. In this condition 50% of ZnII-complexation is ensured even when ZnII soil concentration is ten times less than competitor metals. | Claudia Rocco; Motofumi Suzuki; Ramon Vilar; Enrique Garcia-Espana; Salvador Blasco; Gerald Larrouy-Maumus; Colin Turnbull; Matthias Wissuwa; Xuan Cao; Dominik Weiss | Theoretical and Computational Chemistry; Analytical Chemistry; Agriculture and Food Chemistry; Electrochemical Analysis; Environmental Analysis; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675479ab7be152b1d0409bff/original/application-of-proline-2-deoxymugineic-acid-as-potential-fertilizer-to-alleviate-zinc-deficiency-in-paddy-soils.pdf |
6329d8ab114b7e7b6f169ab0 | 10.26434/chemrxiv-2022-1gqnf-v2 | Rational design of a self-assembling high performance organic nanofluorophore for intraoperative NIR-II image-guided tumor resection of oral cancer | The first line of treatment for most solid tumors is surgical resection of the primary tumor with adequate negative margins. Incomplete resections with positive margins account for over 75% of local recurrences and the development of distant metastases. In cases of oral cavity squamous cell carcinoma (OSCC), the rate of successful tumor removal with adequate margins is just 15-26%. Advanced real-time imaging methods that improve detection of tumor margins can help improve success rates. Fluorescence imaging in the second near-infrared (NIR-II) window has the potential to revolutionize the field due to its superior imaging qualities, but NIR-II dyes with adequate in vivo performance and safety profiles are scarce. We report a novel high-performance organic molecule NIR-II fluorophore, XW-03-66 , with a fluorescence quantum yield (QY) of 6.0% in aqueous media. XW-03-66 self-assembles into nanoparticles (~80 nm) and has a systemic circulation half-life (t 1/2 ) of 11.3 h. In mouse models of HPV+ and HPV- OSCC, XW-03-66 outperformed indocyanine green (ICG), a clinically available NIR dye, and enabled intraoperative NIR-II image-guided resection of the tumor and adjacent draining lymph node with negative margins. In vitro and in vivo toxicity assessments revealed minimal safety concerns for in vivo applications. | Xianwei Sun; Praveen Chintakunta; Andrew Badachhape; Rohan Bhavane; David Yang; Zbigniew Starosolski; Huan-Jui Lee; Ketan Ghaghada; Peter Vekilov; Ananth Annapragada; Eric Tanifum | Biological and Medicinal Chemistry; Materials Science; Nanoscience; Aggregates and Assemblies; Biocompatible Materials; Imaging Agents | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6329d8ab114b7e7b6f169ab0/original/rational-design-of-a-self-assembling-high-performance-organic-nanofluorophore-for-intraoperative-nir-ii-image-guided-tumor-resection-of-oral-cancer.pdf |
650190a5b338ec988a6793b3 | 10.26434/chemrxiv-2023-vt45d | Strain-dependent Enantioselectivity in Mechanochemically Coupled Catalytic Hydrogenation | The specific three-dimensional structure, e.g. the chirality, of the product of many important reactions is determined in large part by the structure of a catalyst, for example the ligand around a metal center, that makes the reaction tractable. Here, we demonstrate that the chiral selectivity of the hydrogenation of a methyl 2-amidoacrylate via a fixed bisphosphine Rh catalyst can be improved by embedding that catalyst into an appropriate heterogenous elastomeric support and transducing the mechanical deformation of the elastomer to the catalyst. The ratio of R and S product isomers is strain-dependent and reversible upon relaxing the support. Stretching the support by 50% in a single dimension increases the R:S ratio of the product by up to 32%. | Xujun Zheng; Chun-Yu Chiou; Robert O'Neill; Chenghao Duan; Yichen Yu; Jack Malek; Roman Boulatov; Stephen Craig; Ross Widenhoefer | Organic Chemistry; Organometallic Chemistry; Physical Organic Chemistry; Catalysis; Ligands (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2023-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650190a5b338ec988a6793b3/original/strain-dependent-enantioselectivity-in-mechanochemically-coupled-catalytic-hydrogenation.pdf |
6182b08cd828a40f2d6a06d2 | 10.26434/chemrxiv-2021-r6q21 | Membrane mixing and dynamics in hybrid POPC/PBd-PEO lipid/block co-polymer giant vesicles | Lipids and block copolymers can individually self-assemble into vesicles, each with their own particular benefits and limitations. Combining polymers with lipids allows for further optimisation of the vesicle membranes for bionanotechnology applications. Here, POPC lipid is mixed with poly(1,2-butadiene-block-ethylene oxide) of two different molecular weights (PBd22-PEO14, Mr = 1800 g.mol-1 and PBd12-PEO11, Mr = 1150 g.mol-1) in order to investigate, how increasing the polymer fraction affects membrane mixing, hydration and fluidity. Intensity contributions of fluorescently labelled lipid and polymer within mixed GUV membranes confirm membrane homogeneity within the hybrids. General polarisation measurements of Laurdan in GUVs showed little change in membrane hydration as polymer fraction is increased, which suggests good structurally compatibility between lipids and polymers that gives rise to well-mixed vesicles. Membrane fluidity in hybrid GUVs was found to decrease non-linearly with increasing polymer fraction. However, the diffusion coefficients for the fluorescent polymer in hybrid membranes did not change significantly with increasing polymer content. While increasing the polymer fraction does reduce the movement of lipids through a polymer-rich matrix, insignificant difference in diffusion coefficients of the polymer suggests that its diffusion is minimally affected by increasing lipid composition in the range studied. These results lay further foundations for the wider development of hybrid vesicles with controlled properties for advanced biotechnologies. | Rashmi Seneviratne; Michael Rappolt; Lars Jeuken; Paul Beales | Physical Chemistry; Materials Science; Polymer Science; Polymer blends; Interfaces; Self-Assembly | CC BY 4.0 | CHEMRXIV | 2021-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6182b08cd828a40f2d6a06d2/original/membrane-mixing-and-dynamics-in-hybrid-popc-p-bd-peo-lipid-block-co-polymer-giant-vesicles.pdf |
63e2a44145d4b84aaea77a1b | 10.26434/chemrxiv-2023-00ff9 | Dative bonding as a mechanism for enhanced catalysis on the surface of MoS2 | Transition-metal dichalcogenide (TMD) layers have been a subject of widespread interest as platforms for electronic devices. However, the low chemical activity of their basal plane results in several technological bottlenecks, including high contact resistance at TMDelectrode interfaces, difficult growth of high-quality gate-oxide layers, and challenging functionalization. The simplest, and perhaps only, approach to overcoming those limitations may be to exploit dative bonding. The effect can enhance binding on TMDs, since their chalcogen nonbonding lone-pair orbitals can function as electron donors. Therefore, it should also be able to impact the surface catalysis for reactions that produce acceptors. This computational study seeks to investigate whether S→P dative bonding may be an effective mechanism for catalysis on the surface of MoS2, and whether the sheet can be functionalized via chemical reactions enabled by the binding of PHn and PCln. The results show that the bonding facilitates the PH functionalization of MoS2. The interaction is strong (1.11 eV), making the whole process exothermic, and the activation energy notably reduced (from 2.08 to 0.5 eV). Furthermore, the mechanism is intrinsically selective, which could prove a vital feature for future advancements in TMD-based electronics, since it could steer selected processes toward surface functionalization or thin-film growth. | Maciej Jan Szary | Theoretical and Computational Chemistry; Materials Science; Catalysis | CC BY NC 4.0 | CHEMRXIV | 2023-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e2a44145d4b84aaea77a1b/original/dative-bonding-as-a-mechanism-for-enhanced-catalysis-on-the-surface-of-mo-s2.pdf |
656eb00f5bc9fcb5c90fbc70 | 10.26434/chemrxiv-2023-n1r3c | Non-equilibrium Trajectory Sampling (NETS) method for generating free-energy landscapes and steady-state distributions | This study presents a novel method for constructing free-energy profiles and steady-state distributions from either equilibrium or non-equilibrium trajectories along a defined reaction coordinate. The method works by tracking the final states of a swarm of short simulations launched from different initial conditions with no prior knowledge of the free energy landscape. Subsequently, this trajectory information is used to build a transition matrix whose primary eigenvector captures the steady-state occupation probability for each value of the reaction coordinate, yielding the free energy profile in equilibrium. This innovative method holds potential for many new materials and engineering applications where it is desired to know the free energy of rate-limiting configurations as may be relevant for transport processes (in, e.g. battery electrolytes and nano-filtration membranes), complexation (in, e.g., self-assembly and ligand-binding interactions) or in tuning properties such as adsorption. We illustrate the effectiveness of the method by capturing the free energy associated with a one-dimensional barrier potential modeling a separation membrane, and the particle distribution associated with thermophoresis under a temperature gradient. Further extensions and applications of the method are also discussed. | Akwasi Nana Prempeh Ansah-Antwi; Pedro H. Amorim Valenca; Mohsen Farshad; Jonathan K. Whitmer | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656eb00f5bc9fcb5c90fbc70/original/non-equilibrium-trajectory-sampling-nets-method-for-generating-free-energy-landscapes-and-steady-state-distributions.pdf |
60c742cd469df420eff43054 | 10.26434/chemrxiv.8637308.v1 | Tunable Circularly Polarized Luminescence from Molecular Assemblies of Chiral AIEgens | <p>Circularly polarized luminescence (CPL) is
important to chiral photonic technologies. In the molecular systems, besides
their intrinsic chemical structures, the architectures of molecular assemblies
at the mesoscopic scale also account for the final macroscopic CPL properties.
Herein, tunable CPL responses can be induced through architectural regulation
of these molecular assemblies in suspension and solid states. A liquid
crystalline assembled system of DPCE-ECh exhibiting smectic C* phase with a
high dissymmetry factor (<i>g</i><sub>CD</sub>
= -0.20 and <i>g</i><sub>lum</sub> = +0.38)
is reported. The intense and apparent
CD and CPL of the film stem from the intrinsic helical structure of the
molecular assembles with<b> </b>weak<b> </b>contribution of Bragg reflection,
where the helical axis is perpendicular to the optical axis and is parallel to the direction of the
glass substrate. To the best of our knowledge,<b> </b>this large <i>g</i><sub>lum</sub> factor is very rare for
organic compounds even in the assembled state formed by annealing at smectic
liquid crystalline temperature. Interestingly, strong
CPL signal with <i>g</i><sub>lum</sub> value
of +0.18 is still recorded when DPCE-ECh is annealed at chiral isotropic liquid (Iso*) state. On the other hand, DPCE-ACh can form two coexistence
phases of chiral hexagonal and smectic liquid-crystalline phases due to
intermolecular hydrogen bonding. The non-periodic
molecular orientations of DPCE-ACh break itself helical structure to give a
weak negtive CPL signal in 10<sup>-3</sup> order. This work thus
provides a new insight for developing efficient chiroptical materials in the
aggregate state and profound implications in high-performance CPL-based device.</p> | Fengyan Song; yanhua Cheng; Qiuming Liu; Jacky W. Y. Lam; Fafu Yang; Ben Zhong Tang | Liquid Crystals; Nanostructured Materials - Materials; Optical Materials; Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742cd469df420eff43054/original/tunable-circularly-polarized-luminescence-from-molecular-assemblies-of-chiral-ai-egens.pdf |
643d3d3d08c86922ff29464f | 10.26434/chemrxiv-2023-bjr33 | Coupled reaction equilibria enable the light-driven formation of metal-functionalized molecular vanadium oxides | The introduction of metal sites into molecular metal oxides, so-called polyoxometalates, is a key approach to tune their structure and reactivity. To-date, the complex solution mechanisms which govern metal-functionalizatio of polyoxometalates is still poorly understood. Here, we reveal the existence of a coupled set of light-dependent and light-independent reaction equilibria control the mono- and di-metal-functionalization of a prototype molecular vanadium oxide cluster. Comprehensive mechanistic analyses show that coordination of a single Mg2+ ion to the native species (NMe2H2)2[V12O32Cl]3- results in formation of the mono-functionalized system (NMe2H2)[(MgCl)V12O32Cl]3-. This species is photoactive, and irradiation with visible light triggers a second, light-dependent reaction equilibrium which drives the formation of the di-metal-functionalized species [(MgCl)2V12O32Cl]3-. The use cations which compete with Mg2+ can effectively inhibit the formation of the metal functionalized clusters. The study therefore demonstrates how external and internal stimuli can be used to control supramolecular polyoxometalate assembly. | Stefan Repp; Moritz Remmers; Alexandra Stefanie Jessica Rein; Dieter Sorsche; Luca M. Carrella; Eva Rentschler; Carsten Streb | Inorganic Chemistry; Coordination Chemistry (Inorg.); Kinetics and Mechanism - Inorganic Reactions; Materials Chemistry; Crystallography – Inorganic | CC BY 4.0 | CHEMRXIV | 2023-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643d3d3d08c86922ff29464f/original/coupled-reaction-equilibria-enable-the-light-driven-formation-of-metal-functionalized-molecular-vanadium-oxides.pdf |
61403d0565db1e2908b61ac9 | 10.26434/chemrxiv-2021-79b8f | Ex Vivo and in Vivo Evaluation of Dodecaborate-Based Clusters Encapsulated in Ferumoxytol Nanoparticles | Host-guest interactions represent a growing research area with recent work demonstrating an ability to chemically manipulate both host molecules as well as guest molecules to vary the type and strength of bonding. Much less is known about the interactions of guest molecules and hybrid materials containing similar chemical features to typical macrocyclic hosts. This work uses in vitro and in vivo kinetic analyses to investigate the interaction of closo-dodecahydrododecaborate derivatives with ferumoxytol, an iron oxide nanoparticle with a carboxylated dextran coating. We find that several boron cluster derivatives can become encapsulated into ferumoxytol and the lack of pH dependence in these interactions suggests that ion pairing, hydrophobic/hydrophilic, or hydrogen bonding are not the driving force for encapsulation in this system. Biodistribution experiments in BALB/c mice show that this system is nontoxic at the reported dosage and demonstrate that encapsulation of dodecaborate-based clusters in ferumoxytol can alter the biodistribution of guest molecules. | Nicholas Bernier; James Teh; Derek Reichel; Joanne Zahorsky-Reeves; J. Manuel Perez; Alexander Spokoyny | Biological and Medicinal Chemistry; Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Polymers; Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61403d0565db1e2908b61ac9/original/ex-vivo-and-in-vivo-evaluation-of-dodecaborate-based-clusters-encapsulated-in-ferumoxytol-nanoparticles.pdf |
60c754f9bb8c1a7b483dc333 | 10.26434/chemrxiv.13947413.v1 | Synthesis and Configurational Assignment of Vinyl Sulfoximines and Sulfonimidamides | Vinyl sulfones and sulfonamides are valued for their use as electrophilic warheads in covalent protein inhibitors. Conversely, the S(VI) aza-isosteres thereof, vinyl sulfoximines and sulfonimidamides, are far less studied and have yet to be applied to the field of protein bioconjugation. Herein, we report a range of different synthetic methodologies for constructing vinyl sulfoximine and vinyl sulfonimidamide architectures that allows access to new areas of electrophilic chemical space. We demonstrate how late stage functionalization can be applied to these motifs to incorporate alkyne tags, generating fully functionalized probes for future chemical biology applications. Finally, we establish a workflow for determining the absolute configuration of enantioenriched vinyl sulfoximines and sulfonimidamides by comparing experimentally and computationally determined electronic circular dichroism spectra, enabling access to configurationally assigned enantiomeric pairs by separation. | Gregory Craven; Edward L. Briggs; Charlotte Zammit; Alex McDermott; Stephanie Greed; Dominic Affron; Charlotte Leinfellner; Hannah Cudmore; Ruth Tweedy; Renzo Luisi; James Bull; Alan Armstrong | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754f9bb8c1a7b483dc333/original/synthesis-and-configurational-assignment-of-vinyl-sulfoximines-and-sulfonimidamides.pdf |
637bf43f53ab8030e32e2b8b | 10.26434/chemrxiv-2022-5t3s9 | Impact of SARS-CoV-2 3CL Protease Mutations on Nirmatrelvir Inhibitory Efficiency. Computational Insights into Potential Resistance Mechanisms | The use of antiviral drugs can promote the appearance of mutations in the target protein that increase the resistance of the virus to the treatment. This is also the case of nirmatrelvir, a covalent inhibitor of the 3CL protease of SARS-CoV-2. In this work we show how the by-residue decomposition of noncovalent interactions established between the drug and the enzyme, in combination with an analysis of natural occurring mutations, can be used to detect potential mutations in 3CL protease conferring resistance to nirmatrelvir. We also investigate the consequences of these mutations on the reaction mechanism to form the covalent enzyme-inhibitor complex. In particular, we show that the E166V variant of the protease shows a smaller affinity by nirmatrelvir and a larger activation free energy for the formation of the covalent complex, both factors contributing to an increased resistance to the treatment with this drug. The conclusions derived from our work can be used to anticipate the consequences of the introduction of nirmatrelvir in the fitness landscape of the virus and to design new inhibitors to prevent resistance mechanisms. | Carlos A. Ramos-Guzmán; Milorad Andjelkovic; Kirill Zinovjev; J. Javier Ruiz-Pernía; Iñaki Tuñón | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637bf43f53ab8030e32e2b8b/original/impact-of-sars-co-v-2-3cl-protease-mutations-on-nirmatrelvir-inhibitory-efficiency-computational-insights-into-potential-resistance-mechanisms.pdf |
61e02e8d80719d7d7e0df5ad | 10.26434/chemrxiv-2022-ls3vz | The Importance of Chemical Activation and the Effect of Low Operation Voltage on the Performance of Pt-alloy Fuel Cell Electrocatalysts | Pt-alloy (Pt-M) nanoparticles (NPs) with less expensive 3d transition metals (M = Ni, Cu, Co) supported on high surface area carbon supports, are currently the state-of-the-art (SoA) solution to reach the production phase in proton exchange membrane fuel cells (PEMFCs). However, while Pt-M electrocatalysts show promise in terms of increased activity for oxygen reduction reaction (ORR) and thus, cost reductions from a significantly lower use of expensive and rare Pt, key challenges in terms of synthesis, activation and stability remain to unlock their true potential. This work systematically tackles them with a combination of electrocatalyst synthesis and characterization methodologies including thin-film rotating disc electrodes (TF-RDE), an electrochemical flow cell linked to an inductively coupled plasma mass spectrometer (EFC-ICP-MS) and testing in 50 cm2 membrane electrode assemblies (MEAs). In the first part of the present work, we highlight the crucial importance of the chemical activation (de-alloying) step on the performance of Pt-M electrocatalysts in the MEA at high current densities (HCDs). In addition, we provide the scientific community a preliminary and facile method of distinguishing between a ‘poorly’ or ‘adequately’ de-alloyed (activated) Pt-alloy electrocatalyst using a much simpler and affordable TF-RDE methodology using the well-known CO-stripping. Since the transition metal cations can also be introduced in a PEMFC due to the degradation of the Pt-M NPs, the second part of the work focuses on presenting clear evidence on the direct impact of the lower voltage limit (LVL) on the stability of Pt-M electrocatalysts. The data suggests that in addition to intrinsic improvements in stability, significant improvements in the PEMFC lifetime can also be obtained via correct MEA design and applied limits of operation, namely restricting not just upper but equally important also lower operation voltage. | Matija Gatalo; Alejandro Martinez Bonastre; Leonard-Jean Moriau; Harriet Burdett; Francisco Ruiz-Zepeda; Edwin Hughes; Adam Hodgkinson; Martin Šala; Luka Pavko; Marjan Bele; Nejc Hodnik; Jonathan Sharman; Miran Gaberšček | Catalysis; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2022-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e02e8d80719d7d7e0df5ad/original/the-importance-of-chemical-activation-and-the-effect-of-low-operation-voltage-on-the-performance-of-pt-alloy-fuel-cell-electrocatalysts.pdf |
648e1a8dbe16ad5c5713cd64 | 10.26434/chemrxiv-2023-2m2l5 | Atomically ordered PdCu electrocatalysts for selective and stable electrochemical nitrate reduction | Electrochemical nitrate reduction (NO3RR) has attracted attention as an emerging approach to mitigate nitrate pollution in groundwater. Here, we report that a highly ordered PdCu alloy-based electrocatalyst exhibits selective (91% N2), stable (480 hours), and near complete (94%) removal of nitrate without loss of catalyst. In situ and ex situ XAS provide evidence that structural ordering between Pd and Cu improves long-term catalyst stability during NO3RR. In contrast, we also report that a disordered PdCu alloy-based electrocatalyst exhibits non-selective (49% N2 and 49% NH4+), unstable, and incomplete removal of nitrate. The copper within disordered PdCu alloys is vulnerable to accepting electrons from hydrogenated neighboring Pd atoms. This resulted in copper catalyst losses which were 10x greater than that of the ordered catalyst. The design of stable catalysts is imperative for water treatment because loss of the catalyst adds to the system cost and environmental impacts. | Jeonghoon Lim; David Cullen; Eli Stavitski; Seung Woo Lee; Marta Hatzell | Catalysis; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648e1a8dbe16ad5c5713cd64/original/atomically-ordered-pd-cu-electrocatalysts-for-selective-and-stable-electrochemical-nitrate-reduction.pdf |
614dcc6fd9c956510ededc59 | 10.26434/chemrxiv-2021-5w56l | Formation Mechanism and Porosity Development in Porous Boron Nitride | In the past decade, porous boron nitride (BN) has proven promising as a novel class of inorganic materials in the field of separations and particularly adsorption. Owing to its high surface area and thermal stability, porous BN has been researched for CO2 capture and water cleaning, for instance. However, most research remains at laboratory scale due to a lack of understanding of the formation mechanism of porous BN, which is still largely a ‘black box’ and prevents scale-up. Partial reaction pathways have been unveiled, but they omit critical steps in the formation, including the porosity development, which is key to adsorption. To unlock the potential of porous BN at a larger scale, we have investigated its formation from the perspective of both chemical formation and porosity development. We have characterised reaction intermediates obtained at different temperatures with a range of analytical and spectroscopic tools. Using these analyses, we propose a mechanism that highlights the key stages of BN formation and its porosity, including the intermediates and gaseous species formed in the process. We identified that the formation of non-porous carbon nitride is crucial to form porous BN with release of porogens, such as HCN and CO2. This work paves the way for scaled-up processes to use porous BN to its full potential at industrial level for gas and liquid separations. | Anouk L'Hermitte; Daniel M. Dawson; Pilar Ferrer; Kanak Roy; Georg Held; Tian Tian; Sharon E. Ashbrook; Camille Petit | Physical Chemistry; Chemical Engineering and Industrial Chemistry; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Structure; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614dcc6fd9c956510ededc59/original/formation-mechanism-and-porosity-development-in-porous-boron-nitride.pdf |
650db05b60c37f4f7641bdfc | 10.26434/chemrxiv-2023-59krd | Enabling High Throughput Kinetic Experimentation by Using Flow as a Differential Kinetic Technique | Kinetic data is most commonly collected through the generation of time-series data under either batch or flow conditions. Existing methods to generate kinetic data in flow collect integral data (concentration over time) only. Here, we report a method for the rapid and direct collection of differential kinetic data (direct measurement of rate) in flow by performing a series of instantaneous rate measurements on sequential small-scale reactions. This technique decouples the time required to generate a full kinetic profile from the time required for a reaction to reach completion, enabling high throughput kinetic experimentation. In addition, comparison of kinetic profiles constructed at different residence times allows the robustness, or stability, of homogeneously catalysed reactions to be interrogated. This approach makes use of a segmented flow platform which was shown to quantitatively reproduce batch kinetic data. The proline mediated aldol reaction was chosen as a model reaction to perform a high throughput kinetic screen of 216 kinetic profiles in 90 hours, one every 25 minutes, which would have taken an estimated continuous 3500 hours in batch, an almost 40-fold increase in experimental throughput matched by a corresponding reduction in material consumption. | Gavin Lennon; Paul Dingwall | Organic Chemistry; Catalysis; Physical Organic Chemistry; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650db05b60c37f4f7641bdfc/original/enabling-high-throughput-kinetic-experimentation-by-using-flow-as-a-differential-kinetic-technique.pdf |
65239c7045aaa5fdbb961cd5 | 10.26434/chemrxiv-2023-r66jc-v2 | Discovery of Antibacterial Manganese(I) Tricarbonyl Complexes through Combinatorial Chemistry | The continuous rise of antimicrobial resistance is a serious threat to human health and already causing hundreds of thousands of deaths each year. While natural products and synthetic organic small molecules have provided the majority of our current antibiotic arsenal, they are falling short in providing new drugs with novel modes of action able to treat multidrug resistant bacteria. Metal complexes have recently shown promising results as antimicrobial agents, but the number of studied compounds is still vanishingly small, making it difficult to identify promising compound classes or elucidate structure-activity relationships. To accelerate the pace of discovery we have applied a combinatorial chemistry approach to the synthesis of metalloantibiotics. Utilizing robust Schiff-base chemistry and combining 7 picolinaldehydes with 10 aniline derivatives, and 5 axial ligands we have prepared a library of 420 novel manganese tricarbonyl complexes. All compounds were evaluated for their antibacterial properties and 10 lead compounds were identified, re-synthesized and fully characterized. All 10 compounds showed high and broad activity against Gram-positive bacteria. The best manganese complex displayed low toxicity against human cells with a therapeutic index of >100. In initial mode of action studies, we show that it targets the bacterial membrane without inducing pore formation or depolarisation. Instead, it releases its carbon monoxide ligands around the membrane and inhibits the bacterial respiratory chain. This work demonstrates that large numbers of metal complexes can be accessed through combinatorial synthesis and evaluated for their antibacterial potential, allowing for the rapid identification of promising metalloantibiotic lead compounds. | Mirco Scaccaglia; Giorgio Pelosi; Silvana Pienlli; Angelo Frei | Biological and Medicinal Chemistry; Inorganic Chemistry; Organometallic Chemistry; Bioinorganic Chemistry; Microbiology; Bioorganometallic Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65239c7045aaa5fdbb961cd5/original/discovery-of-antibacterial-manganese-i-tricarbonyl-complexes-through-combinatorial-chemistry.pdf |
61bc04db75c572331dee6cff | 10.26434/chemrxiv-2021-mskbh | In-situ ellipsometry measurements on the phase segregation of mixed halide lead perovskites | Mixed halide lead perovskite such as methylammonium lead iodide bromides MAPb(BrxI1-x)3 have emerged as one of the most promising materials of future solar cells, offering high power conversion efficiencies and bandgap tunability. Among other factors, the reversible phase segregation under even low light intensities is still limiting their potential use. During this process, the material segregates locally into iodide-rich and bromide-rich phases, lowering the effective bandgap energy. While several studies have been done to illuminate the mechanism and suppression of phase segregation, fundamental aspects remain unclear. Phase compositions after segregation vary extensively between different studies and the exact amounts of phases often remain unmentioned. For iodide-rich phases, the end-point compositions at around x=0.2 are widely accepted but the proportion of the phase is difficult to measure. In this report, we observe the phase segregation using spectroscopic ellipsometry, a powerful, nondestructive technique that has been employed in the study of film degradation before. We obtained dynamic ellipsometric measurements from x=0.5 mixed halide lead perovskite thin films protected by a polystyrene layer under green laser light with a power density of ~11 W/cm2. Changes in the bandgap region can be correlated to the changes in composition caused by phase segregation, allowing for the kinetics to be observed. Time constants between 1.7(± 0.7)×10-3 s-1 for the segregation and 1.5(± 0.6)×10-4 s-1 for recovery were calculated. We expect ellipsometry to serve as a complementary technique to other spectroscopies in studying mixed-halide lead perovskites phase segregation in the future. | Annik Bernhardt; Tharushi Ambagaspitiya; Martin Kordesch; Katherine Cimatu; Jixin Chen | Physical Chemistry; Analytical Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61bc04db75c572331dee6cff/original/in-situ-ellipsometry-measurements-on-the-phase-segregation-of-mixed-halide-lead-perovskites.pdf |
60c74025337d6c7e9ee2666b | 10.26434/chemrxiv.7665620.v1 | Theoretical Investigations of Photoionization Efficiency of Naphthalene | The equilibrium geometry and 48 vibrational normal-mode frequencies of the neutral and cationic ground state and the cationic first excited states of naphthalene isomers were calculated and characterized in the adiabatic representation by using the complete active space self-consistent field (CASSCF) and second order perturbation theory (CASPT2). Photoionization-efficiency (PIE) spectrum of molecular beam conditions in energy range 8 - 11 eV were determined by Kaiser et al. and they were analyzed using time-dependent density functional theory calculations (TDDFT). CASSCF calculations and PIE spectra simulations by one-photon excitation equations were used to optimize the cationic excited (D1) and neutral ground (S0) state structures of naphthalene isomers. The photoionization-efficiency curve was attributed to the S0 D1 electronic transition in naphthalene, and a curve origin was used at 8.14 eV. The ionization-induced geometry changes of the bases are consistent with the shapes of the corresponding molecular orbitals. The displaced harmonic oscillator approximation and Franck-Condon approximation were used to simulate the PIE curve of the D1 S0 transition of naphthalene, and the main vibronic transitions were assigned for the ππ* state. It shows that the vibronic structures were dominated by one of the xxx active totally symmetric modes, with v8 being the most crucial. This indicates that the electronic transition of the D1 state calculated in the adiabatic representation effectively includes a contribution from the adiabatic vibronic coupling through Franck-Condon factors perturbed by harmonic oscillators. The present method can adequately reproduce experimental PIE curve in the molecular beam condition. | Chih-Hao Chin; Tong Zhu; John ZH Zhang | Computational Chemistry and Modeling; Quantum Computing; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74025337d6c7e9ee2666b/original/theoretical-investigations-of-photoionization-efficiency-of-naphthalene.pdf |
626bfd2a5b9009864720cbab | 10.26434/chemrxiv-2022-17trc | Ligand enabled disproportionation of 1,2-diphenylhydrazine at a P(V)-center | We present herein the synthesis of a nearly square pyramidal chlorophosphorane supported by the tetradentate bis(amidophenolate) ligand, N,N’-bis(3,5-di-tert-butyl-2-phenoxy)-1,2-phenylenediamide. After chloride abstraction the resulting phosphonium cation efficiently catalyzes the disproportionation of 1,2-diphenylhydrazine to aniline and azobenzene. Mechanistic studies, spectroscopic analyses and theoretical calculations suggest that it is the combination of high electrophilicity at the cationic P(V)-center, which originates from the geometry constraints imposed by the rigid pincer ligand, and the ability of the o-amidophenolate moieties to act as electron reservoir what leverages this unprecedented reactivity mode for P(V)-centres. This study illustrates the promising role of cooperativity between redox-active ligands and phosphorus for the design of organocatalysts able to promote redox processes. | Simon B. H. Karnbrock; Christopher Golz; Ricardo A. Mata; Manuel Alcarazo | Organic Chemistry; Catalysis | CC BY NC 4.0 | CHEMRXIV | 2022-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626bfd2a5b9009864720cbab/original/ligand-enabled-disproportionation-of-1-2-diphenylhydrazine-at-a-p-v-center.pdf |
67b5f54681d2151a02290f67 | 10.26434/chemrxiv-2025-v96zp | A Comparison of Bead-Spring and Site-Binding Models for Weak Polyelectrolytes | Understanding states of weak polyelectrolytes is essential for designing advanced materials in biological and industrial applications. However, predicting their ionization states in aqueous solutions with added salt remains challenging due to the interplay between long-range Coulomb interactions, conformational degrees of freedom and chemical equilibria. While flexible bead-spring models with an explicit ion treatment provide accurate results, they are computationally expensive. In contrast, Ising-like site-binding models can often be solved in a matter of seconds and a further speed-up is possible using exact reweighting techniques. Notably, these models neglect conformational degrees of freedom and rely on an implicit salt description. To address the question under which circumstances these approximations are justified, we compare a site-binding model to bead-spring models with implicit and explicit ion treatments. Our results show that under strong electrostatic coupling, an explicit ion treatment is critical for accurately capturing ionization behavior. In particular, both, the site-binding model, and the bead-spring model with implicit ion treatment, strongly overestimate correlations between monomers in this regime, leading to significant deviations from the explicit bead-spring model. Conversely, under weak coupling, which is realized in aqueous environments in the presence of monovalent salts, all three models yield reasonable ionization curves. Minor differences arise, with the implicit bead-spring model showing slightly stronger suppression of ionization, while the site-binding model aligns more closely with the explicit bead-spring model due to compensating errors in ion treatment and conformational flexibility. In summary, while all models are effective under weak coupling, the explicit ion treatment within the bead-spring model is essential for capturing accurate ionization behavior under strong coupling. | Loris Burth; David Beyer; Christian Holm | Physical Chemistry; Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b5f54681d2151a02290f67/original/a-comparison-of-bead-spring-and-site-binding-models-for-weak-polyelectrolytes.pdf |
662a599021291e5d1db08e05 | 10.26434/chemrxiv-2024-4mn5r | Aliphatic Ketone Claisen Rearrangement: Troubleshooting the Transetherification Step by Identifying a Stable Acid Catalyst | After optimization for catalyst stability, 4-chlorobenzoic acid emerged as the optimal catalyst for the aliphatic ketone Claisen rearrangement. The protocol enables a one-pot, metal-free, catalytic protocol from allylic alcohols to γ,δ-unsaturated ketones. The optimized process tolerates a range of substrates, including substituents with acid-labile protecting groups. Reaction monitoring and DFT studies of the aliphatic ketone Claisen process agree that the ultimate rearrangement step typically has the highest activation barrier. | Veera Bruce; Kaveh Farshadfar; Aino Rolig; Kari Laasonen; Petri Pihko | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Acid Catalysis | CC BY 4.0 | CHEMRXIV | 2024-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662a599021291e5d1db08e05/original/aliphatic-ketone-claisen-rearrangement-troubleshooting-the-transetherification-step-by-identifying-a-stable-acid-catalyst.pdf |
67bce95d81d2151a02e708ba | 10.26434/chemrxiv-2025-n0tnl | MolGen-Transformer: A molecule language model for the generation and latent space exploration of pi-conjugated molecules | The application of generative artificial intelligence (AI) to molecular discovery has unlocked vast potential for the automated design of new chemical systems. Molecular language models (LM), however, face several challenges that impact their effectiveness, including incomplete coverage of chemical space, due to limitations in training dataset diversity and size, chemical insights within latent space representations, and reconstruction reliability. Here, we present MolGen-Transformer, a generative AI model designed to address these challenges through a latent-space-centered approach. Trained on a large and diverse dataset of approximately 198 million organic molecules, the model achieves 100% molecular reconstruction accuracy, ensuring stable and reliable latent space representations. MolGen-Transformer leverages robust molecular encoding (here, the SELFIES representation) to guarantee valid outputs, enhance computational efficiency, and create a chemically meaningful latent space. To demonstrate the model’s capabilities, we develop and employ three sampling strategies: (1) production of diverse molecules through random latent space sampling, (2) generation of chemically similar molecules with tunable similarity and diversity, and (3) interpolation to identify chemical intermediates between target molecules, to provide insights into the continuity of the latent space. These methods enable flexible exploration of chemical space while addressing limitations of existing approaches. Combining accuracy and scalability, the MolGen-Transformer provides a versatile platform for generating chemically relevant and structurally diverse molecular data. To promote further innovation and facilitate new opportunities for AI-driven molecular discovery, both the model and sampling methods are publicly available. | Chih-Hsuan Yang; Rebekah Duke; Parker Sornberger; Moses Ogbaje; Chad Risko; Baskar Ganapathysubramanian | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence | CC BY NC 4.0 | CHEMRXIV | 2025-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bce95d81d2151a02e708ba/original/mol-gen-transformer-a-molecule-language-model-for-the-generation-and-latent-space-exploration-of-pi-conjugated-molecules.pdf |
63d45b481fe142942f5c37ad | 10.26434/chemrxiv-2023-7lths | The Effect of Ligand-to-Metal Energy Transfer on the Photooxidation Performance of an Isostructural Series of Pyrene-Based Rare-Earth Metal–Organic Frameworks | The rectangular tetratopic linker, 1,3,6,8-tetrakis(p-benzoic acid)pyrene (H4TBAPy) along with rare-earth (RE) ions is used for the synthesis of 9 isostructures of a metal–organic framework (MOF) with shp topology, named RE-CU-10 (RE = Y(III), Gd(III), Tb(III), Dy(III), Ho(III), Er(III), Tm(III), Yb(III) and Lu(III)). The synthesis of each RE-CU-10 analogue requires different reaction conditions to achieve high quality phase pure products. Single crystal X-ray diffraction indicates the presence of a RE9-cluster in Y- to Tm-CU-10, while a unique RE11-cluster is observed for Yb- and Lu-CU-10. The photooxi-dation performance of the reported RE-CU-10 analogues is evaluated, giving insight into the competitive process of ligand-to-metal energy transfer versus the generation of singlet oxygen by RE-CU-10. The singlet oxygen produced is used to detoxify a mustard gas simulant 2-chloroethylethyl sulfide (2-CEES) to 2-chloroethyl ethyl sulfoxide (2-CEESO), with half-lives ranging from 4.0 to 5.8 min, some of the fastest reported to date using UV-irradiation and < 1 mol% catalyst, in methanol under O2 saturation. | Victor Quezada-Novoa; Hatem M. Titi; Francisco Yarur Villanueva; Mark W. B. Wilson; Ashlee J. Howarth | Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d45b481fe142942f5c37ad/original/the-effect-of-ligand-to-metal-energy-transfer-on-the-photooxidation-performance-of-an-isostructural-series-of-pyrene-based-rare-earth-metal-organic-frameworks.pdf |
6638ddde91aefa6ce14a6d83 | 10.26434/chemrxiv-2023-nfq7h-v2 | Simple User-Friendly Reaction Format | Leveraging the increasing volume of chemical reaction data can enhance synthesis planning and improve suc-
cess rates. However, machine learning applications for retrosynthesis planning and forward reaction prediction
tools depend on having readily available, high-quality data in a structured format. While some public and
licensed reaction databases are available, they frequently lack essential information about reaction condi-
tions. To address this issue and promote the principles of findable, accessible, interoperable, and reusable
(FAIR) data reporting and sharing, we introduce the Simple User-Friendly Reaction Format (SURF). SURF
standardizes the documentation of reaction data through a structured tabular format, requiring only a basic
understanding of spreadsheets. This format enables chemists to record the synthesis of molecules in a format
that is both human- and machine-readable, making it easier to share and integrate directly into machine-
learning pipelines. SURF files are designed to be interoperable, easily imported into relational databases, and
convertible into other formats. This complements existing initiatives like the Open Reaction Database (ORD)
and Unified Data Model (UDM). At Roche, SURF plays a crucial role in democratizing FAIR reaction data
sharing and expediting the chemical synthesis process. | David F. Nippa; Alex T. Müller; Kenneth Atz; David B. Konrad; Uwe Grether; Rainer E. Martin; Gisbert Schneider | Theoretical and Computational Chemistry; Organic Chemistry; Chemical Engineering and Industrial Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry; Pharmaceutical Industry | CC BY 4.0 | CHEMRXIV | 2024-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6638ddde91aefa6ce14a6d83/original/simple-user-friendly-reaction-format.pdf |
667e7e245101a2ffa8c71afc | 10.26434/chemrxiv-2024-32xrs-v2 | Electrochemical Synthesis of the in human S-oxide metabolites of phenothiazine containing Anti-Psychotic Medications | The tractable preparation of phase-I drug metabolites is a critical step to understand the first-pass behaviour of novel chemical entities in drug discovery. In this study we have developed a structure electroactivity relationship (SeAR) informed electrochemical reaction of the parent 2-chlorophenothiazine and anti-psychotic, chlorpromazine. The ability to dial-in under current controlled conditions the formation of S-oxide and novel S,S-dioxide metabolites has been achieved for the first time on a multimilligram scale using a direct batch electrode platform. A potential rationale for the electrochemical formation of these metabolites in situ is proposed using molecular docking to a cytochrome P450 enzyme. | Ridho Asra; Aigul Malmakova; Alan Jones | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Organic Synthesis and Reactions; Electrochemical Analysis; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2024-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667e7e245101a2ffa8c71afc/original/electrochemical-synthesis-of-the-in-human-s-oxide-metabolites-of-phenothiazine-containing-anti-psychotic-medications.pdf |
65ace2c6e9ebbb4db9a4d41f | 10.26434/chemrxiv-2024-nh9mx | An Efficient Approach for Obtaining Small and Macro-molecular 1H NMR Spectra Based on Neural Network | Metabolomics plays a vital role in comprehending cellular and organismal metabolic processes. In NMR-based metabolomics studies, specific NMR pulse sequences such as the standard 1D nuclear Overhauser effect spectroscopy (NOESY), 1D Carr-Purcell-Meiboom-Gill (CPMG), and 1D diffusion-edited sequences are commonly utilized to detect distinctive NMR characteristics of small molecule and macromolecule metabolites in plasma or serum samples. However, conducting NMR experiments on multiple samples in metabolomics can be time-consuming. This study introduces the Spectrum-Edited Neural Network (SENNet) for efficient and accurate separation of spectral signals from both macromolecules and small molecules in 1H NMR spectra. The proposed model provides an end-to-end mapping of the entire metabolome NMR spectrum to the macromolecular and small molecule NMR spectra. To validate and optimize the model's hyperparameters, we employed a total of 113 serum samples. Furthermore, the SENNet method was applied to post-process 1D NOESY-presat spectra obtained from 120 plasma samples and 463 serum samples, which were then compared with the corresponding 1D CPMG spectra and 1D diffusion-edited spectra. Our results demonstrate the effective extraction of small molecule signals using the proposed method, as confirmed by comparison with experimental spectra. Principal component analysis (PCA) performed on the macromolecule and small molecule signals reveals comparable statistical information to analyses conducted using experimental data, indicating the efficiency of the SENNet method for signal extraction. This high-throughput NMR post-processing method holds substantial potential for metabolomics research. Additionally, the SENNet method serves as a valuable reference for separating signals from both macro and small molecules in NMR samples. | xiongjie xiao; Qianqian Wang; Xin Chai; Xu Zhang; Bin Jiang; Maili Liu | Analytical Chemistry; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ace2c6e9ebbb4db9a4d41f/original/an-efficient-approach-for-obtaining-small-and-macro-molecular-1h-nmr-spectra-based-on-neural-network.pdf |
60c74f00bdbb890fdba39cb4 | 10.26434/chemrxiv.11671419.v2 | Bypassing the Inertness of Aziridine/CO2 Systems to Access 5-Aryl-2-Oxazolidinones: Catalyst-Free Synthesis Under Ambient Conditions | The development of
sustainable synthetic routes to access valuable oxazolidinones via CO<sub>2</sub>
fixation is an active research area, and the aziridine/carbon dioxide coupling
has aroused a considerable interest. This reaction is featured by a high
activation barrier, so to require a catalytic system, and may present some
other critical issues. Here, we describe the straightforward gram-scale
synthesis of a series of 5-aryl-2-oxazolidinones at ambient temperature and
atmospheric CO<sub>2</sub> pressure, in the absence of any catalyst/co-catalyst.
The key to this innovative procedure consists in the direct transfer of the pre-formed
amine/CO<sub>2</sub> adduct (carbamate) to common aziridine precursors
(dimethylsulfonium salts), replacing the classical sequential addition of amine
(intermediate isolation of aziridine) and then CO<sub>2</sub>. The reaction
mechanism has been investigated by NMR studies and DFT calculations applied to
model cases.<br /> | Giulio Bresciani; Emanuele Antico; Gianluca Ciancaleoni; Stefano Zacchini; Guido Pampaloni; Fabio Marchetti | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f00bdbb890fdba39cb4/original/bypassing-the-inertness-of-aziridine-co2-systems-to-access-5-aryl-2-oxazolidinones-catalyst-free-synthesis-under-ambient-conditions.pdf |
67866d056dde43c9087b064f | 10.26434/chemrxiv-2024-m9tkn-v2 | Using Data Science to Interrogate
Transition State Stabilization in Anion-Binding Catalysis
for Disulfide Ring-Opening Polymerization | In nature, enzymes leverage constituent amino acid residues to create catalytic microenvironment for their active sites to effect high reactivity and selectivity. Multicomponent host−guest assemblies have been exploited to mimic enzymatic microenvironments by preorganizing a network of noncovalent interactions. While anion-binding catalysts such as thioureas have gained widespread success in organic transformation and controlled polymerization, evaluation of the participating structural features in the transition state (TS) stabilization remains challenging. Herein, we report the use of data science tools, i.e., a decision-tree-based machine-learning algorithm and Shapley additive explanations (SHAP) analysis, to model reactivity and regioselectivity in a thiourea-catalyzed ring-opening polymerization of 1,2-dithiolanes. Variation of aryl substituent position and electronic characteristics helps reveal key catalyst features involved in the TS stabilization within the catalytically active, multicomponent host−guest complexes. The analysis of feature importance helps explain the reason behind the optimal performance of (pseudo)halogen-substituted catalysts. Furthermore, the structural basis for the unveiled reactivity-regioselectivity trade-off in the catalysis are established. | Miaomiao Zhang; Yuming Su; Tianyi Du; Shihao Ding; Jieyu Dai; Cheng Wang; Yun Liu | Organic Chemistry; Polymer Science; Physical Organic Chemistry; Supramolecular Chemistry (Org.); Polymerization catalysts | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67866d056dde43c9087b064f/original/using-data-science-to-interrogate-transition-state-stabilization-in-anion-binding-catalysis-for-disulfide-ring-opening-polymerization.pdf |
60c74577469df4670af434f8 | 10.26434/chemrxiv.10028504.v1 | A General Carbonyl Alkylative Amination Process for Tertiary Amine Synthesis | We report a practical
and general solution to this long-standing synthetic challenge can be
accomplished by addition of alkyl radicals to all alkyl-iminium ions. The
process is mediated by the action of visible light and a simple silane reducing
agent, establishing a chain process that permits the combination of an
extremely wide range of aldehydes and secondary amines with alkyl halides. | Roopender Kumar; Nils Floden; William G. Whitehurst; Matthew Gaunt | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74577469df4670af434f8/original/a-general-carbonyl-alkylative-amination-process-for-tertiary-amine-synthesis.pdf |
62c369e67b3b3066cc0d010d | 10.26434/chemrxiv-2022-0l4nt | Methylation Confers Accessibility, Stability and Selectivity to Picrotoxinin | Natural product total synthesis enables gain of function through deep-seated modification of structure. Synthetic difficulty can, however, obstruct meaningful optimization campaigns. To simplify access, the complexity of the target (TGT) can be lowered—a strategy described within function-oriented synthesis. Alternatively, the chemical space immediately surrounding the TGT can be searched for analogs of equal or greater complexity that also simplify access. This strategy—dynamic retrosynthetic analysis—maintains most physicochemical properties of the TGT (locus in chemical space) but opens new synthetic paths unavailable to the natural product itself and can provide functional advantage. Here we experimentally interrogate these ideas by generation of two parallel series of picrotoxinin (PXN) analogs to identify leads with ligand-gated ion channel (LGIC) selectivity. One series derives from PXN via semi-synthesis, and the other from 5MePXN via total synthesis. Methylation at C5 decreases potency against vertebrate ion channels (GABAa receptors) but maintains or increases antagonism of homologous invertebrate GABA-gated chloride channels (RDL receptors). Optimal 5MePXN analogs appear to change the PXN binding pose within GABAARs by disruption of a hydrogen bond network. The C5 methyl also stabilizes the scaffold substantially against irreversible C15 solvolysis by destabilizing an intermediate twist-boat conformer, which returns to 5MePXN instead of progressing to degradant. These discoveries are made possible by the lower synthetic burden of 5MePXN and are illuminated by the parallel analog series, which allows unambiguous identification of the role of the synthetically simplifying C5 methyl. Rapid access to functionally-privileged analogs by TGT point mutation underscores the value of dynamic retrosynthetic analysis as a problem-solving heuristic. | Guanghu Tong; Samantha Griffin; Avery Sader; Anna Crowell; Ken Beavers; Jerry Watson; Zachary Buchan; Shuming Chen; Ryan Shenvi | Physical Chemistry; Organic Chemistry; Agriculture and Food Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c369e67b3b3066cc0d010d/original/methylation-confers-accessibility-stability-and-selectivity-to-picrotoxinin.pdf |
62ab495320a4edd6bf410506 | 10.26434/chemrxiv-2022-jp2vg | Degradation Pathways of Cobalt-free LiNiO2 Cathode in Lithium Batteries | Electrode-electrolyte reactivity (EER) and particle cracking (PC) are considered two main causes of capacity fade in high-nickel layered oxide cathodes in lithium-based batteries. However, whether EER or PC is more critical remains debatable. Herein, the fundamental correlation between EER and PC is systematically investigated with LiNiO2 (LNO), the ultimate cobalt-free lithium layered oxide cathode. Specifically, EER is found more critical than secondary particle cracking (SPC) in determining the cycling stability of LNO; EER leads to primary particle cracking (PPC), but contrary to conventional wisdom, prevents SPC. Two surface degradation pathways are identified for cycled LNO under low and high EERs. A common blocking surface reconstruction layer (SRL) containing electrochemically-inactive Ni3O4 spinel and NiO rock-salt phases is formed on LNO at the charged state in an electrolyte with high EER; in contrast, an electrochemically-active SRL featuring regions of electron- and lithium-ion-conductive LiNi2O4 spinel phase is formed on LNO at the charged state in an electrolyte with low EER, even though bulk LiNi2O4 crystals are believed to be non-existent. These findings unveil the intrinsic degradation pathways of LNO cathode and are foreseen to provide new insights into the development of lithium-based batteries with minimized EER and maximized service life. | Ruijun Pan; Eunmi Jo; Zehao Cui; Arumugam Manthiram | Materials Science; Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ab495320a4edd6bf410506/original/degradation-pathways-of-cobalt-free-li-ni-o2-cathode-in-lithium-batteries.pdf |
6760788f6dde43c9085e8cfa | 10.26434/chemrxiv-2024-bs3gs | Evaluation of Infrared Intensities using Diffusion Monte Carlo | Approaches for evaluating excited state wave functions and energies using diffusion Monte Carlo (DMC) with guiding functions (guided DMC) are discussed. For this work, the guiding functions are functions of a subset of the $3N-6$ coordinates that are needed to describe the structure of the molecule of interest. The DMC wave functions are used to evaluate intensities using two approaches. In the trial wave function approach, the product of the molecular wave function for one of the states involved in the transition and the guiding function for the second state is used to evaluate the matrix elements of the dipole moment. In the descendant weighting approach descendant weights are used to evaluate the value of the wave function for one of the states involved in the transition at the geometries sampled by the DMC wave function for the second state. The descendant weighting approximation is shown to be more accurate as well as computationally more expensive compared to approximations that are based on various forms of the trial wave function approach. Strategies are explored, which combine results of different forms of the trial wave function approximation to minimize the errors in this approach. The trial wave function and descendant weighting approaches are applied to a study of a harmonic oscillator, where the sensitivity of the calculated energies and intensities to the quality of the trial wave function is explored. The two approaches are also applied to calculations of frequencies and intensities of transitions in water, H3O2- a four-dimensional model based on H3O2-, and H5O2+. We also show how comparisons of the results obtained using several forms of the trial wave function approach allow us to explore how couplings among vibrational motions are reflected in the intensities. | Pattrapon Moonkaen; Anne McCoy | Theoretical and Computational Chemistry; Physical Chemistry; Clusters; Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6760788f6dde43c9085e8cfa/original/evaluation-of-infrared-intensities-using-diffusion-monte-carlo.pdf |
64d9e3284a3f7d0c0d24a1b3 | 10.26434/chemrxiv-2023-wqvkv | Cold-bonded biochar-rich lightweight aggregates for net-zero concrete | An emerging strategy to remove CO2 from the atmosphere and compensate for the greenhouse-gas emissions of cement and concrete is based on incorporating biochar into concrete. With this approach, concrete can be turned into a functional carbon sink (C-sink). Until now, biochar has been used without modification to replace part of the cement or of the aggregates in concrete. However, this technology comes with a number of practical problems, which include the high water absorption of the biochar (due to its high specific surface) and hazards (dust, risk of combustion). In this paper we present an alternative approach in which biochar is first processed into lightweight aggregates in a cold-bonding process. To this end, biochar is pelletized together with a small amount of hydraulic binder and with water and forms round pellets that further harden with hydration time. In this way, carbon-rich lightweight aggregates (C-LWA) are obtained that are easier to handle than the pure biochar. The C-LWA pellets have similar porosity and strength as conventional LWA and can be used for similar applications. Yet, the CO2 emissions from sintering traditional LWA are avoided and the C-LWA are instead an effective C-sink. We demonstrate that it is possible to incorporate in the pellets and eventually in the concrete a sufficient amount of carbon to compensate for the original emissions of concrete. The net-zero emissions concrete obtained with this approach possesses mechanical performance sufficient for typical structural applications in buildings. | Mateusz Wyrzykowski; Nikolajs Toropovs; Frank Winnefeld; Pietro Lura | Materials Science; Carbon-based Materials; Composites; Granular Materials | CC BY 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d9e3284a3f7d0c0d24a1b3/original/cold-bonded-biochar-rich-lightweight-aggregates-for-net-zero-concrete.pdf |
60c744b0337d6c3108e26e35 | 10.26434/chemrxiv.8953565.v2 | Global Aromaticity at the Nanoscale | <div><p>Aromaticity is an important concept for predicting
electronic delocalisation in molecules, particularly for designing organic
semiconductors and single-molecule electronic devices. It is most simply
defined by the ability of a cyclic molecule to sustain a ring current when
placed in a magnetic field. Hückel’s rule states that if a ring has [4n+2]
π-electrons, it will be aromatic with an induced magnetisation that opposes the
external field inside the ring, whereas if it has 4n π-electrons, it will be antiaromatic
with the opposite magnetisation. This rule reliably predicts the behaviour of
small molecules, typically with circuits of less than about 22 π-electrons (n =
5). It is not clear whether aromaticity has a size limit and whether Hückel’s
rule is valid in much larger macrocycles. Here, we present evidence for global
aromaticity in a wide variety of porphyrin nanorings, with circuits of up to
162 π-electrons (n = 40; diameter 5 nm). We show that aromaticity can be
controlled by changing the molecular structure, oxidation state and
three-dimensional conformation. Whenever a global ring current is observed, its
direction is correctly predicted by Hückel’s rule. The magnitude of the current
is maximised when the average oxidation state of the porphyrin units is around
0.5–0.7, when the system starts to resemble a conductor with a partially filled
valence band. Our results show that aromaticity can arise in large macrocycles,
bridging the size gap between ring currents in molecular and mesoscopic rings.</p></div> | Michel Rickhaus; Michael Jirasek; Lara Tejerina; Henrik Gotfredsen; Martin D. Peeks; Renee Haver; Hua-Wei Jiang; Timothy D. W. Claridge; Harry L. Anderson | Physical Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744b0337d6c3108e26e35/original/global-aromaticity-at-the-nanoscale.pdf |
643d53c51d262d40eaa4071b | 10.26434/chemrxiv-2022-464nx-v2 | BF3-Catalyzed Intramolecular Fluorocarbamoylation of Alkynes via Halide Recycling | A BF3-catalyzed atom-economical fluorocarbamoylation reaction of alkyne-tethered carbamoyl fluorides is reported. The catalyst acts as both a fluoride source and Lewis acid activator, enabling the formal insertion of alkynes into strong C–F bonds through a halide recycling mechanism. The developed method provides access to 3-(fluoromethylene)oxindoles and γ-lactams with excellent stereoselectivity, including fluorinated derivatives of known protein kinase inhibitors. Experimental and computational studies support a stepwise mechanism for the fluorocarbamoylation reaction involving a turnover-limiting cyclization step, followed by internal fluoride transfer from a BF3-coordinated carbamoyl adduct. For methylene oxindoles, a thermodynamically driven Z-E isomerization is facilitated by a transition state with aromatic character. In contrast, this aromatic stabilization is not relevant for γ-lactams, resulting in a higher barrier for isomerization and the exclusive formation of the kinetic Z-isomer. | E. Ali McKnight; Ramon Arora; Ekadashi Pradhan; Yuriko H. Fujisato; Ayonitemi J. Ajayi; Mark Lautens; Tao Zeng; Christine M. Le | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Acid Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643d53c51d262d40eaa4071b/original/bf3-catalyzed-intramolecular-fluorocarbamoylation-of-alkynes-via-halide-recycling.pdf |
64ae5382ba3e99daeff3459c | 10.26434/chemrxiv-2023-z8wjk | Biochemical transformations of inorganic nanomedicines in buffers, cell cultures and organisms | The field of nanomedicine is rapidly evolving, with new materials and formulations being reported almost daily. In this respect, inorganic and inorganic-organic composite nanomaterials have gained significant attention. However, the use of new materials in clinical trials and their final approval as drugs has been hampered by several challenges, one of which is the complex and difficult to control nanomaterial chemistry that takes place within the body. Several reviews have summarized investigations on inorganic nanomaterial stability in model body fluids, cell cultures, and organisms, focusing on their degradation as well as the influence of corona formation. However, in addition to these aspects, various chemical reactions of nanomaterials, including phase transformation and/or the formation of new/secondary nanomaterials, have been reported. In this review, we discuss recent advances in our understanding of biochemical transformations of medically relevant inorganic (composite) nanomaterials in environments related to their applications. We provide a refined terminology for the primary reaction mechanisms involved to bridge the gaps between different disciplines involved in this research. Furthermore, we highlight suitable analytical techniques that can be harnessed to explore the described reactions. Finally, we highlight opportunities to utilize them for diagnostic and therapeutic purposes and discuss current challenges and research priorities. | Anna Neuer; Inge Herrmann; Alexander Gogos | Biological and Medicinal Chemistry; Materials Science; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ae5382ba3e99daeff3459c/original/biochemical-transformations-of-inorganic-nanomedicines-in-buffers-cell-cultures-and-organisms.pdf |
6617e8f9418a5379b0a1faaf | 10.26434/chemrxiv-2024-pj7s0 | Modular soft stretchable low-cost elastomers for stereolithography printing structures with extreme dissipative properties | Additive manufacturing of elastomers enables the fabrication of many technologically important structures and devices. However, it remains a challenge to develop soft and stretchable elastomers for stereolithography (SLA) printing, one of the most used additive manufacturing techniques for producing objects with relatively high-resolution and smooth finishes. Here, we report a modular, soft, stretchable, and low-cost elastomer resin for SLA printing. The resin consists of mainly commodity acrylates and can be photocured to form a dual-crosslinked network containing covalent and reversible crosslinks. Controlling the ratio of covalent and reversible crosslinks, we create elastomers with an exceptional combination of softness and stretchability (Young’s modulus of 20-150 kPa and tensile breaking strain of 510-1350%) that cannot be achieved by existing SLA resins. We demonstrate printing this resin to produce high-resolution three-dimensional (3D) structures with extreme dissipative properties. Further, we develop a setup to show that the 3D structures can protect brain-like soft gels from impact damage in reducing the severity of impact by 75%. Together with the low-cost of raw chemicals and modular nature of the design, our soft and stretchable elastomer resins provide a new class of soft materials for high-fidelity additive manufacturing of functional architectures. | Daniel Rau; Myoeum Kim; Baoxing Xu; Liheng Cai | Materials Science; Polymer Science; Elastic Materials; Materials Processing | CC BY 4.0 | CHEMRXIV | 2024-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6617e8f9418a5379b0a1faaf/original/modular-soft-stretchable-low-cost-elastomers-for-stereolithography-printing-structures-with-extreme-dissipative-properties.pdf |
60c74021702a9b2fef18a054 | 10.26434/chemrxiv.7496306.v2 | Oligothiophene Synthesis by a Distinct, General C−H Activation Mechanism: Electrophilic Concerted Metalation-Deprotonation (eCMD) | Oxidative
C–H/C–H coupling is a promising synthetic route for the streamlined
construction of conjugated organic materials for optoelectronic applications. Broader
adoption of these methods is nevertheless hindered by the need for catalysts that
excel in forging core semiconductor motifs, such as ubiquitous oligothiophenes,
with high efficiency in the absence of metal reagents. We report a
(thioether)Pd-catalyzed oxidative coupling method for the rapid assembly of both
privileged oligothiophenes and challenging hindered cases, even at low catalyst
loading under Ag- and Cu-free conditions. A combined experimental and
computational mechanistic study was undertaken to understand how a simple
thioether ligand, MeS(CH<sub>2</sub>)<sub>3</sub>SO<sub>3</sub>Na, leads to
such potent reactivity toward electron-rich substrates. The consensus from
these data is that a concerted, base-assisted C–H cleavage transition state is
operative, but thioether coordination to Pd is associated with decreased
synchronicity (bond formation exceeding bond breaking) versus the classic
concerted metalation-deprotonation (CMD) model. Enhanced positive charge
build-up on the substrate results from this perturbation, which rationalizes experimental
trends strongly favoring π-basic sites. The term <i>electrophilic</i> CMD (<i>e</i>CMD)
is introduced to distinguish this mechanism. More O'Ferrall-Jencks analysis
further suggests <i>e</i>CMD should be a
general mechanism manifested by many metal complexes. A preliminary
classification of complexes into those favoring <i>e</i>CMD or standard CMD is proposed, which should be informative for
studies toward tunable catalyst-controlled reactivity. | Long Wang; Brad Carrow | Organic Synthesis and Reactions; Homogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74021702a9b2fef18a054/original/oligothiophene-synthesis-by-a-distinct-general-c-h-activation-mechanism-electrophilic-concerted-metalation-deprotonation-e-cmd.pdf |
6762e58f81d2151a021e7193 | 10.26434/chemrxiv-2024-cjcmp | Linear Viscoelasticity of Polystyrene Vitrimers: Segmental Motions and The Slow Arrhenius Process | Vitrimers are polymer networks connected by associative cross-links – covalent linkages that maintain network connectivity but exchange through reversible chemical reactions. Associative cross-links significantly change the dynamics of the molten polymer. This study focuses on the linear viscoelasticity of polystyrene vitrimers (PS-v) bearing imine cross-links. PS-v samples were prepared by condensation between precursor copolymers with pendant aldehydes and 1,6-hexanediamine cross-linker. The number average molecular weights of the precursors were 6 and 8 kDa, and the amine-to-aldehyde molar ratio (r) ranged between 0.8 and 2.4. The glass transition temperature exhibited a non-monotonic relationship with r. The linear viscoelasticity of PS-v was evaluated using a combination of small amplitude oscillatory shear (SAOS), stress relaxation, and creep and recovery. Time-temperature superposition analyses indicated two distinct relaxation regimes: (I) fast high frequency dynamics with a Williams-Landel-Ferry temperature dependence and (II) slow low frequency dynamics with Arrhenius behavior. The fast regime represented the segmental relaxations of the vitrimer backbone. The slow regime was described as a Slow Arrhenius Process (SAP), in which the long time dynamics have a temperature-independent rheological activation energy. For all PS-v samples in this study, the observed SAP had a much weaker temperature dependence than expected from sticky Rouse model predictions. Increasing r altered the plateau modulus and SAOS cross-over frequency but did not affect the temperature dependences of the segmental motions or SAP. To describe the origin of the SAP, three hypotheses are proposed: cross-linker diffusion, polymer matrix effects, and local elasticity fluctuations. | Daniel Barzycki; Dana Ezzeddine; Sachin Shanbhag; Ralm Ricarte | Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6762e58f81d2151a021e7193/original/linear-viscoelasticity-of-polystyrene-vitrimers-segmental-motions-and-the-slow-arrhenius-process.pdf |
667526b8c9c6a5c07a034ce1 | 10.26434/chemrxiv-2024-l0n7g | A Paramagnetic Nickel–Zinc Hydride Complex | Reaction of a molecular zinc–hydride [{(ArNCMe)2CH}ZnH] (Ar = 2,6-di-isopropylphenyl) with 0.5 equiv. of [Ni(CO)Cp]2 led to the isolation of a nickel–zinc hydride complex containing a bridging 3-centre,2-electron Ni–H–Zn interaction. This species has been characterized in the solid-state by single crystal X-ray diffraction. DFT calculations are consistent with its formulation as a -complex derived from coordination of the zinc–hydride to a paramagnetic nickel(I) fragment. Continuous wave and pulse EPR experiments suggest that this species is not stable in solution and hint that the coordination event may well be dynamic. Further experiments show that in the presence of catalytic quantities of nickel(I) precursors, zinc–hydride bonds can undergo either H/D-exchange with D2 or dehydrocoupling to form Zn–Zn bonds. In combination, the data support the activation and functionalisation of zinc–hydride bonds at nickel(I) centres. | Marina Perez-Jimenez; Blaise Geoghegan; Alberto Collauto; Maxie Roessler; Mark Crimmin | Inorganic Chemistry; Organometallic Chemistry; Bonding; Catalysis; Coordination Chemistry (Organomet.) | CC BY 4.0 | CHEMRXIV | 2024-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667526b8c9c6a5c07a034ce1/original/a-paramagnetic-nickel-zinc-hydride-complex.pdf |
6758ac34085116a133fc9a06 | 10.26434/chemrxiv-2024-ggnch-v2 | Automated Structure Analysis of Small Angle Scattering Data via Machine Learning | Billions of dollars have been invested in recent years to build up national scattering facilities around the world with more advanced configurations and faster data collection for small angle scattering (SAS), a technique that enables in-situ structural analysis of nanoparticles (NP) under stringent sample environments. However, the interpretation of experimental SAS data collected in reciprocal space to determine its corresponding real-space morphology is typically a slow process that requires significant domain expertise, leading to high-throughput scattering facilities such as synchrotron scattering centers collecting large quantities of data that may potentially be left unanalyzed. Here, we report a fast and data-efficient machine learning (ML) framework for identifying NP morphologies and their corresponding structural parameters from both theoretical and experimental SAS data. The developed classification and regression models, which take as input raw scattering curves with minimal pre-processing, are able to accurately identify the morphology and structural dimensions from experimental scattering curves with comparable accuracy to human experts. Critically, we discuss design choices that facilitate the practical application of ML frameworks in scattering facilities. Our ML framework is designed to be easy to train, to work well when extrapolating to structural parameters outside of the parameter range the models were trained on, and to enable verification of ML predictions. The enhanced data analysis efficiency enabled by application of these ML models to real-time in-situ analysis of SAS data has the potential to revolutionize the utilization of synchrotron and neutron scattering facilities for probing nanostructures. | Graham Roberts; Mu-Ping Nieh; Anson Ma; Qian Yang | Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6758ac34085116a133fc9a06/original/automated-structure-analysis-of-small-angle-scattering-data-via-machine-learning.pdf |
60c74060842e65160cdb1c83 | 10.26434/chemrxiv.7700516.v1 | A Stable, Non-corrosive Perfluorinated Pinacolatoborate Mg Electrolyte for Rechargeable Mg Batteries | Mg batteries are a promising energy storage system because of physicochemical merits of Mg metal as an anode material. However, the lack of electrochemically and chemically stable magnesium electrolytes impedes the development of Mg batteries. In this study, a newly designed chloride-free magnesium fluorinated pinacolatoborate, Mg[B((CF<sub>3</sub>)<sub>4</sub>C<sub>2</sub>O<sub>2</sub>)<sub>2</sub>]<sub>2</sub>(abbreviated as <b>Mg-FPB</b>), was synthesized by convenient methods from commercially available reagents and fully characterized. The <b>Mg-FPB</b>electrolyte delivered outstanding electrochemical performance, specifically, 95% coulombic efficiency and 197 mV overpotential for reversible Mg deposition, and anodic stability up to 4.0 V vs Mg. The <b>Mg-FPB</b>electrolyte was applied to demonstrate a high voltage rechargeable Mg/MnO<sub>2</sub>battery with a discharge capacity of 150 mAh/g. | Jian Luo; Yujing Bi; Liping Zhang; Xiaoyin zhang; Tianbiao Liu | Energy Storage; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74060842e65160cdb1c83/original/a-stable-non-corrosive-perfluorinated-pinacolatoborate-mg-electrolyte-for-rechargeable-mg-batteries.pdf |
634fc898de2a21dfe9abaf37 | 10.26434/chemrxiv-2022-t0jzc | Floating Carbon Nitride Composites for Practical Solar Reforming of Pre-treated Wastes to Hydrogen Gas | Photoreforming (PR) is a promising green-energy technology that can use sunlight to mitigate biomass and plastic waste while producing hydrogen gas at ambient pressure and temperature. However, practical challenges including photocatalyst lifetime, recyclability, and low production rates in turbid waste suspensions limit PR’s industrial potential. By immobilising PR catalyst materials (carbon nitride/platinum; CNx|Pt and carbon nitride/nickel phosphide; CNx|Ni2P) on hollow glass microspheres, which act as floating supports enabling practical composite recycling, such limitations can be overcome. Substrates derived from plastic and biomass, including poly(ethylene terephthalate) (PET) and cellulose, are reformed by floating PR composites, which are reused for up to 10 consecutive cycles under realistic, vertical simulated solar irradiation (AM1.5G), reaching activities of 921 ± 166 µmolH2 m−2 h−1 on pre-treated PET. Floating PR composites are also advantageous in realistic waste where turbidity prevents light absorption by non-floating catalyst powders, achieving 503.2 ± 1.9 µmolH2 m−2 h−1 using floating CNx versus non-detectable H2 production with non-floating CNx. Low Pt loadings (0.033 ± 0.0013 % m/m) demonstrate consistent performance and recyclability, allowing efficient use of precious metals for PR hydrogen production at the largest areal scale (217 cm2) reported to date, taking an important step toward practical PR implementation. | Stuart Linley; Erwin Reisner | Catalysis; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2022-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634fc898de2a21dfe9abaf37/original/floating-carbon-nitride-composites-for-practical-solar-reforming-of-pre-treated-wastes-to-hydrogen-gas.pdf |
670e21ea51558a15ef1d17ea | 10.26434/chemrxiv-2024-dxv36-v2 | Assessment of molecular dynamics time series descriptors in protein-ligand affinity prediction. | The advancement of computational methods in drug discovery, particularly through the use of machine learning (ML) and deep learning (DL), has significantly enhanced the precision of binding affinity predictions. Despite progress in computer-aided drug discovery (CADD) accurate prediction of binding affinity remains a challenge due to the complex, non-linear character of molecular interactions. Generalizability continues to limit these models, with performance discrepancies noted between training datasets and external test conditions. This study explores the integration of molecular dynamics (MD) simulations with ML to assess its predictive performance and limitations. In particular MD simulations offer a dynamic perspective by depicting the temporal interactions within protein-ligand complexes, potentially bringing additional information for affinity and specificity estimates. By generating and analyzing over 800 unique protein-ligand MD simulations, we evaluate the utility of MD-derived descriptors based on time series in enhancing predictive accuracies. The findings suggest specific and generalizable features derived from MD data and propose approaches to augment the current in silico affinity prediction methods. | Jakub Poziemski; Artur Yurkevych; Pawel Siedlecki | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2024-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670e21ea51558a15ef1d17ea/original/assessment-of-molecular-dynamics-time-series-descriptors-in-protein-ligand-affinity-prediction.pdf |
60c747e1f96a007ca7286fdb | 10.26434/chemrxiv.11813361.v1 | Shallow Distance Dependence for Proton-Coupled Tyrosine Oxidation in Oligoproline Peptides | We have explored the kinetic effect of increasing
electron transfer distance in a biomimetic, proton coupled electron transfer system
(PCET). Biological electron transfer is often simultaneous with proton transfer
in order to avoid the high-energy, charged intermediates resulting from the
stepwise transfer of protons and electrons. These concerted proton electron
transfer (CPET) reactions are implicated in numerous biological electron
transfer pathways. In many cases, proton transfer is coupled to long-range
electron transfer. While many studies have shown that the rate of electron
transfer is sensitive to the distance between the electron donor and acceptor,
extensions to biological CPET reactions are sparse. The possibility of a unique
electron transfer distance dependence for CPET reactions deserves further
exploration, as this could have implications for how we understand biological
electron transfer. We therefore explored the electron transfer distance
dependence for the CPET oxidation of tyrosine in a model system. We prepared a
series of metallopeptides with a tyrosine separated from a Ru(bpy)<sub>3</sub><sup>2+</sup>
complex by an oligoproline bridge of increasing length. Rate constants for
intramolecular tyrosine oxidation were measured using the flash-quench
transient absorption technique in aqueous solutions. The rate constants for
tyrosine oxidation decreased by 125-fold with three added prolines residues
between tyrosine and the oxidant. By comparison, related intramolecular ET rate
constants in very similar constructs were reported to decrease by 4-5 orders of
magnitude over the same number of prolines. The observed shallow distance
dependence for tyrosine oxidation is proposed to originate, at least in part,
from the requirement for stronger oxidants, leading to a smaller hole transfer
tunneling barrier height. The shallow distance dependence observed here and
extensions to distance dependent CPET reactions have far-reaching implications
for long-range charge transfers | Brian Koronkiewicz; John R. Swierk; Kevin P. Regan; James Mayer | Bioinorganic Chemistry; Kinetics and Mechanism - Inorganic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747e1f96a007ca7286fdb/original/shallow-distance-dependence-for-proton-coupled-tyrosine-oxidation-in-oligoproline-peptides.pdf |
6700cfbb51558a15ef24e984 | 10.26434/chemrxiv-2024-4c82v-v2 | Input Consistency Regularization of Experimental Data for Modeling Functional Characteristics of A2M3O12 Family of Compounds | The prediction confidence is one of the goals of any machine learning-based study with no respect if this is distinguished as the aim of the study or is the associated desired concomitant. The possibility do not import the additional error into the pre-experimental estimation of the studied characteristics should be the goal of machine learning-based approaches in any case limited in their accuracy by the precision and confidence of the experimental data. In this study, we consider the approaches related to the input consistency regularization which may provide with the required enhancement in the prediction confidence and are able to recoup the part of the experimental error associated with obtaining the data using the methods of different precision. The methodology of regularization of the input data consistency is considered in relation to the problem of the predictive modeling of the functional characteristics of A2M3O12 family of ceramics with negative thermal expansion (NTE) property. The methodological part of this study is aimed at several problems. The Hessian-based analysis of the loss function landscape was considered as the criterion of the generalizability and model performance. The continuity of the property change as a function of the data description coupled with the p-values for the experiment-prediction output were considered as the auxiliary criteria concerned with the input consistency regularization. | Natalia Kireeva; Aslan Yu. Tsivadze | Theoretical and Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6700cfbb51558a15ef24e984/original/input-consistency-regularization-of-experimental-data-for-modeling-functional-characteristics-of-a2m3o12-family-of-compounds.pdf |
637cc016c567539e7b91f264 | 10.26434/chemrxiv-2022-ttgpz | Deuteron-proton isotope correlation spectroscopy of molecular solids | A dissolution followed by recrystallization from a deuterated solvent allows the site-selective deuteration of labile protons in molecular solids. High yields of deuteration obtained by this approach facilitates the structure elucidation of powdered solids by solid-state NMR spectroscopy, for example, by acquiring 1D 2H and 2D 2H-1H correlation NMR spectra with short experimental times. Along these lines, we present a cross-polarization 2H-1H isotope correlation spectroscopy (CP-iCOSY) approach for the characterization of deuterated amino acids and pharmaceutical compounds. We show that the high field NMR (28.2 T) coupled with fast magic-angle spinning (MAS) overcomes the sensitivity and resolution barrier for acquiring 2H MAS spectra, enabling the rapid detection of 2H peaks in a few seconds to minutes. Specifically, two-dimensional 2H-1H CP-iCOSY experiment allows the local structures and through-space interactions in a partially deuterated compounds to be elucidated. Analysis of partially deuterated L-histidine·HCl·H2O and dopamine.HCl is presented, whereby the detection of 2D peaks corresponding to 2H-1H pairs separated by >4 Å demonstrates the sensitivity and resolution power of the presented approach for the characterization of solid-state packing interactions. 2D ssNMR results are corroborate by NMR crystallography analysis using Gauge Including Projector Augmented Wave (GIPAW) approach. Molecular-level analysis enabled by this study is of considerable interest for further investigation of labile sites in a variety of molecular solids, reactive surfaces and interfaces, and supramolecular assemblies. | Claire Welton; Julien Trébosc; Sheetal Jain; Manjunatha Reddy G N | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637cc016c567539e7b91f264/original/deuteron-proton-isotope-correlation-spectroscopy-of-molecular-solids.pdf |
655d1092dbd7c8b54bbca93d | 10.26434/chemrxiv-2023-05fw9 | Optical Dispersion Data Analysis of Single Crystal CH3NH3PbBr3 for Optimized Perovskite Solar Cell Active Layer Absorptance | Proper derivation of CH3NH3PbX3 (CH3NH3+ = methyl ammonium or MA+; X- = Cl-, Br-, I-) optical constants is a critical step toward the development of high-performance electronic and optoelectronic perovskite devices. To date, the optical dispersion regimes at, above, and below the band gap of these materials have been inconsistently characterized by omitting or under-approximating anomalous spectral features (from ultraviolet to infrared wavelengths). In this report, we present the rigorous optical dispersion data analysis of single crystal MAPbBr3 involving variable angle spectroscopic ellipsometry data appended with transmission intensity data. This approach yields a more robust derivation of MAPbBr3 optical constants (refractive index, n, and extinction coefficient, k) for both anomalous (absorptance) and normal (no absorptance) optical dispersion regimes. Using the derived optical constants for our MAPbBr3 single crystals, illustrative modeled solar cell device designs are presented in relation to non-realistic designs prepared using representative optical constants reported in the literature to date. In comparison, our derived optical dispersion data enables the modeled design of realistic planar perovskite solar cell (PSC) optical performance where the active layer (MAPbBr3) is optimized for maximum solar radiation absorption. We further demonstrate optimized modeled planar PSC designs with minimal parasitic optical absorptance in non-active PSC device layers resulting in improved performance at broad angles of incidence (approximately 0-70°). Our robust derivation of MAPbBr3 optical properties is expected to impact the optical dispersion data analysis of all perovskite analogs and expedite targeted development of, for example, solar cell, light-emitting diode, photo and X-ray/γ-ray detector, and laser system technologies. | Christopher McCleese; Michael Brennan; Nathan Episcopo; Lirong Sun; Nina Hong; Chintalapalle Ramana; Tod Grusenmeyer; Peter Stevenson | Physical Chemistry; Materials Science; Energy; Hybrid Organic-Inorganic Materials; Optical Materials; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655d1092dbd7c8b54bbca93d/original/optical-dispersion-data-analysis-of-single-crystal-ch3nh3pb-br3-for-optimized-perovskite-solar-cell-active-layer-absorptance.pdf |
6527f2218bab5d205533992c | 10.26434/chemrxiv-2023-7l8l3 | Protein Stability in a Natural Deep Eutectic Solvent: Preferential Hydration or Solvent Slaving? | Deep eutectic solvents (DESs) emerged as potential alternative solvent media in multiple areas, including biomolecular (cryo)preservation. Herein, we studied the stability of a small protein (ubiquitin) in water and a betaine-glycerol-water (B:G:W) (1:2:z; z = 0, 1, 2, 5, 10) DES, through molecular dynamics. An AMBER-based model that accurately describes the density and shear viscosity of the DES is proposed. We find that water molecules are largely trapped in the solvent, precluding the formation of a full hydration layer, seemingly opposite to osmolytes’ preferential exclusion/preferential hydration mechanism. Whereas the protein is stable in the DES, structural fluctuations are largely suppressed and only recovered upon sufficient hydration. This is explained by a solvent-slaving mechanism where -fluctuations are key, also explaining the non-monotonic folding of some proteins in aqueous DESs. A thermal stability enhancement in the DES is also observed, caused by a similar slowdown of the backbone torsional dynamics. Our results support a kinetic stabilization of the protein in the DES, whereas a possible thermodynamic stabilization does not follow a preferential hydration or water entrapment mechanism. | Inês Gomes; Nuno Galamba | Physical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6527f2218bab5d205533992c/original/protein-stability-in-a-natural-deep-eutectic-solvent-preferential-hydration-or-solvent-slaving.pdf |
6694d37c01103d79c50d80ea | 10.26434/chemrxiv-2024-pvxq4 | Solvent Effect on the Hydroxyl Radical Scavenging Activity of New Isothiocyanate Compounds | The role of natural-based isothiocyanates Cp1-Cp4, i.e., allylisothiocyanate, 1-isothiocyanate-3-methylbutane, 4-methylphenyl isothiocyanate, and 2-phenylethyl isothiocyanate in scavenging highly reactive HOꞏ-radical was studied using Density Functional Theory at M06-2X/6-311++G(3df,3pd)//M06-2X/6-311++G(d,p) level of theory. Formal hydrogen transfer, radical adduct formation, and single electron transfer mechanisms were considered in water and pentyl ethanoate (PEA, to mimic the lipid environment). The results illustrated the high HOꞏ-scavenging activity of the isothiocyanate compounds with rate constants of about 108 - 109 M-1s-1. Allylisothiocyanate Cp1 represents the most efficient HOꞏ-scavenger with koverall of 5.20 × 109 M-1s-1 in water, and 1.85 × 109 M-1s-1 in PEA. Moreover, the rate constants of HOꞏ-reactions with the studied isothiocyanates in the aqueous medium are comparable with that of several biological molecules. These results allow us to enrich the data source on effective antioxidants to reduce excess free radicals and limit damaging effects on biological molecules. | Thi Chinh Ngo; Dinh Hieu Truong; Thi Le Anh Nguyen; Quang Khuong Pham; DUY QUANG DAO | Agriculture and Food Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6694d37c01103d79c50d80ea/original/solvent-effect-on-the-hydroxyl-radical-scavenging-activity-of-new-isothiocyanate-compounds.pdf |
636f2dd533f733b525e4c168 | 10.26434/chemrxiv-2022-x1rr3 | Computational Evaluation of Bioactive Compounds from Viscum album (Mistletoe) as Inhibitors of p63 for Pancreatic Cancer Treatment | Pancreatic ductal adenocarcinoma is an aggressive malignancy usually detectable at the advanced stage, with a 5-year survival rate of less than 8%. It has been reported that a gene called tumor-protein 63 (TP63) is expressed in an aggressive form of pancreatic cancer with a squamous signature. Thus, inhibiting the activity of p63 can be a means of treating and managing PDA. Different studies have shown that plant constituents are rich and can be a promising source for discovering drug candidates. The extract from mistletoe (Viscum album) is known to contain anticancer compounds; however, the specific molecular mechanism of the bioactive compounds is unknown. This study examines the pancreatic cancer therapeutic potential of the bioactive compounds in the flavonoid and phenolic acid constituents of mistletoe by adopting structural bioinformatics and advanced theoretical chemistry techniques via molecular docking, molecular dynamics simulation, molecular mechanics/ generalized Born surface area (MM/GBSA) calculations, pharmacokinetic analysis, and density functional theory analysis. The six best compounds from the flavonoid constituent with the highest binding affinity ranging from -6.8 kcal/mol to -6.7 kcal/mol were selected with the control gemcitabine (-5.5 kcal/mol) for further computational analysis after molecular docking. Furthermore, MM/GBSA calculation showed the highest binding energy for the selected docked compounds, which validates their inhibitory potential. Hence, the molecular dynamics simulation, post-simulation analysis, pharmacokinetics model, and DFT results showed that mistletoe compounds are reliable due to their stable interaction with the target protein and drug-likeness properties. | Gbenga Dairo; Ayooluwa Ilesanmi; Toheeb Balogun; Matthew Ward; Mette Soendergaard; John Determan | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Quantum Computing | CC BY NC 4.0 | CHEMRXIV | 2022-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636f2dd533f733b525e4c168/original/computational-evaluation-of-bioactive-compounds-from-viscum-album-mistletoe-as-inhibitors-of-p63-for-pancreatic-cancer-treatment.pdf |
663cb452418a5379b0da5e2d | 10.26434/chemrxiv-2024-7qswj | The Chemistry of the Defensive Secretions of three species of millipedes in the genus Brachycybe | Millipedes have long been known to produce a diverse array of chemical defense agents that deter predation. These compounds, or their precursors, are stored in high concentration within glands (ozadenes) and are released upon disturbance. The subterclass Colobognatha contains four orders of millipedes, all of which are known to produce terpenoid alkaloids—spare the Siphonophorida that produce terpenes. Although these compounds represent some of the most structurally-intriguing millipede-derived natural products, they are the least studied class of millipede defensive secretions. Here, we describe the chemistry of millipede defensive secretions from three species of Brachycybe: Brachycybe producta, Brachycybe petasata, and Brachycybe rosea. Chemical investigations using mass spectrometry-based metabolomics, chemical synthesis, and 2D NMR led to the identification of five alkaloids, three of which are new to the literature. All identified compounds are monoterpene alkaloids with the new compounds representing indolizidine (i.e. hydrogosodesmine) and quinolizidine alkaloids (i.e. homogosodesmine and homo-hydrogosodesmine). The chemical diversity of these compounds tracks the known species phylogeny of this genus, rather than the species geographical proximity. The indolizidines and quinolizidines are produced by non-sympatric sister species, B. producta and B. petasata, while deoxybuzonamine is produced by another set of non-sympatric sister species B. rosea and Brachycybe lecontii. The fidelity between the chemical diversity and phylogeny strongly suggests that millipedes generate these complex defensive agents de novo and begins to provide insights into the evolution of their biochemical pathways. | Paige Banks; Emma M. Funkhouser; Angie M. Macias; Brian Lovett; Shelby Meador; Arden Hatch; H. Martin Garraffo; Kaitie C. Cartwright; Paul Marek; Matt T. Kasson; Tappey H. Jones; Emily Mevers | Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2024-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663cb452418a5379b0da5e2d/original/the-chemistry-of-the-defensive-secretions-of-three-species-of-millipedes-in-the-genus-brachycybe.pdf |
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