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60c745fe0f50db8d0d396386 | 10.26434/chemrxiv.7466426.v2 | Quantifying the hydration structure of sodium and potassium ions: taking additional steps on Jacob’s Ladder | <div><div><div><p>The ability to reproduce the experimental structure of water around the sodium and potassium ions is a key test of the quality of interaction potentials due to the central importance of these ions in a wide range of important phenomena. Here, we simulate the Na+ and K+ ions in bulk water using three density functional theory functionals: 1) The generalized gradient approximation (GGA) based dispersion corrected revised Perdew, Burke, and Ernzerhof functional (revPBE-D3) 2) The recently developed strongly constrained and appropriately normed (SCAN) functional 3) The random phase approximation (RPA) functional for potassium. We compare with experimental X-ray diffraction (XRD) and X-ray absorption fine structure (EXAFS) measurements to demonstrate that SCAN accurately reproduces key structural details of the hydra- tion structure around the sodium and potassium cations, whereas revPBE-D3 fails to do so. However, we show that SCAN provides a worse description of pure water in comparison with revPBE-D3. RPA also shows an improvement for K+, but slow convergence prevents rigorous comparison. Finally, we analyse cluster energetics to show SCAN and RPA have smaller fluctuations of the mean error of ion-water cluster binding energies compared with revPBE-D3.</p></div></div></div> | Timothy Duignan; Gregory K. Schenter; John Fulton; Thomas huthwelker; mahalingam balasubramanian; Mirza Galib; Marcel D. Baer; Jan Wilhelm; Jürg Hutter; Mauro Del Ben; Xiu Song Zhao; Christopher J. Mundy | Computational Chemistry and Modeling; Theory - Computational; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745fe0f50db8d0d396386/original/quantifying-the-hydration-structure-of-sodium-and-potassium-ions-taking-additional-steps-on-jacob-s-ladder.pdf |
63120ac549042a8576c9845f | 10.26434/chemrxiv-2022-n03zl | Unsupervised pharmaceutical polymorph identification and multicomponent particle mapping of ToF-SIMS data by non-negative matrix factorization | Crystal polymorphism of pharmaceutical compounds directly impacts resulting physicochemical characteristics, a critical aspect in active pharmaceutical ingredient (API) production. Tools to characterize and chemically map these polymorphs at the single particle scale remain important to advancing directed manufacture of targeted polymorphs. Here, time-of-flight secondary ion mass spectrometry (ToF-SIMS) was employed for chemically imaging inkjet printed acetaminophen samples. ToF-SIMS generates large datasets of high spatial resolution images. Extracting relevant data and peaks of interest can be laborious for, and biased by, users. Advances in machine learning approaches have introduced many supervised and unsupervised methods for data analysis. In this study, we apply non-negative matrix factorization (NMF) for the unsupervised analysis of ToF-SIMS chemical image data. More specifically, an expanded variant of NMF, NMFk, was employed to determine the dataset’s latent dimensionality. NMFk combines the spectral unmixing of traditional NMF with k-means clustering of the resulting factors and an optimization of the reconstruction and clustering. The method was used to identify the number of polymorph phases – and their representative mass spectra – generated from inkjet printed acetaminophen samples. Amorphous, crystalline form I, and crystalline form II polymorphs were observed. The learned polymorph mass spectra were then used to map the learned polymorphs onto subsequent particle samples of acetaminophen. Finally, NMFk also enabled the decomposition of mixed particle samples (i.e., migraine medicine), learning the number of compounds and their composition. The extracted constituent phase mass spectra – representing single compounds – were searched against mass spectral libraries for identification. | Thomas P. Forbes; Greg Gillen; Amanda J. Souna; Jeffrey Lawrence | Materials Science; Analytical Chemistry; Imaging; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63120ac549042a8576c9845f/original/unsupervised-pharmaceutical-polymorph-identification-and-multicomponent-particle-mapping-of-to-f-sims-data-by-non-negative-matrix-factorization.pdf |
653a8cedc573f893f1260f35 | 10.26434/chemrxiv-2023-8cm07-v2 | Electro/Ni Dual-Catalyzed Decarboxylative C(sp3)−C(sp2) Cross-Coupling Reactions of Carboxylates and Aryl Bromide | Paired redox-neutral electrolysis offers an attractive green platform for organic synthesis by avoiding sacrificial oxidants and reductants. Here, we report the electro/Ni dual-catalyzed redox-neutral C(sp3)−C(sp2) cross-coupling reactions between carboxylates and aryl bromides. At a cathode, an NiII(Ar)(Br) intermediate is formed through the activation of the Ar−Br bond by a NiI-bipyridine catalyst and subsequent one electron reduction. The carboxylates, including amino acid, benzyl carboxylic acid, and 2-phenoxy propionic acid, undergo oxidative decarboxylation at an anode to form carbon based radicals. The combination of the NiII(Ar)(Br) intermediate and the carbon radical results in the formation of C(sp3)−C(sp2) cross-coupling products. The broad reaction scope, excellent functional group tolerance, and good yields of the electro/Ni dual-catalyzed C(sp3)−C(sp2) cross-coupling reaction were confirmed through 48 examples of carboxylates and aryl bromides in small-scale vial reactions and scale-up flow synthesis. The electro/Ni dual-catalyzed cross-coupling reactions described in this study are expected to have broad applications in the construction of C(sp3)−C(sp2) bonds because of the readily available carboxylate nucleophiles and the scalability of electrochemical flow-synthesis technology. | Jian Luo; Michael Davenport; Daniel Ess; Tianbiao Liu | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Electrocatalysis; Homogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2023-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653a8cedc573f893f1260f35/original/electro-ni-dual-catalyzed-decarboxylative-c-sp3-c-sp2-cross-coupling-reactions-of-carboxylates-and-aryl-bromide.pdf |
614305d642198e4c48783b29 | 10.26434/chemrxiv-2021-stm4j-v2 | Double Heterohelicenes Composed of Benzo[b]- and Dibenzo[b,i]phenoxazine: A Comprehensive Comparison of Their Electronic and Chiroptical Properties | Heterohelicenes are potential materials in molecular electronics and optics because of their inherent chirality and various electronic properties originating from the introduced heteroatoms. In this work, we comprehensively investigated two kinds of double NO-hetero[5]helicenes composed of 12H-benzo[b]phenoxazine (BPO) and 13H-dibenzo[b,i]phenoxazine (DBPO). These helicenes exhibit good electron donor property reflecting the electron-rich character of their monomers and were demonstrated to work as p-type semiconductors. The enantiomers of these helicenes show the largest class of dissymmetry factors for circularly polarized luminescence (CPL) (|gCPL| > 10−2) among the previously reported helicenes. Interestingly, the signs of CPL are opposite between BPO- and DBPO-double helicenes of the same helicity. The origin of the large gCPL values and the inversion of the CPL signs was addressed by analysis of the transition electronic dipole moments (TEDM) and transition magnetic dipole moments (TMDM) based on the TD-DFT calculations. | Daisuke Sakamaki; Shunya Tanaka; Katsuki Tanaka; Mayu Takino; Masayuki Gon; Kazuo Tanaka; Takashi Hirose; Daichi Hirobe; Hiroshi M. Yamamoto; Hideki Fujiwara | Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614305d642198e4c48783b29/original/double-heterohelicenes-composed-of-benzo-b-and-dibenzo-b-i-phenoxazine-a-comprehensive-comparison-of-their-electronic-and-chiroptical-properties.pdf |
647bd519be16ad5c576cd7f1 | 10.26434/chemrxiv-2023-nkbn0 | Substrate-selective catalysis enabled synthesis of azaphilone natural products | Achieving substrate-selectivity is a central element of nature’s approach to synthesis; relying on the ability of a catalyst to discriminate, based on small structural changes, which molecules will move forward in a synthesis. This approach can be challenging to duplicate in the laboratory, but can be powerful when realized. In this work, substrate-selective catalysis is leveraged to discriminate between two intermediates that exist in equilibrium, subsequently directing the final cyclization to arrive at either the linear or angular tricyclic core common to subsets of azaphilone natural products. By using a flavin-dependent monooxygenase (FDMO) in sequence with an acyl transferase (AT), the conversion of several orcinaldehyde substrates directly to the corresponding linear tricyclic azaphilones in a single reaction vessel was achieved. Furthermore, mechanistic studies support that a substrate equilibrium together with enzyme substrate-selectivity play an import role in the selectivity of the final cyclization step. A panel of azaphilone natural products and derivatives thereof were synthesized using this strategy. | Ye Wang; Katherine Torma; Joshua Pyser; Paul Zimmerman; Alison Narayan | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Bioorganic Chemistry; Organic Synthesis and Reactions; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647bd519be16ad5c576cd7f1/original/substrate-selective-catalysis-enabled-synthesis-of-azaphilone-natural-products.pdf |
66dad13ccec5d6c1424dbd0b | 10.26434/chemrxiv-2024-gx23r | Controlled Growth of Phase-Pure α-Fe2O3 Nanoparticles on g-C3N4 for the Construction of High-Performance Direct Z-Scheme Heterojunction Photocatalysts | This work presents an innovative two-step approach for constructing efficient direct Z-scheme heterojunction photocatalysts, involving the direct growth of hematite (α-Fe2O3) nanoparticles on graphitic carbon nitride (g-C3N4). The key to this strategy lies in an initial ultrasound-assisted impregnation step that induces the cleavage of g-C3N4 sheets in the presence of FeCl3 precursors while simultaneously promoting the effective anchoring of Fe-N and C-O/C-N species. Interestingly, conversion into hematite nanoparticles is easily achieved in a subsequent short and mild microwave-treatment step, eliminating the need for conventional high-temperature processes. The hematite phase-purity of the nanoparticles, critically controlled by the initial FeCl3 precursor concentration, directly impacts the photocatalytic activity of the g-C3N4@Fe nanohybrid heterojunction. A two-fold enhancement in the photocatalytic degradation of methylene blue compared to α-Fe2O3 and g-C3N4 is achieved for nanohybrids with highest hematite phase-purity. This significant improvement is attributed to the successful formation of a direct Z-scheme g-C3N4/α-Fe2O3 heterojunction photocatalyst as confirmed by electron spin resonance (ESR) analysis. Our two-step approach offers a facile, efficient and scalable route for the development of highly active heterojunction photocatalyst, of promise for the sustainable degradation of contaminants in environmental remediation technologies. | Alejandro Galán-González; Juan G. Galindo-Callén; Isaías Fernández; Nestor J. Zaluzec; Sofie Cambré; Raúl Arenal; Ana M. Benito; Wolfgang K. Maser | Materials Science; Catalysis; Nanoscience; Hybrid Organic-Inorganic Materials; Nanocatalysis - Catalysts & Materials; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66dad13ccec5d6c1424dbd0b/original/controlled-growth-of-phase-pure-fe2o3-nanoparticles-on-g-c3n4-for-the-construction-of-high-performance-direct-z-scheme-heterojunction-photocatalysts.pdf |
63b3e9a5518c1606ee4155ad | 10.26434/chemrxiv-2023-tjt21 | Computational workflows for novel materials: Case study for lanthanide manganese perovskites | Robust computational workflows are important for explorative computational studies, especially for cases where detailed knowledge of the system structure or other properties is not available. In this work, we propose a computational protocol for appropriate method selection in density functional theory, based strictly on open source software. The protocol is applicable to perovskite systems and does not require a starting crystal structure. We validate this protocol using a set of crystal structures of lanthanide manganates, confirming that PBE+U is a reasonable choice for this purpose, along with the OLYP and HCTH120 density functional approximations. We also highlight that +U values derived from linear response theory are robust and their use leads to improved results. We investigate whether the performance of methods for predicting the bond length of related gas phase diatomics correlates with their performance for bulk structures, showing that care is required when interpreting benchmark results. Finally, using defective LaMnO3 as a case study, we investigate whether the three selected methods can computationally reproduce the experimentally determined fraction of MnIV+ at which the orthorhombic to rhombohedral phase transition occurs. The results are mixed, with HCTH120 providing a good quantitative agreement, while PBE+U better capturing the qualitative aspects of this phase transition. | Peter Kraus; Paolo Raiteri; Julian D. Gale | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties; Structure; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-01-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b3e9a5518c1606ee4155ad/original/computational-workflows-for-novel-materials-case-study-for-lanthanide-manganese-perovskites.pdf |
63a7094f81e4ba668c58dba5 | 10.26434/chemrxiv-2022-84ld6 | On the advanced microstructural characterisation of additively manufactured alumina-zirconia based eutectic ceramics: Overview and outlook | Recently, there have been a number of reports on the fabrication of Alumina-Zirconia (Al2O3-ZrO2 (AZ))-based eutectic ceramics using laser additive manufacturing (AM) techniques owing to the exceptional creep and oxidation resistance coupled with excellent microstructural stability in these materials. Moreover, a number of interesting microstructural features (in these materials) have been reported to be formed by the variation of process parameters (especially, laser scanning speed) associated with the aforementioned AM techniques. The present review provides an overview of the present state of research in the area of laser AM AZ-based eutectic ceramics and highlights the challenges and future outlooks in this avenue of research. In addition, the requirement of employing correlative microstructural characterisation in these materials has been highlighted in the outlooks section. | Mainak Saha | Materials Science; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a7094f81e4ba668c58dba5/original/on-the-advanced-microstructural-characterisation-of-additively-manufactured-alumina-zirconia-based-eutectic-ceramics-overview-and-outlook.pdf |
631439eb5351a392b8ee6634 | 10.26434/chemrxiv-2022-vcn22 | Tantalum Ureate Complexes for Photocatalytic Hydroaminoalkylation | Using a tantulum ureate pre-catalyst, photocatalytic hydroaminoalkylation of unactivated alkene with unprotected amine at room temperature is demonstrated. The conbination of Ta(CH2SiMe3)3Cl2 and ureate ligand with saturated cyclic backbone resulted in unique reactivity. The substrate scope of Ta photocatalytic hydroaminoalkylation (β-alkylation of amine) was evaluated. Preliminary investigation on reaction mechanism suggests both similarities and differences with Ta catalyzed hydroaminoalkyaltion under thermo conditions | Han Hao; Manfred Manßen; Laurel Schafer | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Photocatalysis; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631439eb5351a392b8ee6634/original/tantalum-ureate-complexes-for-photocatalytic-hydroaminoalkylation.pdf |
67cae5b06dde43c908ea3d2e | 10.26434/chemrxiv-2025-9qhmg | Small Molecule Activation by Metallylenes and Their Follow-up Reactions | The activation of small molecules is a crucial step in advancing sustainable chemistry, enabling key transformations in fine chemical synthesis and energy storage. While transition metals have traditionally dominated this field, main-group elements—specifically metallylenes, which are heavier analogs of carbenes (silylenes, germylenes, stannylenes, and plumbylenes)—have emerged as viable alternatives due to their unique electronic properties and tunable reactivity. This review explores the mechanisms by which metallylenes activate small molecules, highlighting the influence of ligand design, electronic structure, and geometric factors. We discuss recent advances in the field, including computational insights into metallylene-mediated bond activation and experimental demonstrations of their catalytic potential. Additionally, we examine follow-up reactions such as hydrogenation and hydroboration, which illustrate the versatility of metallylenes in small molecule transformation. By providing a comprehensive overview of the latest developments, this review aims to bridge fundamental principles with potential applications, paving the way for metallylene-based catalysis in sustainable chemistry. | Eveline Tiekink; Matthijs Kragtwijk ; Trevor Hamlin | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2025-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cae5b06dde43c908ea3d2e/original/small-molecule-activation-by-metallylenes-and-their-follow-up-reactions.pdf |
65fded19e9ebbb4db94bedaf | 10.26434/chemrxiv-2024-kqdx3 | Measuring the Adsorption Cross-Section of YOYO-1 to Immobilized DNA Molecules | Many interactions between small molecules and particles occur in solutions. They are surrounded by other molecules that do not react, for example, biological processes in water, chemical reactions in gas or liquid solutions, and environmental reactions in air and water. Predicting the rate of such interactions involves an understanding of a fundamental process called diffusion, the random motion of molecules in solutions exampled by the famous Brownian motion of pollen particles. It has been challenging to conceptualize a mathematical equation to describe the rate, for example calculating the summed probability of all diffusive molecules finding an immobilized target molecule at an interface within a certain period, the elementary step of adsorption and absorption. In this report, we introduced an equation developed very recently to predict the adsorption rate and measured the staining rate of a DNA molecule with a simple organic dye molecule YOYO-1. The adsorption cross-section of the interaction is extracted for the first time to be consistent with the physical sizes of the molecules. This could be an important step toward a genderized method to predict the adsorption rate of many reactions. | Srijana Pandey; Dinesh Gautam; Jixin Chen | Physical Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Chemistry - General; Biophysics; Interfaces | CC BY 4.0 | CHEMRXIV | 2024-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fded19e9ebbb4db94bedaf/original/measuring-the-adsorption-cross-section-of-yoyo-1-to-immobilized-dna-molecules.pdf |
644fd59480f4b75b536e5049 | 10.26434/chemrxiv-2023-900l3 | Revolutionizing Phenotypic Antimicrobial Susceptibility Testing: Lightning-Fast Techniques Based on Cutting-Edge Electrochemistry | Due to the ongoing concern for the development of rapid and accurate antimicrobial susceptibility testing (AST) methods in the field of clinical microbiology, several novel AST systems have been developed to replace the traditional gold standard AST techniques, which are time-consuming and can lead to delayed susceptibility guided therapy outcomes. In this review, the focus is on the phenotypic assays based on electrochemistry that are used to determine bacterial susceptibility towards antibiotics. Electrochemical techniques have gained significant interest in the field of AST due to their rapidity, sensitivity, and specificity, although it is important to note that some of these methods may have limitations regarding the specific classes of antibiotics and bacteria that they can be applied to, which researchers can address by fine-tuning the techniques or incorporating additional controls. By offering significant advantages over traditional AST methods in terms of rapidity and accuracy, electrochemical phenotypic assays could lead to improved patient outcomes. | Pragadeeshwara Rao R | Biological and Medicinal Chemistry; Bioengineering and Biotechnology; Microbiology | CC BY 4.0 | CHEMRXIV | 2023-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644fd59480f4b75b536e5049/original/revolutionizing-phenotypic-antimicrobial-susceptibility-testing-lightning-fast-techniques-based-on-cutting-edge-electrochemistry.pdf |
60c746814c8919704aad2b6c | 10.26434/chemrxiv.11340026.v1 | Unveiling Pseudocapacitive Charge Storage Behavior in FeWO4 Electrode Material by Operando X-ray Absorption Spectroscopy | In nano-sized FeWO<sub>4</sub> electrode material, both Fe and W metal cations are
suspected to be involved in the fast and reversible Faradaic surface
reactions giving rise to its pseudocapacitive signature. As for any
other pseudocapacitive materials, to fully understand the charge storage
mechanism, a deeper insight into the involvement of the electroactive
cations still has to be provided. The present paper illustrates how
operando X-ray absorption spectroscopy (XAS) has been successfully used
to collect data of unprecedented quality allowing to elucidate the
complex electrochemical behavior of this multicationic pseudocapacitive
material. Moreover, these in-depth experiments were obtained in real
time upon cycling the electrode, which allowed investigating the
reactions occurring in the material within a realistic timescale, which
is compatible with electrochemical capacitors practical operation. Both
Fe K-edge and W L<sub>3</sub>-edge measurements point out the involvement of the
Fe<sup>3+</sup>/Fe<sup>2+</sup> redox couple in the charge storage while W<sup>6+</sup> acts as a
spectator cation. The result of this study enables to unambiguously
discriminate between the Faradaic and capacitive behavior of FeWO4.
Beside these valuable insights toward the full description of the charge
storage mechanism in FeWO<sub>4</sub>, this paper demonstrates the potential of
operando X-ray absorption spectroscopy to enable a better material
engineering for new high capacitance pseudocapacitive electrode
materials. | Nicolas Goubard-Bretesché; Olivier Crosnier; Camille Douard; Antonella Iadecola; Richard Retoux; Christophe Payen; Marie-Liesse Doublet; Kazuaki Kisu; Etsuro Iwama; Katsuhiko Naoi; Frédéric Favier; Thierry Brousse | Nanostructured Materials - Materials; Electrochemistry; Solid State Chemistry; Spectroscopy (Inorg.); Theory - Inorganic; Computational Chemistry and Modeling; Theory - Computational; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746814c8919704aad2b6c/original/unveiling-pseudocapacitive-charge-storage-behavior-in-fe-wo4-electrode-material-by-operando-x-ray-absorption-spectroscopy.pdf |
60c74966ee301ca717c79a3e | 10.26434/chemrxiv.11998347.v2 | De Novo Design of New Chemical Entities (NCEs) for SARS-CoV-2 Using Artificial Intelligence | The novel SARS-CoV-2 is the source of a global pandemic COVID-19, which has severely affected the health and economy of several countries. Multiple studies are in progress, employing diverse approaches to design novel therapeutics against the potential target proteins in SARS-CoV-2. One of the well-studied protein targets for coronaviruses is the chymotrypsin-like (3CL) protease, responsible for post-translational modifications of viral polyproteins essential for its survival and replication in the host. There are ongoing attempts to repurpose the existing viral protease inhibitors against 3CL protease of SARS-CoV-2. Recent studies have proven the efficiency of artificial intelligence techniques in learning the known chemical space and generating novel small molecules. In this study, we employed deep neural network-based generative and predictive models for de novo design of new small molecules capable of inhibiting the 3CL protease. The generated small molecules were filtered and screened against the binding site of the 3CL protease structure of SARS-CoV-2. Based on the screening results and further analysis, we have identified 31 potential compounds as ideal candidates for further synthesis and testing against SARS-CoV-2. The generated small molecules were also compared with available natural products. Two of the generated small molecules showed high similarity to a plant natural product, Aurantiamide, which can be used for rapid testing during this time of crisis. | Navneet Bung; Sowmya Ramaswamy Krishnan; Gopalakrishnan Bulusu; Arijit Roy | Biochemistry; Bioengineering and Biotechnology; Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74966ee301ca717c79a3e/original/de-novo-design-of-new-chemical-entities-nc-es-for-sars-co-v-2-using-artificial-intelligence.pdf |
649539c524989702c2d32922 | 10.26434/chemrxiv-2023-cdlf8-v3 | Flavonoids as dual-target inhibitors against α-glucosidase and α-amylase: a systematic review of in vitro studies | Diabetes mellitus remains a major global health burden and great attention is directed at natural therapeutics. This systematic review aimed to evaluate the potential of flavonoids as antidiabetic agents through their ability to inhibit α-amylase and α-glucosidase, two key starch digestive enzymes. Six scientific databases were queried up until August 21, 2022, for in vitro studies reporting the IC50 results of purified flavonoids on α-amylase or α-glucosidase, along with the respective data of acarbose control. A total of 339 articles were assessed as eligible and subjected to the data extraction process, resulting in 1643 retrieved flavonoid structures. Chemical structures were then rigorously standardized and curated to 974 unique compounds, in which 177 flavonoids showed both inhibitions against α-amylase and α-glucosidase. Quality assessment was conducted following a modified CONSORT checklist. The structure-activity relationships revealed that a double bond C2=C3 and a keto group C4=O is essential for simultaneous inhibition. The hydroxyl group at C3 is favourable for α-glucosidase inhibition but detrimental to the effect against α-amylase. Further notable features which affect α-glucosidase and α-amylase inhibition were also discussed. Several limitations were considered, including the inconsistency among included studies, language restriction, and the contemporaneity of the review. In conclusion, the systematic review has summarized some crucial findings in the investigation of flavonoids as dual-target inhibitors against α-glucosidase and α-amylase and proposed several orientations for future research. | Thua-Phong Lam; Ngoc-Vi Nguyen Tran; Long-Hung Dinh Pham; Nghia Vo-Trong Lai; Bao-Tran Ngoc Dang; Ngoc-Lam Nguyen Truong; Song-Ky Nguyen-Vo; Thuy-Linh Hoang; Tan Thanh Mai; Thanh-Dao Tran | Biological and Medicinal Chemistry; Agriculture and Food Chemistry; Food; Drug Discovery and Drug Delivery Systems; Plant Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649539c524989702c2d32922/original/flavonoids-as-dual-target-inhibitors-against-glucosidase-and-amylase-a-systematic-review-of-in-vitro-studies.pdf |
642144ea62fecd2a83811328 | 10.26434/chemrxiv-2023-gvxnv | Structure and Ionic Conductivity of the Li-disordered Bismuth ortho-Thiophosphate Li60– 3xBi16+x(PS4)36 with x = 4.2 to 6.7 | The structure of the first lithium containing bismuth ortho-thiophosphate was solved using a combination of powder X-ray, neutron, and electron diffraction. Li60–3xBi16+x(PS4)36 with x in the range of 4.2 to 6.7 possesses a complex monoclinic structure (space group C2/c, no. 15) and a large unit cell with lattice parameters a = 15.487Å, b = 10.323Å, c = 33.767Å, and = 85.394° for Li44.4Bi21.2(PS4)36. The disordered distribution of lithium ions within the interstices of the dense host-structure as well as the Li ion dynamics and diffusion pathways have been investigated by X-ray and neutron PDF analysis, solid-state NMR spectroscopy, PFG-NMR diffusion measurements, and BVS calculations. The total lithium ion conductivities range from 2.6 × 10−7 to 2.8 × 10−6 S cm−1 at 20 °C with activation energies between 0.29 and 0.32 eV, depending on the bismuth content. Despite the highly disordered nature of lithium ions in Li60–3xBi16+x(PS4)36, the underlying dense host-framework appears to limit the dimensionality of the lithium diffusion pathways and emphasizes once more the necessity of a close inspection of structure-property relationships in solid electrolytes. | Maximilian Plaß; Maxwell Terban; Tanja Scholz; Igor Moundrakovski; Viola Duppel; Robert Dinnebier; Bettina Lotsch | Inorganic Chemistry; Electrochemistry; Solid State Chemistry; Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642144ea62fecd2a83811328/original/structure-and-ionic-conductivity-of-the-li-disordered-bismuth-ortho-thiophosphate-li60-3x-bi16-x-ps4-36-with-x-4-2-to-6-7.pdf |
67548e837be152b1d041a86a | 10.26434/chemrxiv-2024-q8jl1 | Highly Enantioselective Construction of Oxazolidinone Rings via Enzymatic C(sp3)−H Amination | Oxazolidinones are important heterocycles widely utilized in medicinal chemistry for the synthesis of antifungals, antibacterials, and other bioactive compounds and in organic chemistry as chiral auxiliaries for asymmetric synthesis. Herein, we report a biocatalytic strategy for the synthesis of enantioenriched oxazolidinones through the intramolecular C(sp3)‑H amination of carbamate derivatives using engineered myoglobin-based catalysts. This method is applicable to a diverse range of substrates, with high functional group tolerance, providing enantioenriched oxazolidinones in good yields and with high enantioselectivity. The synthetic utility of this methodology is further highlighted by the development of enantiodivergent biocatalysts for this transformation and through the preparative-scale synthesis of key oxazolidinone intermediates for the production of the cholesterol-lowering drugs Ezetimibe and CJ-15-161. An outer sphere mutation, Y146F, was found to be beneficial to favor the productive C–H amination reaction over an unproductive reductive pathway commonly observed in hemeprotein-catalyzed nitrene transfer reactions. This study demonstrates a biocatalytic, enantiodivergent synthesis of oxazolidinones via C-H amination of carbamate derivatives, offering an attractive strategy for the synthesis of these valuable intermediates for applications in medicinal chemistry, target-directed synthesis, and asymmetric synthesis. | Jadab Majhi; Satyajit Roy; Anwita Chattopadhyay; Rudi Fasan | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67548e837be152b1d041a86a/original/highly-enantioselective-construction-of-oxazolidinone-rings-via-enzymatic-c-sp3-h-amination.pdf |
60c753204c89192969ad426e | 10.26434/chemrxiv.13385429.v1 | Rapid Characterisation of Suspensions for Waste Treatment and Resource Recovery | A simple device for the conduct of stepped pressure filtration measurements is described together with methods for making the empirical measurements and interpreting the data obtained. The data interpretation method applies a multi-step systematic approach, with each step supported by statistical justification, to characterise: filter cake particle stress, filtration diffusivity and cake hydraulic resistivity from a single stepped pressure experiment. The methods enable different flocculant materials to be more rapidly and more appropriately screened than conventional jar tests and large scale filtration trials. The methods are applied to the characterisation of a paint residue treated with aluminium sulphate and “PolyClay”.<br />The work shows that the addition of “PolyClay” as a filter aide reduces the hydraulic resistivity at lower solids concentrations but increases it at higher concentrations whilst simultaneously increasing the particle stress. Together these have a combined deleterious effect on the time and energy required to dewater the residues to high solids concentration by filtration. The results also show that a significant change in suspension behaviour occurs between the “PolyClay” doses of 140 mg l<sup>-1</sup> and 660 mg l<sup>-1</sup> and that further changes up to “PolyClay” doses of 1600 mg l<sup>-1</sup> are more modest. The results indicate the existence an opportunity to reduce “PolyClay” dose into a range between 10% and 50% of current practice. In addition the results provide evidence that alternative, centrifuge based, technology is worthy of investigation. | Joshua Wardrop; Sara J. Baldock; ian coote; Rachael Demaine; Peter R. Fielden; Alastair Martin | Analytical Chemistry - General; Analytical Apparatus; Environmental Analysis; Separation Science; Transport Phenomena (Chem. Eng.); Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753204c89192969ad426e/original/rapid-characterisation-of-suspensions-for-waste-treatment-and-resource-recovery.pdf |
60c744b6ee301c8097c791b0 | 10.26434/chemrxiv.9899576.v1 | The Impact of Secondary Coordination Sphere Nucleophiles on Methane Activation: A Computational Study | p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px 'Helvetica Neue'}
<p>Density functional theory and ab initio calculations indicate that nucleophiles can significantly reduce enthalpic barriers to methane C–H bond activation. Different pieces of evidence point to an electrostatic origin for the nucleophile effect such as the sensitivity of the C–H activation barriers to the external nucleophile and to continuum solvent polarity. The data further imply a transition state with significant charge build-up on the active hydrogen of the hydrocarbon substrate. From the present modeling studies, one may propose proteins with hydrophobic active sites, available nucleophiles, and hydrogen bond donors as attractive targets for the engineering of novel methane functionalizing enzymes.</p> | Mary E. Anderson; Thomas Cundari | Computational Chemistry and Modeling; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744b6ee301c8097c791b0/original/the-impact-of-secondary-coordination-sphere-nucleophiles-on-methane-activation-a-computational-study.pdf |
67d32c3381d2151a02425e34 | 10.26434/chemrxiv-2025-9pfz8 | Molecular dynamic simulations of a hexagonal liquid crystalline phase to study drug partitioning and release mechanisms | Liquid crystalline nanoparticles (LCNPs), such as hexosomes (HII), can enhance lipid nanoparticle-mediated drug delivery by improving drug absorption, solubility, and chemical stability. Additionally, LCNPs can be tailored to optimize their function in specific biological environments by incorporating non-external-linker lipids into the HII system lipid composition. In this study, we constructed an HII model system composed of a 90:10 phytantriol:farnesol ratio and performed all-atom molecular dynamics simulations. The simulations demonstrated that the model remained stable across various water-to-lipid ratios, and the impact of the water-to-lipid ratio on the HII structural properties was consistent with previous experimental observations. We then used this model to investigate the localization and interactions of two drug molecules: vancomycin and clarithromycin. The results show that the highly lipophilic clarithromycin predominantly associates with the lipid phase, whereas vancomycin, due to its combination of hydrophobic and hydrophilic residues, tends to localize at the water-lipid interface, interacting with both phases. We also constructed an HII system with repeating HII units enclosed within Pluronic F127 polymers. Simulations revealed that the F127 polymers interact with the lipid phases at the HII interface region, facilitating excess water permeation into the HII phase system. To investigate the initial surface release mechanism of the drug molecules, we performed umbrella sampling (US) simulations. The energy profiles from the umbrella sampling indicate that polymer-lipid-water interactions at the HII interface reduce the energy barrier for drug release, making the release of vancomycin easier compared to clarithromycin. Our in vitro release study further confirmed that vancomycin exhibited higher release compared to clarithromycin. Overall, the model developed in this study provided important molecular-level insights into drug loading, partitioning, and release kinetics from the HII phase system, enabling the design of effective drug delivery formulations. | Diyar Altun; Xiguo He; Christel Bergström; Madlen Hubert; Shakhawath Hossain | Biological and Medicinal Chemistry; Biophysics; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d32c3381d2151a02425e34/original/molecular-dynamic-simulations-of-a-hexagonal-liquid-crystalline-phase-to-study-drug-partitioning-and-release-mechanisms.pdf |
60c7561b702a9b2eb018c860 | 10.26434/chemrxiv.14213528.v1 | A Supramolecular Porous Organic Cage Platform Promotes Electrochemical Hydrogen Evolution from Water Catalyzed by Cobalt Porphyrins | We report a supramolecular porous organic cage
platform composed of cobalt porphyrins for catalyzing the electrochemical hydrogen
evolution reaction (HER) from water at neutral pH. Owing to its permanent
porosity, the supramolecular structure yields a catalyst film with a 5-fold
increase in the number of electrochemically active cobalt atoms and an
improvement in Tafel slope from 170 mV/decade to 119 mV/decade compared to a
planar cobalt porphyrin analog, reaching activities over 19,000 turnovers for
HER over a 24-hour period with 100% Faradaic efficiency. | Peter T. Smith; Bahiru Punja Benke; Lun An; Younghoon Kim; Kimoon Kim; Christopher Chang | Supramolecular Chemistry (Org.); Electrochemistry; Supramolecular Chemistry (Inorg.); Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7561b702a9b2eb018c860/original/a-supramolecular-porous-organic-cage-platform-promotes-electrochemical-hydrogen-evolution-from-water-catalyzed-by-cobalt-porphyrins.pdf |
678c4531fa469535b994504f | 10.26434/chemrxiv-2025-96ddg | A Nitrilium-Type N-Heterocyclic Aryne | The first solution-phase synthesis and reactivity of a nitrilium-type N-hetaryne are described. The 1,2-azaborine-derived 1,6-BN-aryne 2 exhibits [4+2], [3+2], and [2+2] cycloadditions and electrophilic aromatic substitution (EAS) reactivity. The observed regio- and diastereoselectivity of the cycloaddition and EAS products are consistent with a polarized aryne/nitrilium species. A Lewis structure description where the 1,6-BN-aryne 2 resonates between two limiting forms (ketenimine vs. nitrilium) is consistent with DFT calculations. New 1,2-azaborine structures that are functionalized at the C6- and N-positions, including highly strained derivatives that are previously not accessible, can now be accessed using 1,6-BN-aryne 2 as a versatile synthetic building block. | Marisol Alvarado; Lauren Tran; Bo Li; Clovis Darrigan; Hugues Preud'homme; Anna Chrostowska; Shih-Yuan Liu | Theoretical and Computational Chemistry; Organic Chemistry; Inorganic Chemistry; Organic Synthesis and Reactions; Bonding; Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678c4531fa469535b994504f/original/a-nitrilium-type-n-heterocyclic-aryne.pdf |
60c7517bbb8c1a20973dbcdd | 10.26434/chemrxiv.13173659.v1 | Enabling Highly (R)-Enantioselective Epoxidation of Styrene by Engineering Unique Non-Natural P450 Peroxygenases | Unlike the excellent (<i>S</i>)-enantioselective epoxidation of
styrene performed by natural styrene monooxygenase (<i>ee</i> >99%), the (<i>R</i>)-enantioselective epoxidation of
styrene has not yet achieved a comparable efficiency using natural or
engineered oxidative enzymes. This report describes the H<sub>2</sub>O<sub>2</sub>-dependent
(<i>R</i>)-enantioselective epoxidation of
unfunctionalized styrene and its derivatives by site-mutated variants of a
unique non-natural P450BM3 peroxygenase, working in tandem with a dual-functional
small molecule (DFSM). The observed (<i>R</i>)-enantiomeric
excess of styrene epoxidation is up to ~99%, which is unprecedented relative to
natural or engineered oxidative enzymes. The catalytic turnover number is up to
~4500 (with ~98% <i>ee</i>), representing
the best activity of a P450 peroxygenase towards styrene epoxidation, to date.
This study indicates that the synergistic use of protein engineering and an
exogenous DFSM constitutes an efficient strategy to control enantioselectivity
of styrene epoxidation, thus substantially expanding the chemical scope of P450
enzyme functions as useful bio-oxidative catalysts. | Panxia Zhao; Jie Chen; Nana Ma; Jingfei Chen; Xiangquan Qin; Chuanfei Liu; Fuquan Yao; Lishan Yao; Longyi Jin; Zhiqi Cong | Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7517bbb8c1a20973dbcdd/original/enabling-highly-r-enantioselective-epoxidation-of-styrene-by-engineering-unique-non-natural-p450-peroxygenases.pdf |
65cb806d9138d23161086de9 | 10.26434/chemrxiv-2023-48v11-v2 | Synthesis of 1,3-disubstituted bicyclo-[1.1.1]-pentane (BCP) salts: arylsulfonium, arylpyridinium and arylammonium isosteres | Herein, we describe the synthesis of pyridinium, sulfonium and ammonium bicyclo-[1.1.1]-pentane salts as potential aryl isosteres. Arylsulfonium, ammonium and pyridinium salts are central motifs in several natural products, pharmaceuticals, and high value commodities within the industrial chemical sector. The reaction proceeds by a nucleophilic substitution on a bench stable precursor 1,3-diodobicyclo-[1.1.1]-pentane (DIBCP). The transformation displays broad substrate scope, good to excellent yield profile, with several of the BCP products being fully characterised by single crystal X-ray crystallography, highlighting the unique 3-dimensional structure of these potential isosteres. Finally, the pyridinium and quinolinium BCP salts can be cleanly converted into piperidinone and quinolone BCP analogues. | Harvey Monroe; Mark Elsegood; Simon Teat; Gareth Pritchard; Marc Kimber | Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cb806d9138d23161086de9/original/synthesis-of-1-3-disubstituted-bicyclo-1-1-1-pentane-bcp-salts-arylsulfonium-arylpyridinium-and-arylammonium-isosteres.pdf |
653c0a96c573f893f14299ca | 10.26434/chemrxiv-2023-thnkq-v2 | Insulin–Dendrimer Nanocomplex for Multi-Day Glucose-Responsive Therapy in Mice and Swine | The management of diabetes in a manner offering autonomous insulin therapy responsive to glucose-directed need, and moreover with a dosing schedule amenable to facile administration, remains an ongoing goal to improve the standard of care. While basal insulins with reduced dosing frequency, even once-weekly administration, are on the horizon, there is still no approved therapy that offers glucose-responsive insulin function. Herein, a nanoscale complex combining both electrostatic and dynamic-covalent interactions between a synthetic dendrimer carrier and an insulin analogue modified with a high-affinity glucose-binding motif yields an injectable insulin depot affording both glucose-directed and long-lasting insulin availability. Following a single injection, it is even possible to control blood glucose for at least one week in diabetic swine subjected to oral glucose challenges. Measurements of serum insulin concentration in response to challenge show increases in insulin corresponding to elevated blood glucose levels, an uncommon finding even in preclinical work on glucose-responsive insulin. Accordingly, the subcutaneous nanocomplex that results from combining electrostatic and dynamic-covalent interactions between a modified insulin and a synthetic dendrimer carrier affords a glucose-responsive insulin depot for week-long control following a single routine injection. | Sijie Xian; Yuanhui Xiang; Dongping Liu; Bowen Fan; Katarína Mitrová; Rachel Ollier; Bo Su; Muhammad Ali Alloosh; Jiří Jiráček; Michael Sturek; Mouhamad Alloosh; Matthew Webber | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653c0a96c573f893f14299ca/original/insulin-dendrimer-nanocomplex-for-multi-day-glucose-responsive-therapy-in-mice-and-swine.pdf |
60c75208469df42c8ff44aee | 10.26434/chemrxiv.13242068.v1 | Evaluation of Acquisition Modes for the Quantitative Analysis of Cross-Linked Peptides by Targeted and Untargeted Mass Spectrometry | <div>
<div>
<p>Cross-linking
mass spectrometry (XL-MS) is a structural biology technique that can provide
insights into the structure and interactions of proteins and their complexes,
especially those that cannot be easily assessed by other methods. Quantitative
XL-MS has the potential to probe the structural and temporal dynamics of
protein complexes; however, it requires further development. Until recently,
quantitative XL-MS has largely relied upon isotopic labeling and data dependent
acquisition (DDA) methods, limiting the number of biological samples that can
be studied in a single experiment. Here, the acquisition modes available on an
ion mobility (IM) enabled QToF mass spectrometer are evaluated for the
quantitation of cross-linked peptides, eliminating the need for isotopic labels
and thus expanding the number of comparable studies that can be conducted in
parallel. Workflows were optimized using metabolite and peptide standards
analyzed in biological matrices, facilitating modelling of the data and addressing
linearity issues, which allow for significant increases in dynamic range. Evaluation
of the DDA acquisition method commonly used in XL-MS studies indicated
consistency issues between technical replicates and reduced performance in quantitative
metrics. On the contrary, data independent acquisition (DIA) and parallel
reaction monitoring (PRM) modes proved more robust for analyte quantitation.
Mobility enabled modes exhibited an improvement in sensitivity due to the added
dimension of separation, and a simultaneous reduction in dynamic range, which
was largely recovered by correction methods. Hi[3] and probabilistic
quantitation methods were successfully applied to the DIA data, determining the
molar amounts of cross-linked peptides relative to their linear counterparts.</p></div></div> | Hannah Britt; Tristan Cragnolini; Suniya Khatun; Abubakar Hatimy; Juliette James; Nathanael Page; Jonathan Williams; Christ Hughes; Richard Denny; Konstantinos Thalassinos; Hans Vissers | Analytical Chemistry - General; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75208469df42c8ff44aee/original/evaluation-of-acquisition-modes-for-the-quantitative-analysis-of-cross-linked-peptides-by-targeted-and-untargeted-mass-spectrometry.pdf |
641c2f9791074bccd025f33e | 10.26434/chemrxiv-2023-v73sf | Diffusion trapped oxygen in oxide derived Copper electrocatalyst in CO2 reduction | Oxide-derived Cu (OD-Cu) catalysts have shown an excellent ability to ensure C-C coupling in the electrochemical carbon dioxide reduction reaction (eCO2RR). However, these materials extensively rearrange under reaction conditions, thus the nature of the active site remains controversial. Here, we studied the reduction process of OD-Cu via large-scale molecular dynamics at first-principles accuracy introducing experimental conditions. The oxygen concentration in the most stable OD-Cu materials increases with the increase of the pH/potential/specific surface area. In long electrochemical experiments, the catalyst would be fully reduced to Cu, but it takes a considerable amount of time to remove all the trapped oxygen, and the highly reconstructed Cu surface provides various sites to adsorb oxygen under relatively stronger reduction potentials (U = –0.58 VSHE at pH=14, 0.25 VRHE). This work provides insight into the evolution of OD-Cu catalysts and residual oxygen during the reaction conditions and a deep understanding of the nature of active sites. | Zan Lian; Federico Dattila; Núria López | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Machine Learning; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2023-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641c2f9791074bccd025f33e/original/diffusion-trapped-oxygen-in-oxide-derived-copper-electrocatalyst-in-co2-reduction.pdf |
60c756e6bdbb897fc3a3ab0a | 10.26434/chemrxiv.14322194.v1 | ABA Type Amphiphiles with Poly(2-Benzhydryl-2-Oxazine) Moieties: Synthesis, Characterization and Inverse Thermogelation | <div>Thermoresponsive polymers are frequently discussed for various applications. Here, we introduce a novel amphiphilic triblock copolymer, which undergoes inverse thermogelation, i.e. is forms a physical gel upon cooling. The polymers comprises poly(2-benzhydryl-2-oxazine) as the hydrophobic building block, a polymer which has not been reported to date. The physical gels are surprisingly strong with a storage modulus of 22 kPa at 25 wt.% in water. In addition, relatively high yield and flow points were determined by rheology.</div> | Lukas Hahn; Larissa Keßler; Lando Polzin; Lars Fritze; Holger Helten; Robert Luxenhofer | Aggregates and Assemblies; Hydrogels; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756e6bdbb897fc3a3ab0a/original/aba-type-amphiphiles-with-poly-2-benzhydryl-2-oxazine-moieties-synthesis-characterization-and-inverse-thermogelation.pdf |
67ce874b6dde43c9083d99e5 | 10.26434/chemrxiv-2025-8j6lk | Nonadiabatic Dynamics of Intersystem Crossings with the Symmetrical Quasi-Classical Dynamics Method Based on the Meyer--Miller Mapping Hamiltonian | We extended the symmetric quasi-classical (SQC) method based on the Meyer--Miller mapping Hamiltonian (MM) to treat the non-adiabatic dynamics simulation including spin-orbit couplings (SOCs). We studied the photoinduced ultrafast excited state dynamic involving intersystem crossing (ISC) process of the ReBr(CO)_3bpy molecule by performing the dynamics based on a pre-constructed model Hamiltonian as well as with the on-the-fly ab initio calculations. For the model system, the dynamics results obtained with the SQC/MM method consist very well with those obtained with the ML-MCTDH method. The SQC/MM method also outperforms the widely used trajectory surface hopping (TSH) method for the system studied here. For the realistic system, we employed the quasi-diabatic propagation scheme to enable the on-the-fly ab initio dynamics with the SQC/MM method. In this case, the dynamics results obtained with the SQC/MM method are very similar to those obtained with the TSH method, and both of them show great discrepancy with the model system ones, which implies it is necessary to perform the full atom on-the-fly dynamics for some molecular systems. Due to the great performance of the SQC/MM method in this work, we strongly recommend using it in the study of ISC processes in the future, both for model and realistic systems. The implementation of the SQC/MM method in the on-the-fly dynamics including the SOCs also paves the way to employing the SQC/MM or other more advanced semi-classical dynamics methods based on the mapping Hamiltonian to study the ISC processes for complex realistic molecular systems. | Haiyi Huang; Jiawei Peng; Zhenggang Lan; Deping Hu; Ya-Jun Liu | Physical Chemistry; Photochemistry (Physical Chem.); Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ce874b6dde43c9083d99e5/original/nonadiabatic-dynamics-of-intersystem-crossings-with-the-symmetrical-quasi-classical-dynamics-method-based-on-the-meyer-miller-mapping-hamiltonian.pdf |
65f4d7759138d231618d1a7d | 10.26434/chemrxiv-2024-c1gph | Trapping Highly Reactive Photo-Induced Charge-Transfer Complex Between Amine and Imide by Light | Complexation between two organic molecules can occur either for strong electron donor-acceptor pairs in the ground state known as charge-transfer complexes (CTCs), or for pairs of lesser strength in the excited state such as excimers and exciplexes. However, the characterization of chemically distinct CTCs in solution remains elusive. Here, we report a light-induced, solution-persistent 1:1 CTC between an amine and an imide. The pair is not associated in the ground state at room temperature prior to light exposure. The presence and exact molecular compositions of the CTCs could be directly obtained from high-resolution mass spectrometry. Additional spectroscopic and computational evidence reveals that a kinetically trapped ground-state pair is formed following an exciplex-like process between the amine and the imide after photo-excitation. We show that such a photo-induced complex can be used to conduct photochemistry and store photon energy for producing otherwise photochromic products in the dark. | Wenhuan Huang; Xiaolong Zhang; Hao Su; Baicheng Zhang; Airong Feng; Jun Jiang; Biao Chen; Guoqing Zhang | Physical Chemistry; Catalysis; Photocatalysis; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f4d7759138d231618d1a7d/original/trapping-highly-reactive-photo-induced-charge-transfer-complex-between-amine-and-imide-by-light.pdf |
623cbb0e13d47814709ab5d3 | 10.26434/chemrxiv-2022-ngsc5 | Stereocontrolled Total Synthesis of Bastimolide B using Iterative Homologation of Boronic Esters | Bastimolide B is a polyhydroxy macrolide isolated from marine cyanobacteria displaying antimalarial activity. It features a dense array of hydroxylated stereogenic centers with 1,5-relationships along a hydrocarbon chain. These 1,5-polyols represent a particularly challenging motif for synthesis, as the remote position of the stereocenters hampers stereocontrol. Herein, we present a strategy for 1,5-polyol stereocontrolled synthesis based on iterative boronic ester homologation with enantiopure magnesium carbenoids. By merging boronic ester homologation and transition metal-catalyzed alkene hydroboration and diboration, the acyclic backbone of bastimolide B was rapidly assembled from readily available building blocks with full control over the remote stereocenters. | Daniele Fiorito ; Selbi Keskin ; Joseph Bateman ; Malcolm George ; Adam Noble ; Varinder Aggarwal | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623cbb0e13d47814709ab5d3/original/stereocontrolled-total-synthesis-of-bastimolide-b-using-iterative-homologation-of-boronic-esters.pdf |
60c74fd79abda27928f8d910 | 10.26434/chemrxiv.12950390.v1 | Size-Controlled Preparation of Gold Nanoparticles Deposited on Surface-Fibrillated Cellulose obtained by Citric Acid-Modification | <p>Cellulose-based functional materials have gained immense interest due to its low density, hydrophilicity, chirality, and degradability. So far, a facile and scalable preparation of fibrillated cellulose by treating the hydroxy groups of cellulose with citric acid (F-CAC) have been developed, and applied as a reinforcing filler for polypropylene composite. Herein, a size-selective preparation of Au nanoparticles (NPs) stabilized by F-CAC is described. By modifying the conditions of trans-deposition method, established in our group previously, a transfer of Au NPs from poly(<i>N</i>-vinyl-2-pyrrolidone) (PVP) to F-CAC proceeded up to 96% transfer efficiency with retaining its cluster sizes in EtOH. Meanwhile, the deposition efficiency drastically decreased in the case of non-modified cellulose, showing the significance of citric acid-modification. A shift of binding energy at Au 4f core level X-ray photoelectron microscopy (XPS) from 82.0 eV to 83.3 eV indicated that the NPs were stabilized on a F-CAC surface rather than by PVP matrix. The reproducible particle size growth was observed when 2-propanol was used as a solvent instead of EtOH, expanding the range of the available particle size with simple manipulation. The thus-obtained Au:F-CAC nanocatalysts exhibited a catalytic activity toward an aerobic oxidation of 1-indonol in toluene to yield 1-indanone quantitatively, and were recyclable at least 6 times, illustrating high tolerance against organic solvents.</p> | Chutimasakul Threeraphat; Yuta Uetake; Jonggol Tantirungrotechai; Taka-Aki Asoh; Hiroshi Uyama; Hidehiro Sakurai | Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fd79abda27928f8d910/original/size-controlled-preparation-of-gold-nanoparticles-deposited-on-surface-fibrillated-cellulose-obtained-by-citric-acid-modification.pdf |
67af5d8481d2151a026dd529 | 10.26434/chemrxiv-2025-vhmh5 | Role of Polycrystalline F-SnO2 Substrate Topography on Formation Mechanism and Morphology of Pt Nanoparticles by Solid-State-Dewetting | Solid-state-Dewetting (SSD) of thin films is increasingly utilized to fabricate nanoparticles for catalysis. In-depth understanding of particle formation mechanism is crucial to control key properties of catalytic particles such as size, size distribution, and structure. In contrast to most studies on SSD of thin metal films on smooth substrates (e.g., SiO2/Si, …), here we investigate how the topography of practical substrates, such as electrically conductive F-SnO2 (FTO), affects the formation mechanism and size of Pt particles – with potential use as nanoparticle electrodes, e.g., in electrochemical conversion or sensing applications. For this, we combined in situ scanning transmission electron microscopy (STEM) with ex situ rapid thermal annealing (RTA) methodologies. Our results indicate that, by dewetting 5 nm of Pt films on FTO, the Pt nanoparticles arrangement feature a bimodal particle distribution. This is driven by: i) a thinner initial Pt film thickness in the “depths” of the FTO substrate due to shadowing effects (caused by the FTO morphology), and ii) the introduction of surface curvatures in the Pt film due to the topography of the substrates, i.e., the FTO grain structure. Particularly, the latter introduces an additional driving force for the Pt diffusion from peaks and ridges (positive local curvature) to flat terraces (no curvature) and valleys (negative local curvature). | Martin Dierner; Sophia Peters; Mingjian Wu; Carmen Rubach; Shreyas Harsha; Rakesh Kumar Sharma; Yu Zheng Siah; Siow Woon Ng; Marco Altomare; Erdmann Spiecker; Johannes Will | Materials Science; Catalysis; Nanoscience; Thin Films; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67af5d8481d2151a026dd529/original/role-of-polycrystalline-f-sn-o2-substrate-topography-on-formation-mechanism-and-morphology-of-pt-nanoparticles-by-solid-state-dewetting.pdf |
67543afe7be152b1d03a820c | 10.26434/chemrxiv-2024-ptsbg | EFGs: A Complete and Accurate Implementation of Ertl’s Functional Group Detection Algorithm in RDKit | Functional groups are widely used in Organic Chemistry, as they provide a rationale to analyze physicochemical and reactivity properties. In Medicinal Chemistry they are the basis for analyzing ligand-biomacromolecule interactions. Ertl’s algorithm is an approach to extract functional groups in arbitrary organic molecules that do not depend on predefined libraries of functional groups. However, there is a lack of a complete and accurate implementation of Ertl’s algorithm in the widely used RDKit cheminformatic toolkit. In this paper a new RDKit/Python implementation of the algorithm is described, that is both accurate and complete. For a RDKit molecule, it provides: a) a PNG binary string with an image of the molecule with color-highlighted functional groups; b) a list of sets of atom indices (idx), each set corresponding to a functional group; c) a list of pseudo-SMILES canonicalized strings for the full functional groups; d) a list of RDKit labeled mol objects, one for each full functional group. The code is freely available in github.com/bbu-imdea/efgs | Gonzalo Colmenarejo | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67543afe7be152b1d03a820c/original/ef-gs-a-complete-and-accurate-implementation-of-ertl-s-functional-group-detection-algorithm-in-rd-kit.pdf |
6287627bf053df0d4d226dd1 | 10.26434/chemrxiv-2022-g792f | Stereoselective Insertion of Cyclopropenes into Mg–Mg Bonds | The reaction of cyclopropenes with compounds containing Mg–Mg bonds is reported. 1,2-Dimagnesiation occurs exclusively by syn-addition to the least hindered face of the alkene forming a single diastereomeric product. DFT calculations support a concerted and stereoselective mechanism. These findings shed new light on the stereochemistry of reactions involving magnesium reagents. | Feriel Rekhroukh; Linxing Zhang; Richard Kong; Andrew White; Mark Crimmin | Organic Chemistry; Inorganic Chemistry; Organometallic Chemistry; Organic Synthesis and Reactions; Kinetics and Mechanism - Organometallic Reactions; Main Group Chemistry (Organomet.) | CC BY 4.0 | CHEMRXIV | 2022-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6287627bf053df0d4d226dd1/original/stereoselective-insertion-of-cyclopropenes-into-mg-mg-bonds.pdf |
65a10a88e9ebbb4db9fe81a3 | 10.26434/chemrxiv-2024-0719x | Development of a Sulfinamide Crossover Reaction | This study unveils a new catalytic crossover reaction of sulfinamides. Leveraging mild acid catalysis, the reaction demonstrates high tolerance to structural variations, yielding equimolar products across diverse sulfinamide substrates. Notably, small sulfinamide libraries can be selectively oxidized to sulfonamides, providing a new platform for ligand optimization and discovery in medicinal chemistry. This crossover chemotype provides a new tool for high-throughput experimentation in discovery chemistry. | Jiri Misek; Vladimir Nosek | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a10a88e9ebbb4db9fe81a3/original/development-of-a-sulfinamide-crossover-reaction.pdf |
63860e760949e121435a52bd | 10.26434/chemrxiv-2022-pmkj8-v3 | BODIPY-Based Photothermal Agents with Unprecedented Phototoxic Indices for Cancer Treatment | Here we report six novel, easily accessible BODIPY-based agents for cancer treatment. In contrast to established photodynamic therapy (PDT) agents, these BODIPY-based compounds show additional photothermal activity and their cytotoxicity is not dependent on the generation of reactive oxygen species (ROS). The agents show high photocytotoxicity upon irradiation with light and low dark toxicity in different cancer cell lines in 2D culture as well as in 3D multicellular tumour spheroids (MCTSs). The ratio of dark to light toxicity (phototoxic index, PI) of these agents reaches striking values exceeding 830’000 after irradiation with energetically low doses of light at 630 nm. The oxygen-dependent mechanism of action (MOA) of established photosensitizers (PSs) hampers effective clinical deployment of these agents. Under hypoxic conditions (0.2% O2), which are known to limit the efficiency of conventional PSs in solid tumours, photocytotoxicity was induced at the same concentration levels, indicating an oxygen-independent photothermal MOA. With a PI exceeding 360’000 under hypoxic conditions, both PI values are the highest reported to date. We anticipate that small molecule agents with a photothermal MOA, such as the BODIPY-based compounds reported in this work, may overcome this barrier and provide a new avenue to cancer therapy. | Lukas Schneider; Martina Kalt; Samuel Koch; Shanmugi Sithamparanathan; Veronika Villiger; Johann Mattiat; Flavia Kradolfer; Ekaterina Sylshkina; Sandra Luber; Mathias Bonmarin; Caroline Maake; Bernhard Spingler | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Photochemistry (Org.); Drug Discovery and Drug Delivery Systems; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63860e760949e121435a52bd/original/bodipy-based-photothermal-agents-with-unprecedented-phototoxic-indices-for-cancer-treatment.pdf |
63768c860821299df8fb27d7 | 10.26434/chemrxiv-2022-xc09k | Gausemycin antibiotic family act via Ca2+-dependent mem-brane targeting | Recently, we discovered a novel lipoglycopeptide antibiotic family gausemycin with exceptional structural novelty. We reported two major constituents of the family gausemycins A and B and characterized their antimicrobial activities. Here-in we studied the molecular mechanism of action of gausemycins and report the isolation and structure elucidation of other members of the family gausemycins C, D, E and F, the minor components of the mixture. Antimicrobial activity of the new congeners was found to be lower than that of the previously reported gausemycins A and B, thus suggesting the importance of the free δ amino group of Orn2 and O-glycosylation of Tyr5 for biological function. To disclose the mecha-nism of action of gausemycin family we investigated the antimicrobial activity of the most active compounds, gausemy-cins A and B, in the presence of Ca2+, other metal ions, and phosphate. Gausemycins require significantly higher Ca2+ con-centration for maximum activity than daptomycin, but lower than that required for malacidine and cadasides. Species-specific antimicrobial activity was found upon testing against a wide panel of Gram-positive bacteria. Membranes were previously proposed as a plausible target of gausemycins, therefore, we explored their interactions with various model membrane systems, including lipid bilayers and micelles. The pore-forming ability was found to be dramatically depend-ent on Ca2+ concentration and the lipid composition of the membrane. The NMR study of gausemycin B in zwitterionic and anionic micelles suggested putative structure of the gausemycin/membrane complex and revealed binding of Ca2+ by the macrocyclic domain of the antibiotic. | Vladimir Korshun; Tatyana Kravchenko; Alexander Paramonov; Arsen Kudzhaev; Svetlana Efimova; Alexey Khorev; Gulnara Kudryakova; Igor Ivanov; Alexey Chistov; Anna Baranova; Maxim Krasilnikov; Olda Lapchinskaya; Anton Tyurin; Olga Ostroumova; Ivan Smirnov; Stanislav Terekhov; Olga Dontsova; Zakhar Shenkarev; Vera Alferova | Biological and Medicinal Chemistry; Chemical Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63768c860821299df8fb27d7/original/gausemycin-antibiotic-family-act-via-ca2-dependent-mem-brane-targeting.pdf |
6126d63465db1e0ff7a46b2e | 10.26434/chemrxiv-2021-gsp7q-v2 | Heterocyclic Hypervalent Iodine(III) Compounds with Fused Benziodazole and Tetrazole Rings (I-Substituted Tetrazolo[1,5-b][1,2]Benziodazoles) | A series of heterocyclic hypervalent (HV) iodine(III) compounds containing fused tetrazole and benziodazole rings, i.e., derivatives of benziodazolotetrazole (BIAT) with various ligands attached to the iodine atom were prepared and studied. BIAT-Cl was synthesized via chlorination of 5-(2-iodophenyl)-1H-tetrazole and subsequent spontaneous cyclo-dehydrochlorination of the initially formed dichloroiodo compound. The oxidation of the aforementioned parent monovalent iodine substrate with NaIO4 yielded BIAT-OH, which was in turn reacted with acetic anhydride to afford the I-acetoxy derivative BIAT-OAc. BIAT-OMe was obtained by refluxing the latter compound or by dissolving (2-(1H-tetrazol-5-yl)phenyl)(hydroxy)iodonium tosylate in methanol. All heterocyclic HV iodine(III) compounds were characterized by 1H and 13C NMR spectroscopy, ESI-HRMS, and single crystal X-ray crystallography. The reaction of alkenes with BIAT-Cl in the presence of Cu(OTf)2 at room temperature afforded chloro-tetrazolylated products in 70-88% isolated yields. The oxidation of thioanisole with BIAT-Cl under various reaction conditions is also reported. The thermal stabilities of all BIAT derivatives were examined as well. The enthalpies of exothermic degradation were measured by thermal gravimetric analysis coupled with differential scanning calorimetry and were determined to be in the range between −35.3 and −305.3 kJ mol-1, i.e., significantly larger than the enthalpy of decomposition (−29.4 kJ mol-1) of the parent monovalent iodine-containing tetrazole – 5-(2-iodophenyl)-1H-tetrazole. | Rajesh Kumar; Kapil Dev Sayala; Lejla Camdzic; Maxime Siegler; Avichal Vaish; Nicolay Tsarevsky | Inorganic Chemistry; Kinetics and Mechanism - Inorganic Reactions; Reaction (Inorg.); Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6126d63465db1e0ff7a46b2e/original/heterocyclic-hypervalent-iodine-iii-compounds-with-fused-benziodazole-and-tetrazole-rings-i-substituted-tetrazolo-1-5-b-1-2-benziodazoles.pdf |
60f5af8f8f6bf606036f8e39 | 10.26434/chemrxiv-2021-n77jn-v2 | Mechanistic investigation and free energies of the reactive adsorption of ethanol at the alumina/water interface | Controlling the adsorption/desorption of molecules at the solid/water interface is central to a wide range of fields from catalysis to batteries. For instance, adsorbing alcohols at the surface of γ-Al2O3 can prevent its chemical weathering. To make sure that γ-Al2O3 remains a stable catalyst support under operating conditions in liquid water, it is crucial to design alcohols that cannot desorb easily. Taking ethanol as a typical example, we here compare the adsorption/desorption mechanism for two distinct adsorption modes of ethanol at the water/alumina interface using various DFT-based approaches. Thermodynamic integration simulations unambiguously identify ethoxy as the more stable adsorption mode. The presence of liquid water yields to adsorption barriers fo adsorption barriers
of at least 20 kJ·mol-1. To better assess the effect of water, we perform 3D well-tempered metadynamics simulations that include a bias accounting for solvation effects and proton transfers at the interface. Activating the proton shuffling allows to explore a variety of protonation and hydration configurations and yields to higher barriers (up to 40 kJ·mol−1) than the ones predicted by thermodynamic integration where the solvent reorganisation was assumed to be decoupled from the desorption. This study illustrates the importance of treating explicitly solvation effects when modelling reactions at the solid/liquid interface. | Jérôme Rey; Paul Clabaut; Romain Réocreux; Stephan Steinmann; Carine Michel | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f5af8f8f6bf606036f8e39/original/mechanistic-investigation-and-free-energies-of-the-reactive-adsorption-of-ethanol-at-the-alumina-water-interface.pdf |
62c82c69cd7a9916c3be842c | 10.26434/chemrxiv-2022-sd5vw | Development of a Transferable Coarse-Grained Model of Polydimethylsiloxane | Polydimethylsiloxane (PDMS) is a popular silicon-based polymer with advanced applications in microfluidics and nanocomposites. The slow dynamics of polymer chains in such complex systems hinders molecular dynamics investigations based on all-atom force fields. This limitation can be overcome by exploiting finely tuned coarse-grained (CG) models. This paper develops a transferable CG model of PDMS, compatible with the recent Martini 3 force field, using structural and thermodynamic properties as targets in the parametrization, including a vast set of experimental free energies of transfer. We validate the model transferability by reproducing the correct scaling laws for the PDMS gyration radius in the melt and good and bad solvents. We successfully test the model by describing the phase behavior of a PDMS-peptide triblock copolymer system. This work sets the stage for computational studies involving the interaction between PDMS and many synthetic and biological molecules modeled within the Martini framework. | Sonia Cambiaso; Giulia Rossi; Davide Bochicchio | Theoretical and Computational Chemistry; Polymer Science; Organic Polymers; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c82c69cd7a9916c3be842c/original/development-of-a-transferable-coarse-grained-model-of-polydimethylsiloxane.pdf |
63f3b5899da0bc6b334254c5 | 10.26434/chemrxiv-2023-jlftz-v2 | Ion Correlation and Negative Transference in Lithium-bearing Non-Aqueous Oligomeric Electrolyte Solutions | Polyelectrolyte solutions (PESs) recently have been proposed as high conductivity, high lithium transference number (t+) electrolytes where the majority of the ionic current is carried by the electrochemically active Li-ion. While PESs are intuitively appealing because anchoring the anion to a polymer backbone selectively slows down anionic motion and therefore increases t+, increasing the anion charge will act as a competing effect, decreasing t+. In this work we directly measure ion mobilities in a model non-aqueous polyelectrolyte solution using electrophoretic Nuclear Magnetic Resonance Spectroscopy (eNMR) to probe these competing effects. While previous studies that rely on ideal assumptions predict that PESs will have higher t+ than monomeric solutions, we demonstrate that below the entanglement limit, both conductivity and t+ decrease with increasing degree of polymerization. For polyanions of 10 or more repeat units, at 0.5m Li+ we directly observe Li+ move in the wrong direction in an electric field, evidence of a negative transference number due to correlated motion through ion clustering. This is the first experimental observation of negative transference in a non-aqueous polyelectrolyte solution. We also demonstrate that t+ increases with increasing Li+ concentration. Using Onsager transport coefficients calculated from experimental data, and insights from previously published molecular dynamics studies we demonstrate that despite selectively slowing anion motion using polyanions, distinct anion-anion correlation through the polymer backbone and cation-anion correlation through ion aggregates reduce the t+ in non-entangled PESs. This leads us to conclude that short-chained polyelectrolyte solutions are not viable high transference number electrolytes. | Helen Bergstrom; Kara Fong; David Halat; Carl Karouta; Hasan Celik; Jeffrey Reimer; Bryan McCloskey | Materials Science; Energy; Chemical Engineering and Industrial Chemistry; Polyelectrolytes - Materials; Transport Phenomena (Chem. Eng.); Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f3b5899da0bc6b334254c5/original/ion-correlation-and-negative-transference-in-lithium-bearing-non-aqueous-oligomeric-electrolyte-solutions.pdf |
63fdbd2f32cd591f1299af21 | 10.26434/chemrxiv-2023-vphs1 | Thermal Decomposition of Trimethylindium and Indium Trisguanidinate Precursors for InN Growth: An Ab-Initio and Kinetic Modelling Study | Indium nitride (InN) is an interesting material for future electronic and photonic-related applications, as it combines high electron mobility and low-energy band gap for photoabsorption or emission-driven processes. In this context, atomic layer deposition (ALD) techniques have been previously employed for InN growth at low temperatures (typically < 350 C), reportedly yielding crystals with high quality and purity. In general, this technique is assumed to not involve any gas phase reactions as a result from the time-resolved insertion of volatile molecular sources into the gas chamber. Nonetheless, such temperatures could still favour the precursor decomposition in gas phase during the In half-cycle, therefore altering the molecular species that undergoes physisorption and, ultimately, driving the reaction mechanism to pursue other pathways. Thence, we herein evaluate the thermal decomposition of relevant In precursors in gas phase, namely trimethylindium (TMI) and tris(N,N-diisopropyl-2-dimethylamido-guanidinato) (III) (ITG), by means of thermodynamic and kinetic modelling. According to the results, at T= 593 K, TMI should exhibit partial decomposition of ~8% after 400 s to first generate methylindium (MI) and ethane (C2H6), a percentage that increases to ~34% after 1 hour of exposure inside the gas chamber. Therefore, this precursor should be present in an intact form to undergo physisorption during the In half-cycle of the deposition experiment (< 10 s). On the other hand, the ITG decomposition starts already at the temperatures used in the bubbler and it will slowly decompose as it is evaporated during the deposition process. At T= 300 C, the decomposition is a fast process that reaches 90% completeness after 1 s, and where equilibrium, at which almost no ITG remains, is achieved before 10 s. In this case, the decomposition pathway is likely to occur via elimination of carbodiimide ligand. Ultimately, these results should contribute for a better understanding of the reaction mechanism involved in the InN growth from these precursors. | Giane Damas; Karl Rönnby; Henrik Pedersen; Lars Ojamäe | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science | CC BY 4.0 | CHEMRXIV | 2023-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63fdbd2f32cd591f1299af21/original/thermal-decomposition-of-trimethylindium-and-indium-trisguanidinate-precursors-for-in-n-growth-an-ab-initio-and-kinetic-modelling-study.pdf |
62169942c3e9da33d574d611 | 10.26434/chemrxiv-2022-8ptd2 | Chemoselective, Metal-free, (Hetero)Arene Electroreduction Enabled by Rapid Alternating Polarity | Arene semi-reduction remains a challenge when multiple re-ductively labile functional groups are present or when using heteroarene substrates. Conventional chemical and even elec-trochemical Birch-type reductions suffer from a lack of chemoselectivity due to a reliance on alkali metals or harshly reducing conditions. This study reveals that a simpler avenue is available for such reductions by simply altering the wave-form of current delivery, namely rapid alternating polarity (rAP). The developed method, which proceeds in protic sol-vent and can be easily scaled up, does not require any metal additives or stringently anhydrous conditions. The scope of this dearomatization is broad, tolerating numerous functional groups and providing rapid access to previously challenging molecules. While the mechanism has not been fully deci-phered, the key feature of the rAP reduction is that the main competing process, namely proton reduction, can be sup-pressed. As such, unique arene reductions can be accom-plished even outside solvent electrochemical window or in the presence of Brønsted acids. | Kyohei Hayashi; Jeremy Griffin; Kaid Harper; Yu Kawamata; phil baran | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62169942c3e9da33d574d611/original/chemoselective-metal-free-hetero-arene-electroreduction-enabled-by-rapid-alternating-polarity.pdf |
60c748a30f50db88d83967c1 | 10.26434/chemrxiv.11952516.v1 | ML4Chem: A Machine Learning Package for Chemistry and Materials Science | ML4Chem is an open-source machine learning library for chemistry and materials science. It
provides an extendable platform to develop and deploy machine learning models and pipelines and
is targeted to the non-expert and expert users. ML4Chem follows user-experience design and offers
the needed tools to go from data preparation to inference. Here we introduce its atomistic module
for the implementation, deployment, and reproducibility of atom-centered models. This module is
composed of six core building blocks: data, featurization, models, model optimization, inference,
and visualization. We present their functionality and ease of use with demonstrations utilizing
neural networks and kernel ridge regression algorithms. | Muammar El Khatib; Wibe de Jong | Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748a30f50db88d83967c1/original/ml4chem-a-machine-learning-package-for-chemistry-and-materials-science.pdf |
60c749d8bb8c1a4f5a3daecf | 10.26434/chemrxiv.11396904.v2 | Reaction Mechanism of the Metal Precursor Pulse in Plasma-Enhanced Atomic Layer Deposition of Cobalt and the Role of Surface Facet | Cobalt is a potential
candidate in replacing copper for interconnects and has been applied in the
trenches and vias in semiconductor industry. A non-oxidizing reactant is
required in plasma-enhanced atomic layer deposition (PE-ALD) of thin films of metals
to avoid O-contamination. PE-ALD of Co has been demonstrated experimentally,
but the growth mechanism and key reactions are not clear. In this paper, the reaction
mechanism of metal cyclopentadienyl (Cp, C<sub>5</sub>H<sub>5</sub>) precursors
(CoCp<sub>2</sub>) and NH<sub>x</sub>-terminated Co surface is studied by
density functional theory (DFT) calculations. The Cp ligands are eliminated by
CpH formation via a hydrogen transfer step and desorb from metal surface. The surface
facet plays an important role in the reaction energies and activation barriers.
The results show that on the NH<sub>x</sub>-terminated surfaces corresponding
to ALD operating condition (temperature range 550K to 650K), the two Cp ligands
are eliminated completely on Co(100) surface during the metal precursor pulse,
resulting in Co atom deposited on the Co(100) surface. But the second Cp ligand
reaction of hydrogen transfer is thermodynamically unfavourable on the Co(001)
surface, resulting in CoCp fragment termination on Co(001) surface. The final
terminations after metal precursor pulse are 3.03 CoCp/nm<sup>2</sup> on NH<sub>x</sub>-terminated
Co(001) surface and 3.33 Co/nm<sup>2</sup> on NH<sub>x</sub>-terminated Co(100)
surface. These final structures after metal precursor pulse are essential to
model the reaction during the following N-plasma step..<br /> | Ji Liu; hongliang lu; david wei zhang; Michael Nolan | Coating Materials; Materials Processing; Thin Films; Computational Chemistry and Modeling; Theory - Computational; Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749d8bb8c1a4f5a3daecf/original/reaction-mechanism-of-the-metal-precursor-pulse-in-plasma-enhanced-atomic-layer-deposition-of-cobalt-and-the-role-of-surface-facet.pdf |
65c61d739138d23161c0b7c1 | 10.26434/chemrxiv-2023-5tlfk-v3 | Metal-organic polyhedron from flexible tetrakis(thiobenzyl-carboxylate)-Tetrathiafulvalene | The synthesis of crystalline self-assembled materials starting from building blocks with a large degree of freedom is challenging. Furthermore, incorporating redox-active moieties in self-assembled metal organic polyhedra is of the outmost interest to modulate the properties of the cavity through redox stimuli. Herein is presented the synthesis of a novel electroactive ligand bearing four coordinating moieties around an S-alkylated tetrathiafulvalene (TTF) scaffold. The redox behavior of the ligand is similar to a tetra-S-alkylated TTF. In the solid state, it presents a densely packed H-bonded 1D polymeric structure. Upon reaction with Cu(OAc)2 in the presence of dimethylformamide or dimethylacetamide, two novel M4L4-type metal-organic polyhedra (MOPs) bearing paddlewheel metal clusters as connecting nodes are obtained. The structural features and electrochemical properties of the ligand and the MOPs are devised. Both MOPs adopt the same structure characterized by a tetrahedral arrangement of the four TTF moieties. | Yohan Cheret; Narcis Avarvari; Nicolas Zigon | Organic Chemistry; Organometallic Chemistry; Supramolecular Chemistry (Org.); Coordination Chemistry (Organomet.) | CC BY 4.0 | CHEMRXIV | 2024-02-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c61d739138d23161c0b7c1/original/metal-organic-polyhedron-from-flexible-tetrakis-thiobenzyl-carboxylate-tetrathiafulvalene.pdf |
60c74d36567dfe7005ec5307 | 10.26434/chemrxiv.12598487.v1 | In Silico Analysis of Sea Urchin Pigments as Potential Therapeutic Agents Against SARS-CoV-2: Main Protease (Mpro) as a Target. | The SARS-CoV-2 outbreak has spread rapidly and globally generating a new coronavirus disease (COVID-19) since December 2019 that turned into a pandemic. Effective drugs are urgently needed and drug repurposing strategies offer a promising alternative to dramatically shorten the process of traditional de novo development. Based on their antiviral uses, the potential affinity of sea urchin pigments to bind main protease (Mpro) of SARS-CoV-2 was evaluated in silico. Docking analysis was used to test the potential of these sea urchin pigments as therapeutic and antiviral agents. All pigment compounds presented high molecular affinity to Mpro protein. However, the 1,4-naphtoquinones polihydroxilate (Spinochrome A and Echinochrome A) showed high affinity to bind around the Mpro´s pocket target by interfering with proper folding of the protein mainly through an H-bond with Glu166 residue. This interaction represents a potential blockage of this protease´s activity. All these results provide novel information regarding the uses of sea urchin pigments as antiviral drugs and suggest the need for further in vitro and in vivo analysis to expand all therapeutic uses against SARS-CoV-2. <br /> | Tamara Rubilar; Elena Susana Barbieri; Ayelén Gázquez; Marisa Avaro; Mercedes Vera-Piombo; Agustín Gittardi; Erina Noé Seiler; Jimena Pía Fernandez; Lucas Sepulveda; Florencia Chaar | Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d36567dfe7005ec5307/original/in-silico-analysis-of-sea-urchin-pigments-as-potential-therapeutic-agents-against-sars-co-v-2-main-protease-mpro-as-a-target.pdf |
64981a432e632767b0c16c73 | 10.26434/chemrxiv-2023-5s4nc | Origin of Broad Emission Induced by Rigid Aromatic Ditopic Cations in Low-Dimensional Metal Halide Perovskites | The development of broadband emitters based on metal halide perovskites (MHPs) requires the elucidation of structure-emission property correlations. Herein, we report a combined experimental and theoretical study on a series of novel low-dimensional lead-chloride perovskites including ditopic aromatic cations. Synthesized lead-chloride perovskites and their bromide analogues show both narrow and broad photoluminescence emission properties as a function of the cation and halide nature. Structural analysis shows a correlation between the rigidity of the ditopic cations with the lead-halide octahedral distortions. Density functional theory calculations reveal, in turn, the pivotal role of octahedral distortions in the formation of self-trapped excitons which are responsible for the insurgence of broad emission and large Stokes shifts together with a contribution of halide vacancies. For the considered MHPs series the use of conventional octahedral distortion parameters allows to nicely describe the trend of emission properties thus providing a solid guide for further materials design. | Lorenzo Malavasi; Waldemar Kaiser; Filippo De Angelis; Edoardo Mosconi; Marta Morana; Rossella Chiara; Daniele Meggiolaro; Pietro Galinetto; Benedetta Albini | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-06-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64981a432e632767b0c16c73/original/origin-of-broad-emission-induced-by-rigid-aromatic-ditopic-cations-in-low-dimensional-metal-halide-perovskites.pdf |
65cfb263e9ebbb4db9859eb7 | 10.26434/chemrxiv-2024-hfw3p | Enhanced Ligand Discovery through Generative AI and Latent-Space Exploration: Application to the Mizoroki-Heck Reaction | The identification of catalysts that promote chemical reactions is a critical challenge in the production of pharmaceuticals. One of the main bottlenecks in this process is the synthesis of vast libraries of precatalysts, although assessing catalyst effectiveness can be rapidly conducted through high-throughput experimentation. The rational design and development of high-performing precatalysts can circumvent this challenge and lead to important advances. In this study, we apply the transformer-based Kernel-Elastic Autoencoder (KAE) equipped with a conditioned latent space, enabling the targeted generation of ligands with desired steric and electronic properties. Our KAE model has facilitated the identification of a monodentate alkynylphosphine, dubbed MachinePhos A, as an effective precatalyst for forming carbon-carbon bond. Its utility was demonstrated experimentally in the Mizoroki-Heck reaction, using a variety of nitrogen-rich arenes pertinent to pharmaceutical applications. | Wenxin Lu; Haote Li; Jan Paul Menzel; Abbigayle E. Cuomo; Andrea M. Nikolic; H. Ray Kelly; Yu Shee; Sanil Sreekumar; Frederic Buono; Jinhua J. Song; Robert H. Crabtree; Victor S. Batista; Timothy R. Newhouse | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cfb263e9ebbb4db9859eb7/original/enhanced-ligand-discovery-through-generative-ai-and-latent-space-exploration-application-to-the-mizoroki-heck-reaction.pdf |
661fbad021291e5d1d0572a6 | 10.26434/chemrxiv-2024-m179z | Assembly of differently sized supercharged protein nanocages into superlattices for construction of binary nanoparticle-protein materials | This study focuses on the design and characterization of binary nanoparticle superlattices: Two differently sized, supercharged protein nanocages are used to create a matrix for nanoparticle arrangement. We have previously established the assembly of protein nanocages of the same size. Here, we present a novel approach for biohybrid material synthesis by successfully assembling two differently sized supercharged protein nanocages with different symmetries. Typically, the ordered assembly of objects with non-matching symmetry is challenging, but our electrostatic-based approach overcomes the symmetry mismatch by exploiting electrostatic interactions between oppositely charged cages. Moreover, our study showcases the use of nanoparticles as contrast enhancer in an elegant way to gain insights into the structural details of crystalline biohybrid materials. The assembled materials were characterized with various methods, including transmission electron microscopy (TEM) and single-crystal small-angle X-ray scattering (SAXS). We employed focused ion beam milling (FIB) under cryogenic temperatures to further characterize the nanoparticle sublattices via cryo-TEM. Notably, for the first time, we refined superlattice structure data obtained from single-crystal SAXS experiments, providing conclusive evidence of the final assembly type. Our findings highlight the versatility of protein nanocages for creating novel types of binary superlattices. Because the nanoparticles do not influence the type of assembly, protein cage matrices can combine various nanoparticle in the solid state. This study not only contributes to the expanding repertoire of nanoparticle assembly methods but also demonstrates the power of advanced characterization techniques in elucidating the structural intricacies of these biohybrid materials. | Tobias Beck; Michael Rütten; Laurin Lang; Henrike Wagler; Marcel Lach; Thomas Keller; Andreas Stierle; Helen Ginn | Nanoscience; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661fbad021291e5d1d0572a6/original/assembly-of-differently-sized-supercharged-protein-nanocages-into-superlattices-for-construction-of-binary-nanoparticle-protein-materials.pdf |
656794ed29a13c4d4748686c | 10.26434/chemrxiv-2023-vnxgr | Label-free Single-molecule Immunoassay | Single-molecule immunoassay is a reliable technique for the detection and quantification of low-abundance blood biomarkers, which are essential for early disease diagnosis and biomedical research. However, current single-molecule methods all require signal amplification via labelling, which brings a variety of unwanted consequences, such as matrix effects and autofluorescence interference. Here, we introduce a real-time mass imaging-based label-free single-molecule immunoassay (LFSM-immunoassay). Featuring plasmonic scattering microscopy-based real-time mass imaging, a 2-step sandwich assay format-enabled background reduction, and minimization of matrix effects by dynamic tracking of single binding events, the LFSM-immunoassay enables ultra-sensitive and direct protein detection at the single-molecule level in neat blood sample matrices. We demonstrated that the LFSM-immunoassay can measure sub-femtomolar levels of interleukin-6 and prostate-specific antigen in whole blood with 8 log dynamic range. To show its translational potential to clinical settings, we measured NT-proBNP (N-terminal pro-brain natriuretic peptide) in 28 patient serum samples using a 20 minute LFSM-immunoassay, and the results show a strong linear correlation (r > 0.99) with clinical lab reported values. | Xiaoyan Zhou; Chao Chen; Guangzhong Ma; Mohammad Javad Chemerkouh; Christine Snozek; Eric Yang; Brandyn Braswell; Zijian Wan; Shaopeng Wang | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656794ed29a13c4d4748686c/original/label-free-single-molecule-immunoassay.pdf |
60c73dde842e656f82db1846 | 10.26434/chemrxiv.6217451.v1 | Photocatalytic Hydrogen Evolution from Water Using Heterocyclic Conjugated Microporous Polymers: Porous or Non-Porous? | <p>Three series of conjugated microporous
polymers (CMPs) were studied as photocatalysts for producing hydrogen from
water using a sacrificial hole-scavenger. In all cases, dibenzo[<i>b</i>,<i>d</i>]thiophene
sulfone polymers outperformed their fluorene analogs. A porous network, S-CMP3,
showed the highest hydrogen evolution rate of 6076 µmol h<sup>-1</sup>
g<sup>-1</sup> (λ > 295 nm) and 3106 µmol h<sup>-1</sup>
g<sup>-1</sup> (λ > 420 nm), with an external quantum
efficiency of 13.2% at 420 nm. S-CMP3 outperforms its linear structural
analog, P35, while in other cases, non-porous linear polymers are superior to
equivalent porous networks. This suggests that microporosity can be beneficial
for sacrificial photocatalytic hydrogen evolution, but not for all monomer
combinations.</p> | Reiner Sebastian Sprick; Yang Bai; Catherine M. Aitchison; Duncan J. Woods; Andrew I. Cooper | Organic Polymers; Heterogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dde842e656f82db1846/original/photocatalytic-hydrogen-evolution-from-water-using-heterocyclic-conjugated-microporous-polymers-porous-or-non-porous.pdf |
625530ddebac3a4918d21843 | 10.26434/chemrxiv-2022-s8xc3 | Development of Poly(2-oxazoline)s and poly(2-oxazine)s based formulation library and estimation of polymer/drug compatibility. | The main objective of this study is to formulate a library of difficult to solubilize drugs with four slightly different poly(2-oxazoline)s (POx) and poly(2-oxazine)s (POzi) based amphiphilic triblock copolymers and to elucidate whether the drug-polymer compatibility, as estimated by solubility parameters (SPs) might be used as tool to guide formulation development. The theoretical and experimental SPs of different homo-/triblock copolymers and 21 different hydrophobic drugs were calculated by two group contribution methods (i.e. Hoftyzer Van-Krevelen and Yamamoto molecular break method) and determined experimentally by solubility testing in list of selective solvents (for polymers only). The obtained SPs were further utilized to calculate the distance between polymers and drugs (Ra) in 3 dimensional Hansen space. Out of 21 structurally diverse drugs, the loading capacity (LC) was found to be higher than 40, 30, 20 and 10 wt.% for 4, 4, 3 and 5 drugs, respectively. In the remaining of 5 drugs the maximum achievable LC was found below 10 wt.%. The experimental results obtained by formulation development were not in accordance with the results predicted by Ra calculation. In contrast to several reports found in the literature, the determination of SPs and concurrent compatibility estimation appeared not to be a suitable tool to predict polymer-drug compatibility in the present system. As the predictive power of SPs is based on simple mathematical calculations, limiting the precise prediction of overall polarity, hydrogen bonding ability of molecules and interplay between the hydrophilic and hydrophobic domains resulting in differing deviations than predicted interactions thus might compromise the predictive power of HSPs. | Malik Salman Haider; Robert Luxenhofer | Polymer Science; Nanoscience; Drug delivery systems; Organic Polymers | CC BY 4.0 | CHEMRXIV | 2022-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625530ddebac3a4918d21843/original/development-of-poly-2-oxazoline-s-and-poly-2-oxazine-s-based-formulation-library-and-estimation-of-polymer-drug-compatibility.pdf |
60c759a74c89193107ad4dfc | 10.26434/chemrxiv.14377016.v3 | Cooperative Single-Atom Active Centers for Attenuating Linear Scaling Effect in Nitrogen Reduction Reaction | We elucidate how the cooperation of two active centers can attenuate the
linear scaling effect in NRR, through the first-principle study on 39 SACs
comprised of two adjacent (~4 Å apart) four N-coordinated metal centers (MN<sub>4</sub>
duo) embedded in graphene. | Ke Ye; Min Hu; Qin-Kun Li; Yi Luo; Jun Jiang; Guozhen Zhang | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759a74c89193107ad4dfc/original/cooperative-single-atom-active-centers-for-attenuating-linear-scaling-effect-in-nitrogen-reduction-reaction.pdf |
65020473b6ab98a41c6445b0 | 10.26434/chemrxiv-2023-7pglw | Lasso Peptides: Exploring the Folding Landscape of Nature’s Smallest Interlocked Motifs | Lasso peptides are a class of natural products characterized by a threaded structure. Given their small size and stability, chemical synthesis would offer tremendous potential for the development of novel therapeutics. However, the accessibility of the pre-folded lasso architecture has limited this advance. To better understand the folding process de novo, simulations are used herein to characterize the folding propensity of microcin J25 (MccJ25), a lasso peptide known for its antimicrobial properties. New algorithms are developed to unambiguously distinguish threaded from non-threaded precursors and determine handedness, a key feature in natural lasso peptides. We find that MccJ25 indeed forms right-handed pre-lassos, in contrast to past predictions but consistent with all natural lasso peptides. Additionally, the native pre-lasso structure is shown to be metastable prior to ring formation but to readily transition to entropically-favored unfolded and non-threaded structures, suggesting de novo lasso folding is rare. However, by modifying the ring forming residues with the appendage of thiol and thioester functionalities, we are able to increase the stability of pre-lasso conformations. Furthermore, conditions leading to protonation of a histidine imidazole side chain further stabilize the modified pre-lasso ensemble. This work highlights the use of computational methods to characterize lasso folding and demonstrates that de novo access to lasso structures can be facilitated by optimizing sequence, unnatural modifications, and reaction conditions like pH. | Gabriel da Hora; Myongin Oh; Marcus Mifflin; Lori Digal; Andrew Roberts; Jessica Swanson | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Biophysics; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65020473b6ab98a41c6445b0/original/lasso-peptides-exploring-the-folding-landscape-of-nature-s-smallest-interlocked-motifs.pdf |
67437a205a82cea2faabeafe | 10.26434/chemrxiv-2024-tzs1z-v2 | Examining proton conductivity of metal-organic frameworks by means of machine learning | The tunable structure of metal–organic frameworks (MOFs) is an ideal platform to meet contradictory requirements for proton exchange membranes: a key component of fuel cells. Nonetheless, rational design of proton-conducting MOFs remains a challenge owing to the intricate structure–property relationships that govern the target performance. In the present study, the modeling of quantities available for hundreds of MOFs was scaled up to many thousands of entities using supervised machine learning. The experimental dataset was curated to train multimodal transformer-based networks, which integrated crystal-graph, energy grid, and global-state embeddings. Uncertainty-aware models revealed superprotonic conductors among synthesized MOFs that have not been previously investigated for the application in question, thus highlighting magnesium-containing frameworks with aliphatic linkers as high-confidence candidates for experimental validation. Furthermore, classifiers trained on the activation energy threshold effectively discriminated between well-known proton conduction mechanisms, thereby providing physical insights beyond the black-box routine. Thus, our findings prove high potential of data-driven materials design, which is becoming a valuable addition to experimental studies on proton-conducting MOFs. | Ivan Dudakov; Sergei Savelev; Iurii Nevolin; Artem Mitrofanov; Vadim Korolev; Yulia Gorbunova | Theoretical and Computational Chemistry; Materials Science; Hybrid Organic-Inorganic Materials; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67437a205a82cea2faabeafe/original/examining-proton-conductivity-of-metal-organic-frameworks-by-means-of-machine-learning.pdf |
65c584a866c13817293fc498 | 10.26434/chemrxiv-2024-g4vxk | Alkene-Coordinated Palladium(0) Cross-Coupling Precatalysts: Comparing Oxidative Addition and Catalytic Reactivity for Dimethyl Fumarate and Maleic Anhydride Stabilizing Ligands
| Air-stable palladium (0) precatalysts are advantageous for facilitating a variety of chemical transformations, and are desir-able precursors for high-throughput experimentation studies. We report investigations into air-stable Pd(0) precatalysts stabi-lized by dimethyl fumarate (DMFU) as an electron-deficient alkene. A Pd(0) DMFU complex with a diazabutadiene (DAB) supporting ligand readily undergoes substitution with both monodentate and bidentate phosphines to form phosphine–Pd–DMFU complexes in situ. These complexes undergo oxidative addition with ArBr substrates, and are also effective precata-lysts for Heck coupling, Suzuki-Miyaura coupling, and Miyaura borylation. Catalytic comparisons of the DAB–Pd–DMFU precursor to other Pd sources reveals benefits and limitations of this system, including high activity in Heck coupling, and challenges with in situ catalyst generation | Gilian Thomas; Jared Litman; Binh Dang Ho; Jingjun Huang; Kalina Blonska; Nathan Schley; David Leitch | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c584a866c13817293fc498/original/alkene-coordinated-palladium-0-cross-coupling-precatalysts-comparing-oxidative-addition-and-catalytic-reactivity-for-dimethyl-fumarate-and-maleic-anhydride-stabilizing-ligands.pdf |
66c0c5a4a4e53c4876b3c43d | 10.26434/chemrxiv-2024-2112n | On the importance of configuration search to the predictivity of lanthanide selectivity | The lanthanide elements are crucial components in numerous technologies, yet their industrial production through liquid-liquid extraction continues to be economically and environmentally costly due to the challenge of separating elements with similar physico-chemical properties. While computational ligand screening has shown promise towards discovering efficient extractants, the complexity of constructing chemically-sensible 3D structures (often by-hand), coupled with the high cost of quantum chemistry calculations, often limits exploration of the vast ligand chemical and conformational space in favor of local exploration around known chemistries. Moreover, metal complexes can have many stable configurations whose differences in energies exceed the small energy differences that determine extractant selectivity for certain lanthanides. Because of this difference, incorrect selectivity predictions can be made if the lowest energy coordination complex is not identified and modeled. To address this issue, we present a high- throughput computational workflow that automates the construction and quantum mechanical modeling of 3D lanthanide-extractant complexes. This approach allows for an unbiased search of distinct configurational and compositional variations for each metal, enabling accurate predictions of their solution structures and lanthanide selectivity. As showcased by three extractants from diverse chemical categories—a crown ether, a phenanthroline monocarboxamide, and a malonamide—it is found that sampling the lanthanide-ligand configuration space is critical to correctly predicting the solvation structure and experimental lanthanide selectivity trends. | Thomas Summers; Michael Taylor; Logan Augustine; Jan Janssen; Danny Perez; Enrique Batista; Ping Yang | Theoretical and Computational Chemistry; Inorganic Chemistry; Lanthanides and Actinides; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c0c5a4a4e53c4876b3c43d/original/on-the-importance-of-configuration-search-to-the-predictivity-of-lanthanide-selectivity.pdf |
60c73f1bbdbb892c73a37f23 | 10.26434/chemrxiv.7233878.v1 | Capabilities of Anion and Cation on Hydrogen-bond Transition from the Mode of Ordinary Water to (Mg, Ca, Sr)(Cl, Br)2 Hydration | <div>Charge injection in terms of divalent cations and halide anions on the O:H-O network and properties with discrimination of the solute capabilities on transition O:H-O bonds from the mode of ordinary water of hydrating in terms of fraction number and stiffness.<br /></div> | Yongli Huang; Chang Sun | Solution Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1bbdbb892c73a37f23/original/capabilities-of-anion-and-cation-on-hydrogen-bond-transition-from-the-mode-of-ordinary-water-to-mg-ca-sr-cl-br-2-hydration.pdf |
63231273334f1de1cbf4bb45 | 10.26434/chemrxiv-2022-bv6cs | Spatially Offset Raman Spectroscopy (SORS) as analytical tool for the sustainable analysis of packed meat | As a highly sensitive food, the safety of meat is an important issue in the context of food safety. The current analytical methods for detection are based on different, invasive proce-dures. The analysis of these foods therefore causes avoidable food losses in the case of foods that are still suitable for consumption. Spatially offset Raman spectroscopy (SORS) is a po-tential alternative analytical method, as it offers the possibility to measure through packag-ing. Using packaged chicken breast as an example, we simulated two different storage condi-tions and compared these samples to control samples using SORS. To validate the group as-signment and to monitor the resulting changes, total bacterial count and NMR spectra of the meat extracts were measured and evaluated. We overcame the various difficulties in the multivariate data evaluation of the through package measured Raman spectra and were able to classify samples deviating from the control group with very high accuracies and simulta-neous absence of false positive results. | Lyn Christiansen; Nele Paasch; Markus Weidner; Lara Cordsen; René Bachmann | Analytical Chemistry; Agriculture and Food Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63231273334f1de1cbf4bb45/original/spatially-offset-raman-spectroscopy-sors-as-analytical-tool-for-the-sustainable-analysis-of-packed-meat.pdf |
60c74464469df4c848f43307 | 10.26434/chemrxiv.9784799.v1 | A Molecular Logic Gate Enables Super-Resolved Imaging of Intracellular Lipid Droplets | <div>Photoactivatable dyes enable single-molecule imaging in biology. Despite progress in the development of new fluorophores and labeling strategies, many cellular compartments remain difficult to image beyond the limit of diffraction in living cells. For example, lipid droplets, which are organelles that contain mostly neutral lipids, have eluded single-molecule imaging. To visualize these challenging subcellular targets, it is necessary to develop new fluorescent molecular devices beyond simple on/off switches. Here, we report a fluorogenic molecular logic gate that can be used to image single molecules associated with lipid droplets with excellent specificity. This probe requires the subsequent action of light, a lipophilic environment and a competent nucleophile to produce a fluorescent product. The combination of these requirements results in a probe that can be used to image the boundary of lipid droplets in three dimensions with resolutions beyond the limit of diffraction. Moreover, this probe enables single-molecule tracking of lipids within and between droplets in living cells.</div> | Adam Eördögh; Carolina Paganini; Dorothea Pinotsi; Paolo Arosio; Pablo Rivera-Fuentes | Biophysics; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74464469df4c848f43307/original/a-molecular-logic-gate-enables-super-resolved-imaging-of-intracellular-lipid-droplets.pdf |
670ff240cec5d6c14259736b | 10.26434/chemrxiv-2024-sslzp-v3 | Equilibrium and Non-equilibrium Ensemble Methods for Accurate, Precise and Reproducible Absolute Binding Free Energy Calculations | Free energy calculations for protein-ligand complexes have become widespread in recent years owing to several conceptual, methodological and technological advances. Central among these is the use of ensemble methods which permits accurate, precise and reproducible predictions and are necessary for uncertainty quantification. Absolute binding free energies (ABFEs) are challenging to predict using alchemical methods and their routine application in drug discovery has remained out of reach until now. Here, we apply ensemble alchemical ABFE methods to a large dataset comprising 219 ligand-protein complexes and obtain statistically robust results with high accuracy (< 1 kcal/mol). We compare equilibrium and non-equilibrium methods for ABFE predictions at large scale and provide a systematic critical assessment of each method. The equilibrium method is more accurate, precise, faster, computationally more cost-effective and requires a much simpler protocol, making it preferable for large scale and blind applications. We find that the calculated free energy distributions are non-normal and discuss the consequences. We recommend a definitive protocol to perform ABFE calculations optimally. Using this protocol, it is possible to perform thousands of ABFE calculations within a few hours on modern exascale machines. | Agastya Prakash Bhati; Shunzhou Wan; Peter V. Coveney | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2024-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670ff240cec5d6c14259736b/original/equilibrium-and-non-equilibrium-ensemble-methods-for-accurate-precise-and-reproducible-absolute-binding-free-energy-calculations.pdf |
63d42e751125960c4f7cc083 | 10.26434/chemrxiv-2023-n4qvm | Secondary Organic Aerosol from Biomass Burning Phenolics Could Increase Brown Carbon Lifetimes, Seed Ice Clouds, and Transport Pollutants | Biomass burning events emit large amounts of phenolic compounds, which are oxidized in the atmosphere and form secondary organic aerosol (SOA). Using the poke-flow technique, we measured room-temperature and relative humidity (RH)-dependent viscosities of SOA generated by the oxidation of three biomass burning phenolic compounds: catechol, guaiacol, and syringol. All systems had viscosity < 3 × 10³ Pa s at RH ⪆ 40% and > 2 × 10⁸ Pa s at RH ⪅ 3%. At RH values of 0-10%, the viscosities of these SOA were at least 2 orders of magnitude higher than the viscosity of primary organic aerosol (POA) from biomass burning. These results suggest that mixing biomass burning SOA and POA may extend the lifetime of the brown carbon in the atmosphere. Based on an extrapolation of our results to tropospheric temperature and RH values, phenolic SOA is in a glassy state (𝜂 > 10¹² Pa s) above ∼6 km in the troposphere, potentially acting as heterogeneous ice nuclei in clouds, thereby influencing climate. Furthermore, the mixing time of organic molecules in a 200 nm phenolic SOA particle exceeds 1 h above 3 km in the troposphere, which has implications for the long-range transport of pollutants. | Kristian J. Kiland; Fabian Mahrt; Long Peng; Sepehr Nikkho; Julia Zaks; Giuseppe V. Crescenzo; Allan K. Bertram | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry | CC BY 4.0 | CHEMRXIV | 2023-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d42e751125960c4f7cc083/original/secondary-organic-aerosol-from-biomass-burning-phenolics-could-increase-brown-carbon-lifetimes-seed-ice-clouds-and-transport-pollutants.pdf |
60c7481f702a9bf50518af0f | 10.26434/chemrxiv.11858010.v1 | A New Benchmark Set for Excitation Energy of Charge Transfer States: Systematic Investigation of Coupled-Cluster Type Methods | There are numerous publications on benchmarking quantum chemistry methods for excited states. These studies rarely include Charge Transfer (CT) states although many interesting phenomena in e.g. biochemistry and material physics involve transfer of electron between fragments of the system. Therefore, it is timely to test the accuracy of quantum chemical methods for CT states, as well. In this study we first suggest a set benchmark systems consisting of dimers having low-energy CT states. On this set, the excitation energy has been calculated with coupled cluster methods including triple excitations (CC3, CCSDT-3, CCSD(T)(a)* ), as well as with methods including full or approximate doubles (CCSD, STEOM-CCSD, CC2, ADC(2), EOM-CCSD(2)). The results show that the popular CC2 and ADC(2) methods are much more inaccurate for CT states than for valence states. On the other hand, CCSD seems to have similar systematic overestimation of the excitation energies for both valence and CT states. Concerning triples methods, the new CCSD(T)(a)* method including non-iterative triple excitations preforms very well for all type of states, delivering essentially CCSDT quality results.<br /> | Balázs Kozma; Attila Tajti; Baptiste Demoulin; Róbert Izsák; Marcel Nooijen; Péter Szalay | Physical and Chemical Properties; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7481f702a9bf50518af0f/original/a-new-benchmark-set-for-excitation-energy-of-charge-transfer-states-systematic-investigation-of-coupled-cluster-type-methods.pdf |
611607d6424ea3b36e88d306 | 10.26434/chemrxiv-2021-1drg9 | Host-Guest Interactions in C2H2/CO2 Discriminative Covalent Organic Framework Probed by Solid-State NMR | Covalent organic frameworks (COF) are promising porous materials for energy-efficient gas separation. However, understanding of the interaction between the host framework and the guest gas molecules, which is crucial for the development of the COF adsorbents, remains insufficient. Here, we look into the host-guest interactions between C2H2/CO2 molecules and a propyl sodium sulfonate group functionalized COF. Gas sorption studies indicate that the synthesized COF, termed Py-Na COF, exhibits C2H2/CO2 discriminative adsorption at ambient temperature. The underlying discriminative mechanism is studied by in situ 23Na solid-state NMR combined with molecular dynamics (MD) and density functional theory (DFT) calculations. The interactions between the C2H2/CO2 molecules and the host sodium ion play an essential role in C2H2/CO2 discrimination in Py-Na COF. | Weiming Jiang; Ping Wang; Ken-ichi Otake; Susumu Kitagawa; Yasuto Noda; Kazuyuki Takeda; Kiyonori Takegoshi | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611607d6424ea3b36e88d306/original/host-guest-interactions-in-c2h2-co2-discriminative-covalent-organic-framework-probed-by-solid-state-nmr.pdf |
61b0e306689c874c47daa008 | 10.26434/chemrxiv-2021-668nw | Technical and economic performance of the dithionite-assisted organosolv fractionation of lignocellulosic biomass | The development of biomass pretreatment approaches that, next to (hemi)cellulose valorization, aim at the conversion of lignin to chemicals is essential for the long-term success of a biorefinery. Herein, we discuss a dithionite-assisted organosolv fractionation (DAOF) of lignocellulose in n-butanol and water to produce cellulosic pulp and mono-/oligo-aromatics. The present study frames the technicalities of this biorefinery process and relates them to the features of the obtained product streams. Via the extensive characterization of the solid pulp (by acid hydrolysis-HPLC, ATR-FTIR, XRD, SEM and enzymatic hydrolysis-HPLC), of lignin derivatives (by GPC, GC-MS/FID, 1H-13C HSQC NMR, and ICP-AES) and of carbohydrate derivatives (by HPLC) we comprehensively identify and quantify the different products of interest. These results were used for inspecting the economic feasibility of DAOF. The adoption of a dithionite loading of 16.7% w/wbiomass and of an equivolumetric mixture of n-butanol and water, which led to a high yield of monophenolics (~20%, based on acid insoluble lignin, for the treatment of birch sawdust), was identified as the most profitable process configuration. Furthermore, the treatment of various lignocellulosic feedstocks was explored, which showed that DAOF is particularly effective for processing hardwood and herbaceous biomass. Overall, this study provides a comprehensive view of the development of an effective dithionite-assisted organosolv fractionation method for the sustainable upgrading of lignocellulosic biomass. | Filippo Brienza; Korneel Van Aelst; François Devred; Delphine Magnin; Maxim Tschulkow; Philippe Nimmegeers; Steven Van Passel; Bert F. Sels; Patrick Gerin; Damien Debecker; Iwona Cybulska | Chemical Engineering and Industrial Chemistry; Natural Resource Recovery; Reaction Engineering | CC BY NC 4.0 | CHEMRXIV | 2021-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b0e306689c874c47daa008/original/technical-and-economic-performance-of-the-dithionite-assisted-organosolv-fractionation-of-lignocellulosic-biomass.pdf |
673339bef9980725cff0eabe | 10.26434/chemrxiv-2024-wtrg5 | Photodissociation Dynamics of Indole using Multi-Configuration Time-dependent Hartree Method | Indole, being a biologically relevant and abundant chromophore, is a prime molecule of interest both in experimental and computational research. In previous works, the nature of the dissociative states for indole and indole derivatives were predicted. In this work, the N-H photodissociation dynamics of indole have been studied using nonadiabatic quantum dynamics. First, the important vibrational modes responsible for the photodissociation were detected using vibrational analysis. Potential energy cuts (PECs) along important vibrational modes have been calculated using the complete active space self-consistent field (CASPT2) method with (10,9) active space. The multi-mode multi-state model vibronic Hamiltonian is constructed by the parameters obtained from the fitting of ab initio PECs, including Morse and harmonic functions, and vibronic couplings. Nonadiabatic quantum dynamics is performed using the multi-configuration time-dependent Hartree (MCTDH) method, considering four electronic states and four vibrational modes. N-H stretching mode, Q42 turns out to be the most important of all modes, showing an anharmonic, dissociative 𝛑-𝛔* state at the third excited state. The out-of-plane C-N-H bending i.e. mode Q3 is found to facilitate the dissociation process. Additionally, effects of inclusion of Q8 and Q17, which are mixed motion modes with contribution from N-H displacement, were also assessed. Two timescales obtained from the population dynamics, 37 fs and 383 fs, are attributed to internal conversion from the second excited La state to the 𝛑-𝛔* states and photodissociation at the 𝛑-𝛔*, respectively, and are in good agreement with timescales obtained from femtosecond time-resolved ionization experiments. After 500 fs of dynamic propagation, around 55% reaction probability for N-H fission in indole is recorded. This study of photofission of indole is crucial for understanding photodynamics of similar large molecules with high accuracy. | Soumyadip Ray; Sudip Sasmal; Padmabati Mondal | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673339bef9980725cff0eabe/original/photodissociation-dynamics-of-indole-using-multi-configuration-time-dependent-hartree-method.pdf |
654b7fdcdbd7c8b54bd8142b | 10.26434/chemrxiv-2023-18zk5-v3 | Amorphous aggregates with a very wide size distribution play a central role in crystal nucleation | There is mounting evidence that crystal nucleation from supersaturated solution involves the formation and reorganization of prenucleation clusters, contradicting classical nucleation theory. Here, a range of amino acids and peptides is investigated using light scattering, mass spectrometry, and in situ terahertz Raman spectroscopy, showing that the presence of amorphous aggregates is a general phenomenon in supersaturated solutions. Significantly, these aggregates are found on a vast range of length scales from dimers to 30-mers to the nanometer and even micrometer scale, suggesting a continuous distribution throughout this range. Larger amorphous aggregates are sites of spontaneous crystal nucleation and act as intermediates for laser-induced crystal nucleation. These results are shown to be consistent with a nonclassical nucleation model in which barrierless (homogeneous) nucleation of amorphous aggregates is followed by the nucleation of crystals from solute-enriched aggregates. This provides a novel perspective on crystal nucleation. | Zhiyu Liao; Ankita Das; Christina Glen Robb; Rebecca Beveridge; Klaas Wynne | Physical Chemistry; Physical and Chemical Processes; Spectroscopy (Physical Chem.); Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654b7fdcdbd7c8b54bd8142b/original/amorphous-aggregates-with-a-very-wide-size-distribution-play-a-central-role-in-crystal-nucleation.pdf |
60c74ad9bdbb89d921a39451 | 10.26434/chemrxiv.11950491.v3 | Restricted-Variance Molecular Geometry Optimization Based on Gradient-Enhanced Kriging | Machine learning techniques, specifically gradient-enhanced Kriging (GEK), have been implemented for molecular geometry optimization. GEK-based optimization has many advantages compared to conventional - step-restricted second-order truncated expansion - molecular optimization methods. In particular, the surrogate model given by GEK can have multiple stationary points, will smoothly converge to the exact model as the number of sample points increases, and contains an explicit expression for the expected error of the model function at an arbitrary point. Machine learning is, however, associated with abundance of data, contrary to the situation desired for efficient geometry optimizations. In the paper we demonstrate how the GEK procedure can be utilized in a fashion such that in the presence of few data points, the surrogate surface will in a robust way guide the optimization to a minimum of a potential energy surface. In this respect the GEK procedure will be used to mimic the behavior of a conventional second-order scheme, but retaining the flexibility of the superior machine learning approach. Moreover, the expected error will be used in the optimization to facilitate restricted-variance optimizations (RVO). A procedure which relates the eigenvalues of the approximate guessed Hessian with the individual characteristic lengths, used in the GEK model, reduces the number of empirical parameters to optimize to two - the value of the trend function and the maximum allowed variance. These parameters are determined using the extended Baker (e-Baker) and part of the Baker transition-state (Baker-TS) test suites as a training set. The so-created optimization procedure is tested using the e-Baker, the full Baker-TS, and the S22 test suites, at the density-functional-theory and second order Møller-Plesset levels of approximation. The results show that the new method is generally of similar or better performance than a state-of-the-art conventional method, even for cases where no significant improvement was expected. | Gerardo Raggi; Ignacio Fernández Galván; Christian L. Ritterhoff; Morgane Vacher; Roland Lindh | Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ad9bdbb89d921a39451/original/restricted-variance-molecular-geometry-optimization-based-on-gradient-enhanced-kriging.pdf |
61e85c70deeafa633d22b7de | 10.26434/chemrxiv-2021-fpqst-v3 | Measuring Attitude Towards Chemistry, Biology, and Math at a Hispanic-Serving Institution | This work describes the evaluation of the Attitude toward the Subject of Chemistry Inventory (ASCI), as well as two modifications (one for measuring attitude toward math and one for measuring attitude toward biology), for college students at a Hispanic Serving Institution. Instrument reliability was tested via multiple administrations of the instruments,and confirmatory factor analysis supported a two-factor structure similar to an existing model of a revised version of the ASCI for all three instruments. The similar factor structure of the three instruments, coupled with interviews with students, provide validity evidence for the instruments and support an interpretation that one of the subscales aligns with a cognitive aspect of attitude while the other subscale aligns with an affective aspect. The results of these instruments indicate that students have a more positive attitude towards biology than either chemistry or math, and more positive affective attitude than cognitive attitude for all three subjects, although student attitudes show little change with respect to biology, chemistry, or math during a typical semester. However, major perturbations, such as switching to remote instruction mid-semester, can lead to small but significant increases and decreases in attitude. | Jordan Chang; Erik Menke | Chemical Education; Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e85c70deeafa633d22b7de/original/measuring-attitude-towards-chemistry-biology-and-math-at-a-hispanic-serving-institution.pdf |
67dadd0d81d2151a0204a203 | 10.26434/chemrxiv-2025-hz7h1 | Polarization-induced breaching of liquid/liquid interface formed with water-in-salt electrolytes | The solvation properties of water-in-salt-electrolytes (WiSE) have been extensively studied by spectroscopic and computational means, and were shown to impart them with unique chemical and physical properties when compared to more classical superconcentrated aqueous solutions. More specifically, the formation of ionic aggregates in solutions containing large concentration of TFSI anions was shown to alter the water and anions reactivity at electrochemical interfaces, often improving the performance of aqueous rechargeable batteries. However, insights into the role of WiSE solvation structure on ion transfer at electrochemical interfaces are scarce. Herein, interfaces between two immiscible electrolytes (ITIES) are used to study the energetics for ion transfer between aqueous LiCl and LiTFSI solutions and dichloroethane. Combining electrochemical measurements at microinterfaces with metadynamics molecular dynamics (MD) simulations, the effect of solvation properties on the energy for transferring Li+ and Cl-/TFSI- ions across the liquid/liquid interface is studied. While increasing the LiCl concentration increases the amount of ion pairs, it only marginally impacts the ions transfer energy. Instead, using large LiTFSI concentrations at which ionic aggregates are formed, ion transfer across the liquid/liquid interface shows a unique behavior that departs from that observed for polarizable or non-polarizable interfaces. Ions do not freely cross the interface, with a transfer energy found ≈8-10 kcal/mol. However, upon polarization, ionic aggregates are found to breach the liquid/liquid interface, locally mixing both solutions. We believe that such finding calls for reevaluating our current understanding of ion transfer across chemical interfaces in superconcentrated electrolytes, including liquid/liquid interfaces used in membrane-less electrochemical systems. | Lihao Feng; Michael Goldstein; Yang Wang; Udayan Mohanty; Alexis Grimaud | Physical Chemistry; Energy; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dadd0d81d2151a0204a203/original/polarization-induced-breaching-of-liquid-liquid-interface-formed-with-water-in-salt-electrolytes.pdf |
60c746a1337d6c0302e271d8 | 10.26434/chemrxiv.10269653.v2 | Protein-Modification of Lysine with 2-(2-Styrylcyclopropyl)ethanal | <div>A new lysine‐reactive cyclopropropyl aldehyde for the covalent modification of proteins was developed. The reagent exploits a divinylcyclopropane‐cycloheptadiene rearrangement to render the initial condensation irreversible. A labelling study on eGFP demonstrated excellent chemoselectivity for the modification of amine‐nucleophiles with the possibility of subsequent modifications.</div> | Caroline Apel; Marc-André Kasper; Christian
E. Stieger; Christian P. R. Hackenberger; Mathias Christmann | Bioorganic Chemistry; Organic Synthesis and Reactions; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746a1337d6c0302e271d8/original/protein-modification-of-lysine-with-2-2-styrylcyclopropyl-ethanal.pdf |
6375ab44be365eca032252e6 | 10.26434/chemrxiv-2022-r9tmg-v2 | Cassini-oval description of atomic binding: a new method to evaluate atomic hardness | This paper reports that the binding process of two heteronuclear atoms can be described by Cassini oval in dynamic form, every molecular state corresponds to one of these graphs. the approach is based on a constraint rule between hardness and deformation of atomic particles, then the critical phenomena of
molecular deformation are discovered and the calculated potential energy at the critical point is consistent with the experimental dissociation energy of molecules, the new scale uses atomic hardness coefficient as a
dimensionless quantity, which accurately reproduces the molecular energies. | weicheng zeng | Theoretical and Computational Chemistry; Inorganic Chemistry; Bonding; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6375ab44be365eca032252e6/original/cassini-oval-description-of-atomic-binding-a-new-method-to-evaluate-atomic-hardness.pdf |
60c73d0e567dfe7a6cec35c4 | 10.26434/chemrxiv.5387833.v1 | Electron-phonon coupling and polaron mobility in hybrid perovskites from first-principles | Density functional theory electronic structures, maximally localized Wannier funcitons and linear response theory are used to compute the electron and hole mobility of both inorganic, Cs-containing, and hybrid, CH<sub>3</sub>NH<sub>3</sub>-containing, lead bromide perovskites. When only phonon scattering is considered we find hole mobilities at room temperature in the 40-180~cm<sup>2</sup>V<sup>-1</sup>s<sup>-1</sup> range, in good agreement with experimental data for highly-ordered crystals. The electron mobility is about an order of magnitude larger, because low-energy phonons are ineffective over the Pb 6<i>p</i> shell. Most importantly, our parameter-free approach, finds a <i>T</i><sup>-3/2</sup> power-law temperature dependence of the mobility, which is a strong indication of polaronic transport. Our work then offers an independent theoretical validation of the many hypotheses about the polaronic nature of the charge carriers in lead halide perovskites. | Carlo Motta; Stefano Sanvito | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2017-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0e567dfe7a6cec35c4/original/electron-phonon-coupling-and-polaron-mobility-in-hybrid-perovskites-from-first-principles.pdf |
60c751854c8919b01fad3f96 | 10.26434/chemrxiv.12670676.v2 | Reversibly Sampling Conformations and Binding Modes Using Molecular Darting | <div>Sampling multiple binding modes of a ligand in a single molecular dynamics simulation is difficult. A given ligand may have many internal degrees of freedom, along with many different ways it might orient itself a binding site or across several binding sites, all of which might be separated by large energy barriers. We have developed a novel Monte Carlo move called Molecular Darting (MolDarting) to reversibly sample between predefined binding modes of a ligand. Here, we couple this with nonequilibrium candidate Monte Carlo (NCMC) to improve acceptance of moves.</div><div>We apply this technique to a simple dipeptide system, a ligand binding to T4 Lysozyme L99A, and ligand binding to HIV integrase in order to test this new method. We observe significant increases in acceptance compared to uniformly sampling the internal, and rotational/translational degrees of freedom in these systems.</div> | Samuel C. Gill; David Mobley | Computational Chemistry and Modeling; Statistical Mechanics | CC BY 4.0 | CHEMRXIV | 2020-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751854c8919b01fad3f96/original/reversibly-sampling-conformations-and-binding-modes-using-molecular-darting.pdf |
62288a12c45c0b1e512b006a | 10.26434/chemrxiv-2022-gxt5n | Oxide-supported carbonates reveal a unique descriptor for catalytic performance in the oxidative coupling of methane (OCM) | The oxidative coupling of methane (OCM) is a promising reaction for direct conversion of methane to higher hydrocarbons. The reaction can be performed over oxide-based catalysts with very diverse elemental composition. Yet, despite decades of research, no general common structure-activity relationship has been deduced. Our recent statistical meta-analysis across a wide range of catalyst compositions reported in the literature suggested that only the catalysts combining thermodynamically stable (under reaction conditions) carbonate and thermally stable oxide support exhibit good catalytic performance. Guided by these findings we explore now experimentally correlations between descriptors for structure, stability and decomposition behavior of supported metal carbonates vs. the materials’ respective performance in OCM catalysis. In this study, carbonates of Rb, Cs and Mg were supported on oxides of Sm, Y, Gd, Ce, Sr and Ba, tested in OCM and studied by IR spectroscopy and thermal analysis. From the evaluation of six proposed property-descriptors we derive a statistically robust volcano-type correlation between the onset temperature of carbonate decomposition and the C2 yield, indicating the importance of CO2 adsorption and surface carbonates in selective methane conversion. Moreover, we discuss mechanisms that can account for the observed property-performance correlation across a wide range of OCM catalysts. Carbonate species are suggested to block highly reactive sites during OCM catalysis, which reduces overoxidation and enables the formation of C2 products. | Huan Wang; Roman Schmack; Sergey Sokolov; Evgenii Kondratenko; Aliaksei Mazheika; Ralph Kraehnert | Physical Chemistry; Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62288a12c45c0b1e512b006a/original/oxide-supported-carbonates-reveal-a-unique-descriptor-for-catalytic-performance-in-the-oxidative-coupling-of-methane-ocm.pdf |
659c604966c138172900a95e | 10.26434/chemrxiv-2024-qm8jp | Enantioselective Sulfonimidamide Acylation via a Cinchona Alkaloid-Catalyzed Desymmetrization: Scope, Data Science, and Mechanistic Investigation | Methods to access chiral sulfur (VI) pharmacophores are of interest in medicinal and synthetic chemistry. We report the desymmetrization of unprotected sulfonimidamides via asymmetric acylation with a cinchona-phosphinate catalyst. The desired products are formed in excellent yield and enantioselectivity with no observed bis-acylation. A data science-driven approach to substrate scope evaluation was coupled to high throughput experimentation (HTE) to facilitate statistical modeling in order to inform mechanistic studies. Reaction kinetics, catalyst structural studies, and density functional theory (DFT) transition state analysis elucidated the turnover-limiting step to be the collapse of the tetrahedral intermediate and provided key insights into the catalyst-substrate structure-activity relationships responsible for the origin of enantioselectivity. This study offers a reliable method for accessing enantioenriched sulfonimidamides to propel their application as pharmacophores and serves as an example of the mechanistic insight that can be gleaned from integrating data science and traditional physical organic techniques. | Brittany Haas; Ngiap-Kie Lim; Janis Jermaks; Eden Gaster; Melody Guo; Thomas Malig; Jacob Werth; Haiming Zhang; F. Dean Toste; Francis Gosselin; Scott Miller; Matthew Sigman | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organocatalysis | CC BY 4.0 | CHEMRXIV | 2024-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659c604966c138172900a95e/original/enantioselective-sulfonimidamide-acylation-via-a-cinchona-alkaloid-catalyzed-desymmetrization-scope-data-science-and-mechanistic-investigation.pdf |
6163e065cada1f3518d240a2 | 10.26434/chemrxiv-2021-zcdzn | Highly Selective Anion Recognition, Extraction and Deep Removal Using a Superphane | Highly selective anion recognition and extraction are critical and challenging to deep removal of pollutants from the environment and effective recovery of valuable chemicals from low–content (at sub–ppm or ppb level) sources. Herein, we detail the gram–scale synthesis of a superphane 2, a new supramolecular host that was found capable of encapsulating ReO4– with high selectivity, as suggested by the single–crystal structures, NMR spectroscopy and theoretical calculations. Under solid–liquid extraction condidtions, 2 proved able to extract perrhenate from the solid mixture containing trace ReO4– (as low as 200 ppb) with near 100% selectivity over other 7 competing anions. Under liquid–liquid extraction conditions, using 2 as the supramolecular extractant, over 99.99% of ReO4– could be separated from the complex simulated aqueous waste streams containing ppm–level perrhenate and large excess of competing ions. Notably, after extraction, 2 could be recycled and reused by simple treatment with NaHCO3. This study opens up the door to development of superphane–based advanced materials for deep elimination of pollutants from the envirenment and purification of chemicals of interest with high efficiency and selectivity. | Wei Zhou; Aimin Li; Qing He | Organic Chemistry; Supramolecular Chemistry (Org.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6163e065cada1f3518d240a2/original/highly-selective-anion-recognition-extraction-and-deep-removal-using-a-superphane.pdf |
6422cf2691074bccd06d1d38 | 10.26434/chemrxiv-2023-5v9s0 | Multimodal and Dynamic Cross-Linking of Modular Thiolated Alginate-Based Bioinks | Engineered extracellular matrix-mimicking hydrogels can facilitate 3D cell culture and fabrication of tissue-like constructs and biologically relevant disease models. Processing of cell-laden hydrogels using additive manufacturing techniques further allows for the development of tissue-mimetic structures with higher spatial complexity. Whereas a wide range of printable hydrogels is available, they tend to lack biological functionality and cell compatibility. Here we show an enzymatically mediated thiol-based cross-linking strategy for the design of modular and cytocompatible hydrogel-based bioinks for 3D bioprinting of dynamic multi-material architectures. Alginate is functionalized with cysteines modified with an enzyme-labile thiol protection group. Deprotection using penicillin G acylase (PGA) generates free thiols on-demand, enabling hydrogel cross-linking using thiol-reactive cross-linkers and intramolecular disulfides while avoiding undesired and uncontrolled thiol oxidation. Remaining free thiols can be used for post-printing hydrogel functionalization and lamination of multilayer structures. Moreover, the addition of PGA to a thermo-reversible hydrogel support bath enables the bioprinting of cell-laden 3D structures with high cell viability and excellent shape fidelity. The possibilities to enzymatically generate free thiols during bioprinting facilitate cross-linking and tuning of bioink properties using cytocompatible chemistries and allow for the printing of complex and dynamic cell-laden structures. | Sajjad Naeimipour; Fatemeh Rasti Boroojeni; Philip Lifwergren; Robert Selegård; Daniel Aili | Biological and Medicinal Chemistry; Materials Science; Biocompatible Materials; Biological Materials; Bioengineering and Biotechnology; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6422cf2691074bccd06d1d38/original/multimodal-and-dynamic-cross-linking-of-modular-thiolated-alginate-based-bioinks.pdf |
666a97a112188379d8fe6fb8 | 10.26434/chemrxiv-2024-68h4g-v2 | Photoresponsive block copolymer nanostructures through implementation of arylazopyrazoles | Responsive nanomaterials that can undergo reversible changes in morphology are interesting for the development of functional materials that interact with and respond to their environment. Amphiphilic block copolymers are well known for their ability to create a wide range of supramolecular nanostructures in solution. Arylazopyrazoles (AAPs) are versatile molecular photoswitches, which change their configuration and hydrophobicity via irradiation with UV light (365 nm, Z isomer, less hydrophobic) and green light (520 nm, E isomer, more hydrophobic). In this work, photoswitchable block copolymers containing arylazopyrazole tetraethylene glycol methacrylate (AAPMA) and oligo(ethylene glycol) methacrylate (OEGMA) forming amphiphilic POEGMA b PAAPMA with varying block lengths are prepared by RAFT polymerization. The photochemical properties of AAP persist in the polymers. Due to their amphiphilic structure, the polymers self-assemble into supramolecular morphologies in water. Remarkably, photoisomerization results in a reversible change in the self-assembly behavior. Specifically, spherical and cylindrical micelles are observed for POEGMA33-b-PAAPMA47 when illuminated under green or UV light during assembly. Furthermore, the morphology of assembled structures can be reversibly switched by subsequent irradiation with UV and green light. | Katharina Ziegler; Lisa Schlichter; Yorick Post; André Gröschel; Bart Jan Ravoo | Polymer Science | CC BY NC 4.0 | CHEMRXIV | 2024-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666a97a112188379d8fe6fb8/original/photoresponsive-block-copolymer-nanostructures-through-implementation-of-arylazopyrazoles.pdf |
60c74a24bdbb89f715a3930a | 10.26434/chemrxiv.12159114.v1 | Modulation of Charge Transfer by N-Alkylation to Control Photoluminescence Energy and Quantum Yield | Charge transfer in organic fluorophores is a fundamental photophysical process that can be either beneficial, e.g., facilitating thermally activated delayed fluorescence, or detrimetnal, e.g., mediating emission quenching. <i>N</i>-Alkylation is shown to provide straightforward synthetic control of the charge transfer, emission energy and quantum yield of amine chromophores. We demonstrate this concept using quinine as a model. <i>N</i>-Alkylation causes changes in its emission that mirror those caused by changes in pH (i.e., protonation). Unlike protonation, however, alkylation of quinine’s two N sites is performed in a stepwise manner to give kinetically stable species. This kinetic stability allows us to isolate and characterize an <i>N</i>-alkylated analog of an ‘unnatural’ protonation state that is quaternized selectively at the less basic site, which is inaccessible using acid. These materials expose (i) the through-space charge-transfer excited state of quinine and (ii) the associated loss pathway, while (iii) developing a simple salt that outperforms quinine sulfate as a quantum yield standard. This <i>N</i>-alkylation approach can be applied broadly in the discovery of emissive materials by tuning charge-transfer states. | Andrew T. Turley; Andrew Danos; Antonio Prlj; Andrew
P. Monkman; Basile F.E. Curchod; Paul R. McGonigal; Marc Etherington | Physical Organic Chemistry; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a24bdbb89f715a3930a/original/modulation-of-charge-transfer-by-n-alkylation-to-control-photoluminescence-energy-and-quantum-yield.pdf |
60c73d92bdbb897f59a37c9d | 10.26434/chemrxiv.5907394.v1 | Characterization of Protease-Activated Receptor (PAR) Ligands: Parmodulins Are Reversible Allosteric Inhibitors of PAR1-Driven Calcium Mobilization in Endothelial Cells | We report a detailed protocol for an intracellular calcium mobilization assay with adherent endothelial cells in multiwell plates that was used to study a number of different PAR1 and PAR2 ligands, including an alkynylated version of the PAR1 antagonist RWJ-58259 that is suitable for the preparation of tagged or conjugate compounds. Using the cell line EA.hy926, it was necessary to perform media exchanges with automated liquid handling equipment in order to obtain optimal and reproducible antagonist concentration-response curves. The assay was used to confirm that vorapaxar acts as an irreversible antagonist of PAR1 in endothelium, and parmodulin 2 (ML161) and the related parmodulin RR-90 were found to inhibit PAR1 reversibly, in a manner consistent with negative allosteric modulation. Detailed synthetic protocols are also provided for several known and novel PAR ligands.<br /> | Disha M. Gandhi; Mark W. Majewski; Ricardo Rosas; Kaitlin Kentala; Trevor J. Foster; Eric Greve; Chris Dockendorff | Bioorganic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2018-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d92bdbb897f59a37c9d/original/characterization-of-protease-activated-receptor-par-ligands-parmodulins-are-reversible-allosteric-inhibitors-of-par1-driven-calcium-mobilization-in-endothelial-cells.pdf |
64659661f2112b41e9baeff7 | 10.26434/chemrxiv-2023-7m9bn | Data Base similarity (DBsimilarity) of Natural Products to aid compound identification on MS and NMR pipelines, similarity networking and more | Introduction: This paper proposes DBsimilarity to organize structural databases into Similarity Networks to better understand the rich information available. Method: DBsimilarity was written in Jupyter Notebooks to be easy to follow and values readability. It converts SDF files into CSV files, adds chemoinformatics data, constructs a MZMine custom database file and a NMRfilter candidate list of compounds for rapid dereplication of MS and 2D NMR data, calculates similarities between compounds, and constructs CSV files to be converted to Similarity Networks using Cytoscape. Results: The Lotus database was used as source for Ginkgo biloba compounds and DBsimilarity was used to create Similarity Networks that includes NPClassifier classification to indicate biosynthesis pathways. Following, a database of validated antibiotics natural products was combined with the G. biloba database to indicate promising compounds. The presence of 11 compounds in both datasets points to a possible antibiotic property of G. biloba, and 122 other compounds similar to those known antibiotics is found. Next, DBsimilarity was used to filter the NPAtlas database (selecting only those with MIBIG reference) to identify potential antibacterial compounds using the ChEMBL database as reference. It was possible to promptly identify 5 compounds found in both databases, and 167 other worth investigating compounds similar to those known antibiotics. Conclusion: Chemical and biological properties are determined by molecular structures. DBsimilarity enables the creation of interactive Similarity Networks using Cytoscape. It is also in line with recent review that highlights significant sources of errors in compound identification: poor biological plausibility and unrealistic chromatographic behaviors. | Ricardo Moreira Borges; Gabriela de Assis Ferreira; Mariana Martins Campos; Andrew Magno Teixeira; Aline Camargo Jesus de Souza Wuillda; Fernanda das Neves Costa; Fernanda Oliveira Chagas | Organic Chemistry; Analytical Chemistry; Natural Products; Analytical Chemistry - General; Chemoinformatics | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64659661f2112b41e9baeff7/original/data-base-similarity-d-bsimilarity-of-natural-products-to-aid-compound-identification-on-ms-and-nmr-pipelines-similarity-networking-and-more.pdf |
669535b201103d79c513aabf | 10.26434/chemrxiv-2024-8nj9k | Molecular modeling of luciferyl adenylate deprotonation in the active site of Photinus pyralis luciferase | Firefly bioluminescence is a product of chemical reactions that involve luciferin chromophore oxidation in the active site of luciferase proteins. We perform a series of classical molecular dynamic simulations and combined quantum and molecular mechanics (QM/MM) calculations to expose the molecular mechanism of C4 carbon atom deprotonation in luciferyl adenylate molecule. QM/MM calculations confirm that ND-protonated His245 residue is a suitable proton acceptor in the wild type Photinus pyralis luciferase. Classical molecular dynamic simulations reveal oxygen binding cavities inside the protein including the one located close to the C4 atom of luciferin. In mutant forms that lack direct interactions with the His245 side chain, a proton wire comprising water molecules stimulates either protonation of the phosphate group of the luciferyl adenylate forming an unstable intermediate or keto-enol tautomerization of luciferin. The comparison of the ionization potentials of molecular systems with the ‘deprotonated’ C4 carbon atom revealed that the ionization energy for the enol tautomeric form is close to the system with the His245 proton acceptor. Thus, existence of the keto-enol tautomerization channel might explain bioluminescence in case of absence of the amino acid proton acceptor. | Igor Polyakov ; Maria Khrenova | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Biophysics; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669535b201103d79c513aabf/original/molecular-modeling-of-luciferyl-adenylate-deprotonation-in-the-active-site-of-photinus-pyralis-luciferase.pdf |
61ce54fe7284d0be45fe00f0 | 10.26434/chemrxiv-2021-w09lc | Synthesis of a Möbius carbon nanobelt | New technologies for the creation of topological carbon nanostructures have significantly advanced synthetic organic chemistry and materials science. While simple molecular nanocarbons with a belt topology have been constructed recently, analogous carbon nanobelts with a twist, i.e., Möbius carbon nanobelts (MCNBs), have not yet been synthesized due to their high intrinsic strain. Herein, we report the synthesis, isolation, and characterization of a MCNB. Calculations of strain energies suggested that large MCNBs are synthetically accessible. Designing a macrocyclic precursor with an odd number of repeat units led to a successful rational synthetic route via Z-selective Wittig reactions and nickel-mediated intramolecular homocoupling reactions, which yielded (25,25)MCNB over 14 steps. NMR and theoretical calculations revealed that the twist moiety of the Möbius band moves quickly around the MCNB molecule in solution. The topological chirality originating from the Möbius structure was confirmed experimentally using chiral HPLC separation and CD spectroscopy. | Kenichiro Itami; Yasutomo Segawa; Tsugunori Watanabe; Kotono Yamanoue; Motonobu Kuwayama; Kosuke Watanabe; Jenny Pirillo; Yuh Hijikata | Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2021-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ce54fe7284d0be45fe00f0/original/synthesis-of-a-mobius-carbon-nanobelt.pdf |
60c73cc9f96a008f11285ca2 | 10.26434/chemrxiv.14737362.v1 | HMPA-Free Generation of Trialkylsilyl Lithium Reagents and Its Application to Synthesis of Silylboronic Esters | Trialkylsilyl lithium species have turned out to be facilely generated by treating hexaalkyl disilanes with methyl lithium in the presence of tris(<i>N,N</i>-tetramethylene)phosphoric triamide (TPPA) as an activator, which can be trapped by boron electrophiles to afford silylboronic esters including long-awaited Me<sub>3</sub>Si–B(pin). | Shintaro Kamio; Taiki Imagawa; Masaaki Nakamoto; Martin Oestreich; Hiroto Yoshida | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc9f96a008f11285ca2/original/hmpa-free-generation-of-trialkylsilyl-lithium-reagents-and-its-application-to-synthesis-of-silylboronic-esters.pdf |
666c8eba5101a2ffa89b5e67 | 10.26434/chemrxiv-2024-9bmfj-v3 | Large Language Models for Inorganic Synthesis Predictions | We evaluate the effectiveness of pre-trained and fine-tuned large language models (LLMs) for predicting the synthesizability of inorganic compounds and the selection of precursors needed to perform inorganic synthesis. The predictions of fine-tuned LLMs are comparable to—and sometimes better than—recent bespoke machine learning models for these tasks, but require only minimal user expertise, cost, and time to develop. Therefore, this strategy can serve both as an effective and strong baseline for future machine learning studies of various chemical applications and as a practical tool for experimental chemists. | Seongmin Kim; Yousung Jung; Joshua Schrier | Theoretical and Computational Chemistry; Inorganic Chemistry; Reaction (Inorg.); Solid State Chemistry; Artificial Intelligence; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666c8eba5101a2ffa89b5e67/original/large-language-models-for-inorganic-synthesis-predictions.pdf |
60c742d1842e652531db2115 | 10.26434/chemrxiv.8786048.v1 | In Vivo Biocompatibility and Immunogenicity of Metal-Phenolic Gelation | In vivo forming hydrogels are of interest for diverse biomedical applications due to their ease-of-use and minimal invasiveness and therefore high translational potential. Supramolecular hydrogels that can be assembled using metal–phenolic coordination of naturally occurring polyphenols and group IV metal ions (e.g. Ti<sup>IV </sup>or Zr<sup>IV</sup>) provide a versatile and robust platform for engineering such materials. However, the in situ formation and in vivo response to this new class of materials has not yet been reported. Here, we demonstrate that metal–phenolic supramolecular gelation occurs successfully in vivo and we investigate the host response to the material over 14 weeks. The Ti<sup>IV</sup>–tannic acid materials form stable gels that are well-tolerated following subcutaneous injection. Histology reveals a mild foreign body reaction, and titanium biodistribution studies show low accumulation in distal tissues. Compared to poloxamer-based hydrogels (commonly used for in vivo gelation), Ti<sup>IV</sup>–tannic acid materials show substantially improved in vitro drug loading and release profile for the corticosteroid dexamethasone (from <1 day to >10 days). These results provide essential in vivo characterization for this new class of metal–phenolic hydrogels, and highlight their potential suitability for biomedical applications in areas such as drug delivery and regenerative medicine.<br /> | Mattias Björnmalm; Lok Man Wong; Jonathan Wojciechowski; Jelle Penders; Conor Horgan; Marsilea Booth; Nicholas Martin; Susanne Sattler; Molly Stevens | Biocompatible Materials; Biological Materials; Drug delivery systems; Nanostructured Materials - Nanoscience; Bioengineering and Biotechnology | CC BY 4.0 | CHEMRXIV | 2019-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742d1842e652531db2115/original/in-vivo-biocompatibility-and-immunogenicity-of-metal-phenolic-gelation.pdf |
65e98407e9ebbb4db92609b2 | 10.26434/chemrxiv-2024-v2g59 | Exact-factorization study of the photochemistry of phenol | We present an analysis of the performance of the coupled-trajectory schemes for nonadiabatic dynamics derived from the exact factorization of the electron-nuclear wavefunction and implemented in the G-CTMQC code. These algorithms can be seen as variations of the standard Ehrenfest method and Tully surface hopping, which are based, however, on independent trajectories. The reported analysis aims to compare the coupled-trajectory and the independent-trajectory schemes, and to benchmark the numerical results against exact quantum waavepacket dynamics. To this end, we employ an analyitical molecular model with two nuclear degrees of freedom and three electronic states that allows us to describe the photo-induced hydrogen dissociation in phenol. The analysis focuses on different electronic and nuclear properties calculated along the nonadiabatic dynamics of phenol. | Audrey Pollien; Evaristo Villaseco Arribas; David Lauvergnat; Federica Agostini | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e98407e9ebbb4db92609b2/original/exact-factorization-study-of-the-photochemistry-of-phenol.pdf |
6294aa80d3c73a4e7dd58485 | 10.26434/chemrxiv-2022-2prdx | A Mean-Field Model for Oxygen Reduction Electrocatalytic Activity on High-Entropy Alloys | High-entropy alloys (HEAs) represent near-equimolar points in the middle of a vast composition space of multi-metallic catalysts. Successful modeling of the catalytic activity of these complex materials allows to search this composition space for optimal catalysts. Previous models of HEA catalytic activity have been based on local and intricate descriptions of the atomic environment on the catalyst surface to predict accurate adsorption energies. These are subsequently used to model the catalytic activity. In this study, we show that by approximating the ligand effect of the surrounding atoms around an adsorption site with a mean-field perturbation corresponding to equimolar AgIrPdPtRu, the same trend in the predictions of the oxygen reduction reaction catalytic activities are obtained for a majority of the quinary Ag-Ir-Pd-Pt-Ru composition space. By comparing to models that consider the ligand effect locally, we show that the extent of such a mean-field approximation is valid up to and including equimolar ternary alloys, corresponding to 60.3 % of the quinary composition space. When extrapolating to make predictions far from near-equimolar compositions, such as for binary alloys, the mean field has been sufficiently perturbed to cause large discrepancies compared to the local models. Here, the intricate models thus prove more useful for discovering optimal catalysts. | Jack K. Pedersen; Christian M. Clausen; Lars Erik J. Skjegstad; Jan Rossmeisl | Theoretical and Computational Chemistry; Materials Science; Catalysis; Alloys; Computational Chemistry and Modeling; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6294aa80d3c73a4e7dd58485/original/a-mean-field-model-for-oxygen-reduction-electrocatalytic-activity-on-high-entropy-alloys.pdf |
60c741eb702a9b4a6218a35f | 10.26434/chemrxiv.8184395.v1 | Interplay of Direct and Indirect Charge Transfer Pathways in Donor-Bridge-Acceptor Systems | Charge transfer in donor-bridge-acceptor (DBA) structures typically takes place through the combination of donor-bridge and bridge-acceptor overlap integrals forming an effective, indirect electronic coupling between the donor (D) and acceptor (A) moieties. Here, we examine the effects of an additional direct DA electronic coupling on charge transfer processes in DBA systems with local interaction to thermal baths. First, using the exact Nakajima-Zwanzig master equation (NZME) for the reduced density matrix, we rigorously define probability currents as the coherent part of the NZME, thereby allowing us to quantify the contribution of the different electronic pathways (direct and indirect) to the charge transfer dynamics. Focusing on two minimal DBA systems of three sites (V and L models), and adopting well-developed methods, we find that the interplay between different transfer pathways can be assessed by the McConnell formula in the weak systembath coupling regime. We then demonstrate that the combination of indirect and direct donor-acceptor coupling either enhances or leads to a destructive quantum interference effect on charge transport processes, depending on the energy landscape of the DBA system.<br /> | Junjie Liu; Dvira Segal | Physical and Chemical Processes; Quantum Mechanics; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741eb702a9b4a6218a35f/original/interplay-of-direct-and-indirect-charge-transfer-pathways-in-donor-bridge-acceptor-systems.pdf |
64bb8f22ae3d1a7b0d246266 | 10.26434/chemrxiv-2023-hrsvj | Prediction of Binding Pose and Affinity of SARS-CoV-2 Main Protease and Repositioned Drugs by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations | COVID-19 remains a global pandemic, necessitating the urgent development of more effective therapeutics. By combining molecular docking, molecular dynamics (MD), and fragment molecular orbital (FMO) calculations, the binding structure and properties with Mpro were predicted for Nelfinavir (NLF), which was identified as a candidate compound through drug repositioning targeting the Main Protease (Mpro) produced by the causative virus, SARS-CoV-2. For the four docking poses selected by scoring using FMO energy, 100 structures each from the MD trajectory were sampled, and FMO calculations were performed and ranked based on binding energy. Besides the interaction between NLF and each Mpro residue, the desolvation effect of the pocket affected the ranking order. Furthermore, we identified several residues important in ligand recognition, including Glu47, Asp48, Glu166, Asp187, and Gln189, all of which interacted strongly with NLF. Asn142 was mentioned as a residue with hydrogen bonds or CH/π interaction with NLF; however, it was considered a transient interacting residue because of its unstable structure. Moreover, the tert-butyl group of NLF had no interaction with Mpro. Identifying weak interactions provides candidates for substituting ligand functional groups and important suggestions for drug discovery using drug repositioning. Our approach provides a new guideline for structure-based drug design starting from a candidate compound whose complex crystal structure has not been obtained. | Yuma Handa; Koji Okuwaki; Yusuke Kawashima; Ryo Hatada; Yuji Mochizuki; Yuto Komeiji; Shigenori Tanaka; Takayuki Furuishi; Etsuo Yonemochi; Teruki Honma; Kaori Fukuzawa | Physical Chemistry; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64bb8f22ae3d1a7b0d246266/original/prediction-of-binding-pose-and-affinity-of-sars-co-v-2-main-protease-and-repositioned-drugs-by-combining-docking-molecular-dynamics-and-fragment-molecular-orbital-calculations.pdf |
650c59f060c37f4f76332ea7 | 10.26434/chemrxiv-2023-lh7bq-v2 | Martini 3 Coarse-Grained Force Field for cholesterol | Cholesterol plays a crucial role in biomembranes by regulating various properties such as fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the Martini model, Martini 3, offers significant improvements in interaction balance, molecular packing, and the inclusion of new bead types and sizes. However, the release of the new model resulted in the need to re-parameterize many core molecules, including cholesterol. Here, we describe the development and validation of a Martini 3 cholesterol model, addressing issues related to its bonded setup, shape, volume and hydrophobicity. The proposed model mitigates some limitations of its Martini 2 predecessor while maintaining or improving overall behavior. | Luís Borges-Araújo; Ana Borges-Araújo; Tugba Ozturk; Daniel P. Ramirez-Echemendia; Balázs Fábián; Timothy S. Carpenter; Sebastian Thallmair; Jonathan Barnoud; Helgi I. Ingólfsson; Gerhard Hummer; D. Peter Tieleman; Siewert J. Marrink; Paulo C. T. Souza; Manuel N. Melo | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-09-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650c59f060c37f4f76332ea7/original/martini-3-coarse-grained-force-field-for-cholesterol.pdf |
6278afa7d555502f05935b4a | 10.26434/chemrxiv-2022-xt610 | Chemical catalyst/protein hybrid as artificial histone-modifying enzyme for epigenome manipulation | Chemical biology approaches that can manipulate the epigenome hold promise to elucidate the role of epigenetics in gene regulation and may have utility in translational research. However, there are few methods to artificially introduce epigenetic modifications in living cells without reliance on endogenous enzymes. Here, we develop a chemical catalyst/protein hybrid promoting regioselective histone acylation, comprised of the cell-permeable lysine-acylating chemical catalyst TMP-BAHA and the nucleosome-binding fusion protein LANA-inserted eDHFR (LieD). Molecular modelling and molecular dynamics simulations with an atomistic model suggested that the catalyst-binding pocket of LieD was close to H2B lysine-120 (H2BK120). Consistent with this, TMP-BAHA bound to LieD and efficiently promoted H2BK120 acetylation in cells, which inhibited both H2BK120 ubiquitination and H3K79 dimethylation, active marks of gene transcription. Furthermore, the system incorporated other natural and unnatural acylations at target lysines, enabling study of endogenous histones. Our results suggest that a chemical catalyst/protein hybrid, such as the TMP-BAHA/LieD system, can function as an artificial histone-modifying enzyme and thus expands the toolbox of chemical biology for epigenome manipulation. | Akiko Fujimura; Hisashi Ishida; Tamiko Nozaki; Yuto Azumaya; Tadashi Ishiguro; Tomoya Kujirai; Hitoshi Kurumizaka; Hidetoshi Kono; Kenzo Yamatsugu; Shigehiro Kawashima; Motomu Kanai | Biological and Medicinal Chemistry; Organic Chemistry; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6278afa7d555502f05935b4a/original/chemical-catalyst-protein-hybrid-as-artificial-histone-modifying-enzyme-for-epigenome-manipulation.pdf |
60c74b63842e656255db3146 | 10.26434/chemrxiv.12301457.v1 | Potential Non-Covalent SARS-CoV-2 3C-like Protease Inhibitors Designed Using Generative Deep Learning Approaches and Reviewed by Human Medicinal Chemist in Virtual Reality | <div>
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<p>One of the most important SARS-CoV-2 protein targets for therapeutics is the 3C-like protease
(main protease, Mpro). In our previous work1we used the first Mpro crystal structure to become
available, 6LU7. On February 4, 2020 Insilico Medicine released the first potential novel
protease inhibitors designed using a de novo,AI-driven generative chemistry approach. Nearly
100 X-ray structures of Mpro co-crystallized both with covalent and non-covalent ligands have
been published since then. Here we utilize the recently published 6W63 crystal structure of
Mpro complexed with a non-covalent inhibitor and combined two approaches used in our
previous study: ligand-based and crystal structure-based. We published 10 representative
structures for potential development with 3D representation in PDB format and welcome
medicinal chemists for broad discussion and generated output analysis. The molecules in SDF
format and PDB-models for generated protein-ligand complexes are available here and at
https://insilico.com/ncov-sprint/.Medicinal chemistry VR analysis was provided by Nanome team
and the video of VR session is available at https://bit.ly/ncov-vr.
</p>
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</div> | Alex Zhavoronkov; Bogdan Zagribelnyy; Alexander Zhebrak; Vladimir Aladinskiy; Victor Terentiev; Quentin Vanhaelen; Dmitry S. Bezrukov; Daniil Polykovskiy; Rim Shayakhmetov; Andrey Filimonov; Michael Bishop; Steve McCloskey; Edgardo Leija; Deborah Bright; Keita Funakawa; Yen-Chu Lin; Shih-Hsien Huang; Hsuan-Jen Liao; Alex Aliper; Yan Ivanenkov | Chemoinformatics | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b63842e656255db3146/original/potential-non-covalent-sars-co-v-2-3c-like-protease-inhibitors-designed-using-generative-deep-learning-approaches-and-reviewed-by-human-medicinal-chemist-in-virtual-reality.pdf |
60c7520ebdbb897bf6a3a1d5 | 10.26434/chemrxiv.13246715.v1 | Late Stage Diversification of an Unsymmetrical Ligand Scaffold for Multi-functional cis-Pd2L4 Nanocage Libraries | <p>Although many impressive
metallo-supramolecular architectures have been reported, they tend towards high
symmetry structures and avoid extraneous functionality to ensure high-fidelity
in the self-assembly process. This minimalist approach, however, limits the
range of accessible structures and thus their potential applications. Herein is
described a late stage diversification strategy towards ligand scaffolds that
are both low symmetry and incorporate exohedral functional moieties. Key to
this design is the use of CuAAC chemistry, as the triazole is capable of acting
as both a coordinating heterocycle and a tether between the ligand framework
and functional unit simultaneously. In this manner a common precursor was used
to generate ligands with various functionalities, allowing control of electronic
properties, whilst maintaining the core structure of the resultant <i>cis</i>-Pd<sub>2</sub>L<sub>4</sub>
nanocage assemblies. The isostructural nature of the scaffold frameworks
enabled formation of combinatorial libraries from the self-assembly of ligand
mixtures, generating multi-functional, low-symmetry architectures.</p> | James Lewis | Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7520ebdbb897bf6a3a1d5/original/late-stage-diversification-of-an-unsymmetrical-ligand-scaffold-for-multi-functional-cis-pd2l4-nanocage-libraries.pdf |
61da3e6981f3fe78d49fd38a | 10.26434/chemrxiv-2022-xdrpf-v2 | Photochemical Degradation of Short-Chain Chlorinated Paraffins in Aqueous Solution by Hydrated Electrons and Hydroxyl Radicals | Short-chain chlorinated paraffins (SCCPs) are a complex mixture of polychlorinated alkanes (C10-C13, chlorine content 40-70%), and have been categorized as persistent organic pollutants. However, there are knowledge gaps about their environmental degradation, particularly the effectiveness and mechanism of photochemical degradation in surface waters. Photochemically-produced hydrated electrons (e-(aq)) have been shown to degrade highly chlorinated compounds in environmentally-relevant conditions more effectively than hydroxyl radicals (·OH), which can degrade a wide range of organic pollutants. This study aimed to evaluate the potential for e-(aq) and ·OH to degrade SCCPs. To this end, the degradation of SCCP model compounds was investigated under laboratory conditions that photochemically produced e-(aq) or ·OH. Resulting SCCP degradation rate constants for e-(aq) were on the same order of magnitude as well-known chlorinated pesticides. Experiments in the presence of ·OH yielded similar or higher second-order rate constants. Trends in e-(aq) and ·OH SCCP model compounds degradation rate constants of the investigated SCCPs were consistent with that of other chlorinated compounds, with higher chlorine content producing in higher rate constants for e-(aq) and lower for ·OH. Above a chlorine:carbon ratio of approximately 0.6, the e-(aq) second-order rate constants were higher than rate constants for ·OH reactions. Results of this study furthermore suggest that SCCPs are likely susceptible to photochemical degradation in sunlit surface waters, facilitated by dissolved organic matter that can produce e-(aq) and ·OH when irradiated. | Brian DiMento; Cristina Tusei; Christoph Aeppli | Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61da3e6981f3fe78d49fd38a/original/photochemical-degradation-of-short-chain-chlorinated-paraffins-in-aqueous-solution-by-hydrated-electrons-and-hydroxyl-radicals.pdf |
67aabdf6fa469535b9cd8a68 | 10.26434/chemrxiv-2025-nqfl9 | A Nitrilium ion-trapping path to substituted thiadiazoles and oxadiazoles | We have repurposed the Huisgen rearrangement towards a multicomponent synthesis of 2-amino-1,3,4-thiadiazoles and 2-amino-1,3,4-oxadiazoles. The starting materials – 5-sustituded-1H-tetrazoles, TCDI or CDI, and amines – are readily accessible and allow for modular construction of heterocyclic scaffolds. To demonstrate the enabling aspect of this transformation towards late-stage modification of medicinally relevant molecules, we have prepared a thiadiazole-containing crisaborole derivative. | Matthew Diamandas; Kane A. C. Bastick; Daniel Ou; Betty Huang; Andrei Yudin | Organic Chemistry; Combinatorial Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67aabdf6fa469535b9cd8a68/original/a-nitrilium-ion-trapping-path-to-substituted-thiadiazoles-and-oxadiazoles.pdf |
655e12a129a13c4d47bd0a43 | 10.26434/chemrxiv-2023-55ml6 | Molybdenum(0) tricarbonyl complex supported by an azacalixpyridine ligand: Synthesis, characterization, surface deposition and conversion to a molybdenum(VI) trioxo complex with O2 | Adsorption of metal-organic complexes on metallic surfaces to produce well-defined single site catalysts is a novel approach combining the advantages of homogeneous and heterogeneous catalysis. To avoid the “surface trans-effect” a dome-shaped molybdenum(0) tricarbonyl complex supported by an tolylazacalix[3](2,6)pyridine ligand is synthesized. This vacuum-evaporable complex both activates CO and reacts with molecular oxygen (O2) to form a Mo(VI) trioxo complex which in turn is capable of catalytically mediating oxygen transfer. The molybdenum tricarbonyl- and trioxo complexes are investigated in the solid state, in homogeneous solution and on noble metal surfaces (Cu, Au) employing a range of spectroscopic and analytical methods. | Kai Uwe Clausen; Alexander Schlimm; Katja Bedbur; Christian Näther; Thomas Strunskus; Ling Fu; Manuel Gruber; Richard Berndt; Felix Tuczek | Catalysis; Organometallic Chemistry; Nanoscience; Nanocatalysis - Catalysts & Materials; Small Molecule Activation (Organomet.); Spectroscopy (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655e12a129a13c4d47bd0a43/original/molybdenum-0-tricarbonyl-complex-supported-by-an-azacalixpyridine-ligand-synthesis-characterization-surface-deposition-and-conversion-to-a-molybdenum-vi-trioxo-complex-with-o2.pdf |
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