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62b06a21e84dd18777fb5fa3 | 10.26434/chemrxiv-2022-qzjnv | Spatial and Valence Matched Neutralizing DNA-Nanostructure Blocks Wild-Type SARS-CoV-2 and Omicron Variant Infection | Natural ligand-receptor interactions that play pivotal roles in biological events are ideal models for design and assembly of artificial recognition molecules. Herein, aiming at the structural characteristics of the spike trimer and infection mechanism of SARS-CoV-2, we have designed a DNA framework-guided spatial patterned neutralizing aptamer trimer for SARS-CoV-2 neutralization. The ~5.8 nm tetrahedral DNA framework affords precise spatial organization and matched valence as four neutralizing aptamers (MATCH-4), which matches with nanometer precision the topmost surface of SARS-CoV-2 spike trimer, enhancing the interaction between MATCH-4 and spike trimer. Moreover, the DNA framework provides a dimensionally com-plementary nanoscale barrier to prevent the spike trimer-ACE2 interaction and the conformational transition, thereby inhibiting SARS-CoV-2-host cell fusion and infection. As a result, the spatial and valence-matched MATCH-4 ensures improved binding affinity and neutralizing activity against SARS-CoV-2 and its varied mutant strains, particularly current Omicron variant that are evasive of the majority of existing neutralizing antibodies. In addition, because neutralizing aptamers specific to other targets can be evolved and assembled, the present design has the potential to inhibit other wide-range and emerging pathogens. | Shuang Wan; Siwen Liu; Miao Sun; Jialu Zhang; Xinyu Wei; Ting Song; Yuhao Li; Liu Xinyang; Honglin Chen; Chaoyong Yang; Yanling Song | Biological and Medicinal Chemistry; Analytical Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b06a21e84dd18777fb5fa3/original/spatial-and-valence-matched-neutralizing-dna-nanostructure-blocks-wild-type-sars-co-v-2-and-omicron-variant-infection.pdf |
630c84e2521cb7040aaa8fdd | 10.26434/chemrxiv-2022-6d4k9 | Unravelling the molecular structure and confinement of an or-ganometallic catalyst heterogenized within amorphous porous polymers | The catalytic activity of multifunctional microporous materials is directly linked to the spatial arrangement of their struc-tural building blocks. Despite great achievements in the design and use of isolated catalytic sites within such materials, the precise determination of their atomic-level structure and their local environment still remains a fundamental chal-lenge, especially when they are hosted in non-crystalline solids. Here, we show that by combining NMR measurements with pair distribution function (PDF) analysis and computational chemistry, a very accurate picture of the organometallic Cp*Rh catalytic sites inside the cavity of porous organic polymers can be determined. Two microporous supports based on bipyridine and biphenyl motifs functionalized with NH2 or NO2 groups were considered. Making use of differential PDF, Dynamic Nuclear Polarization (DNP) enhanced solid-state NMR spectroscopy on 15N labelled–NH2 and –NO2 materi-als, and 129Xe NMR, the detailed structure of the heterogenized organometallic complex and its confinement within the amorphous porous organic polymers is revealed with a precision of 0.1 Å, fully matched by the computed models. While the same well-defined molecular structure is observed for the organometallic catalyst independently of the functionalisa-tion of the porous organic polymer, subtle changes are detected in the average ligand-pore wall distance and interactions in the two materials. | Ribal Jabbour; Christopher Ashling; Arafat Hossain Khan; Dorothea Wisser; Pierrick Berruyer; Ashta Ghosh; Alisa Ranscht; David A. Keen; Eike Brunner; Jérôme Canivet; Thomas D. Bennett; Caroline Mellot-Draznieks; Anne Lesage; Florian M. Wisser | Inorganic Chemistry; Analytical Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630c84e2521cb7040aaa8fdd/original/unravelling-the-molecular-structure-and-confinement-of-an-or-ganometallic-catalyst-heterogenized-within-amorphous-porous-polymers.pdf |
60c7500a469df4176ff447bb | 10.26434/chemrxiv.12982433.v1 | Flavin-Dependent Halogenases Catalyze Enantioselective Olefin Halocyclization | <div><div><div><p>Catalytic enantioselective halocyclization of alkenes is a powerful bond forming tool in synthetic organic chemistry and a key step in the biosynthesis of several natural products. To date, however, no examples of enantioselective halocyclization of simple achiral olefins catalyzed by enzymes have been reported. Herein, we report that flavin-dependent halogenases (FDHs) previously engineered to catalyze site-selective aromatic halogenation can also catalyze bromolactonization of olefins with high enantioselectivity and near-native catalytic proficiency. Analysis of the selectivity of FDH variants along the lineage for the most selective enzymes reveals mutations responsible for the emergence of halocyclase activity, and docking simulations provide insight into the origins of improvements imparted by these mutations. High selectivity was achieved by characterizing and mitigating the release of HOBr from FDH variants using a combination of protein engineering and reaction optimization. Given the range of different halocyclization reactions and other organic transformations that proceed via oxidative halogenation, this expansion of FDH catalytic activity bodes well for the development of a wide range of biocatalytic halogenation reactions.</p></div></div></div> | Dibyendu Mondal; Brian F. Fisher; Yuhua Jiang; Jared C. Lewis | Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7500a469df4176ff447bb/original/flavin-dependent-halogenases-catalyze-enantioselective-olefin-halocyclization.pdf |
665c88d491aefa6ce19d05a4 | 10.26434/chemrxiv-2024-pp22n | Tetra-Donor Pyrazine based Thermally Activated Delayed Fluorescence Emitters for Electroluminescence and Amplified Spontaneous Emission | Thermally activated delayed fluorescence (TADF) materials are expected to address triplet-related losses in electrically driven organic lasers, as the electrically generated triplets in the materials can be converted to radiative singlets through reverse intersystem crossing (RISC). This offers a way to bypass triplet absorption and annihilation in organic semiconductor lasers (OSLs). In this work we present two versatile TADF emitters 4tCzPz and 4αCbPz for application in OLEDs and OSLs. Both emitters possess moderately high ΔEST (~0.30 eV) and show high ΦPL in solution and solid state and prominent stimulated emission features in solution. Films of 4tCzPz and 4αCbPz doped in mCBP show an amplified spontaneous emission (ASE) threshold of 41.0 and 44.9 µJ/cm2, respectively. The OLEDs with 4tCzPz and 4αCbPz emitted with peak wavelengths of 492 nm and 475 nm, respectively, and showed corresponding maximum external quantum efficiencies, EQEmax, of 24.6 and 21.3%. Our research shows that D-A TADF materials hold significant potential not only as emitters for OLEDs but also in OSLs. | Dongyang Chen; Junyi Gong; Jeannine Grüne; Tomas Matulaitis; Alexander Gillett; Xiao-Hong Zhang; Ifor Samuel; Graham Turnbull; Eli Zysman-Colman | Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665c88d491aefa6ce19d05a4/original/tetra-donor-pyrazine-based-thermally-activated-delayed-fluorescence-emitters-for-electroluminescence-and-amplified-spontaneous-emission.pdf |
63b43fa2ff46518c32406a1f | 10.26434/chemrxiv-2023-tg7fs | Structure and thermodynamics of water adsorption in NU- 1500-Cr | The mechanism of water adsorption in NU-1500-Cr, a high-performance atmospheric water harvest- ing metal-organic framework (MOF), is investigated using a combination of molecular dynamics simulations and infrared spectroscopy. Calculations of thermodynamic and dynamical properties of water as a function of relative humidity allow for following the adsorption process from the initial hydration stage to complete filling of the MOF pores. Initial hydration begins at the water molecules that saturate the open Cr3+ sites of the framework, which is then followed by the formation of water chains that extend along the channels connecting the hexagonal pores of the framework. Water present in these channels gradually coalesces and fills the hexagonal pores sequentially after the channels are completely hydrated. The development of hydrogen-bond networks inside the MOF pores as a function of relative humidity is characterized at the molecular level using experimental and computational infrared spectroscopy. A detailed analysis of the OH-stretch vibrational band indicates that the low- frequency tail, which is common in the experimental infrared spectra of water in MOFs, stems from strongly polarized hydrogen-bonded water molecules, suggesting the presence of some structural dis- order in the experimental samples. Strategies for designing efficient water harvesting MOFs are also proposed based on the mechanism of water adsorption in NU-1500-Cr. | Ching-Hwa Ho; Mason L. Valentine; Zhijie Chen; Haomiao Xie; Omar K. Farha; Wei Xiong; Francesco Paesani | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Interfaces; Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b43fa2ff46518c32406a1f/original/structure-and-thermodynamics-of-water-adsorption-in-nu-1500-cr.pdf |
670e40d451558a15ef220213 | 10.26434/chemrxiv-2024-2xzct-v2 | Catalytic Large Atomic Model (CLAM): A Machine-Learning-Based Interatomic Potential Universal Model | Catalysis involves complex reactions with dynamic changes in catalyst morphology, challenging the capabilities of traditional Density Functional Theory (DFT) methods. To address this, we present the Catalytic Large Atomic Model (CLAM), a machine-learning-based interatomic potential designed for heterogeneous catalysis. Trained on a comprehensive dataset that includes metals, alloys, oxides, clusters, zeolites, 2D materials, and small molecules, CLAM ensures high accuracy across diverse catalytic systems. We also introduce a "local fine-tuning" algorithm that enhances the model’s applicability by accelerating structural optimizations and transition state searches while maintaining precision. Additionally, CLAM facilitates rapid reaction network construction and efficient kinetic analysis. This work advances computational catalysis by providing a universal and robust tool for catalyst design and mechanism exploration. | Zhihong Wu; Lei Zhou; Pengfei Hou; Yuyan Liu; Taoli Guo; Jin-Cheng Liu | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2024-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670e40d451558a15ef220213/original/catalytic-large-atomic-model-clam-a-machine-learning-based-interatomic-potential-universal-model.pdf |
64d26ca44a3f7d0c0dd3be86 | 10.26434/chemrxiv-2023-4xz3w | Scope and computational insights into enantioselective C–H amination through silver-catalyzed nitrene transfer | Chiral, non-racemic amines and amino alcohols are prevalent in drugs, bioactive natural products and ligands for transi-tion metal catalysis. Asymmetric nitrene transfer is an efficient and powerful strategy to prepare enantioenriched amines from abundant C–H bonds; however, there is a continued need for general and inexpensive transition metal catalysts sup-ported by easily tunable ligands. Herein, we report silver salts ligated to an unusual bis(oxazoline) (BOX) ligand, readily accessible through a modular synthetic approach, catalyze site- and enantioselective nitrene transfers into benzylic, al-lylic and unactivated C–H bonds of carbamate esters. The resulting 1,3-aminoalcohol building blocks are delivered in good yields and moderate-to-excellent enantioselectivities up to 99%. Computational models were employed to rational-ize the observed stereochemical outcomes and set the stage for the predictive design of second-generation silver cata-lysts. These in-depth computational investigations implicate a complex combination of features in promoting enantiose-lectivity, including substrate distortion from a square-planar geometry at silver and stabilizing C–H/π interactions be-tween ligand and substrate. Careful analyses of the enantiodetermining transition states employing diverse substrates revealed the dominant factors controlling selectivity for each substrate class, thus enabling the rational design of ligand and catalyst combinations that furnish a broader scope of chemo-, site- and enantioselective C–H bond aminations. | Emily Schroeder; Yue Fu; Jed Kim; Wentan Liu; Peng Liu; Jennifer Schomaker | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d26ca44a3f7d0c0dd3be86/original/scope-and-computational-insights-into-enantioselective-c-h-amination-through-silver-catalyzed-nitrene-transfer.pdf |
64b560a6b605c6803be18fe0 | 10.26434/chemrxiv-2023-dk9sn-v2 | Tuning morphology, stability and optical properties of CsSnBr<sub>3</sub> nanocrystals through bismuth doping for visible-light-driven applications | In this investigation, we have demonstrated the synthesis of lead-free, CsSnBr<sub>3</sub> (CSB) and 5 mol% bismuth (Bi) doped CSB (CSB′B) nanocrystals, with a stable cubic perovskite structure following a facile hot injection technique. The Bi substitution in CSB was found to play a vital role in reducing the size of the nanocrystals significantly, from 316±93 to 87±22 nm. Additionally, Bi doping has inhibited the oxidation of Sn<sup>2+</sup> of CSB perovskite. A reduction in the optical band gap from 1.89 to 1.73 eV was observed for CSB′B and the PL intensity was quenched due to the introduction of Bi<sup>3+</sup> dopant. To demonstrate one of the visible-light-driven applications of the nanocrystals, photodegradation experiments were carried out as a test case. Interestingly, under UV-vis irradiation, the degradation efficiency of CSB′B is roughly one order lower than that of P25 titania nanoparticles, however, it is almost five times higher when driven by visible light under identical conditions. Moreover, by employing experimental parameters, DFT-based first-principles calculations were performed, which demonstrated an excellent qualitative agreement between experimental and theoretical outcomes. The as-synthesized Bi-doped CSB might be a stable halide perovskite with potential in visible-light-driven applications. | Md Asif Adib; Fahmida Sharmin; Mohammed Basith | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b560a6b605c6803be18fe0/original/tuning-morphology-stability-and-optical-properties-of-cs-sn-br-sub-3-sub-nanocrystals-through-bismuth-doping-for-visible-light-driven-applications.pdf |
67cec10c6dde43c908420904 | 10.26434/chemrxiv-2024-wdtz9-v3 | Machine learning transition state geometries and applications in reaction property prediction | The calculation of transition state (TS) geometries is essential for understanding reaction mechanisms and rational synthetic methodology design. However, traditional methods like density functional theory (DFT) are often too computationally expensive for large-scale TS identification and are significantly slower than high-throughput experimental screening methods. Recent advancements in machine learning (ML) offer promising alternatives, enabling the direct prediction of TS geometries, reducing the reliance on expensive quantum mechanical (QM) calculations and affording predictions ahead of experiment. The works explored here include the broader application of ML in reaction property prediction, emphasising how accurate TS geometries can serve as vital input data to improve model accuracy. A comprehensive review of ML methods developed to explicitly predict TS geometries are then presented, with attention to their application in downstream tasks, such as energy barrier calculations, and their use as initial structures for further optimisation via QM methods. Finally, a critical evaluation of the accuracy and limitations of existing TS prediction methods are discussed, highlighting challenges that impede wider adoption and areas where further research is needed. | Isaac W. Beaglehole; Miles J. Pemberton; Elliot H. E. Farrar; Matthew N. Grayson | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2025-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cec10c6dde43c908420904/original/machine-learning-transition-state-geometries-and-applications-in-reaction-property-prediction.pdf |
6523570645aaa5fdbb926f06 | 10.26434/chemrxiv-2023-56p2r | Stochastic electrochemical measurement of biofouling layer on gold | Adsorption of a biofouling layer on the surface of biosensors decreases the electrochemical activity and hence shortens the service life of biosensors, particularly implantable and wearable biosensors. Real time quantification of the loss of activity is important for in situ assessment of performance while presenting an opportunity to compensate for the loss of activity and recalibrate the sensor to extend the service life. Here we introduce an electrochemical noise measurement technique as a tool for quantification of the formation of a biofouling layer on the surface of gold. The technique uniquely affords thermodynamic and kinetic information without applying an external bias (potential and/or current) hence allowing the system to be appraised in its innate state. The technique relies on the analysis of non-Faradaic current and potential fluctuations that are intrinsically generated by the interaction of charged species at the electrode surface, i.e. gold. An analytical model is extended to explain the significance of parameters drawn from the statistical analysis of the noise signal. This concept is then examined in buffered media in the presence of albumin, a common protein in blood and a known source of fouling layer in biological systems. Results indicate that the statistical analysis of the noise signal can quantify the loss of electrochemical activity which is also corroborated by impedance spectroscopy as complementary technique. | Sina S. Jamali; Samuel V. Somerville; Justin J. Gooding | Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry; Analytical Chemistry - General; Electrochemical Analysis; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6523570645aaa5fdbb926f06/original/stochastic-electrochemical-measurement-of-biofouling-layer-on-gold.pdf |
66b0967f01103d79c5c870da | 10.26434/chemrxiv-2024-gc8vm | Biocompatible Flash Chemiluminescent Assay Enabled by Sterically Hindered Spiro-Strained-Oxetanyl-1,2-Dioxetane | Chemiluminescence is the emission of light that occurs as a result of a chemical reaction. Depending on the rate of chemiexcitation, light emission can occur as a long-lasting, low-intensity, glow-type reaction or a rapid, highly intense flash-type reaction. Assays using a flash-type mode of action provide enhanced detection sensitivity compared to those using a glow-type mode. Recently, our group discovered that applying spiro-strain to 1,2-dioxetanes significantly increases their chemiexcitation rate, thereby transforming glow-type chemiluminescence into flash-type chemiluminescence. However, further examination of the structure-activity relationships revealed that the spiro-strain severely compromises the chemical stability of the 1,2-dioxetanes. We hypothesized that a combination of spiro-strain, steric hindrance, and an electron-withdrawing effect, will result in a chemically stable spiro-strained dioxetane with an accelerated chemiexcitation rate. Indeed, spiro-fused tetramethyl-oxetanyl exhibited a 128-fold faster chemiexcitation rate compared to adamantyl while maintaining similar chemical stability, with a half-life of over 400 hours in PBS 7.4 buffer at room temperature. Turn-on probes composed of tetramethyl-oxetanyl spiro-dioxetane exhibited significantly improved chemical stability in bacterial and mammalian cell media compared to previously developed dioxetane probes fused to a cyclobutyl unit. The superior chemical stability enables a tetramethyl-oxetanyl dioxetane probe to detect β-gal activity with enhanced sensitivity in E. coli bacterial assays and leucine aminopeptidase activity in tumoral cell lines. Overall, the development of the tetramethyl-oxetanyl dioxetane luminophore enables us to enhance the detection sensitivity of chemiluminescent probes while maintaining high chemical stability. The results obtained in this study should assist in designing of improved chemiluminescent probes and underscore the significance of strain-release techniques in enhancing the detection sensitivity of chemiluminescence assays.
| Omri Shelef; Anne Krinsky; Moriah Jospe-Kaufman ; Zuzana Babjaková; Micha Fridman; Ronit Satchi-Fainaro ; Urs Spitz; Doron Shabat | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b0967f01103d79c5c870da/original/biocompatible-flash-chemiluminescent-assay-enabled-by-sterically-hindered-spiro-strained-oxetanyl-1-2-dioxetane.pdf |
678ac2affa469535b96f8f12 | 10.26434/chemrxiv-2025-d77dr | Synthesis and Characterization of Bimetallic Copper (I) Complexes Supported by a Hexadentate Naphthyridine-Based Macrocycle Ligand | Herein, we describe the synthesis and characterisation of N,N′–di–tert–butyl–3,7–diaza–1,5(2,7)–1,8–naphthyridinacyclooctaphane and its coordination chemistry with CuI centres. The macrocyclic naphtyridinaphane ligand (tBuN6) reacts selectively with 2 equivalents of tetrakis acetonitrile copper (I) precursor, yielding the bimetallic CuI–complex [Cu2(tBuN6)(MeCN)2][BF4]2, 1·BF4. Each CuI–atom has a pentacoordinate geometry, with elongated distances with the amine N–donors (2.25 Å), in which the fifth coordination position belongs to a cuprophilic interaction with its vicinal CuI–atom (2.74 Å). Complex 1·BF4 exists in equilibrium in acetonitrile solutions with complex 2, [Cu2(tBuN6)2][BF4]2, and free [Cu(MeCN)4[BF4] due to ligand/solvent exchange. Complex 2 can be formed in high yields when tBuN6 is combined with 1 equivalent of [Cu(MeCN)4[BF4]. Both CuI–atoms remain pentacoordinate with the same Cu···Cu distance but with increased distances with the amine N–donors (2.31 Å). Ligand tBuN6, however, exhibits two different conformations in the solid structure: syn(boat/boat) for the ligand with amine N–donors attached to the CuI–centre, and syn(chair/chair) for the ligand with free amine N–donors. Complex 1·BF4 reacts with 1 equivalent of [Bu4N][Cl] generating selectively complex 3, [Cu2(μ–Cl)(tBuN6)][BF4]. The presence of the bridging Cl–atom shortens the Cu···Cu distance (2.51 Å) and increases the stability of the dicopper complex in acetonitrile solutions and solid state. Counter ion exchange of 1·BF4 with sodium tetrakis 3,5–bis(trifluoromethyl)phenyl borate (NaB(ArF)4) generates 1·B(ArF)4, which behaves similarly to 1·BF4 in acetonitrile solutions. However, in tetrahydrofuran (THF) solutions, 1·B(ArF)4 exhibits higher stability, with no observed formation of complex 2. In THF, complex 1·B(ArF)4 contains one MeCN–bridging molecule, which is described as a three-centre two-electron bonding [Cu2(μ–MeCN)(tBuN6)][B(ArF)4]2. When complex 1·B(ArF)4 is placed under CO atmosphere in THF solutions, the syn,syn biscarbonyl complex 4·B(ArF)4 [Cu2(tBuN6)(CO)2][B(ArF)4]2 is generated. This complex is sufficiently stable in solution under CO and Ar atmosphere to be characterised by NMR and IR spectroscopy, with two stretching bands observed for the CO bound to the CuI–centres at 2102 and 2088 cm–1. | Carlos Martínez-Ceberio; Francisco José Fernández–de–Córdova; Orestes Rivada-Wheelaghan | Inorganic Chemistry; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678ac2affa469535b96f8f12/original/synthesis-and-characterization-of-bimetallic-copper-i-complexes-supported-by-a-hexadentate-naphthyridine-based-macrocycle-ligand.pdf |
62fdc5098bffee6b408fcecc | 10.26434/chemrxiv-2022-4g18f-v2 | On the definition of chirality and enantioselective fields | In solid state physics, any symmetry breaking is known to be associated with emergence of an order parameter. However, the order parameter for molecular and crystal chirality, which is a consequence of parity and mirror symmetry breaking, has not been known since its discovery. In this article, the authors show that the order parameter for chirality can be defined by electric toroidal monopole G_0. By this definition, one becomes able to discuss external filed that can distinguish two different enantiomers only by physical fields. In addition, dynamics and fluctuations of the order parameter G_0 can be discussed, with which one can obtain fruitful insights on a spin filtering effect called CISS (Chirality Induced Spin Selectivity). Emergence of time-reversal-odd dipole M_z by time propagation of G_0 quantities is discussed to explain the enantioselective effect (chiral resolution) at a ferromagnetic surface. | Hiroshi Yamamoto; Jun-ichiro Kishine; Hiroaki Kusunose | Physical Chemistry; Organic Chemistry; Materials Science; Stereochemistry; Quantum Mechanics; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fdc5098bffee6b408fcecc/original/on-the-definition-of-chirality-and-enantioselective-fields.pdf |
60c747390f50db0b7c396570 | 10.26434/chemrxiv.11555580.v1 | Xe···OCS: Relatively Straightforward? | <div>The Xe···OCS complex is studied using microwave spectroscopy. Nine isotopologues are measured, and a mass-dependent rm(2) structure is presented. The experiments are supported with a wide array of calculations, including CCSD(T), SAPT, as well as double-hybrid DFT. Trends in the structures of six Rg···OCS complexes (He, Ne, Ar, Kr, Xe, and Hg) are investigated, with particular attention to the deformation of the OCS monomer and relativistic effects. The experimental near-equilibrium structure of Xe···OCS can be predicted to within 11 milliangstrom in the Xe···C distance by correlated wavefunction theory.<br /></div> | Peter Kraus; Daniel A. Obenchain; Sven Herbers; Dennis Wachsmuth; Irmgard Frank; Jens-Uwe Grabow | Quantum Mechanics; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747390f50db0b7c396570/original/xe-ocs-relatively-straightforward.pdf |
60c752b04c89192986ad417e | 10.26434/chemrxiv.13337399.v1 | Boronic Acid with High Oxidative Stability and Utility in Biological Contexts | <p>Despite their desirable attributes, boronic acids have had a minimal impact in biological contexts. A significant problem has been their oxidative instability. At physiological pH, phenylboronic acid and its boronate esters are oxidized by reactive oxygen species at rates comparable to those of thiols. After considering the mechanism and kinetics of the oxidation reaction, we reasoned that diminishing electron density on boron could enhance oxidative stability. We found that a boralactone, in which a carboxyl group serves as an intramolecular ligand for the boron, increases stability by 10<sup>4</sup>-fold. Computational analyses revealed that the resistance to oxidation arises from diminished stabilization of the p orbital of boron that develops in the rate-limiting transition state of the oxidation reaction. Like simple boronic acids and boronate esters, a boralactone binds covalently and reversibly to 1,2-diols, such as those in saccharides. The kinetic stability of its complexes is, however, at least 20-fold greater. A boralactone also binds covalently to a serine side chain in a protein. These attributes confer unprecedented utility upon boralactones in the realms of chemical biology and medicinal chemistry.</p> | Brian Graham; Ian W. Windsor; Brian Gold; Ronald Raines | Bioorganic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Biochemistry; Chemical Biology; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752b04c89192986ad417e/original/boronic-acid-with-high-oxidative-stability-and-utility-in-biological-contexts.pdf |
653783c1c3693ca993007bd3 | 10.26434/chemrxiv-2023-jhbh4 | Novel 5-Substituted Oxindoles Derivatives as Bruton's Tyrosine Kinase Inhibitors: Design, Synthesis, Docking, Molecular Dynamic Simulation, and Biological Evaluation | Bruton's tyrosine kinase (BTK) is a non-RTK cytoplasmic kinase predominantly expressed by haemopoietic lineages, particularly B-cells. A new Oxindole-based focused library was designed to identify potent compounds targeting the BTK protein as anticancer agents. This study used rational approaches like structure-based pharmacophore modelling, docking, and ADME properties to select compounds. The Molecular dynamics simulation analysis carried out at 20 ns supported the stability of compound 9g within the binding pocket. All the compounds were synthesized and subjected to biological screening on two BTK-expressing cancer cell lines, RAMOS and K562, and six non-BTK cancer cell lines, A549, HCT116 (parental and p53-/-), U2OS, JURKAT, and CCRF-CEM, and two non-malignant cell lines, BJ and MRC-5. This study resulted in the identification of four new compounds, 9b, 9f, 9g, and 9h, which displayed potent activity against BTK-high RAMOS cells. These four compounds, each possessing free binding energies of -10.8, -11.1, -11.3, and -10.8 Kcal/mol, demonstrated antiproliferative and cytotoxic effects in RAMOS cells with IC50 values falling within the lower sub-micromolar range. | Vani Madhuri Velavalapalli; Venkatanarayana Chowdary Maddipati; Soňa , Gurská; Narendran Annadurai; Barbora Lišková; Naresh Kumar Katari; Petr Džubák; Marián Hajdúch; Viswanath Das; Rambabu Gundla | Biological and Medicinal Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653783c1c3693ca993007bd3/original/novel-5-substituted-oxindoles-derivatives-as-bruton-s-tyrosine-kinase-inhibitors-design-synthesis-docking-molecular-dynamic-simulation-and-biological-evaluation.pdf |
65612dc85bc9fcb5c94eff91 | 10.26434/chemrxiv-2023-v23n6 | Modification of Polysulfide Surfaces with Low-Power Lasers | The modification of polymer surfaces using laser light is important for many applications in the nano-, bio- and chemical sciences. Such capabilities have supported advances in biomedical devices, electronics, information storage, microfluidics, and other functional material applications. In most cases, these modifications require high power lasers that are expensive and require specialized equipment and facilities to minimize risk of hazardous irradiation. Additionally, polymer systems that can be easily modified by lasers are often complex and costly to prepare. In this report, these challenges are addressed with the discovery of low-cost sulfur copolymers that can be rapidly modified with lasers emitting low-power infrared and visible light. The featured copolymers are made from elemental sulfur and either cyclopentadiene or dicyclopentadiene—all inexpensive building blocks. The addition of Fe2O3 nanoparticles to the polymer matrix enhanced the rate of modification, enabling polymer ablation at lower laser powers for the dicyclopentadiene-derived polymer, which had a high glass transition temperature. Using a panel of lasers with discreet wavelengths (532, 638 and 786 nm) and powers, a variety of surface modifications could be made on the polymers such as controlled swelling or etching via ablation. The facile synthesis and laser modification of these polymer systems were exploited in applications such as direct laser lithography and erasable information storage. | Abigail Mann; Lynn Lisboa; Samuel Tonkin; Jason Gascooke; Justin Chalker; Christopher Gibson | Physical Chemistry; Polymer Science; Organic Polymers; Photochemistry (Physical Chem.); Surface; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65612dc85bc9fcb5c94eff91/original/modification-of-polysulfide-surfaces-with-low-power-lasers.pdf |
676e7bb3fa469535b9f6b6d7 | 10.26434/chemrxiv-2024-480z6 | Plasticizer blending improved regenerated cellulose films as an alternative to plastics | Plasticizers are widely used to improve the elasticity of regenerated cellulose films, but academic research has thus far ignored the possibility of plasticizer blending. We studied the effects of glycerol, sorbitol, and maltitol on film properties based on a systematic design for mixture experiments and determined regression models to correlate blend composition with film properties. Our results showed that plasticizer blending enabled us to control film tensile strength and water vapour and oxygen permeabilities, which are key indicators to evaluate film efficacy in barrier packaging applications. Our films showed lower water vapor and oxygen permeabilities than commercial uncoated cellophane film and could potentially provide a renewable alternative to conventional polyolefin films with further improvements. These results are important and they indicate that plasticizer blending provides a novel and simple methodology to improve regenerated cellulose films to meet the increasing demand for alternatives to conventional plastics in packaging and other applications. | Pauliina Ahokas; Vesa Kunnari; Johanna Majoinen; Ali Harlin; Mikko Mäkelä | Polymer Science; Chemical Engineering and Industrial Chemistry; Biopolymers; Cellulosic materials; Polymer blends; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676e7bb3fa469535b9f6b6d7/original/plasticizer-blending-improved-regenerated-cellulose-films-as-an-alternative-to-plastics.pdf |
66ea498451558a15ef4f4a00 | 10.26434/chemrxiv-2024-vxdq4 | 2D TiNBr as photocatalyst for overall water splitting | Two-dimensional (2D) Janus materials gain increasing attention as water splitting photocatalysts for hydrogen production. We use first-principles calculations to predict a stable 2D Janus $T$-TiNBr structure, with strong near-ultraviolet sunlight absorption and band edges that align favorably with the water redox potentials for oxygen and hydrogen evolution. We show that the optical and electronic properties of $T$-TiNBr can be modulated to a certain extend by applying external uniaxial strain. Explicit calculations of the redox reactions reveal that solar-driven water splitting is viable at the N-side of $T$-TiNBr, while the Br-side requires modifications such as vacancy creation, the application of an external potential, or adjustment of the pH conditions. | Yatong Wang; Geert Brocks; Ceren Tayran; Süleyman Er | Physical Chemistry; Catalysis; Photocatalysis; Physical and Chemical Properties; Surface; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ea498451558a15ef4f4a00/original/2d-ti-n-br-as-photocatalyst-for-overall-water-splitting.pdf |
664c089b21291e5d1dd48726 | 10.26434/chemrxiv-2024-9701j | Regioselective halogenation of lavanducyanin by a site-selective vanadium-dependent chloroperoxidase | Halogenated phenazine meroterpenoids are a structurally unusual family of marine actinobacterial natural products that exhibit antibiotic, anti-biofilm, and cytotoxic bioactivities. Despite a lack of established phenazine halogenation biochemistry, genomic analysis of Streptomyces sp. CNZ-289, a prolific lavanducyanin and C2-halogenated derivative producer, suggested the involvement of vanadium-dependent haloperoxidases. We subsequently discovered lavanducyanin halogenase (LvcH), characterized it in vitro as a regioselective vanadium-dependent chloroperoxidase, and applied it in late-stage chemoenzymatic synthesis. | Jackson Baumgartner; Shaun McKinnie | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Natural Products; Biochemistry; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664c089b21291e5d1dd48726/original/regioselective-halogenation-of-lavanducyanin-by-a-site-selective-vanadium-dependent-chloroperoxidase.pdf |
62278c38c45c0b4f6729dda1 | 10.26434/chemrxiv-2022-197kq | Robust Analysis of 4e− vs 6e− reduction of
Nitrogen on metal surfaces and single atom alloys | The electrochemical synthesis of hydrazine is an exciting avenue in the sustainable production of commonly used chemicals. Taking inspiration from the mechanistic selectivity of reactions such as 2e- vs 4e- ORR, we explore how to fine tune catalysts for hydrazine synthesis through the 4e- electrochemical nitrogen reduction reaction (NRR) over the popular 6e- (NRR) used for ammonia synthesis. Optimal 4e- NRR performance requires sufficient activity as well as selectivity over 6e- (NRR), other mechanistic NRR reaction branching points and the hydrogen evolution reaction. In this study, we perform first principles calculations in conjunction with uncertainty quantification on various monometallic and single atom alloy surfaces to study activity and selectivity of 4e- NRR. Through free energy diagrams, estimation of scaling relations and a theoretical activity volcano, we observe that catalysts exhibiting low activity due to weak binding for NH3, favor hydrazine synthesis. We also find that single atom alloys follow the same scaling relations as monometallic surfaces. Through uncertainty quantification, we form distributions of limiting potentials and establish a correlation between the activity of a catalyst with the skewness of its limiting potential distribution. We further quantify first principles calculations uncertainty for branching points within various 4e- NRR branching points. Reaction branching point analysis and the tradeoff between activity and selectivity of the catalysts points to the significant challenges of pushing NRR towards hydrazine synthesis. | Lydia Maria Tsiverioti; Lance Kavalsky; Venkatasubramanian Viswanathan | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62278c38c45c0b4f6729dda1/original/robust-analysis-of-4e-vs-6e-reduction-of-nitrogen-on-metal-surfaces-and-single-atom-alloys.pdf |
60c74164702a9b606018a23f | 10.26434/chemrxiv.7841270.v3 | Reaction-based Enumeration, Active Learning, and Free Energy Calculations to Rapidly Explore Synthetically Tractable Chemical Space and Optimize Potency of Cyclin Dependent Kinase 2 Inhibitors | We report a new computational technique, PathFinder, that uses retrosynthetic analysis followed by combinatorial synthesis to generate novel compounds in synthetically accessible chemical space. Coupling PathFinder with active learning and cloud-based free energy calculations allows for large-scale potency predictions of compounds on a timescale that impacts drug discovery. The process is further accelerated by using a combination of population-based statistics and active learning techniques. Using this approach,
we rapidly optimized R-groups and core hops for inhibitors of cyclin-dependent kinase 2. We explored greater than 300 thousand ideas and identified 35 ligands with diverse commercially available R-groups and a predicted IC<sub>50</sub> < 100 nM, and four unique cores with a predicted IC<sub>50</sub> < 100 nM. The rapid turnaround time, and scale of chemical exploration, suggests that this is a useful approach to accelerate the discovery of novel chemical matter in drug discovery campaigns. | Kyle Konze; Pieter Bos; Markus Dahlgren; Karl Leswing; Ivan Tubert-Brohman; Andrea Bortolato; Braxton Robbason; Robert Abel; Sathesh Bhat | Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74164702a9b606018a23f/original/reaction-based-enumeration-active-learning-and-free-energy-calculations-to-rapidly-explore-synthetically-tractable-chemical-space-and-optimize-potency-of-cyclin-dependent-kinase-2-inhibitors.pdf |
620b1bff0c0bf09733e9cde8 | 10.26434/chemrxiv-2022-5gfvq | A Step-by-step Guide on How to Construct quasi-Markov State Models to Study Functional Conformational Changes of Biological Macromolecules | Conformational changes play an important role for many biomolecules to perform their functions. In recent years, Markov State Model (MSM) has become a powerful tool to investigate these functional conformational changes by predicting long time-scale dynamics from many short molecular dynamics (MD) simulations. In MSM, dynamics are modelled by a first-order master equation, in which a biomolecule undergoes Markovian transitions among conformational states at discrete time intervals, called lag time. The lag time has to be sufficiently long to build a Markovian model, but this parameter is often bound by the length of MD simulations available for estimating the frequency of interstate transitions. To address this challenge, we recently employed the generalized master equation (GME) formalism (e.g., the quasi-Markov State Model or qMSM) to encode the non-Markovian dynamics in a time-dependent memory kernel. When applied to study protein dynamics, our qMSM can be built from MD simulations that are an order-of-magnitude shorter than MSM would have required. The construction of qMSM is more complicated than that of MSMs, as time-dependent memory kernels need to be properly extracted from the MD simulation trajectories. Here, we present a step-by-step guide on how to build qMSM from MD simulation datasets, and the materials accompanying this protocol are publicly available on Github: https://github.com/ykhdrew/qMSM_tutorial. We hope this protocol is useful for researchers who want to apply qMSM and study functional conformational changes in biomolecules. | Andrew Kai-hei Yik; Yunrui Qiu; Ilona Christy Unarta; Siqin Cao; Xuhui Huang | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2022-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620b1bff0c0bf09733e9cde8/original/a-step-by-step-guide-on-how-to-construct-quasi-markov-state-models-to-study-functional-conformational-changes-of-biological-macromolecules.pdf |
63990b5b0a81278284e0a1b5 | 10.26434/chemrxiv-2022-n21z9 | A biomimetic approach to promote cellular uptake and enhance photoacoustic properties of tumor-seeking dyes | The attachment of glucose to drugs and imaging agents enables cancer cell targeting via interactions with GLUT1 overexpressed on the cell surface. While an added benefit of this modification is the remarkable solubilizing effect of carbohydrates, in the context of imaging agents, aqueous solubility does not guarantee decreased π-stacking or aggregation. The resulting broadening of the absorbance spectrum is a detriment to photoacoustic (PA) imaging since the signal intensity, accuracy, and image quality all rely on reliable spectral unmixing. To address this major limitation and further enhance the tumor-targeting ability of imaging agents, we have taken a biomimetic approach to design a multivalent glucose moiety (mvGlu). We show-case the utility of this new group by developing aza-BODIPY-based contrast agents boasting a significant PA signal enhancement greater than 11-fold after spectral unmixing. Moreover, when applied to targeting cancer cells, effective staining could be achieved with ultra-low dye concentrations (50 nM) and compared to a non-targeted analog, the signal intensity was >1000-fold higher. Lastly, we employed the mvGlu technology to develop a logic-gated acoustogenic probe to detect intratumoral Cu(I), which is an emerging cancer biomarker, in a murine model of breast tumor. This was exciting application not possible using other acoustogenic probes previously developed for copper sensing. | Amanda East; Michael Lee; Chang Jiang; Qasim Sikander; Jefferson Chan | Biological and Medicinal Chemistry; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2022-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63990b5b0a81278284e0a1b5/original/a-biomimetic-approach-to-promote-cellular-uptake-and-enhance-photoacoustic-properties-of-tumor-seeking-dyes.pdf |
66585599418a5379b0a2df82 | 10.26434/chemrxiv-2024-plfkz-v2 | Scaling relations on high-entropy alloy catalyst surfaces | Scaling and Brønsted-Evans- Polanyi (BEP) relations have proven immensely powerful in catalysis theory. The relations provide an understanding of the Sabatier principle in a quantitative fashion, such that we can calculate the adsorption energy that most optimally compromises between a low reaction barrier and a not too strong adsorption. Scaling and BEP relations are usually mapped out for pure metal surfaces and it is not directly clear how they translate to complex alloy surfaces, e.g. high-entropy alloys (HEAs). The scaling relation between *OH and *OOH is one of the most studied and best understood. Generally, both *OH and *OOH adsorb on a single surface atom, so HEAs do not change the established scaling relation, but rather widen the distribution of available adsorption energies. The situation can be different for reactions at multi-atom surface sites. In the reaction between O* and *CO to form CO2, the species interact with more surface atoms at the initial state compared to the transition state, so for a given reaction energy, HEAs allow for lower activation energies than pure metals. The reason is that HEA surfaces can make the transition state more similar to the initial state, without the need of steps or other geometric features. | Ana-Iulia Hutu; Emmanouil Pervolarakis; Ioannis N. Remediakis; Henrik Høgh Kristoffersen; Jan Rossmeisl | Theoretical and Computational Chemistry; Catalysis; Theory - Computational; Electrocatalysis; Heterogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2024-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66585599418a5379b0a2df82/original/scaling-relations-on-high-entropy-alloy-catalyst-surfaces.pdf |
62701711ef2adefa4145e29a | 10.26434/chemrxiv-2022-qs19c | Rapid GC-MS as a Screening Tool for Forensic Fire Debris Analysis | Techniques developed for the screening of forensic samples can be useful for increasing sample throughput and decreasing backlog in forensic laboratories. One such technique, rapid gas chromatography mass spectrometry (GC-MS), allows for fast sample screening (≈1 min) and has gained interest in recent years for forensic applications. This work focuses on the development of methods for ignitable liquid analysis using rapid GC-MS. A sampling protocol and temperature program were developed for the analysis of these volatile samples. Using the optimized method for analysis, the limits of detection for compounds commonly found in ignitable liquids ranged from 0.012 mg/mL to 0.018 mg/mL. Once the analysis method was developed, neat ignitable liquids (i.e., gasoline and diesel fuel) were analyzed, and major components in each liquid were identified. The identification of gasoline and diesel fuel in the presence of substrate interferences was then assessed through the analysis of simulated fire debris samples. Three different substrates were spiked with each ignitable liquid, burned, and analyzed. Major compounds in both liquids were identified using the total ion chromatograms, relevant extracted ion profiles, and deconvolution methods. | Briana Capistran; Edward Sisco | Analytical Chemistry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62701711ef2adefa4145e29a/original/rapid-gc-ms-as-a-screening-tool-for-forensic-fire-debris-analysis.pdf |
60c7476dbb8c1a4fad3daa77 | 10.26434/chemrxiv.11659563.v1 | Integrating Deep Neural Networks and Symbolic Inference for Organic Reactivity Prediction | <div>Accurate <i>in silico</i> models for the prediction of novel chemical reaction outcomes can be used to guide the rapid discovery of new reactivity and enable novel synthesis strategies for newly discovered lead compounds. Recent advances in machine learning, driven by deep learning models and data availability, have shown utility throughout synthetic organic chemistry as a data-driven method for reaction prediction. Here we present a machine-intelligence approach to predict the products of an organic reaction by integrating deep neural networks with a probabilistic and symbolic inference that flexibly enforces chemical constraints and accounts for prior chemical knowledge. We first train a graph convolutional neural network to estimate the likelihood of changes in covalent bonds, hydrogen counts, and formal charges. These estimated likelihoods govern a probability distribution over potential products. Integer Linear Programming is then used to infer the most probable products from the probability distribution subject to heuristic rules such as the octet rule and chemical constraints that reflect a user's prior knowledge. Our approach outperforms previous graph-based neural networks by predicting products with more than 90% accuracy, demonstrates intuitive chemical reasoning through a learned attention mechanism, and provides generalizability across various reaction types. Furthermore, we demonstrate the potential for even higher model accuracy when complemented by expert chemists contributing to the system, boosting both machine and expert performance. The results show the advantages of empowering deep learning models with chemical intuition and knowledge to expedite the drug discovery process.</div> | Wesley Wei Qian; Nathan T. Russell; Claire L. W. Simons; Yunan Luo; Martin D. Burke; Jian Peng | Organic Synthesis and Reactions; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7476dbb8c1a4fad3daa77/original/integrating-deep-neural-networks-and-symbolic-inference-for-organic-reactivity-prediction.pdf |
65b3d2ece9ebbb4db909a6bb | 10.26434/chemrxiv-2024-mqxlc | High-Efficiency Non-Thermal Plasma Synthesis of Imine Macrocycles | Macrocycles are candidates for wide-ranging applications, yet their synthesis can be low-yielding, poorly reproducible, and resource-intensive, limiting their use. Here, we explore the use of Non-Thermal Plasma (NTP) as an efficient method for the synthesis of imine macrocycles. NTP-mediated macrocyclisations consistently achieved high yields of up to 97 % in reduced reaction times compared to the standard non-plasma method, and were successfully carried out with a range of different aldehyde substrates. Control experiments were performed to explore the origin of the observed improvements. The results indicate that NTP methods could be advantageous for macrocycle synthesis, particularly for substrates that are sensitive to elevated temperature, and other materials formed via imine condensation. | Patrycja Roszkowska; Abbie Scholes; James L Walsh; Timothy L Easun; Anna Grace Slater | Organic Chemistry; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Supramolecular Chemistry (Org.); Reaction Engineering; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b3d2ece9ebbb4db909a6bb/original/high-efficiency-non-thermal-plasma-synthesis-of-imine-macrocycles.pdf |
669a847901103d79c5982b86 | 10.26434/chemrxiv-2024-1csk5 | Mechanistic Differences between Linear vs Spirocyclic Dialkyldiazirine Probes for Photoaffinity Labeling | Dialkyldiazirines have emerged as a photo-reactive group of choice for interactome mapping in live cell experiments. Upon irradiation, ‘linear’ dialkyldiazirines produce dialkylcarbenes which are susceptible to both intramolecular reactions and unimolecular elimination processes, as well as diazoalkanes, which also participate in intermolecular labeling. Cyclobutylidene has a nonclassical bonding structure and is stable enough to be captured in bimolecular reactions. Cyclobutanediazirines have more recently been studied as photoaffinity probes based on cyclobutylidene, but the mechanism, especially with respect to the role of putative diazo intermediates, was not fully understood. Here, we show that photolysis (365 nm) of cyclobutanediazirines can produce cyclobutylidene intermediates as evidenced by formation of their expected bimolecular and unimolecular products, including methylenecyclopropane derivatives. Unlike linear diazirines, cyclobutanediazirine photolysis in the presence of tetramethylethylene produces a [2+1] cycloaddition adduct. By contrast, linear diazirines produce diazo compounds upon low temperature photolysis in THF, whereas diazo compounds are not detected in similar photolyses of cyclobutanediazirines. Diazocyclobutane, prepared by independent synthesis, is labile, reactive toward water and capable of protein alkylation. The rate of diazocyclobutane decomposition is not affected by 365 nm light, suggesting that the photochemical conversion of diazocyclobutane to cyclobutylidene is not an important pathway. Finally, chemical proteomic studies revealed that a likely consequence of this primary conversion to a highly reactive carbene is a marked decrease in labeling by cyclobutanediazirine- based probes relative to linear diazirine counterparts both at the individual protein and proteome- wide levels. Collectively, these observations are consistent with a mechanistic picture for cyclobutanediazirine photolysis that involves carbene chemistry with minimal formation of diazo intermediates, and contrasts with the photolyses of linear diazirines where alkylation by diazo intermediates plays a more significant role. | Jessica O'Brien; Louis Conway; Paramesh Ramaraj; Appaso Jadhav; Jun Jin; Jason Dutra; Parrish Evers; Shadi Masoud; Manuel Schupp; Iakovos Saridakis; Yong Chen; Nuno Maulide; John Pezacki; Christopher am Ende; Christopher Parker; Joseph Fox | Organic Chemistry; Bioorganic Chemistry; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669a847901103d79c5982b86/original/mechanistic-differences-between-linear-vs-spirocyclic-dialkyldiazirine-probes-for-photoaffinity-labeling.pdf |
64f9e169b6ab98a41c04442f | 10.26434/chemrxiv-2023-jtvvr-v2 | Molecularly defined lubricant hydrocarbons from olefin metathesis | Hydrocarbon-based lubricants are ubiquitous in industrial applications but are typically complex mixtures of branched molecules that are challenging to characterize and to relate to their macroscopic properties. Consequently, lubricants are typically optimized empirically for specific applications by blending base oils and organic or inorganic additives. Here, we report the synthesis and characterization of molecularly defined lubricants via metathesis of branched terminal olefins followed by hydrogenation of the internal olefin products. The resulting saturated hydrocarbons are characterized by ultra-high-field (28.2 T) 1H and 13C NMR spectroscopies to establish their molecular structures and resolve different stereoisomers, showing the utility of state-of-the-art spectroscopic tools for resolving structures of branched alkanes. Furthermore, the molecular-level diffusion and bulk viscosity properties compare favorably to classical synthetic lubricants based on hydrogenated polyalphaolefin blends, establishing olefin metathesis as a selective and scalable route to high-performance lubricant oils with defined molecular structures. | Zachariah Berkson; Snædís Björgvinsdóttir; Alexander Barnes; Roland Riek; Roman Schowner; Michael Buchmeiser; Stephen Gibson; Gregory Price; Glenn Sunley; Christophe Copéret | Organic Chemistry; Catalysis; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f9e169b6ab98a41c04442f/original/molecularly-defined-lubricant-hydrocarbons-from-olefin-metathesis.pdf |
60c756b7842e657805db4561 | 10.26434/chemrxiv.14312087.v1 | Green Preparation of High Surface Area Cu-Au Bimetallic Nanostructured Materials by Co-Electrodeposition in a Deep Eutectic Solvent | In this work we present an electrodeposition method in a deep eutectic
solvent (DES) to prepare bimetallic high surface area nanostructures of Cu and
Au with tunable structure and composition. The metal electrodeposition performed
in green choline chloride within a urea deep eutectic solvent allows us to
tailor the size, morphology and elemental composition of the deposits. We
combine electrochemical methods with scanning electron microscopy (SEM), X-ray
photoelectron spectroscopy (XPS) and energy dispersive X-ray spectroscopy (EDS)
to characterize the electrodeposited nanostructured materials. We assess the
increase of the electroactive surface area through the analysis of the lead
underpotential deposition (UPD) on the prepared films. We observe a 5 to
15-fold increase of the active surface area compared to flat surfaces of
polycrystalline Cu or Au. Our work reports, for the first time, a green route
for the electrodeposition of Cu-Au bimetallic nanostructures in a deep eutectic
solvent. | Elena Plaza Mayoral; Paula Sebastián Pascual; Kim Nicole Dalby; Kim Degn Jensen; Ib Chorkendorff; Hanne Falsig; María Escudero-Escribano | Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756b7842e657805db4561/original/green-preparation-of-high-surface-area-cu-au-bimetallic-nanostructured-materials-by-co-electrodeposition-in-a-deep-eutectic-solvent.pdf |
60c74719702a9b3c0b18ad2f | 10.26434/chemrxiv.10299506.v3 | Tuning the Magnetic Vortex State in Magnetite Nanodiscs for Remote Control of Biological Signalling | In this work, we demonstrate the application of anisotropic magnetite nanodiscs (MNDs) as transducers of torque to mechanosensory cells under weak, slowly varying magnetic fields (MFs). These MNDs possess a ground state vortex configuration of magnetic spins which affords greater colloidal stability due to eliminated dipole-dipole interactions characteristic of isotropic magnetic particles of similar size. We first predict vortex magnetization using micromagnetic stimulations in sub-micron anisotropic magnetite particles and then use electron holography to experimentally investigate the magnetization of MNDs 98–226 nm in diameter. When MNDs are coupled to MFs, they transition between vortex and in-plane magnetization allowing for the exertion of the torque on the pN scale, which is sufficient to activate mechanosensitive ion channels in cell membranes.<br /> | Danijela Gregurec; Alexander W. Senko; Andrey Chuvilin; Pooja Reddy; Ashwin Sankararaman; Dekel Rosenfeld; Po-Han Chiang; Francisco Garcia; Ian Tafel; Georgios Varnavides; Eugenia Ciocan; Polina Anikeeva | Biocompatible Materials; Biological Materials; Magnetic Materials; Nanostructured Materials - Materials; Nanodevices; Magnetism; Cell and Molecular Biology; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74719702a9b3c0b18ad2f/original/tuning-the-magnetic-vortex-state-in-magnetite-nanodiscs-for-remote-control-of-biological-signalling.pdf |
67d9cd316dde43c90851a9cf | 10.26434/chemrxiv-2025-q6rfm | Cavity quantum electrodynamics complete active space self consistent field theory | The qualitative description of strongly correlated systems interacting with quantized cavity modes poses significant theoretical challenges due to the combinatorial scaling of electronic and photonic degrees of freedom. Recent advances addressing this complexity include quantum electrodynamics (QED) generalizations of complete active space configuration interaction (QED-CASCI) and density matrix renormalization group (QED-DMRG) methods. In this work, we introduce a QED extension of state-averaged complete active space self-consistent field theory (QED-SA-CASSCF), which incorporates cavity-induced correlations through a second-order orbital optimization framework with robust convergence properties. The implementation enables symmetry-free orbital relaxations to account for photon-mediated symmetry breaking in polaritonic systems. Numerical validation on the LiH molecule coupled to an optical cavity demonstrates that the QED-SA-CASSCF method achieves significantly improved accuracy in modeling ground-state and polariton potential energy surfaces (PESs) compared to QED-CASCI. This advancement provides a systematic approach for studying cavity-altered chemical landscapes while retaining the balance between static correlation treatment and computational feasibility inherent to multiconfigurational methods. | Nam Vu; Kenny Ampoh; Jonathan Foley | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2025-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d9cd316dde43c90851a9cf/original/cavity-quantum-electrodynamics-complete-active-space-self-consistent-field-theory.pdf |
60c7581b842e653712db47e5 | 10.26434/chemrxiv.14498664.v1 | Molecular-Level Understanding of the Influence of Ions and Water on HMGB1 Adsorption Induced by Surface Hydroxylation of Titanium Implants | <div><div><div><p>Due to its excellent chemical and mechanical properties, titanium has become the material of choice for orthopedic and dental implants to promote rehabilitation via bone anchorage and osseointegration. Titanium osseointegration is partially related to its capability to form a TiO<sub>2</sub> surface layer and its ability to interact with key endogenous proteins immediately upon implantation, establishing the first bone-biomaterial interface. Surgical trauma caused by implantation results in the release of High Mobility Group Box 1 (HMGB1) protein, which is a prototypic DAMP (Damage Associated Molecular Pattern) with multiple roles in inflammation and tissue healing. To develop different surface strategies that improve the clinical outcome of titanium-based implants by controlling their biological activity, a molecular-scale understanding of HMGB1-surface interactions is desired. Here, we use molecular dynamics (MD) computer simulations to provide direct insight into the HMGB1 interactions and the possible molecular arrangements of HMGB1 on fully hydroxylated and non-hydroxylated rutile (110) TiO<sub>2</sub> surfaces. The results establish that HMGB1 is most likely to be adsorbed directly onto the surface regardless of surface hydroxylation, which is undesirable because it could affect its biological activity by causing structural changes to the protein. The hydroxylated TiO<sub>2</sub> surface shows a greater affinity for HMGB1 than the non-hydroxylated surface. The water layer on the non-hydroxylated TiO<sub>2</sub> surface prevents ions and the protein from directly contacting the surface. However, it was observed that if the ionic strength increases, the total number of ions adsorbed on the two surfaces increases, and the protein’s direct adsorption ability decreases. These findings will help to understand the HMGB1-TiO<sub>2</sub> interactions upon implantation, as well as the development of different surface strategies by introducing ions or ionic materials to the titanium implant surface to modulate its interactions with HMGB1 to preserve biological function.</p></div></div></div> | Dineli T. S. Ranathunga; Alexandra Arteaga; Claudia C. Biguetti; Danieli C. Rodrigues; Steven O. Nielsen | Biological Materials; Coating Materials; Bioengineering and Biotechnology; Bioinformatics and Computational Biology; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7581b842e653712db47e5/original/molecular-level-understanding-of-the-influence-of-ions-and-water-on-hmgb1-adsorption-induced-by-surface-hydroxylation-of-titanium-implants.pdf |
60c740b8bdbb892569a381e5 | 10.26434/chemrxiv.7277354.v2 | Drug Analogs from Fragment Based Long Short-Term Memory Generative Neural Networks | <p>Several recent reports have shown that long short-term memory generative
neural networks (LSTM) of the type used for grammar learning efficiently learn
to write SMILES of drug-like compounds when trained with SMILES from a database
of bioactive compounds such as ChEMBL and can later produce focused sets upon
transfer learning with compounds of specific bioactivity profiles. Here we
trained an LSTM using molecules taken either from ChEMBL, DrugBank, commercially
available fragments, or from FDB-17 (a database of fragments up to 17 atoms) and
performed transfer learning to a single known drug to obtain new analogs of
this drug. We found that this approach readily generates hundreds of relevant and
diverse new drug analogs and works best with training sets of around 40,000
compounds as simple as commercial fragments. These data suggest that
fragment-based LSTM offer a promising method for new molecule generation.</p> | Mahendra Awale; Finton Sirockin; Nikolaus Stiefl; Jean-Louis Reymond | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740b8bdbb892569a381e5/original/drug-analogs-from-fragment-based-long-short-term-memory-generative-neural-networks.pdf |
67d76b3d81d2151a02a2743b | 10.26434/chemrxiv-2025-prsq2 | Ascorbate Peroxidase (APEX2) Activates Dihydrotetrazine Oxidation for Rapid Bioorthogonal Chemistry in Living Cells | It is shown that genetically expressible APEX2 efficiently catalyzes the oxidation of dihydrotetrazine (DHTz) to give tetrazine products that engage in rapid bioorthogonal reactions with trans-cyclooctene dienophiles. Through in vitro studies, it is shown that the APEX2-catalyzed DHTz oxidation is accelerated by superoxide dismutase— an enzyme found in all mammalian cells that regulates oxidative stress by disproportioning superoxide into O2 and H2O2. While the addition of H2O2 is not required for APEX2-catalyzed DHTz oxidation, the catalytic efficiency is increased substantially to kcat/KM 4.90 × 103 M–1s–1 by the addition of a small amount of H2O2 (10 μM). These ‘minimal peroxide’ conditions are mild compared to the higher H2O2 concentrations that are typically employed in phenolic oxidation reactions promoted by APEX2. The ability of APEX2 to promote DHTz oxidation for subsequent Diels-Alder chemistry was demonstrated in live HeLa cells that, through a dual-transfection protocol, contained cytosolic APEX2 and a HaloTag-DHTz conjugate. Upon oxidation, the resulting tetrazine was conjugated in situ to a fluorophore-tagged TCO, and conjugation efficiency was assayed through in-gel fluorescence, western blot analysis, and confocal microscopy. In live PC3 cells, it was further shown that APEX2 catalyzed the oxidation of a DHTz that had been selectively conjugated to endogenous monoacylglycerol lipase (MAGL) via a selective covalent warhead. | Sophia Neglia; Amanda Tallon; Christopher am Ende; Colin Thorpe; Joseph Fox | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d76b3d81d2151a02a2743b/original/ascorbate-peroxidase-apex2-activates-dihydrotetrazine-oxidation-for-rapid-bioorthogonal-chemistry-in-living-cells.pdf |
60c73e579abda28cf0f8b884 | 10.26434/chemrxiv.6871775.v1 | Structural Macrokinetics of Biomimetic Processes in Artificial Cells | It is known that all cytophysiological processes occur on the cell ultrastructure, which is a heterogeneous (heterophase) medium. So the kinetics of metabolic processes should be considered as a structural macrokinetics of this partially ordered medium (soft matter). Our model reproduces the structural-macrokinetic aspect of a number of metabolic phenomena, based on the physico-chemical analogies with the biological cell. Thus, the semipermeability of bioorganic membranes is simulated by semiconductive polymer inorganic dynamic membranes, exergonic chemoosmotic redox processes are equivalent to cellular respiration, biomimetic self-oscillating reactions are analogues of oscillatory metabolic processes and finally the structure formation in these models is also provided by reaction-diffusion mechanisms. | Oleg Gradov; Margaret Gradova | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2018-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e579abda28cf0f8b884/original/structural-macrokinetics-of-biomimetic-processes-in-artificial-cells.pdf |
60c73e579abda2ee2bf8b888 | 10.26434/chemrxiv.6874886.v1 | A Master Class in Dimensional Analysis: the Universal Gas Constant | We present a spreadsheet-assisted exercise using Microsoft Excel software for the<br />determination of the universal gas constant, R, in 35,712 different units. This large<br />number of units arises from a simple enumeration of possible pressure-volume unit<br />combinations and energy unit combinations covering SI (metric), Imperial (British), and<br />American units. In turn, various units for force and area used for defining pressure, and<br />various units for force and distance used for defining energy are explored. This<br />presentation serves as an excellent exercise for high school and undergraduate students to<br />master the skill of dimensional analysis, unit conversions, and basic combinatorics in<br />general chemistry and physical chemistry courses. Instructors can also use the described<br />exercise of constructing conversion matrices to train students in how to efficiently use the<br />Microsoft Excel spreadsheet program. | john andraos | Chemical Education - General; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e579abda2ee2bf8b888/original/a-master-class-in-dimensional-analysis-the-universal-gas-constant.pdf |
65a998a89138d231613cf980 | 10.26434/chemrxiv-2024-f6tnd | Development of a Sulfamate Tethered Aza-Michael Cyclization Allows for the Preparation of (-)-Negamycin tert-Butyl Ester | We present the first examples of intramolecular aza-Michael cyclizations of sulfamates and sulfamides onto pendant
α,β-unsaturated esters, thioesters, amides, and nitriles. Stirring substrate with catalytic quantities of the appropriate base delivers product in good yield and excellent diastereoselectivity. The reactions are operationally simple, can be performed open to air, and are tolerant of a variety of important functional groups. We highlight the utility of this technology by using it in the preparation of a (-)-negamycin derivative. | Shyam Sathyamoorthi; Harshit Joshi; Appasaheb Nirpal; Debobrata Paul; Steven Kelley; Joel Mague | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2024-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a998a89138d231613cf980/original/development-of-a-sulfamate-tethered-aza-michael-cyclization-allows-for-the-preparation-of-negamycin-tert-butyl-ester.pdf |
6549f90148dad2312040361e | 10.26434/chemrxiv-2023-f3dcl | Activation of anthraquinone’s electrophilicity by light
for a dynamic C-O bond | Coupling of photoswitching with dynamic covalent chemistry enables the control of the formation and cleavage of covalent bonds by light irradiation. Peri-aryloxyanthraquinones feature an exclusive ability to switch electrophilicity by interconversion between para- and ana-quinone isomers, which was used for the first time for implementation of a dynamic C-O bond. Photogenerated ana-isomers undergo a concerted oxa-Michael addition of phenols to give hitherto unknown 4-hydroxy-10,10-diaryloxyanthracen-9-ones. These species were found to be in equilibrium with the corresponding ana-quinones, thus forming a dynamic covalent system of a new type. Withdrawal of the colored ana-quinones from the equilibria by visible-light irradiation resulted in two para-quinones with “locked” aryloxy groups. | Vasily Bykov; Stepan Ukhanev; Igor Ushakov; Anna Vologzhanina; Evgenii Antsiferov; Lyubov Klimenko; Andrey Lvov | Organic Chemistry; Photochemistry (Org.); Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6549f90148dad2312040361e/original/activation-of-anthraquinone-s-electrophilicity-by-light-for-a-dynamic-c-o-bond.pdf |
66ab726bc9c6a5c07ab183cc | 10.26434/chemrxiv-2024-zz2wc | Light-Driven, Reversible Spatiotemporal Control of Dynamic Covalent Polymers | Dynamic covalent polymer networks exhibit a cross-linked structure like conventional thermosets and elastomers, although their topology can be reorganized by thermoactivated bond exchange. This characteristic enables a unique combination of repairability, recyclability and dimensional stability, crucial for a sustainable industrial economy. We herein report the application of a photoswitchable nitrogen superbase for the spatially resolved and reversible control over dynamic bond exchange within a thiol-ene photopolymer. By the exposure to UV or visible light, we successfully gain control over the associative exchange between thioester links and thiol groups, and thereby the macroscopic mechanical material properties, in a locally controlled manner. Consequently, the resulting reorganization of the global network topology enables us to utilize our material for previously unrealizable advanced applications such as spatially resolved, reversible reshaping as well as micro-imprinting over multiple steps. Finally, the presented concept contributes fundamentally to the evolution of dynamic polymers and provides universal applicability in covalent adaptable networks relying on a base-catalyzed exchange mechanism. | David Reisinger; Alexander Sietmann; Ankita Das; Sarah Plutzar; Elisabeth Rossegger; Matthias Walluch; Stefan Holler-Stangl; Thomas S. Hofer; Fabian Dielmann; Frank Glorius; Sandra Schlögl | Materials Science; Polymer Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ab726bc9c6a5c07ab183cc/original/light-driven-reversible-spatiotemporal-control-of-dynamic-covalent-polymers.pdf |
6730e5c1f9980725cfc0807d | 10.26434/chemrxiv-2024-lnmv4 | Greenhouse Gas Accounting Procedures in Low Carbon Fuel Policies Lead to Undervalued Benefits of Miscanthus-based Sustainable Aviation Fuel | Low carbon fuel policies such as the U.S. Renewable Fuel Standard (RFS), Canada Clean Fuel Regulations (CFR), and California Low Carbon Fuel Standard (LCFS) are intended to reduce the greenhouse gas (GHG) emissions from transportation. Cellulosic feedstocks, optimized biorefineries, and favorable farming locations can significantly reduce biofuel carbon intensity (CI). Despite the emergence of field-to-fuel GHG monitoring technologies that could verify such benefits, programmatic constraints in CI accounting procedures may limit fuel producers’ ability to capitalize on these opportunities. To elucidate the implications of this challenge, this work examines a miscanthus-to-sustainable aviation fuel (SAF) pathway (i) to demonstrate how program provisions drive estimates of biofuel CIs and (ii) to explore potential CI and financial benefits of spatially explicit life cycle assessment (LCA). In comparing policy-based vs. spatially explicit CI scores (estimated via DayCent and BioSTEAM) for SAF production from miscanthus via alcohol-to-jet (ATJ), programmatic CI accounting requirements underestimated GHG benefits in 60-99% of simulated scenarios. These underestimates result in policy-induced SAF price differentials of -1.19 [(-)3.46 to (-)0.23], -0.07 [(-)1.06 to (+)0.37], and -0.48 [(-)2.46 to (+)0.16] $·L-1 for the RFS, CFR, and LCFS, respectively. Ultimately, this work demonstrates the importance of LCA methodological specifications in low carbon fuel policies. | Dalton Stewart; Wenjun Guo; Yalin Li; Xinxin Fan; Jonathan Coppess; Madhu Khanna; Jeremy Guest | Chemical Engineering and Industrial Chemistry; Industrial Manufacturing | CC BY 4.0 | CHEMRXIV | 2024-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6730e5c1f9980725cfc0807d/original/greenhouse-gas-accounting-procedures-in-low-carbon-fuel-policies-lead-to-undervalued-benefits-of-miscanthus-based-sustainable-aviation-fuel.pdf |
60c759b5ee301c5837c7b974 | 10.26434/chemrxiv.14723658.v1 | Structure Determination, Thermal Stability and Dissolution Rate of δ Indomethacin | <div>
<p>The structure solution of the
δ-polymorph of indomethacin was obtained using three-dimensional electron
diffraction. This form shows a significantly enhanced dissolution rate compared
with the more common and better studied α- and γ-polymorphs, indicating an
increased bioavailability for medicinal applications. The structure was solved
in non-centrosymmetric space group <i>P</i>2<sub>1</sub>
and comprises two molecules in the asymmetric unit. Packing and molecule
conformation closely resemble indomethacin methyl ester and indomethacin
methanol solvate. Knowledge of the structure allowed the rational
interpretation of spectroscopic IR and Raman data for δ-polymorph and a
tentative interpretation for still unsolved indomethacin polymorphs. Finally,
we observed a solid-solid transition from δ-polymorph to α-polymorph that can
be driven by similarities in molecular conformation.</p>
</div>
<br /> | Iryna Andrusenko; Victoria Hamilton; Arianna E. Lanza; Charlie
L. Hall; Enrico Mugnaioli; Jason Potticary; Asma Buanz; Simon Gaisford; Anna Piras; Ylenia Zambito; Simon R. Hall; Mauro Gemmi | Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759b5ee301c5837c7b974/original/structure-determination-thermal-stability-and-dissolution-rate-of-indomethacin.pdf |
66f67e54cec5d6c1426408df | 10.26434/chemrxiv-2024-fgzjq | Achieving Pressure Consistency in Mechanochemical Simulations of Chemical Reactions Under Pressure | The eXtended Hydrostatic Compression Force Field (X-HCFF) is a mechanochemical approach in which a cavity is used to exert hydrostatic pressure on a target system. The cavity used in this method is set up to represent the van-der-Waals (VDW) surface of the system by joining spheres sized according to the respective atomic VDW radii. The size of this surface can be varied via a scaling factor, and it can be shown that the compression forces exerted in X-HCFF in its current implementation depend on this factor. To address this dependency, we have developed a rescaling formalism for the applied forces, allowing us to drastically reduce the dependency of the compression forces on the chosen scaling factor. Independency from the scaling factor is important as the scaling of the VDW spheres is often used to ensure an overlap of cavities in supramolecular complexes, which is necessary for the simulation of chemical reactions. Our rescaling formalism reduces the empiricism of the X-HCFF approach and boosts its applicability in the field of computational high-pressure chemistry. | Jonas Bentrup; Rahel Weiß; Felix Zeller; Tim Neudecker | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f67e54cec5d6c1426408df/original/achieving-pressure-consistency-in-mechanochemical-simulations-of-chemical-reactions-under-pressure.pdf |
60c751a59abda215c3f8dc54 | 10.26434/chemrxiv.13194983.v1 | Iron Catalyzed α-C-H Cyanation of Simple and Complex Tertiary Amines | This manuscript details the development of a general and mild protocol for the α-C-H cyanation of tertiary amines as well as its application in late stage functionalization. Suitable substrates include tertiary aliphatic, benzylic, and aniline-type substrates as well as complex substrates. Functional groups tolerated under the reaction conditions include various heterocycles, as well as ketones, amides, olefins, and alkynes. This broad substrate scope is remarkable, as comparable reaction protocols for α-C-H cyanation frequently occur via free radical mechanisms, and are thus fundamentally limited in their functional group tolerance. In contrast, the presented catalyst system tolerates functional groups that typically react with free radicals, suggesting an alternative reaction pathway. All components of the described system are readily available, allowing implementation of the presented methodology without the need for lengthy catalyst synthesis. | Ozgur YIlmaz; Cagatay Dengiz; Marion Emmert | Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2020-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751a59abda215c3f8dc54/original/iron-catalyzed-c-h-cyanation-of-simple-and-complex-tertiary-amines.pdf |
60c749170f50db575b39686f | 10.26434/chemrxiv.12026736.v1 | PROTEIN-NUCLEIC ACID INTERFACE (PNAI) INHIBITOR DRUG MOLECULES FOR SARS-COV-2 | <p>In this research we used the structure of SARS-CoV-2
related, recently mapped, atomic
structure of nsp10/16 proteins for docking with some known drug molecular
structures at pH 7 and 5. Chosen
molecules were azo -N=N- and -COOH derivatives. It was revealed that the molecules
showed good binding energy with nsp10/16
protein at both pH. These molecules can act as protein-nucleic acid
interface (PNAI) inhibitor drug molecules. Such molecules can be used in
combination with polymerase and protease inhibitors for treatment of SARS-CoV-2.
</p> | Hamdullah Khadim Sheikh; Tanzila Arshad; Zainab Sher Mohammad; Iqra Arshad; Mohtasheemul Hassan | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749170f50db575b39686f/original/protein-nucleic-acid-interface-pnai-inhibitor-drug-molecules-for-sars-cov-2.pdf |
668ff5bb5101a2ffa8163f3b | 10.26434/chemrxiv-2024-t81cl | A New Time-resolved Luminescent Sensor | We present a new time-resolved chemosensor for the detection of Ba2+ ions. Our sensor is based on
an iridium(III) compound with dual (fluorescent and phosphorescent) emission. The nature of the
luminescent response of the sensor depends on its state; specifically, the phosphorescent emission of
the free state at long wavelengths is strongly suppressed, while that of the Ba2+-chelated compound
is strongly enhanced. Furthermore, the residual phosphorescent emission of the free compound
decays with two short decay constants, τ 1
free ∼ 3.5 ns (88%) and τ 2
free ∼ 209 ns (12%), while the
chelated compound decays with two long decay constants, τ 1ch ∼ 429 ns (21%) and τ 2 ch ∼ 1128 ns
(76%). This exceptional behaviour, supported by quantum chemical calculations, allows a time-
based separation between the signal of the free and the chelated species. Among other applications,
our sensor could be the basis of a Ba2+ tagging detector for neutrinoless double beta decay searches
in xenon. | Ane I. Aranburu; Mikel Elorza; Claire Tonnelé; Pablo R.G. Valle; Ariadna Pazos; Alexey Brodolin; Pablo Herrero-Gómez; J. Eduardo Barcelon; Gabriel Molina-Terriza; Francesc Monrabal; Celia Rogero; Fernando P. Cossío; Juan José Gómez-Cadenas; Zoraida Freixa; NEXT Collaboration | Materials Science; Organometallic Chemistry; Dyes and Chromophores; Photosensitizers; Transition Metal Complexes (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2024-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668ff5bb5101a2ffa8163f3b/original/a-new-time-resolved-luminescent-sensor.pdf |
65b370d666c13817294ec784 | 10.26434/chemrxiv-2024-3zrx2 | Predicting Solvatochromism of Chromophores in Proteins through QM/MM and Machine Learning | Solvatochromism occurs in both homogeneous solvents and more complex biological environments such as proteins. While in both cases the solvatochromic effects report on the surroundings of the chromophore, their interpretation in proteins becomes more complicated, not only because of structural effects induced by the protein pocket, but also because the protein environment is highly anisotropic. This is particularly evident for highly conjugated and flexible molecules such as carotenoids, whose excitation energy is strongly dependent on both the geometry and the electrostatics of the environment. Here we introduce a machine learning (ML) strategy trained on QM/MM calculations of geometrical and electrochromic contributions to carotenoids' excitation energies. We employ this strategy to compare the solvatochromism in protein and solvent environments. Despite the important specifities of the protein, ML models trained on solvents can faithfully predict excitation energies in the protein environment, demonstrating the robustness of the chosen descriptors. | Amanda Arcidiacono; Edoardo Cignoni; Patrizia Mazzeo; Lorenzo Cupellini; Benedetta Mennucci | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b370d666c13817294ec784/original/predicting-solvatochromism-of-chromophores-in-proteins-through-qm-mm-and-machine-learning.pdf |
6759c511085116a13314f215 | 10.26434/chemrxiv-2024-9cjzc-v4 | Techno-economic Analysis and Optimization of Water-Gas Shift Membrane Reactors for Low-Carbon Hydrogen Production | Hydrogen (H2) is an important energy carrier for transitioning into a decarbonized economy. H2-producing membrane reactors (MRs), such as those used for fuel reforming or water-gas shift reactions, can enable low-cost low-carbon H2 production from a variety of feedstocks, e.g., biomass, coal, or natural gas. This is a consequence of the enhanced feed utilization (i.e., kg of H2 produced per kg of
eed) for the MR compared to conventional multi-step H2 generation/purification schemes. Furthermore, H2 MRs simultaneously separate H2 and concentrate CO2, thereby increasing the overall process efficiency and facilitating pre-combustion carbon capture. This work describes an equation-oriented, technoeconomic optimization model for a water-gas shift membrane reactor (WGS-MR) integrated within a 155,000 kg·H2 day−1 capacity biomass gasification process with carbon capture to produce low-carbon H2. We
estimate using a WGS-MR decreased the levelized cost of H2 (LCOH) by ∼10% from $3.33 kg·H2−1 to $3.01 kg·H2−1 (2016 USD) compared to the baseline process with conventional WGS reactors and pressure swing adsorption. Sensitivity analysis elucidates the influence of operating conditions (e.g., temperature, pressure, space velocity) on performance (i.e., CO conversion, H2 recovery). Finally, we show that the LCOH could be further decreased to $2.57 kg·H2−1 (∼23% lower than the baseline) through feedstock blending (50 wt% biomass/50 wt% coal) or $2.17 kg·H2−1 (∼35% lower than the baseline) through onsite utilization of captured CO2 by avoiding transport and storage costs. This study provides a blueprint for applying MRs in low-carbon H2 production and motivates further studies on their optimal integration. | Damian T. Agi; Hani A.E. Hawa; Alexander W. Dowling; Kyle Hawley | Energy; Chemical Engineering and Industrial Chemistry; Natural Resource Recovery; Reaction Engineering; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6759c511085116a13314f215/original/techno-economic-analysis-and-optimization-of-water-gas-shift-membrane-reactors-for-low-carbon-hydrogen-production.pdf |
64b6f4cbb053dad33a7a30c6 | 10.26434/chemrxiv-2023-sxjng | Searching for heritability in prebiotically realistic membrane-bound systems | Membrane-bound compartments are ubiquitous in modern organisms meaning that they evolved early in Earth history. Vesicles composed of short-chain amphiphile molecules are some of the simplest prebiotically-plausible compartments and are capable of growth and division. Here we investigate the capacity of vesicle properties to transition between multiple metastable states in a historically contingent manner, thus implying heritability. We prepared 1:1 decanoic acid : decylamine vesicles in water or a mixture of organic compounds as might have been present on early Earth (EPS: enriched prebiotic soup). In some samples we added a detergent Triton X-100, which tends to increase vesicle size heterogeneity and promote vesicle remodeling. All four vesicle-containing mixtures were subjected to transfer-with-dilution: after a 24-hour incubation (one generation) we transferred 10% of the mix into 9X volume of a fresh, vesicle-containing mixtures. Sample with a history of transfer were compared to no-transfer controls (NTCs), which were initiated each generation using the same fresh vesicle-containing mixture but did not receive 10% of the prior generation. We compared transfer samples to NTCs for Nile Red fluorescence, vesicle size, and overall chemical composition, as measured by liquid chromatography/mass spectrometry (LC/MS). In samples with Triton, but not those without, we observe oscillation-like changes in Nile Red fluorescence, with significant temporal autocorrelation. In all samples, we observe non-linear changes in vesicle size over the course of 30 generations. Overall chemical composition did not change significantly due to transfers. These findings, while not definitive, suggest the possible presence of heritability in vesicles composed of short-chain amphiphiles. | Tymofii Sokolskyi; Pavani Ganju; Ronan Montgomery-Taylor; David Baum | Biological and Medicinal Chemistry; Earth, Space, and Environmental Chemistry; Biophysics; Chemical Biology; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b6f4cbb053dad33a7a30c6/original/searching-for-heritability-in-prebiotically-realistic-membrane-bound-systems.pdf |
644c14200d87b493e373c866 | 10.26434/chemrxiv-2023-b88nb | Crowding alters F-actin secondary structure and hydration | Actin, a key component of the cytoskeleton in eukaryotic cells, plays a crucial role in regulating cell morphology and transport. The morphology, mechanical, and biochemical properties of these filaments and bundles are determined by their monomer structure and by protein-protein contacts. Crowded environments are known to organize filaments into bundles. However, less is known how crowding and bundling affect the structure of F-actin. Here, we employed two-dimensional infrared (2D IR) spectroscopy and structure-based spectral calculations to investigate the morphology-dependent secondary-structure and local environments in filaments and weakly or strongly bundled networks. The results indicate that actin undergo secondary structural changes upon bundling, resulting in a decrease in beta-sheet and increase in the loop conformations. Moreover, strongly bundled networks experience a decrease in backbone solvent exposure, with relatively low perturbation of alpha-helix and the beta-sheet nearly ``locked" in buried positions. Similar changes are observed in the loops, which become less hydrated but exhibit a dynamic environment. In summary, our study provides insights into the structure and structure-dependent local environment of actin biopolymers under morphology control by PEG, emphasizing the significance of loop structure as a critical player in actin network morphology and stability. | Xiaobing Chen; Steven Roeters; Francis Cavanna; José Alvarado; Carlos Baiz | Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644c14200d87b493e373c866/original/crowding-alters-f-actin-secondary-structure-and-hydration.pdf |
60c74e49bdbb892c04a39b6c | 10.26434/chemrxiv.12732293.v1 | Controlling Pd Morphology in Electrodeposition from Nanoparticles to Dendrites via the use of Mixed Solvents | <p>By changing the mole fraction of water (cwater) in the solvent acetonitrile (MeCN), we report a simple procedure
to control nanostructure morphology during electrodeposition. We focus on the
electrodeposition of palladium (Pd) on electron beam transparent boron-doped
diamond (BDD) electrodes. Three solutions are employed MeCN rich (90% v/v MeCN,
cwater = 0.246), equal volumes (50% v/v
MeCN, cwater = 0.743) and water rich (10% v/v
MeCN, cwater = 0.963) with electrodeposition
carried out under diffusion-controlled conditions for fixed time periods (50,
150 and 300 s). Scanning transmission electron microscopy (STEM) reveals that
in MeCN rich solution, Pd atoms, amorphous atom clusters and (majority) nanoparticles
(NPs) result. As water content is increased, NPs are again evident but also
elongated and defected nanostructures which grow in prominence with time. In
the water rich environment, NPs and branched, concave<sup> </sup>and star-like
Pd nanostructures are now seen, which with time translate to aggregated porous
structures and ultimately dendrites. We attribute these observations to the
role MeCN adsorption on Pd surfaces plays in retarding metal nucleation and
growth.</p> | Haytham Hussein; Houari Amari; Ben Breeze; Richard Beanland; Julie Macpherson | Aggregates and Assemblies; Catalysts; Nanostructured Materials - Materials; Electrochemical Analysis; Nanofabrication; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e49bdbb892c04a39b6c/original/controlling-pd-morphology-in-electrodeposition-from-nanoparticles-to-dendrites-via-the-use-of-mixed-solvents.pdf |
62c7271b332f0246ccdf786d | 10.26434/chemrxiv-2022-g5qfr | Using Genetic Algorithms to Discover Novel Ground- State Triplet Conjugated Polymers | Stable ground-state triplet π-conjugated copolymers have many interesting electronic and optoelectronic properties. However, the large number of potential monomer combinations makes it impractical to synthesize or even just use density functional theory (DFT) to calculate their triplet ground-state stability. Here, we present a genetic algorithm implementation that uses the semi-empirical GFN2- xTB to find ground-state triplet polymer candidates. We find over 1400 polymer candidates with a triplet ground-state stability of up to 4 eV versus the singlet. Additionally, we explore the properties of the monomers of those candidates in order to understand the design rules which promote the formation of a stable ground-state triplet in π-conjugated polymers. | Omri Abarbanel; Geoffrey Hutchison | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Properties; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c7271b332f0246ccdf786d/original/using-genetic-algorithms-to-discover-novel-ground-state-triplet-conjugated-polymers.pdf |
66a153f901103d79c5885be9 | 10.26434/chemrxiv-2024-2h7kn-v2 | Role of grain-level chemo-mechanics in composite cathode degradation of solid-state lithium batteries | Solid-state Li-ion batteries, utilizing Ni-rich oxide cathodes, hold promise for high-energy electrochemical storage. However, Li intercalation-induced dimensional changes can lead to crystal defect formation in these cathodes, and contact mechanics problems between cathode and solid electrolyte. Understanding the interplay between cathode microstructure, operating conditions, micromechanics of battery materials, and capacity decay remains a challenge. Here, we present a microstructure-sensitive chemo-mechanical model to study the impact of grain-level chemo-mechanics on the degradation of composite cathodes. We reveal that crystalline anisotropy, state-of-charge-dependent Li diffusion rates, and lattice dimension changes drive dislocation formation in cathodes and contact loss at the cathode/electrolyte interface. These dislocations induce large lattice strain and trigger oxygen loss and structural degradation preferentially near the surface area of cathode particles. Moreover, contact loss is caused by the micromechanics resulting from the crystalline anisotropy of cathodes and the mechanical properties of solid electrolytes, not just operating conditions. These findings highlight the significance of grain-level cathode microstructures in causing cracking, formation of crystal defects, and chemo-mechanical degradation of solid-state batteries. | Chuanlai Liu; Franz Roters; Dierk Raabe | Energy; Energy Storage | CC BY 4.0 | CHEMRXIV | 2024-07-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a153f901103d79c5885be9/original/role-of-grain-level-chemo-mechanics-in-composite-cathode-degradation-of-solid-state-lithium-batteries.pdf |
66e2164312ff75c3a11287f6 | 10.26434/chemrxiv-2024-spksf-v2 | Chemoinformatic characterization of NAPROC-13: A database for natural product 13C NMR dereplication | Natural products (NPs) are secondary metabolites of natural origin with broad applications across various human activities, particularly discovering bioactive compounds. Structural elucidation of new NPs entails significant cost and effort. On the other hand, the dereplication of known compounds is crucial for the early exclusion of irrelevant compounds in contemporary pharmaceutical research. NAPROC-13 stands out as a publicly accessible database, providing structural and 13C NMR spectroscopic information for over 25,000 compounds, rendering it a pivotal resource in natural product (NP) research, favoring open science. This study seeks to quantitatively analyze the chemical content, structural diversity, and chemical space coverage of NPs within NAPROC-13, compared to FDA-approved drugs and a very diverse subset of NPs, UNPD-A. Findings indicated that NPs in NAPROC-13 exhibit comparable properties to those in UNPD-A, albeit showcasing a notably diverse array of structural content, scaffolds, ring systems of pharmaceutical interest, and molecular fragments. NAPROC-13 covers a specific region of the chemical multiverse (a generalization of the chemical space from different chemical representations) regarding physicochemical properties and a region as broad as UNPD-A in terms of structural features represented by fingerprints. | Juan F. Avellaneda-Tamayo; Naicolette A. Agudo-Muñoz; Javier E. Sánchez-Galán; José Luis López-Pérez; José L. Medina-Franco | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e2164312ff75c3a11287f6/original/chemoinformatic-characterization-of-naproc-13-a-database-for-natural-product-13c-nmr-dereplication.pdf |
61f9d733e59d8774a451dcb7 | 10.26434/chemrxiv-2022-6s38f | Towards hydrogen and halogen bonded frameworks based on 3,5-bis(triazolyl)pyridinium motifs
| We attempted to use hydrogen, iodo and seleno 3,5-bis(triazolyl)pyridinium (btp) motifs to form 3D supramolecular frameworks assembled by hydrogen, halogen or chalcogen bonding to anions. Initially, we prepared flexible ditopic and tetratopic receptors where the pyridinium nitrogen atom was functionalized with a benzylic group but were unable to crystallise extended frameworks. We subsequently developed the use of Zincke methodology to prepare rigid ditopic and tetratopic hydrogen and halogen bonding tectons, and were able to crystallize the sulfate derivative of a tetratopic receptor, although unfortunately this did not have the desired open framework. Several crystal structures were obtained with the receptors and monovalent anions, including one containing an unusually short iodotriazole∙∙∙Cl– halogen bond. Generally, the btp triazole groups show a tendency to rotate away from the desired conformation and it appears that this may contribute to difficulties in obtaining 3D frameworks even when the receptors have a rigid core. | Emer Foyle; Hui Min Tay; Nicholas White | Organic Chemistry; Inorganic Chemistry; Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.); Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f9d733e59d8774a451dcb7/original/towards-hydrogen-and-halogen-bonded-frameworks-based-on-3-5-bis-triazolyl-pyridinium-motifs.pdf |
60c74bb20f50db77b6396ca6 | 10.26434/chemrxiv.12370469.v1 | HaloTag-Targeted Sirtuin Rearranging Ligand (SirReal) for the Development of Proteolysis Targeting Chimeras (PROTACs) Against the Lysine Deacetylase Sirtuin 2 (Sirt2) | We have discovered the sirtuin rearranging ligands (SirReals) as a novel class of highly potent and selective inhibitors of the NAD+-dependent lysine deacetylase sirtuin 2 (Sirt2). In previous studies, conjugation of a SirReal with a ligand for the E3 ubiquitin ligase cereblon to form a so-called proteolysis targeting chimera (PROTAC), enabled small molecule-induced degradation of Sirt2. Here, we report the structure-based development of a chloroalkylated SirReal that induces the degradation of Sirt2 mediated by Halo-tagged E3 ubiquitin ligases. Using this orthogonal approach for Sirt2 degradation, we show that also other E3 ligases than cereblon, such as the E3 ubiquitin ligase parkin, can be harnessed for small molecule-induced Sirt2 degradation, thereby emphasizing the great potential of parkin to be utilized as an E3 ligase for new PROTACs approaches. Thus, our study provides new insights into targeted protein degradation in general and Sirt2 degradation in particular. | Matthias Schiedel; Attila Lehotzky; Sándor Szunyogh; Judit Oláh; Sören Hammelmann; Nathalie Wössner; Dina Robaa; Oliver Einsle; Wolfgang Sippl; Judit Ovádi; Manfred Jung | Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bb20f50db77b6396ca6/original/halo-tag-targeted-sirtuin-rearranging-ligand-sir-real-for-the-development-of-proteolysis-targeting-chimeras-prota-cs-against-the-lysine-deacetylase-sirtuin-2-sirt2.pdf |
63c608a07c5fef5f0324298f | 10.26434/chemrxiv-2023-qf1k5 | Site-Selective C–H Alkenylation of N-Heteroarenes by Ligand-Directed Co/Al and Co/Mg Cooperative Catalysis | We report herein the design and development of cobalt/aluminum- and cobalt/magnesium bimetallic catalysts, supported by a phosphine/secondary phosphine oxide (PSPO) bifunctional ligand, for the site-selective C–H alkenylation of nitrogen-containing heteroaromatic compounds with alkynes. These catalysts enable the alkenylation of pyridine, pyridone, and imidazo[1,2-a]pyridine derivatives at the C–H site proximal to the Lewis basic nitrogen or oxygen atom, which represents a selectivity profile distinct from that of the previously developed cobalt–diphosphine/aluminum Lewis acid catalyst. The alkenylated products were obtained in moderate to good yields with syn-selectivity across various heterocycles as well as differently substituted internal alkynes. Kinetic isotope effect experiments on the pyridine C–H alkenylation suggest that the C–H activation occurs in an irreversible manner, while its relevance to the rate-limiting step depends on the reaction conditions. Density functional theory calculations indicate that ligand-to-ligand hydrogen transfer is the mechanism that operates commonly across the substrates used in the present study. | Naohiko Yoshikai; Yuri Saito; Jun Kikuchi; Chen Wang | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2023-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c608a07c5fef5f0324298f/original/site-selective-c-h-alkenylation-of-n-heteroarenes-by-ligand-directed-co-al-and-co-mg-cooperative-catalysis.pdf |
60c74146bb8c1a41473d9ef2 | 10.26434/chemrxiv.7993607.v1 | “Ghost Peak” Driven Structural Elucidation of a Photocatalytic Degradation Product from Brexpiprazole | <p><b> </b>Brexpiprazole
which marketed as Rexulti<sup>® </sup>is a second-generation
atypical
antipsychotic. A seemingly
random and uncontrollable “ghost
peak” that vary from below the detection limit to ∼0.2% was observed occasionally during the
development of HPLC method for brexpiprazole drug substance. The “ghost peak”
was finally characterized as a <i>syn</i> head-to-tail dimer
of brexpiprazole by UV, IR, LC–MS/TOF, 1D and 2D NMR. It was formed rapidly through
photocatalytic [2 + 2] pericyclic reaction and can reach approximately
1.7% in five minutes once the analytes were exposed to sunlight at noon. By
contrast, the occurrence of this “ghost peak” in
brexpiprazole can be suppressed when the solutions were prepared and stored
away from sunlight.</p> | Tao Zhuang; Fang Du; Jing Li; Haiqing Wang; Liang Chen; Bifeng Liu; Guisen Zhang | Organic Compounds and Functional Groups; Spectroscopy (Anal. Chem.); Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74146bb8c1a41473d9ef2/original/ghost-peak-driven-structural-elucidation-of-a-photocatalytic-degradation-product-from-brexpiprazole.pdf |
60c740e4bdbb89762ca3822c | 10.26434/chemrxiv.7868351.v1 | PT-Symmetry in Hartree–Fock Theory | <div>
<div>
<p>P T -symmetry — invariance with respect to combined space reflection P and time reversal T — provides a weaker condition than (Dirac) Hermiticity for ensuring a real energy spectrum of a general non-Hermitian Hamiltonian. PT -symmetric Hamiltonians therefore form an intermediate class between Hermitian and non-Hermitian Hamiltonians. In this work, we derive the conditions for PT-symmetry in the context of electronic structure theory, and specifically, within the Hartree–Fock (HF) approximation. We show that the HF orbitals are symmetric with respect to the P T operator if and only if the effective Fock Hamiltonian is PT -symmetric, and vice versa. By extension, if an optimal self-consistent solution is invariant under PT , then its eigenvalues and corresponding HF energy must be real. Moreover, we demonstrate how one can construct explicitly PT -symmetric Slater determinants by forming PT doublets (i.e. pairing each occupied orbital with its PT -transformed analogue), allowing PT -symmetry to be conserved throughout the self-consistent process. Finally, considering the H2 molecule as an illustrative example, we observe PT-symmetry in the HF energy landscape and find that the symmetry-broken unrestricted HF wave functions (i.e. diradical configurations) are P T -symmetric, while the symmetry-broken restricted HF wave functions (i.e. ionic configurations) break PT -symmetry.</p>
</div>
</div> | Hugh G.
A. Burton; Alex Thom; Pierre-Francois Loos | Theory - Computational; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e4bdbb89762ca3822c/original/pt-symmetry-in-hartree-fock-theory.pdf |
667b20105101a2ffa87e38af | 10.26434/chemrxiv-2024-qx0k8 | Multifarious Heteroatom-doped/enriched Carbon-based Materials for Energy Storage Prospectives: A Crucial Insight | Chemically doped carbon-based candidates have emerged as a significant driving force across multifarious research domains including ORR, electrochemical sensing, Energy storage and conversion, and solar cell technologies, etc., This comprehensive review takes a critical stance, shedding light on the exceptional supercapacitance performance found within heteroatom-doped/enriched carbon derivatives. This includes an array of candidates such as graphene, carbon nanotubes, carbon nanofibers, boron carbonitride, g-C3N4, mesoporous carbon, ordered mesoporous carbon, and oxygen-enriched porous carbon. The review delves into diverse synthetic methodologies, encompassing chemical vapor deposition, thermal annealing, hydrothermal, microwave routes, and arc discharge techniques for each of these carbon-based materials. Furthermore, an in-depth exploration of the underlying electrochemical mechanisms governing supercapacitive performance is provided. Notably, the synthesis and energy storage proficiency of heteroatom-enriched materials like g-C3N4 and BCN are meticulously scrutinized. The influence of heteroatom doping on crucial characteristics like wettability, and porosity is deeply examined, boosted by compelling empirical substantiation. Adding intrigue, the merits, and drawbacks inherent to each synthetic approach are thoughtfully presented systematically. As a result, this article stands as a highly valuable resource, offering substantial support and insightful information tailored to young researchers. By furnishing a panoramic survey of diverse synthetic avenues and an in-depth analysis of supercapacitive performances across distinct classes of heteroatom-doped/enriched carbon materials, we aspire for this work to become an indispensable reference. | Suresh Balaji Srinivasan; Sangamithirai Devendiran; Kirankumar Venkatesan Savunthari; Pandurangan Arumugam; Sanjeev Mukerjee | Physical Chemistry; Energy; Energy Storage; Physical and Chemical Properties; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667b20105101a2ffa87e38af/original/multifarious-heteroatom-doped-enriched-carbon-based-materials-for-energy-storage-prospectives-a-crucial-insight.pdf |
60c73dd7bb8c1a6f273d981c | 10.26434/chemrxiv.6209984.v1 | A New Adsorption Rate Equation in Batch Systems | <p><b>In
this paper, the deficiencies and cause of previous adsorption kinetic models
were revealed, new adsorption rate equation has been proposed and its validities
were verified by kinetic analysis of various experimental data.</b> <b>This
work is a new view on the adsorption kinetics rather than a comment on the
previous adsorption papers.</b></p> | yongson hong; Kye-Ryong Sin; Jong-Su Pak; Chol-Min Pak | Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2018-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd7bb8c1a6f273d981c/original/a-new-adsorption-rate-equation-in-batch-systems.pdf |
60c74c9d702a9b861a18b6cd | 10.26434/chemrxiv.12488525.v1 | Recent Advances in Stereochemistry Reveal Classification Shortcomings | We contend that the
Polytope model utilized by IUPAC to specify stereoisomerism for species ML<i><sub>n</sub></i> with <i>n</i> > 3 should be universally applied. Such application recently led to the
synthesis of isolable compounds displaying a new fundamental form of isomerism,
akamptisomerism, pertinent to ML<sub>2</sub> stereocenters. We review 443807
molecules that could be classified as akamptisomers. Some akamptisomers are described as being
“wrong” by existing IUPAC rules, hindering molecular conception. For many classes of medicinal and technology-related
molecules, software packages like ChemDraw mostly do not handle akamptisomers
correctly, databases such as CAS provide 2D representations inconsistent with
those presented in the original publications, and often the akamptisomeric
identity of compounds remains unknown.
These features hinder both human and machine-learning approaches to
chemical design. Further, the existence
of previously unrecognized isomeric forms has broad implications for patents
and pharmaceutical-registration requirements. Hence, the immediate
re-examination of stereochemistry is demanded. | Peter J. Canfield; Linda J. Govenlock; Jeffrey Reimers; Maxwell J. Crossley | Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c9d702a9b861a18b6cd/original/recent-advances-in-stereochemistry-reveal-classification-shortcomings.pdf |
60c75768f96a004e62288c63 | 10.26434/chemrxiv.13679143.v2 | Ligand-Metal Charge Transfer Induced via Adjustment of Textural Properties Controls the Performance of Single-Atom Catalysts During Photocatalytic Degradation | Because of their peculiar nitrogen-rich
structure, carbon nitrides are convenient polydentate ligands for designing
single-atom-dispersed photocatalysts. However, the relation of catalysts
textural properties with their photophysical properties and as a result
activity in photocatalytic applications is rarely elaborated. Herein we report
the preparation and characterization of a series of single-atom heterogeneous
catalysts featuring highly-dispersed Ag and Cu species on mesoporous graphitic
C<sub>3</sub>N<sub>4</sub>. We show that adjustment of materials textural
properties and thereby metal single atoms coordination mode enables ligand-to-metal
(LMCT) or ligand-to-metal-to-ligand charge transfer (LMLCT), a property tha was
long speculated in single-atom catalysis but never observed. We employ the
developed materials in the degradation of organic pollutant under irradiation
with visible light. Kinetic investigations under flow conditions show that
single atoms of Ag and Cu decrease the amount of toxic organic fragmentation
products, while leading to a higher selectivity towards full calcination. The
results correlate with the selected mode of charge transfer in the designed
photocatalysts and provide a new understanding of the surface state
of single-atom catalysts. The concepts can be exploited further to rationally
design and optimize other single-atom materials. | Jiaxu Liu; Yajun Zou; Daniel Cruz; Aleksandr Savateev; Markus Antonietti; Gianvito Vilé | Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75768f96a004e62288c63/original/ligand-metal-charge-transfer-induced-via-adjustment-of-textural-properties-controls-the-performance-of-single-atom-catalysts-during-photocatalytic-degradation.pdf |
62dab9db3787f1c14dc1fa9e | 10.26434/chemrxiv-2022-phxng-v2 | Mechanistic Insights of IscU Conformation Regulation for Fe–S Cluster Biogenesis Revealed by Variable-Temperature Electrospray Ionization Native Ion Mobility Mass Spectrometry | ABSTRACT: Iron-sulfur (Fe-S) cluster cofactors are required for the function of many critical cellular processes. These cofactors are assembled and inserted into apo target proteins by conserved Fe-S cluster biosynthetic pathways. In the ISC system of E. coli, the scaffold protein IscU assembles Fe-S cluster intermediates from iron, electrons, and inorganic sulfur, which is provided by the cysteine desulfurase enzyme IscS. IscU also binds to Zn, which mimics and competes for binding with the Fe-S cluster. Crystallographic and nuclear magnetic resonance (NMR) spectroscopic studies reveal that IscU is a metamorphic protein that exists in multiple conformational states, which include at least a structured form and a disordered form. The structured form of IscU is favored by metal binding and is stable in a narrow temperature range, undergoing both cold and hot denaturation. However, there is controversy over whether the structured or disordered form of IscU binds to IscS and functions in Fe-S cluster assembly. The recent development of variable-temperature electrospray ionization (vT-ESI) native ion mobility mass spectrometry (nIM-MS) enables probing the temperature dependence of macromolecular conformation and binding events in a single experiment. Here, vT-ESI nIM-MS results established that IscU exists in structured, intermediate, and disordered conformations. IscU samples shift towards high-charge states that have more extended conformations under extreme temperatures, consistent with cold/heat denaturation. A comparison of Zn-IscU and apo-IscU reveals that Zn(II) binding (i) attenuates the cold/heat-denaturation of IscU and promotes the refolding of IscU; (ii) favors the structured aand intermediate conformations and inhibits the disordered high charge states; and (iii) attenuates collisional induced unfolding (CIU) of intermediate conformations. Moreover, IscS was shown to alter the local conformation around the IscU active site, resulting in weakened Zn(II) affinity. Overall, these findings provide structural rationalization of the role of Zn(II) on stabilizing IscU conformation and the role of IscS on altering the IscU active site to prepare for Zn(II) release and cluster synthesis. This work highlights how vT-ESI-nMS can be applied as a powerful tool in mechanistic enzymology by providing details of relationships among temperature, protein conformations, and ligand/protein binding. | Cheng-Wei Lin; Shelby D. Oney-Hawthorne; Syuan-Ting Kuo; David P. Barondeau; David H. Russell | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62dab9db3787f1c14dc1fa9e/original/mechanistic-insights-of-isc-u-conformation-regulation-for-fe-s-cluster-biogenesis-revealed-by-variable-temperature-electrospray-ionization-native-ion-mobility-mass-spectrometry.pdf |
6398c7ba04bc66e09214d22f | 10.26434/chemrxiv-2022-b56l1 | Proton-Coupled Triplet-Triplet Energy Transfer: Carbon Monoxide Photorelease from Porphyrin-Flavonol Hybrids | A new photochemical mechanism, termed proton-coupled
energy transfer (PCEnT), was recently
discovered in anthracene-phenol-pyridine triads
(Pettersson Rimgard et al., Science 2022, 377,
742). It couples an electronic transition to nuclear
motions allowing Förster (dipole-dipole) energy
transfer even though there is no overlap of the
donor emission and acceptor absorption spectra.
Here, we extend this concept to triplet-triplet
energy transfer (TEnT) from light-harvesting
porphyrin to a covalently bound flavonol group. While direct TEnT to the flavonol acceptor would be
highly endergonic, it becomes feasible thanks to the flavonol energy stabilization upon intramolecular
proton transfer in the triplet state. We describe the overall mechanism as proton-coupled TEnT
(PCTEnT) – a one-photon process that enables the activation of a UV-absorbing chromophore by visible
light. Several porphyrin-flavonol hybrids containing 4 flavonol units attached to the porphyrin meso
positions were designed as photoactivatable carbon monoxide (CO)-releasing molecules
(photoCORMs). The photoreaction mechanism was studied by steady-state and transient absorption
spectroscopy techniques and complementary quantum-chemical calculations. While intrinsically toxic,
CO is an endogenous signaling molecule with therapeutic potential that regulates various physiological
processes, and photoCORMs offer precise spatial and temporal control of CO administration. We
evaluated the viability of the human hepatoblastoma HepG2 cells in the presence of the studied hybrids
and tested the effects associated with the intracellular release of CO and the production of singlet
oxygen. We demonstrate that the PCTEnT process could be used to devise new photoactivatable
molecular devices with potential biological applications. | Andrea Ramundo; Jiri Janos; Lucie Muchova; Maria Srankova; Libor Vitek; Petr Slavicek; Petr Klán | Physical Chemistry; Organic Chemistry; Photochemistry (Physical Chem.); Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6398c7ba04bc66e09214d22f/original/proton-coupled-triplet-triplet-energy-transfer-carbon-monoxide-photorelease-from-porphyrin-flavonol-hybrids.pdf |
60c744fc469df46c73f43427 | 10.26434/chemrxiv.9942038.v1 | Tyrosinase-Mediated Oxidative Coupling of Tyrosine Tags on Peptides and Proteins | We report a strategy for chemical protein modification by using tyrosinase enzymes to oxidize exposed tyrosine residues on protein N or C-termini. We explore the chemical space for coupling partners in this reaction and find combinations that can proceed in near quantitative conversion. This strategy is used to conjugate a dye onto a Trastuzumab antibody fragment and a Protein L fragment and demonstrate that these constructs can be used as immunostaining reagents. | Alan Marmelstein; Marco Lobba; Casey S. Mogilevsky; Johnathan Maza; Daniel D. Brauer; Matthew Francis | Bioengineering and Biotechnology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744fc469df46c73f43427/original/tyrosinase-mediated-oxidative-coupling-of-tyrosine-tags-on-peptides-and-proteins.pdf |
60c7453b702a9bb38e18a998 | 10.26434/chemrxiv.9985124.v1 | The Dynamic Ligand Field of a Molecular Qubit: Decoherence Through Spin–Phonon Coupling | Quantum coherence of S = 1/2 transition metal-based quantum bits (qubits) is strongly influenced by the magnitude of spin–phonon coupling. While this coupling is recognized as deriving from dynamic distortions about the first coordination sphere of the metal, a general model for understanding and quantifying ligand field contributions has not been established. Here we derive a general ligand field theory model to describe and quantify the nature of spin–phonon coupling terms in S = 1/2 transition metal complexes. We show that the coupling term for a given vibrational mode is governed by: 1) the magnitude of the metal-based spin–orbit coupling constant, 2) the magnitude and gradient in the ligand field excited state energy, and 3) dynamic relativistic nephelauxetic contributions reflecting the magnitude and gradient in the covalency of the ligand–metal bonds. From an extensive series of density functional theory (DFT) and time-dependent DFT (TDDFT) calculations calibrated to a range of experimental data, spin–phonon coupling terms describing minimalistic <i>D</i><sub><i>4h</i></sub>/<i>D</i><sub><i>2d</i></sub> [CuCl<sub>4</sub>]<sup>2-</sup> and <i>C</i><sub><i>4v</i></sub> [VOCl<sub>4</sub>]<sup>2-</sup> complexes translate to and correlate with experimental quantum coherence properties observed for Cu(II)- and V(IV)-based molecular qubits with different ligand sets, geometries, and coordination numbers. While providing a fundamental framework and means to benchmark current qubits, the model and methodology described herein can be used to screen any S = 1/2 molecular qubit candidate and guide the discovery of room temperature coherent materials for quantum information processing. | Ruben Mirzoyan; Ryan Hadt | Magnetism; Spectroscopy (Inorg.); Theory - Inorganic; Transition Metal Complexes (Inorg.); Theory - Computational; Quantum Computing; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7453b702a9bb38e18a998/original/the-dynamic-ligand-field-of-a-molecular-qubit-decoherence-through-spin-phonon-coupling.pdf |
6549cec0c573f893f1f96b14 | 10.26434/chemrxiv-2023-9c2v5 | Correlating Kinetics and Thermodynamics of Conformational Changes in Ammonium Complexes of a Flexible Naphthocage | Although conformational changes are fundamental processes in many natural and synthetic supramolecular systems, understanding of the relationship between conformational kinetics and thermodynamics of host-guest binding is very limited because low-energy structural changes are usually fast and difficult to monitor. Described in this work is a kinetic study of the conformational conversion of the inclusion complexes consists of a flexible naphthocage host and quaternary ammonium guests featuring a relatively slow “guest dissociation-host conformational change-guest re-association” con-formational exchange mechanism. For guests of comparable structural features, the overall rate of the conformational change is found to be inversely correlated to the thermodynamic stability of the host-guest complexes, which in turn is related to both the overall structure and local steric properties of the guests. Results from this work that bridge the kinet-ics and thermodynamics of molecular recognition to conformational changes are valuable for an in-depth understanding of the kinetic contributions in guest binding and selectivity. | Shan He; Mao Quan; Liu-Pan Yang; Ho Yu Au-Yeung; Wei Jiang | Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6549cec0c573f893f1f96b14/original/correlating-kinetics-and-thermodynamics-of-conformational-changes-in-ammonium-complexes-of-a-flexible-naphthocage.pdf |
60c74631bb8c1a03ad3da82a | 10.26434/chemrxiv.11094986.v1 | Insight on the Factors Controlling the Equilibrium of Allylic Azides | <p>Several
allylic azides with different double bond substitution were studied to
understand the factors governing their equilibrium using density functional
theory along with quantum theory of atoms in molecules, Non-covalent Interactions
and Natural Bond Orbitals approaches. The results showed the hydroxyl group or
heteroatoms in allylic azides interact with the molecule through an
electrostatic weak interaction in each pair of regioisomers. The equilibrium
shifts of substituted allylic azides, compared to non-substituted allylic
azides, are not attributed to the presence of specific interactions, such as
hydrogen bond. The observed equilibrium shifts stem mainly from the strengthening
and weakening of negative
hyperconjugative interactions, which is affected by the weak interaction
involving the proximal substituent in each regioisomer. A good linear correlation
was obtained between the hyperconjugative energies of pC=C→s*<i>Z</i><sub>b</sub> interactions and the calculated percentages of
secondary azide and tertiary azides in the equilibrium mixture. Also, the
effect of aromatic ring substituent was analysed using such approaches. This
study not only provides insight into the factor controlling the stabilities of
the substituted allylic azides, but also settle the basis to predict the regioisomer predominance in
the equilibrium mixture.</p> | Margarita Vallejos; Guillermo Labadie | Physical Organic Chemistry | CC BY NC 4.0 | CHEMRXIV | 2019-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74631bb8c1a03ad3da82a/original/insight-on-the-factors-controlling-the-equilibrium-of-allylic-azides.pdf |
666c53df01103d79c536c54a | 10.26434/chemrxiv-2024-1bwbj | Structure-reactivity relationships in a small library of imine-type dynamic covalent materials: Determination of rate and equilibrium constants enables model prediction and validation of a unique mechanical softening in dynamic hydrogels | The development of next generation soft and recyclable materials prominently features the use of dynamic (reversible) chemistries such as host-guest, supramolecular, and dynamic covalent. The advantages of dynamic systems are their injectability (shear-thinning and self-healing), reprocessability, and dynamic (time-dependent) mechanical properties, sometimes uncovering unique behavior or functions in the desired application. These properties arise from the inherent relationship between the rate and equilibrium constants (RECs) of molecular junctions (cross-links) and the resulting macroscopic behavior of dynamic networks. However, there are few examples of explicitly measured rate and equilibrium constants establishing this connection between RECs and materials properties, particularly for polymeric hydrogel systems. Here we use dynamic covalent imine formation to study how single-point compositional changes in amine nucleophiles affect binding constants and resulting hydrogel mechanical properties. We find that there is over a 3 decade change in RECs, in both model small molecule studies and model polymeric backbones. Based on established relationships in the literature, we then developed a simple model to describe the cross-linking equilibrium and predict changes in hydrogel mechanical properties. This allowed us to uncover a regime where adding crosslinker before saturation can decrease the crosslink density of a hydrogel. Having determined explicit equilibrium constants, we were then able to demonstrate the veracity of this predicted behavior experimentally. Notably this emergent behavior is not accounted for in covalent hydrogel theory. This study expands upon the structure-reactivity relationships for imine formation, highlighting how quantitative determination of rate and equilibrium constants facilitates predicting the macroscopic behavior of soft materials. Furthermore, while the present study focuses on dynamic covalent imine formation, the underlying principles of this work are applicable to the general bottom-up design of soft and recyclable dynamic materials. | Francis Luke Culliford Morgan; Ivo Anton Octave Beeren; Jurica Bauer; Lorenzo Moroni; Matthew Brandon Baker | Physical Chemistry; Polymer Science; Hydrogels; Chemical Kinetics; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666c53df01103d79c536c54a/original/structure-reactivity-relationships-in-a-small-library-of-imine-type-dynamic-covalent-materials-determination-of-rate-and-equilibrium-constants-enables-model-prediction-and-validation-of-a-unique-mechanical-softening-in-dynamic-hydrogels.pdf |
630d1f6f90802d52c16eceb2 | 10.26434/chemrxiv-2022-4g7rx | An ecosystem for digital reticular chemistry | The space of all plausible materials for a given application is so large that it cannot be explored using a brute-force approach.
This is, in particular, the case for reticular chemistry which provides materials designers with a practically infinite playground on different length scales.
One promising approach to guide the design and discovery of materials is machine learning, which typically involves learning a mapping of structures onto properties from data.
While there have been plenty of examples of the use of machine learning for reticular materials, the progress in the field seems to have stagnated.
From our perspective, an important reason is that digital reticular chemistry is still more an art than a science in which many parts are only accessible to experienced groups. The lack of standardization across all the steps of the machine learning pipeline makes it practically impossible to directly compare machine learning models and build on top of prior results.
To confront these challenges, we present mofdscribe: a software ecosystem that accompanies—seasoned as well as novice—digital reticular chemists on all steps from ideation to model publication.
Our package provides reference datasets (including a completely new one), more than 35 reported as well as completely novel featurization strategies, data splitters, and validation helpers which can be used to benchmark new modeling strategies on standard benchmark tasks and to report the results on a public leaderboard.
We envision that this ecosystem allows for a more robust, comparable, and productive area of digital reticular chemistry. | Kevin Maik Jablonka; Andrew S. Rosen; Aditi S. Krishnapriyan; Berend Smit | Theoretical and Computational Chemistry; Materials Science; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630d1f6f90802d52c16eceb2/original/an-ecosystem-for-digital-reticular-chemistry.pdf |
60c74666469df47973f4363e | 10.26434/chemrxiv.8798285.v2 | Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics. | <div><div><div><p>SAXS experiments provide low-resolution but valuable information about the dynamics of biomolecular systems, which could be ideally integrated into MD simulations to accurately determine conformational ensembles of flexible proteins. The applicability of this strategy is hampered by the high computational cost required to calculate scattering intensities from three-dimensional structures. We previously presented a hybrid resolution method that makes atomistic SAXS-restrained MD simulation feasible by adopting a coarse-grained approach to efficiently back-calculate scattering intensities; here, we extend this technique, applying it in the framework of metainference with the aim to investigate the dynamical behavior of flexible biomolecules. The efficacy of the method is assessed on the K63-diubiquitin, showing that the inclusion of SAXS-restraints is effective in generating a reliable conformational ensemble, improving the agreement with independent experimental data.</p></div></div></div> | Cristina Paissoni; Alexander Jussupow; Carlo Camilloni | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74666469df47973f4363e/original/determination-of-protein-structural-ensembles-by-hybrid-resolution-saxs-restrained-molecular-dynamics.pdf |
61d5a13381f3fe21639ad5c9 | 10.26434/chemrxiv-2022-2ssz2-v3 | Silicon-Vacancy Nanodiamonds as High Performance Near-Infrared Emitters for Live-Cell Dual-Color Imaging and Thermometry | Nanodiamonds (NDs) with color centers are excellent emitters for various bioimaging and quantum biosensing applications. In our work, we explored new applications of NDs with silicon-vacancy centers (SiV) obtained by high-pressure high-temperature (HPHT) synthesis based on metal-catalyst-free growth. They are coated with a polypeptide biopolymer which is essential for efficient cellular uptake. The unique optical properties of NDs with SiV are their high photostability and narrow emission in the near-infrared region. Our results demonstrate for the first time that NDs with SiV allow live-cell dual-color imaging and intracellular tracking. Also, intracellular thermometry as well as challenges associated with SiV atomic defects in NDs are investigated and discussed for the first time. NDs with SiV nanoemitters provide new avenues for live-cell bioimaging, diagnostic (SiV as a nanosized thermometer), and theranostic (nanodiamonds as drug carrier) applications. | Weina Liu; Md Noor A Alam; Yan Liu; Viatcheslav N. Agafonov; Haoyuan Qi; Kaloian Koynov; Valery A. Davydov; Rustem Uzbekov; Ute Kaiser; Theo Lasser; Fedor Jelezko; Tanja Weil; Anna Ermakova | Materials Science; Nanoscience; Biocompatible Materials; Carbon-based Materials; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d5a13381f3fe21639ad5c9/original/silicon-vacancy-nanodiamonds-as-high-performance-near-infrared-emitters-for-live-cell-dual-color-imaging-and-thermometry.pdf |
60c743e09abda27983f8c253 | 10.26434/chemrxiv.9307844.v2 | Adhesion-Peptide Conjugates of Thermo-Responsive Polymers Co-Electrospun into Fibrous Scaffolds Enable Growth and Enzyme-Free Recovery of Quiescent Human Corneal Stromal Cells (hCSCs) | <p>Here we report the development of a PLA/thermo-responsive (PDEGMA) blend 3D electrospun fibre-based scaffold to create an enzymatic-free 3D cell culture platform for the expansion of mammalian cells with the desired phenotype for clinical use. Human corneal stromal cells (hCSCs) were used as an exemplar as they have been observed to de-differentiate to an undesirable myo-fibroblastic phenotype when cultured by conventional 2D cell culture methods. Scaffolds were functionalised with a cell adherence peptide sequence GGG-YIGSR by thiol-ene chemistry to improve cell adherence and phenotype support. This was obtained by functionalising the thermo-responsive polymer with a thiol (PDEGMA/PDEGSH) by co-polymerisation. These incorporated thiols react with the norbornene acid functionalised peptide (GGG-YIGSR) under UV exposure. Presence of the thiol in the scaffold and subsequent peptide attachment on the scaffolds were confirmed by fluorescence labelling, ToF-SIMS and XPS analysis. The biocompatibility of the peptide containing scaffolds was assessed by the adhesion, proliferation and immuno-staining of hCSCs. Significant increase in hCSCs adherence and proliferation was observed on the peptide containing scaffolds. Immuno-staining showed maintained expression of the desired phenotypic markers ALDH, CD34 and CD105, while showing no or low expression of the undesired phenotype marker α-SMA. This desired expression was observed to be maintained after thermo-responsive passaging and observed higher when cells were cultured on PLA scaffolds with 10 wt% PDEGMA/4 mole% PDEGS-Nor-GGG-YIGSR. This paper describes the fabrication and application of a first generation, biocompatible thermo-responsive peptide conjugates fibrous scaffolds. The ease of fabrication, successful adherence and expansion of a therapeutically relevant cell type makes these scaffolds a promising new class of materials for the application of cell culture expansion platforms in the biomaterials and tissue engineering field.</p> | Floor Ruiter; Laura E. Sidney; Kristi L. Kiick; Joel I. Segal; cameron alexander; Felicity R. A. J. Rose | Biological Materials; Fibers | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743e09abda27983f8c253/original/adhesion-peptide-conjugates-of-thermo-responsive-polymers-co-electrospun-into-fibrous-scaffolds-enable-growth-and-enzyme-free-recovery-of-quiescent-human-corneal-stromal-cells-h-cs-cs.pdf |
66e0814bcec5d6c142b257f9 | 10.26434/chemrxiv-2024-8r8j1-v2 | End-To-End Learning of Classical Interatomic Potentials for Benchmarking Anion Polarization Effects in Lithium Polymer Electrolytes | Solid polymer electrolytes are an exciting solution for safe and stable solid lithium electrode battery systems but are hindered by low ionic conductivity and low lithium transference. All-atom molecular dynamics simulation has become an invaluable tool to probe lithium diffusion mechanisms and accelerate the discovery of promising polymer chemistries. Because of their low computational cost and despite their approximate nature, only classical interatomic potentials can access the time and length scales for appropriate statistics of polymer kinetics. Machine learning (ML) potentials trained end-to-end on ab initio data have proven more accurate but cannot be scaled to the necessary time- and length- scales yet. Historical approaches to parameterize classical force fields have been incremental, reliant on a manual combination of top-down and bottom-up fitting, and are often paywalled and hard to reproduce. We introduce a computational learning workflow to predict classical interatomic potential parameters using quantum mechanical computations as training data that combines the automation and end-to-end fitting of ML with traditional class 1 and class 2 functional forms. The fitting strategy produced potentials whose simulations improved the accuracy of lithium coordination environments, diffusivities, and conductivities relative to experimental approaches when compared to both naive and hand-tuned parameters for liquid and solid organic electrolyte systems. We show that chemistry-informed regularization is necessary to constrain predicted parameters in order to reproduce experimental solvation and kinetic properties. Finally, we explore the limitations of non-polarizable, fixed point-charge schemes in describing electrolyte anions and compare the effects of two alternative schemes to fit point-charge distributions. The two strategies result in distinct lithium coordination mechanisms and highlight that closest parity to DFT forces and energies does not correlate to correct trends with lithium salt concentration in kinetic and solvation properties for fixed-point-charge classical interatomic potentials. | Pablo A. Leon; Avni Singhal; Jurgis Ruza; Jeremiah Johnson; Yang Shao-Horn; Rafael Gomez-Bombarelli | Theoretical and Computational Chemistry; Materials Science; Energy; Computational Chemistry and Modeling; Artificial Intelligence; Energy Storage | CC BY 4.0 | CHEMRXIV | 2024-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e0814bcec5d6c142b257f9/original/end-to-end-learning-of-classical-interatomic-potentials-for-benchmarking-anion-polarization-effects-in-lithium-polymer-electrolytes.pdf |
65f168bae9ebbb4db99c2f73 | 10.26434/chemrxiv-2023-8s9dz-v3 | On analytical corrections for restraints in absolute binding free energy calculations | Double decoupling absolute binding free energy simulations require an intermediate state at which the ligand is held solely by restraints in a position and orientation resembling the bound state. One possible choice consists of one distance, two angle and three dihedral angle restraints. Here, I demonstrate that in practically all cases, the analytical correction derived under the rigid rotator harmonic oscillator approximation is sufficient to account for the free energy of the restraint. | Stefan Boresch | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f168bae9ebbb4db99c2f73/original/on-analytical-corrections-for-restraints-in-absolute-binding-free-energy-calculations.pdf |
656099ac29a13c4d47e3ea06 | 10.26434/chemrxiv-2023-3xspw | Direct Control of Electron Spin at Chiral Active Sites for Highly Efficient Oxygen
Reduction Reaction | The oxygen reduction reaction (ORR) in acidic suffers from sluggish kinetics owing to the
spin-dependent electron transfer process. However, the direct generation of spin-polarized
electron at catalytic active sites remains elusive and the underlying mechanism is still
controversial due to the lack of intrinsically homochiral catalysts. To address this challenge,
we demonstrate the topological homochiral PdGa (TH PdGa) crystal with chiral active sites
for ORR. Spin-resolved photoemission and theoretical simulations probed the in-situ
generated spin polarizations at Pd sites. Both structural chirality and spin-orbital coupling
are essential for inducing spin polarization. TH PdGa with remarkable concentration of
spin-polarized electron outperforms the benchmark Pt/C by about 70 times in terms of
kinetic current density at 0.85 V vs. the reversible hydrogen electrode (RHE) and over 200
times in terms of the turnover frequency. This work allows us to elucidate the respective
contributions of spin polarization to the enhanced acidic ORR activity. | Xia Wang; Mayra Peralta; Xiaodong Li; Paul V. Möllers; Dong Zhou; Patrick Merz; Ulrich Burkhardt; Horst Borrmann; Robredo Magro Iñigo; Shekhar Chandra; Helmut Zacharias; Xinliang Feng; Claudia Felser | Catalysis; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656099ac29a13c4d47e3ea06/original/direct-control-of-electron-spin-at-chiral-active-sites-for-highly-efficient-oxygen-reduction-reaction.pdf |
66ebd79a51558a15ef7356e6 | 10.26434/chemrxiv-2024-gp12h | High resolution imaging of non-equilibrium colloidal self-assembly enabled by photopolymerization | The self-organization of colloidal nanoparticles into complex structures, both in equilibrium and out-of-equilibrium, is a critical area in colloidal science with potential applications in creating new functional materials. While equilibrium assemblies yield thermodynamically stable and periodic structures, non-equilibrium (or active) assemblies exhibit dynamic, reconfigurable behavior in response to external stimuli. As a consequence, understanding the structure-function relationships in these assemblies remain challenging due to their transient, highly dynamic nature and the limitations of current characterization methods. In this work, we present a novel methodology for Fixation and Resolution of Colloidal Active Matter Ensembles (FRAME). FRAME combines UV photopolymerization to immobilize non-equilibrium (active) colloidal assembly with high-resolution imaging techniques, such as 3D confocal microscopy and SEM, for subsequent structural characterization. We demonstrate this method on Optical Matter (OM) structure formed by an optical trap at glass/water interface where it enables the preservation and detailed analysis of OM structures, using colloidal nanoparticles ranging from 200 nm to 1 μm. We demonstrate the method's efficacy by validating that the immobilization process does not alter the structural properties, allowing for accurate structural analysis. Additionally, this approach enables the capture of dynamic snapshots of the assembly during its formation, providing critical insights into its transient behavior. FRAME offers a new avenue for investigating non-equilibrium colloidal assemblies, paving the way for their rational design and application across a broad range of colloidal systems. | Jagannath Satpathy; Jui-Kai Chen; Gang Wen; Hiroshi Masuhara; Sudipta Seth; Volker Leen; Susana Rocha; Johan Hofkens; Boris Louis; Roger Bresolí-Obach | Nanoscience | CC BY 4.0 | CHEMRXIV | 2024-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ebd79a51558a15ef7356e6/original/high-resolution-imaging-of-non-equilibrium-colloidal-self-assembly-enabled-by-photopolymerization.pdf |
60c74d264c891927d8ad3781 | 10.26434/chemrxiv.12592418.v1 | Copper(II) Complexes of N-Propargyl Cyclam Ligands Reveal a Range of Coordination Modes and Colours, and Unexpected Reactivity | <p>Herein we describe single crystal
X-ray diffraction and spectroscopic investigations of the coordination
chemistry of copper(II) complexes of cyclam derivatives with between 1 and 4
pendant alkynes. The crystal structures of these copper complexes unexpectedly reveal
a range of coordination modes, and the surprising occurrence of five unique
complexes within a single recrystallisation of the tetra-<i>N</i>-propargyl cyclam ligand. One of these species exhibits weak
intramolecular copper-alkyne coordination, and another is formed by a surprising
intramolecular copper-mediated hydroalkoxylation reaction with the solvent
methanol, transforming one of the pendant alkynes to an enol ether. Multiple
functionalisation of the tetra-<i>N</i>-propargyl
ligand is demonstrated <i>via</i> a ‘tetra-click’
reaction with benzyl azide, and the copper-binding behaviour of the resulting
tetra-triazole ligand is characterised spectroscopically.</p> | Andrew Counsell; Mingfeng Yu; Mengying Shi; Angus Jones; James M. Batten; Peter Turner; Matthew Todd; Peter Rutledge | Coordination Chemistry (Inorg.); Ligands (Inorg.); Transition Metal Complexes (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d264c891927d8ad3781/original/copper-ii-complexes-of-n-propargyl-cyclam-ligands-reveal-a-range-of-coordination-modes-and-colours-and-unexpected-reactivity.pdf |
60c74e57f96a00f8e3287ad5 | 10.26434/chemrxiv.12743552.v1 | Ideal–Gas Thermochemical Properties for Alkanolamine and Related Species Involved in Carbon Capture Applications | <div>Ideal{gas thermochemical properties (enthalpy, entropy, Gibbs energy, and heat capacity, Cp) of 49 alkanolamines potentially suitable for CO2 capture applications and their carbamate and protonated forms were calculated using two high{order electronic structure methods, G4 and G3B3 (or G3//B3LYP). We also calculate for comparison results from the commonly used B3LYP/aug-cc-pVTZ method. This data is useful for the construction of molecular{based thermodynamic models of CO2 capture processes involving these species. The Cp data for each species over the temperature range 200 K{1500 K is presented as functions of temperature in the form of NASA seven-term polynomial expressions, permitting the set of thermochemical properties to be calculated over this temperature range. The accuracy of the G3B3 and G4 results is estimated to be 1 kcal/mol and the B3LYP/aug-cc-pVTZ results are of nferior quality..</div> | Nayyereh hatefi; William Smith | Computational Chemistry and Modeling; Thermodynamics (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e57f96a00f8e3287ad5/original/ideal-gas-thermochemical-properties-for-alkanolamine-and-related-species-involved-in-carbon-capture-applications.pdf |
60c74cf5842e653091db33a4 | 10.26434/chemrxiv.12571241.v1 | Multitask Bioactivity Predictions Using Structural Chemical and Cell Morphology Information | <p>The understanding of the Mechanism-of-Action (MoA) of compounds and the prediction of potential drug targets has an important role in small-molecule drug discovery. The aim of this work was to compare chemical and cell morphology information for bioactivity prediction. The comparison was performed by using bioactivity data from the ExCAPE database, image data from the Cell Painting data set (the largest publicly available data set of cell images with approximately ~30,000 compound perturbations) and Extended Connectivity Fingerprints (ECFPs) using the multitask Bayesian Matrix Factorisation (BMF) approach Macau. We found that the BMF Macau and Random Forest (RF) performance was overall similar when ECFP fingerprints were used as compounds descriptors. However, BMF Macau outperformed RF in 155 out of 224 target classes (69.20%) when image data was used as compounds information. By using BMF Macau 100 (corresponding to about 45%) and 90 ( about 40%) of the 224 targets were predicted with high predictive performance (AUC > 0.8) with ECFP data and image data as side information, respectively. There were targets better predicted by image data as side information, such as b-catenin, and others better predicted by fingerprint-based side information, like proteins belonging to the G-Protein Coupled Receptor 1 family, which could be rationalized from the underlying data distributions in each descriptor domain. In conclusion, both cell morphology changes and structural chemical information contain information about compound bioactivity, which is also partially complementary, and can hence contribute to <i>in silico </i>mechanism of action analysis. </p> | Maria-Anna Trapotsi; Ian Barrett; Lewis Mervin; Avid M. Afzal; Noé Sturm; Ola Engkvist; Andreas Bender | Bioinformatics and Computational Biology; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cf5842e653091db33a4/original/multitask-bioactivity-predictions-using-structural-chemical-and-cell-morphology-information.pdf |
66d35333a4e53c4876431377 | 10.26434/chemrxiv-2024-ncn19 | Leveraging Metal Complexes for Microsecond Lifetime-Based Chloride Sensing | Chloride is the most abundant anion in cell physiology and plays many critical roles in maintaining cellular homeostasis. However, current chloride sensors are rare, with inherent sensitivity in their emission properties, such as vulnerability to pH changes or short emission lifetimes. These limitations restrict their application in aqueous media and imaging. In this work, we employed a transition metal complex bearing pyridinium as a recognition unit for chloride and studied the phosphorescence emission properties. Iridium(III) complex 1 was synthesized as an alternative chloride-sensitive luminophore. The conjugable design also allows customization for desired applications. Complex 1 exhibited high sensitivity and selectivity in chloride sensing across different physiological environments, regardless of pH fluctuation and ionic strength. Additionally, complex 1 featured a long microsecond emission lifetime. The chloride sensing ability of complex 1 can be measured through both luminescence intensity and long-lived phosphorescent lifetime simultaneously, providing an alternative potential route for chloride imaging. | Jared Morse; Nnamdi Ofodum; Fung-Kit Tang; Matthias Schmidt; Xiaocun Lu; Kaho Leung | Inorganic Chemistry; Analytical Chemistry; Organometallic Chemistry; Bioinorganic Chemistry; Sensors | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d35333a4e53c4876431377/original/leveraging-metal-complexes-for-microsecond-lifetime-based-chloride-sensing.pdf |
646dc5b8268ed316c94f592f | 10.26434/chemrxiv-2023-rb5st | Engineering Ferroelectricity and Giant Piezoelectricity in h-BN | Hexagonal Boron Nitride (h-BN), a well-known layered van der Waals (vdW) material that exhibits
no spontaneous electric polarization due to its centrosymmetric structure. Extensive Density
Functional Theory (DFT) calculations are used to demonstrate that doping through the substitution
of B by isovalent Al and Ga breaks the inversion symmetry and induces local dipole moments
along the c-axis, which promotes a ferroelectric (FE) alignment over anti-ferroelectric. For doping
concentrations below 25%, a “protruded layered” structure in which the dopant atoms protrude out
of the planar h-BN layers is energetically more stable than the flat layered structure of pristine
h-BN or a wurtzite structure similar to w-AlN. The computed polarization, between 7.227 – 21.117
μC/cm2 depending on dopant concentration and the switching barrier (16.684 – 45.838 meV) for the
FE polarization reversal are comparable to that of other well known FEs. Interestingly, doping of
h-BN also induces a large negative piezoelectric response in otherwise non-piezoelectric h-BN. For
example, we compute d33 of -24.214 pC/N for Ga0.125B0.875N, which is about 5 times larger than
that of pure w-AlN (5 pC/N), although the computed e33 (-1.164 C/m2) is about 1.6 times lower
than that of pure w-AlN (1.462 C/m2). Because of the layered structure, the rather small elastic
constant C33 provides the origin of this large d33. Moreover, doping makes h-BN an electric auxetic
piezoelectric. We also show that ferroelectricity in doped h-BN may persist down to its trilayer,
which indicates high potential for applications in FE non-volatile memories. | Mohammad Noor-A-Alam; Michael Nolan | Theoretical and Computational Chemistry; Physical Chemistry; Physical and Chemical Properties; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646dc5b8268ed316c94f592f/original/engineering-ferroelectricity-and-giant-piezoelectricity-in-h-bn.pdf |
60c74f46702a9b9f6d18bb55 | 10.26434/chemrxiv.12885203.v1 | Persistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis | Testing
the premise of evolutionarily optimized protein dynamics has remained an experimental
challenge. Most measurements fail to
isolate specific structural motions. Our
simulations show that the structural variation of a single protein in time
results in variation in the vibrations leading to the observed broad and
featureless optical absorption. However,
when the thermal population of a protein’s configurations are considered,
vibrations with functional displacements are concentrated in specific frequency
bands. These emergent dynamics are
apparent in anisotropic optical absorbance, indicating an experimental avenue
for measuring these motions and their impact on biological function. | Tod D. Romo; Alan Grossfield; Andrea Markelz | Biochemistry; Bioinformatics and Computational Biology; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Biophysical Chemistry; Spectroscopy (Physical Chem.); Statistical Mechanics; Structure; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f46702a9b9f6d18bb55/original/persistent-protein-motions-in-a-rugged-energy-landscape-revealed-by-normal-mode-ensemble-analysis.pdf |
6647c0bb418a5379b092e068 | 10.26434/chemrxiv-2024-hts0l | Ultrathin Boron Growth onto Nanodiamond Surfaces via Electrophilic Boron Precursors | Diamond as a templating substrate is largely unexplored and the unique properties of diamond including its large bandgap, thermal conductance and lack of cytotoxicity make it versatile in emergent technologies in medicine and quantum sensing. Surface termination of an inert diamond substrate and its chemical reactivity are key in generating new bonds for nucleation and growth of an overlayer material. Oxidized high-pressure high-temperature (HPHT) nanodiamonds NDs are largely terminated by alcohols that act as nucleophiles to initiate covalent bond formation when an electrophilic reactant is available. In this work we demonstrate a templated synthesis of ultrathin boron on ND surfaces using trigonal boron compounds. Boron trichloride (BCl3), boron tribromide (BBr3) and borane (BH3) were found to react with ND substrates at room temperature in inert conditions. BBr3 and BCl3 were highly reactive with the diamond surface and sheet-like structures were produced and was verified with electron microscopy. Surface sensitive spectros-copies were used to probe the molecular and atomic structure of the ND constructs’ surface and quantification showed the boron shell was less than 1 nm thick after 1-24 hour reaction protocols. Observations of the reaction supports a self-terminating mechanism, similar to atomic layer depo-sition growth and is likely due to the quenching of alcohols on the diamond surface. The boron-diamond nanostructures were found to aggregate in dichloromethane and were dispersed in various solvents and characterized with dynamic light scattering for future cell imaging or cancer therapy applications using boron neutron capture therapy (BNCT). The unique templating mech-anism based on nucleophilic alcohols and electrophilic trigonal precursors allows for covalent bond formation and will be of interest to researchers using diamond for quantum sensing, additive manufacturing and BNCT. | Krishna Govindaraju; Tyanna Supreme; Daniel Labunsky; Nicole Martin; Juan Miguel Del Rosario; Alana Washington; Ezhioghode Uwadiale; Solomon Adjei II; Sandra Ladjadj; Cynthia Melendrez; Sang-Jun Lee; Virginia Altoe; Avery Green; Sebastian Riano; Sami Sainio; Dennis Nordlund; Abraham Wolcott | Physical Chemistry; Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6647c0bb418a5379b092e068/original/ultrathin-boron-growth-onto-nanodiamond-surfaces-via-electrophilic-boron-precursors.pdf |
653b3f3348dad2312073e584 | 10.26434/chemrxiv-2023-f61jq | Exploring the Effect of Temperature on the Concentration of Salicylic Acid in Acetylsalicylic Acid | Aspirin is used for a variety of reasons, from reducing fever to providing relief for mild pain associated with headaches, menstrual cramps, and arthritis. Its versatility leads to aspirin tablets being present in almost every home, which makes the consequences of their mishandling that much more impactful. Generally, patients are instructed not to store aspirin in areas exposed to excess heat and humidity as they cause aspirin to break down into salicylic acid and acetic acid. Salicylic acid is the substance responsible for aspirin’s medicinal properties, and fluctuations in its concentration can lead to dosage inaccuracies. This leads to questions and concerns about the correlation between temperature and the concentration of salicylic acid within hydrolyzed aspirin. Within this paper, it was found that there is a directly proportional relationship between temperature and the concentration of salicylic acid in acetylsalicylic, as the concentration steadily increases as the temperature increases. | Rojina Karimirad | Biological and Medicinal Chemistry; Organic Chemistry; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2023-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653b3f3348dad2312073e584/original/exploring-the-effect-of-temperature-on-the-concentration-of-salicylic-acid-in-acetylsalicylic-acid.pdf |
62e912b6adfd3562d224510c | 10.26434/chemrxiv-2022-gp9dm-v2 | Protein control of photochemistry and transient intermediates in phytochromes | Phytochromes are ubiquitous photoreceptors responsible for sensing light in plants, fungi and bacteria. Their photoactivation is initiated by the photoisomerization of the embedded bilin chromophore, which triggers a large conformational change in the protein. The initial photoisomerization and the following structural changes propagating from the chromophore to the entire protein are controlled by a delicate interplay of interactions between the chromophore and the protein residues.
Although the numerous studies, the molecular details of this control remain elusive.
Here, we apply an integrated computational approach that combines non-adiabatic and adiabatic molecular dynamics simulations to the Deinococcus radiodurans bacteriophytochrome. Our simulations show that the photoisomerization of the chromophore proceeds through a hula-twist mechanism whose kinetics is mainly determined by the hydrogen-bonding interaction of the chromophore with a close-by histidine. The resulting photoproduct rapidly relaxes in an early intermediate thanks to a stabilizing effect of a tyrosine, and finally evolves into a late intermediate, characterized by a more disordered binding pocket and a weakening of the aspartate-to-arginine salt-bridge interaction, whose cleavage is essential to interconvert the phytochrome to the final active state. | Giacomo Salvadori; Veronica Macaluso; Giulia Pellicci; Lorenzo Cupellini; Giovanni Granucci; Benedetta Mennucci | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2022-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e912b6adfd3562d224510c/original/protein-control-of-photochemistry-and-transient-intermediates-in-phytochromes.pdf |
65cc8f3f66c13817299de2b9 | 10.26434/chemrxiv-2024-7dt0s | ADSORPTION OF ACID BROWN-340 ON SILICA BASED ADSORBENT | Acid Brown-340 is a valuable and prominent dye which Having Serious effect on our environments due to its acidic nature. Usually, this dye is coming out of different industries and accumulate in various water bodies such as lakes, ocean and freshwater ecosystem. In this Present study silica monolith particles were synthesized by the renovated sol-gel process under controlled environment of heating steps. The newly prepared functionalized silica monolith particles were used as an adsorbent for the removal of acid brown-340 from aqueous solution. particles originating from silica monolith were effective adsorbent for the removal of selective dye due to its various sorts such as enlarged surface area, high permeability due to monolith like nature leading to high loading capability, and mechanical strength to various PH. Adsorption capacity of silica was firm with respect to different parameters at certain point of time. By adjusting certain parameter such as PH at range 2-8 Concentration taken as range from 0.02-0.1 and time as taken as range from 15mins to 75mins. Then Acid brown-340 shows the greatest adsorption with particles originating from silica monolith when the optimized values of the parameters for acid brown-340 are PH is 2, adsorbent dose is 0.06g, and Contact time is 75 min. | Salman Khan | Analytical Chemistry; Analytical Chemistry - General; Analytical Apparatus; Environmental Analysis | CC BY NC 4.0 | CHEMRXIV | 2024-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cc8f3f66c13817299de2b9/original/adsorption-of-acid-brown-340-on-silica-based-adsorbent.pdf |
66a11b80c9c6a5c07ac62dc2 | 10.26434/chemrxiv-2024-b74fc | What can chemical bonding tell us about photoinduced self-healing reactions in inorganic semiconductors? Insight from Bismuth-Antimony Selenide | Photo-reactive self-healing semiconductors with suitable bandgaps for solar energy conversion offer an intriguing path to making resilient and low-cost photovoltaic devices through the introduction of a self-recovery path. However, only few inorganic photovoltaic materials have such quality, and the underlying chemical properties that enable it are unknown, which poses a significant limit to our ability to study and discover new self-healing semiconductors. Recently, we have found antimony trichalcogenide (Sb2Se3, Sb2S3) and chalcohalides (e.g., SbSeI) can undergo a reversible photo-induced phase transition (PIPT) in which the structure is restored after photo-induced damage is incurred to the materials. This group of materials offer a unique opportunity for studying PIPT and its limits. In particular, this group of materials facilitates the study of functional permutation to specific crystalline sites, and to finding the limits of PIPT occurrence, which sheds light on the origin of the PIPT and self-recovery of this class of materials. We found that PIPT magnitude decays upon gradual BiSb(1) substitution in a Sb2-xBixSe3 homologous series, until nearly one in five Sb ions is substituted with Bi. Then, PIPT diminishes completely. The homologous series occurs along a transition from a covalent to metavalent chemical bonding. By expanding our search, we find a correlation between bonding type and photoreactivity does exist but is an insufficient condition. Instead we suggest that sufficient bonding states at the bottom of the conduction band are also required. This study pushes the limits of designing self-healing inorganic semiconductors for various applications and provides tools to further expansion. | Anchal Vashishtha; Subila KB; Yaniv Dror; Jitendra Kumar; Priyakumari CP; Eran Edri | Materials Science; Inorganic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a11b80c9c6a5c07ac62dc2/original/what-can-chemical-bonding-tell-us-about-photoinduced-self-healing-reactions-in-inorganic-semiconductors-insight-from-bismuth-antimony-selenide.pdf |
6396cbe244ccbc532518d142 | 10.26434/chemrxiv-2022-qkwz5 | Molecular Modelling of Ionic Liquids: Perfluorinated Anionic Species with Enlarged Halogen Substitutions | Ionic liquids as promising green solvents are widely applied in laboratory and industrial applications. Despite the massive experimental efforts on various applications, accurate computational modelling of such complex solution remains challenging. Our previous extensive numerical experiences on bulk properties, solvation and partition of external drug-like molecules between water and ionic-liquids phases lead to the recommended modelling regime of 0.8-scaled RESP charges and the GAFF2 parameter set. Such a protocol has been found to be effective in reproducing the experimental thermodynamic properties that require balanced descriptions of solute-solvent and solvent-solvent interactions. A deficiency in the previous benchmark set is the lack of voluminous and highly halogen-substituted anions. Therefore, in this work, we explore the calculation of ionic liquids involving large voluminous perfluorinated anionic species. Also, the ESP analysis confirms the similarity of the ESP produced by the gas-phase HF/6-31G* generated atomic charges and the higher-level implicit-solvent calculations. The quality of the HF/6-31G*-targeted charges is further validated by a direct face-to-face comparison of the bulk density estimated from molecular simulation under different charge sets, consolidating the protocol for model construction. | Zhaoxi Sun; Lei Zheng; Zuo-yuan Zhang; Yalong Cong; Jingjing Yang; Xiaohui Wang | Theoretical and Computational Chemistry; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science; Theory - Computational; Thermodynamics (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6396cbe244ccbc532518d142/original/molecular-modelling-of-ionic-liquids-perfluorinated-anionic-species-with-enlarged-halogen-substitutions.pdf |
643871371d262d40ea682a5b | 10.26434/chemrxiv-2023-60glz-v2 | Mannich base PIP-199 is a chemically unstable pan-assay interference compound | PIP-199 is the only reported small molecule inhibitor of FANCM-RMI, a key protein-protein interaction that governs genome instability in the genetic disorders Fanconi Anemia and Bloom’s Syndrome. PIP-199 and close analogues that share the same indole-derived Mannich base core scaffold have been used as commercially available tool compounds for studying a wide range of therapeutically relevant biological pathways and targets, including the Alternative Lengthening of Telomeres (ALT), G-quadruplexes, pro-apoptotic proteins, and quorum sensing. Herein, we report the first published synthesis of PIP-199 and related analogues, demonstrating that the parent compound immediately decomposes in common aqueous buffers and some organic solvents. We characterize the breakdown products and show that PIP-199 and its more hydrolytically stable analogues show no observable activity in binding and competitive biophysical assays for FANCM-RMI. We conclude that PIP-199 is not an effective tool compound for biological studies, and that apparent activity in cellular studies likely arises from non-specific toxicity of mixed breakdown products. More generally, apparent inhibitors that share this indole-derived Mannich scaffold potentially represent a new family of pan-assay interference compounds (PAINS) that should be thoroughly assessed for aqueous stability prior to use in biological studies. | Xinyi Wu; Haritha Sudhakar; Lisa Alcock; Yu Heng Lau | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643871371d262d40ea682a5b/original/mannich-base-pip-199-is-a-chemically-unstable-pan-assay-interference-compound.pdf |
60c744be9abda20ea1f8c448 | 10.26434/chemrxiv.9913046.v1 | Identification of Important Normal Modes in Nonadiabatic Dynamics Simulations by Coherence, Correlation, and Frequency Analyses | <div>Nonadiabatic dynamics simulations of molecular systems with a large number of nuclear degrees of freedom become increasingly feasible, but there is still a need to extract from such simulations a small number of most important modes of nuclear motion, for example to obtain general insight or to construct low-dimensional model potentials for further simulations. Standard techniques for this dimensionality reduction employ statistical methods that identify the modes that account for the largest variance in nuclear positions. However, large-amplitude motion is not necessarily a good proxy for the influence of a mode on the excited-state wave function evolution. Hence, here we report a number of analysis techniques aimed at extracting from nonadiabatic dynamics simulations the vibrational modes that are most strongly affected by the electronic excitation process and that most significantly affect the interaction of the electronic states. The first technique identifies coherent nuclear motion after excitation from the ratio between total variance and variance of the average trajectory. The second strategy employs linear regression to find normal modes that have a statistically significant effect on excitation energies, energy gaps, or wave function overlaps. The third approach uses time-frequency analysis to find normal modes where the vibrational frequencies change in the course of the dynamics simulation. All three techniques are applied to the case of surface hopping trajectories of [Re(CO)<sub>3</sub>(Im)(Phen)]<sup>+</sup> (Im=imidazole; Phen=1,10-phenanthroline), showing that in this transition metal complex the nonadiabatic dynamics is dominated by a small number of carbonyl and phenanthroline in-plane stretch modes.</div><div><br /></div> | Sebastian Mai; Leticia Gonzalez | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744be9abda20ea1f8c448/original/identification-of-important-normal-modes-in-nonadiabatic-dynamics-simulations-by-coherence-correlation-and-frequency-analyses.pdf |
61b634d3d10aa546150e4dbe | 10.26434/chemrxiv-2021-ldl9p | Ring-Opening of Epoxides by Pendant Silanols | We present a new ring-opening reaction of epoxides by pendant silanols, catalyzed by either Ph3C+BF4– or BINOL-phosphoric acid. In all cases examined, the reaction is perfectly regioselective and diastereoselective. Silanol epoxides derived from trans-allylic alcohols, cis-allylic alcohols, trans-homoallylic alcohols, and cis-homoallylic alcohols were all compatible and gave products from either endo- or exo-ring opening. With silanol epoxides derived from 4-alkenyl silanols, an unusual rearrangement to tetrahydrofuran products was observed, which is likely the result of tandem nucleophilic attacks. The utility of this methodology was demonstrated in a short preparation of protected D-arabitol. | SHYAM SATHYAMOORTHI; Someshwar Nagamalla; Joel Mague | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2021-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b634d3d10aa546150e4dbe/original/ring-opening-of-epoxides-by-pendant-silanols.pdf |
60c747acbdbb89687ea38e4e | 10.26434/chemrxiv.11743752.v1 | Evolving Oxeto-Indolinic Polycycles from Indoles by Means of a Visible-Light [2+2] Heterocycloaddition Dearomatization Process | A large variety of highly functionalized N-containing polycycles (35 examples) are synthetized from simple indoles and aromatic ketones through a mild visible-light-driven [2+2]-heterocycloaddition process. Tetrahydrooxeto[2,3b]indole scaffolds, with up to three contiguous all-substituted stereo-centers are generated in high yield (up to >98%) and excellent site- regio- and diastereocontrol (>20:1). The use of visible light (405 or 465 nm) ensures enhanced performances by switching off undesired photodimerization reactions. Mechanistic investigations revealed that the operative reaction mechanism is dependent by the nature of the used ketone-substrate. | Javier Mateos; Alberto Vega-Peñaloza; Pietro Franceschi; Francesco Rigodanza; Philip Andreetta; Xavier Companyó; Giorgio Pelosi; Marcella Bonchio; Andrea Sartorel; Luca Dell'Amico | Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747acbdbb89687ea38e4e/original/evolving-oxeto-indolinic-polycycles-from-indoles-by-means-of-a-visible-light-2-2-heterocycloaddition-dearomatization-process.pdf |
61c0428a203b4083de9381f4 | 10.26434/chemrxiv-2021-n5660-v2 | Facile Synthesis of the Dicyanophosphide Anion via Electrochemical Activation of White Phosphorus: An Avenue to Organophosphorus Compounds | Organophosphorus compounds (OPCs) have gained tremendous interest in the past decades due to their wide applications ranging from synthetic chemistry to materials and biological sciences. We describe herein a practical and versatile approach for the transformation of white phosphorus (P4) into useful OPCs with high P atom economy via a key bridging anion [P(CN)2]–. This anion can be prepared on a gram scale directly from P4 through an unprecedented electrochemical process. A variety of OPCs involving phosphinidenes, cyclophosphanes and phospholides have been made readily accessible from P4 in a two-step manner. Our approach has a significant impact on the future preparation of OPCs in laboratory and industrial settings. | Yanbo Mei; Zeen Yan; Liu Leo Liu | Organic Chemistry; Inorganic Chemistry; Organic Synthesis and Reactions; Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c0428a203b4083de9381f4/original/facile-synthesis-of-the-dicyanophosphide-anion-via-electrochemical-activation-of-white-phosphorus-an-avenue-to-organophosphorus-compounds.pdf |
672203c8f9980725cf6a5c23 | 10.26434/chemrxiv-2024-wkw04 | Transmembrane peptide-loaded ionic liquid nanocarriers for targeting ErbB2-positive cancer | The transmembrane peptide domains (TMs) of membrane proteins are involved in signal transduction and are crucial for receptor dimerization. Human epidermal growth factor receptor 2 (HER2 or ErbB2) promotes accelerated cancer cell proliferation and survival and is overexpressed in over 20% of all malignancies. We target ErbB2 in a set of ErbB2-positive cancer cell lines by chemically synthesized peptides mimicking the full ErbB2 TM, which inhibited downstream MAPK and PI3K/Akt signaling and drastically reduced cell viability. Loading the ErbB2 TM into surface-active ionic liquid nanocarriers demonstrated a synergic effect on cell viability via cell membrane disruption with simultaneous inhibition of the downstream signaling cascades. Thus, this proof-of-concept study demonstrates TM peptides in conjunction with surface-active ionic liquid carriers as a promising strategy for targeted cancer treatment and broad application, exemplified on ErbB2 receptor as a target here. | Helal Abujubara; Pankaj Bharmoria; Samantha Alvarez; Enoch Appiah; Kasper Moth-Poulsen; Volkan Sayin; Alesia Tietze | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2024-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672203c8f9980725cf6a5c23/original/transmembrane-peptide-loaded-ionic-liquid-nanocarriers-for-targeting-erb-b2-positive-cancer.pdf |
60c751d8567dfe5fbbec5b2b | 10.26434/chemrxiv.13218107.v1 | Enhanced Voltammetric Anion Sensing at Halogen and Hydrogen Bonding Ferrocenyl SAMs | Halogen bonding mediated electrochemical anion sensing has very recently been established as a potent platform for the selective and sensitive detection of anions, although the principles that govern binding and subsequent signal transduction remain poorly understood. Herein we address this challenge by providing a comprehensive study of novel redox-active halogen bonding (XB) and hydrogen bonding (HB) ferrocene-isophthalamide-(iodo)triazole receptors in solution and at self-assembled monolayers (SAMs). Under diffusive conditions the sensory performance of the XB sensor was significantly superior. In molecular films the XB and HB binding motifs both display a notably enhanced, but similar, response to specific anions. Importantly, the enhanced response of these films is rationalised by a consideration of the (interfacial) dielectric microenvironment. These effects, and the resolved relationship between anion binding and signal transduction, underpin an improved fundamental understanding of anion sensing at redox-active interfaces which will benefit not just the development of more potent, real-life relevant sensors, but also new tools to study host-guest interactions at interfaces. | Robert Hein; Xiaoxiong Li; Paul D. Beer; Jason J Davis | Supramolecular Chemistry (Org.); Thin Films; Electrochemistry; Sensors; Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751d8567dfe5fbbec5b2b/original/enhanced-voltammetric-anion-sensing-at-halogen-and-hydrogen-bonding-ferrocenyl-sa-ms.pdf |
60c75275842e653b40db3d98 | 10.26434/chemrxiv.13299074.v1 | Engineering of TMDC-OSC Hybrid Interfaces: The Thermodynamics of Unitary and Mixed Acene Monolayers on MoS2 | Here, we use temperature-programmed desorption (TPD) and Monte Carlo (MC) simulations<br />of TPD traces to characterize the desorption kinetics of pentacene (PEN) and perfluoropentacene (PFP) on MoS2 as a model system for OSCs on TMDCs. We show that the monolayers of PEN and PFP are thermally stabilized compared to their multilayers, which allows to prepare nominal monolayers by selective desorption of multilayers. This stabilization is, however, caused by entropy due to a high molecular mobility rather than an enhanced molecule-substrate bond. Consequently, the nominal monolayers are not densely packed films. | Stefan
R. Kachel; Pierre Martin Dombrowski; Tobias Breuer; Michael Gottfried; Gregor Witte | Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75275842e653b40db3d98/original/engineering-of-tmdc-osc-hybrid-interfaces-the-thermodynamics-of-unitary-and-mixed-acene-monolayers-on-mo-s2.pdf |
60c753bb469df46b1ef44df9 | 10.26434/chemrxiv.13542101.v1 | Water Dispersible Sulfo-Polyester Resins with Controlled Nano-Sized Particles | <div>Water dispersible polyester resins derived from dimethyl terephthalate, dimethyl 5-sulfoisophthalate sodium salt, 1,2-propane diol and diethylene glycol were prepared. A</div><div>Design of Experiment (DOE) was explored by varying the concentration of the ionic 5-sulfo-isophthalate sodium salt and diethylene glycol at various molecular weights and found to</div><div>correlate with particle size dispersion of the sulfonated resins in water. An empirical model for the resin glass transition was also obtained through experimental design.</div> | Guerino Sacripante; Daniel Foucher | Nanostructured Materials - Materials; Nanofabrication | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753bb469df46b1ef44df9/original/water-dispersible-sulfo-polyester-resins-with-controlled-nano-sized-particles.pdf |
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