id
stringlengths 24
24
| doi
stringlengths 28
32
| title
stringlengths 8
495
| abstract
stringlengths 17
5.7k
| authors
stringlengths 5
2.65k
| categories
stringlengths 4
700
| license
stringclasses 3
values | origin
stringclasses 1
value | date
stringdate 1970-01-01 00:00:00
2025-03-24 00:00:00
| url
stringlengths 119
367
⌀ |
|---|---|---|---|---|---|---|---|---|---|
6682935101103d79c59fa4a6 | 10.26434/chemrxiv-2024-zfzpp | SPCal - An open source, easy-to-use processing platform for ICP-TOFMS based single event data | Single particle inductively coupled plasma – mass spectrometry (SP ICP-MS) has evolved into one of the most powerful techniques for the bottom-up characterisation of nanoparticle suspensions. The latest generations of time-of-flight mass analysers offer new perspectives on single particles by rapidly collecting full mass spectra and providing information on particle composition and abundances even in unknown samples. However, SP ICP-TOFMS is associated with vast data sizes with complex structure, which can hamper its applicability and the interrogation of specific particle features. Unlocking the full potential of SP ICP-TOFMS requires dedicated, easy-to-use software solutions to navigate through data sets and promote transparent, efficient and precise processing. SPCal is an open-source SP data processing platform, which we have previously released for quadrupole-based data. In this work, we expand its reach by enabling the analysis of TOF-based SP data sets additionally. We have incorporated various tools to facilitate the handling, manipulation and calibration of large data sets and provide the required statistical fundament and models to promote accurate thresholding. Non-target screening tools are integrated to pinpoint particulate elements in unknown samples without the requirement for a-priori investigations or modelling. Next to basic functions like the calibration of size and mass distributions, methods to carry out cluster analysis (PCA, HAC) provide the means to study groups of particles based on their composition and conditional data filtering allows the interrogation of particle populations by selectecting specific features. | Thomas Lockwood; Lukas Schlatt; David Clases | Analytical Chemistry; Nanoscience; Chemoinformatics; Mass Spectrometry; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6682935101103d79c59fa4a6/original/sp-cal-an-open-source-easy-to-use-processing-platform-for-icp-tofms-based-single-event-data.pdf |
6720e3f17be152b1d0274dbc | 10.26434/chemrxiv-2024-pktbw | Optimizing Excited-State Energies and Electron Transfer Dynamics in Benzothiadiazole-Based Organic Photocatalysts for Improved Efficiency | Organic photocatalysts play a pivotal role in advancing green and sustainable chemistry by enabling efficient and selective photochemical transformations and reducing the need for traditional hazardous reagents and energy-intensive processes. This work uses the donor-acceptor natures, steric effects, and conjugation lengths of six benzothiadiazole (BTD) based organic dyes (PC1-PC6) to control their charge transfer (CT) and locally excited (LE) states. Thus, effective photosensitization and photoredox characteristics are brought about for photocatalytic applications. Additionally, theoretical research shows that the carbazole-linked-BTD with methyl (PC2 and PC3) demonstrates an effective CT feature in the T1 state. While the LE nature of the methyl-free carbazole-linked-BTD dye (PC1) is excellent. TPA-linked-BTD dyes (PC4-PC5), on the other hand, have good LE properties in the T1 state except for mono-TPA-linked-BTD derivative (PC6). For S1 state features, though, the tendency was in the reverse direction. In the S1 state, all the compounds (PC1-PC4) exhibit outstanding HLCT capabilities except the methylated BTD dyes that contain triphenylamine donors (PC5-PC6). The letter compounds possess CT nature in the S1 state. Overall, the donor’s strength and steric effect of the methyl group were found to tune the nature of S1 and T1 states of these photocatalysts with both photosensitization and photoredox qualities. Thus, A universal technique for screening BTD-based dyes has been developed, guided by theoretical insights and confirmed through practical validation. It demonstrates exceptional photocatalytic performance, outperforming traditional benchmark photocatalysts, and holds significant promise for advancing the field. With a wide spectrum of functional group tolerance, the catalysts can selectively oxidize both primary and secondary amine derivatives. | Anupam Das; Ambika Pathak; Panaha Panaha; K. R. Justin Thomas | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Theory - Computational; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6720e3f17be152b1d0274dbc/original/optimizing-excited-state-energies-and-electron-transfer-dynamics-in-benzothiadiazole-based-organic-photocatalysts-for-improved-efficiency.pdf |
628bf284708767f45f5d3cfa | 10.26434/chemrxiv-2022-c4mz6 | Total Synthesis of Darobactin A | The total synthesis of darobactin A, a recently isolated antibiotic that selectively targets Gram-negative bacteria, has been accomplished in a convergent fashion with a longest linear sequence of 16 steps from ᴅ-Garner’s aldehyde and ʟ-serine. Scalable routes towards three non-canonical amino acids were developed to enable the synthesis. The closure of the bismacrocycle was realized through sequential, halogen-selective Larock indole syntheses, where the proper order of cyclizations proved crucial for the formation of the desired atropisomer of the natural product. | Marko Nesic; David B. Ryffel; Jonathan Maturano; Michael Shevlin; Scott R. Pollack; Donald R. Gauthier Jr.; Pablo Trigo-Mouriño; Li-Kang Zhang; Danielle Schultz; Jamie M. McCabe Dunn; Louis-Charles Campeau; Niki R. Patel; David A. Petrone; David Sarlah | Organic Chemistry; Natural Products; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628bf284708767f45f5d3cfa/original/total-synthesis-of-darobactin-a.pdf |
6461fd1ca32ceeff2daf0c20 | 10.26434/chemrxiv-2023-g4zwj | Enantioselective Synthesis of Chiral Amides by Phosphoric Acid-Catalyzed Asymmetric Wolff Rearrangement | The enantioselective addition of potent nucleophilic reagents to ketene compounds poses challenges due to the presence of significant background reactions, along with simultaneous stereoselectivity and enantioselectivity issues in the reaction process. We present a method for enantioselective amination of ketenes employing α-aryl-α-diazoketones as ketene precursors and phosphoric acids as catalysts. Upon exposure to visible light, diazoketones undergo Wolff rearrangement to gradually generate ketenes. Subsequently, the phosphoric acid not only accelerates capture of ketenes by amines, forming a singular configuration of aminoenol intermediates, but also promotes the enantioselective proton transfer of the intermediates to yield product. Mechanism studies elucidate the reaction pathways and explain how the catalysts expedite this transformation and control enantioselectivity. | Jia-Bin Pan; Zhi-Chun Yang; Xuan-Ge Zhang; Mao-Lin Li; Qi-Lin Zhou | Organic Chemistry; Catalysis; Acid Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6461fd1ca32ceeff2daf0c20/original/enantioselective-synthesis-of-chiral-amides-by-phosphoric-acid-catalyzed-asymmetric-wolff-rearrangement.pdf |
663ec94791aefa6ce1b04e77 | 10.26434/chemrxiv-2024-1917n | Precision Synthesis of Chimeric Peptides through Site-Specific Azomethine Ylide–Dehydroalanine Cycloaddition | Site-selective conjugation of peptides is crucial for constructing structurally uniform peptide chimeras for applications such as drug discovery and drug delivery. Nevertheless, the site-specific late-stage transformation of peptides is challenging due to the presence of multiple nucleophilic sites, such as lysine ε-amine. In this work, we developed a three-component assembly method involving N-terminus/dehydroalanine (Dha)-selective peptide–peptide connections via a 1,3-dipolar cycloaddition reaction, resulting in the formation of peptide chimeras with complete endo-diastereoselectivity. Tolerating a broad range of functional groups, including the ɛ-amine of a lysine residue, the present method offers an opportunity for the expedient and modular assembly of readily accessible aldehyde, N-terminus-unprotected peptides, and peptide-based dehydroalanines into the chemically robust pyrrolidine ring. | Masaki Iwata; Naohiko Yoshikai; Kazuya Kanemoto | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663ec94791aefa6ce1b04e77/original/precision-synthesis-of-chimeric-peptides-through-site-specific-azomethine-ylide-dehydroalanine-cycloaddition.pdf |
65c26bc166c138172917f6cf | 10.26434/chemrxiv-2024-v787g-v2 | The Enantioselective Organocatalytic [1,2]-Rearrangement of Allylic Ammonium Ylides | The [1,2]-rearrangement of allylic ammonium ylides is traditionally observed as a competitive minor pathway alongside the thermally allowed [2,3]-sigmatropic rearrangement. The challenges associated with developing a catalytic enantioselective variant are amplified as concerted [1,2]-rearrangements are forbidden, with these processes proposed to proceed through homolytic C-N bond fission of the ylide, followed by stereoselective radical-radical recombination. Herein a Lewis basic chiral isothiourea facilitates catalytic [1,2]-rearrangement of prochiral aryl ester ammonium salts to generate unnatural α-amino acid derivatives with unprecedented levels of enantiocontrol (up to 97:3 er) and up to total selectivity over the thermally allowed [2,3]-rearrangement. Key factors in favouring the [1,2]-rearrangement include exploitation of (i) disubstituted terminal allylic substituents, (ii) cyclic N-substituted ammonium salts and (iii) elevated reaction temperatures. Mechanistic studies involving 13C-labelling and crossover reactions, combined with radical trapping experiments and observed changes in product enantioselectivity are consistent with a radical solvent cage effect, with maximum product enantioselectivity observed with promotion of “in-cage” radical-radical recombination. Computational analysis indicates that the distribution between [1,2]- and [2,3]-rearrangement products arises predominantly from C-N bond homolysis of an intermediate ammonium ylide, followed by recombination of the a-amino radical at either the primary or tertiary site of an intermediate allylic radical. Electrostatic interactions involving the bromide counterion and the rearrangement transition states control the facial selectivity of the [1,2]- and [2,3]-rearrangements, while the difficulty of forming a bond in the more sterically hindered tertiary position of the allylic substituent disfavors the formation of the [2,3]-product. These results will impact further investigations and understanding into enantioselective radical-radical reactions. | Will Hartley; Mark Greenhalgh; Kevin Kasten; Taisiia Feoktistova; Henry Wise; Jacqueline Laddusaw; Aileen Frost; Sean Ng; Alexandra Slawin; Bela Bode; Paul Ha-Yeon Cheong; Andrew Smith | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Organocatalysis | CC BY 4.0 | CHEMRXIV | 2024-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c26bc166c138172917f6cf/original/the-enantioselective-organocatalytic-1-2-rearrangement-of-allylic-ammonium-ylides.pdf |
61d8856a6be42069a9258f7a | 10.26434/chemrxiv-2022-c7z49 | Diastereoselective Indole-Dearomative Cope Rearrangements by Compounding Minor Driving Forces. | Reported herein is the discovery of a diastereoselective indole-dearomative Cope rearrangement. A suite of minor driving forces (substrate destabilizing effects; product stabilizing effects) are what promote this otherwise unfavorable dearomatization reaction. These include the following that work in concert to overcome the penalty for dearomatization: (i.) steric congestion in the starting material, (ii.) alkylidene malononitrile and stilbene conjugation events in the product, and (iii.) an unexpected intramolecular p–p* stack on the product side of the equilibrium. The key substrates are rapidly assembled from alkylidenemalononitriles and indole-phenylmethanol derivatives resulting in many successful examples (high yields and diastereoselectivity). The products are structurally complex bearing vicinal stereocenters generated by the dearomative Cope rearrangement. They also contain a variety of functional groups for interconversion to complex architectures. On this line, also described herein are proof-of-concept strategies for achieving enantioselectivity and conversion of the dearomative products to valuable and functionalized small drug-like molecules. | Subhadip De; Breanna Tomiczek; Yinuo Yang; Kenneth Ko; Ion Ghivirga; Adrian Roitberg; Alexander Grenning | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d8856a6be42069a9258f7a/original/diastereoselective-indole-dearomative-cope-rearrangements-by-compounding-minor-driving-forces.pdf |
60c75578702a9b9fc118c6e6 | 10.26434/chemrxiv.14113700.v1 | Anion Specific Effects Drive the Formation of Li-Salt Based Aqueous Biphasic Systems | <p>Aqueous
biphasic systems (ABS) can form when mixing water with two compounds such as
polymers, ionic-liquids or simple salts. While this phenomenon has been known for
decades and found applications in various fields such as biology, recycling or
even more recently electrochemistry, the physics behind the formation of ABSs
remains ill-understood. It was recently demonstrated that ABSs can be composed
of two salts sharing the same cation (Li<sup>+</sup>) but different anions
(sulfonamide and halide). Interestingly, their formation could not be explained
by the position of the anions within the chaotropic/kosmotropic series and was
rather proposed to originate from an anion size mismatch, albeit the size for
these anions was never measured yet owing to the lack of a proper experimental
methodology. Here, we combine experimental techniques and molecular simulations
to assess the specific effects (size, shape, hydrophobic/hydrophilic character)
of a series of anions and correlate them with the formation of ABSs. We
demonstrate that while the anion size mismatch is a prerequisite for the
formation of Li-salts based ABSs, their shape can also play an important role,
providing general guidelines for forming new ABSs with potential future
applications. </p> | Nicolas Dubouis; Arthur France-Lanord; Amandine Brige; Mathieu Salanne; Alexis Grimaud | Theory - Computational; Energy Storage; Interfaces; Solution Chemistry; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75578702a9b9fc118c6e6/original/anion-specific-effects-drive-the-formation-of-li-salt-based-aqueous-biphasic-systems.pdf |
63c042a6a5c354ac5a91396b | 10.26434/chemrxiv-2023-9lh21 | Role of Cholesterol in Interaction of Ionic Liquid with Model Lipid Membranes and Associated Permeability | In this work, we have investigated the impact of composition of cholesterol in the lipid membrane composed of phosphatidylcholine (POPC) or phosphatidylglycerol (POPG) on the membrane permeability induced by 1-dodecyl-3-methylimidazolium bromide ([C12MIM]+Br-) ionic liquid using various biophysical techniques. We investigated four different compositions of cholesterol (10, 20, 30, and 40 mole%) both with POPC and POPC phospholipids. Membrane permeability was determined using steady-fluorescence-based dye leakage assay. Further, interaction of ionic liquid with lipid membranes was investigated using ζ-potential measurements, and dynamic light scattering for measuring the size distribution. POPC and POPG membranes both show a reduction in [C12MIM]+ induced membrane permeability in the presence of cholesterol which continues with a further increase in cholesterol content. The overall reduction in membrane permeability is more in POPG LUVs in the presence of 30 and 40 mol% cholesterol content. Besides this, cholesterol also impacts the [C12MIM]+Br--induced fusion of POPC and POPG LUVs at higher ionic liquid concentrations. POPG membranes become more fusion prone in the presence of cholesterol as compared to POPC lipid membrane. | Sandeep Kumar; Navleen Kaur; Venus Singh Mithu | Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c042a6a5c354ac5a91396b/original/role-of-cholesterol-in-interaction-of-ionic-liquid-with-model-lipid-membranes-and-associated-permeability.pdf |
63394724e665bd8f781a5b94 | 10.26434/chemrxiv-2022-khww5 | N-Acryloylindole-alkyne (NAIA) enables profiling new ligandable hotspots in chemoproteomics experiments and imaging thiol oxidation | We report a new class of compounds, N-acryloylindole-alkynes (NAIAs), as promising cysteine-reactive probes for proteome-wide cysteine profiling and imaging of thiol oxidative modifications. NAIAs showed superior cysteine reactivity owing to delocalization of π electrons of the acrylamide warhead over the whole indole scaffold, resulting in its activation for faster reaction with cysteines. This allows NAIAs to ligand functional cysteines more effectively than IAA, as well as to image oxidized thiols in cells facing oxidative stress by confocal fluorescence microscopy. In MS-based ABPP experiments, NAIAs successfully captured a new pool of ligandable cysteines and proteins even compared to the current state-of-the-art cysteine profiling data. Competitive ABPP experiments further demonstrate the ability of NAIA to discover hit compounds targeting these new cysteines and proteins. This work should initiate development of new cysteine-reactive probes, particularly those with activated acrylamide, for advancing cysteine imaging and profiling, and covalent ligand screening for drug research. | Hinyuk Lai; Tin-Yan Koo; Daniel K. Nomura; Clive Yik-Sham CHUNG | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63394724e665bd8f781a5b94/original/n-acryloylindole-alkyne-naia-enables-profiling-new-ligandable-hotspots-in-chemoproteomics-experiments-and-imaging-thiol-oxidation.pdf |
60c74af3702a9b5fd418b36e | 10.26434/chemrxiv.12234416.v2 | Stereoretention in Styrene Heterodimerisation Promoted by One-Electron Oxidants | <p>Radical cations generated from the oxidation of C=C p-bonds are synthetically useful reactive intermediates for C–C and C–X bond formation. Radical cation formation, induced by sub-stoichiometric amounts of external oxidant, are important intermediates in the Woodward-Hoffmann thermally disallowed [2+2] cycloaddition of electron-rich alkenes. Using density functional theory (DFT), we report the detailed mechanisms underlying the intermolecular heterodimerisation of anethole and β-methylstyrene to give unsymmetrical, tetra-substituted cyclobutanes. Reactions between <i>trans</i>-alkenes favour the <i>all-trans</i> adduct, resulting from a kinetic preference for <i>anti</i>-addition reinforced by reversibility at ambient temperatures since this is also the thermodynamic product; on the other hand, reactions between a <i>trans</i>-alkene and a <i>cis</i>-alkene favour <i>syn</i>-addition, while exocyclic rotation in the acyclic radical cation intermediate is also possible since C-C forming barriers are higher. Computations are consistent with the experimental observation that hexafluoroisopropanol (HFIP) is a better solvent than acetonitrile, in part due to its ability to stabilize the reduced form of the hypervalent iodine initiator by hydrogen bonding, but also through the stabilisation of radical cationic intermediates along the reaction coordinate.</p> | Xinglong Zhang; Robert Paton | Stereochemistry; Computational Chemistry and Modeling; Theory - Computational; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74af3702a9b5fd418b36e/original/stereoretention-in-styrene-heterodimerisation-promoted-by-one-electron-oxidants.pdf |
61540b199e38408c36442853 | 10.26434/chemrxiv-2021-8p816 | Simple Nonionic Omnisoluble Tetraphenylporphyrin for Relative Referencing of Singlet Oxygen Quantum Yield | Meso-tetrakis-(3,4,5-tris{2-[2-(2-methoxyethoxy)ethoxy]ethoxy}phenyl)porphyrin TEG12PH2 is reported as an ‘omnisoluble’ TPP reference for singlet oxygen (1O2) generation quantum yield (ΦSO) estimation. TEG12PH2 is a highly soluble, nonionic compound possessing excellent 1O2 QY in a wide variety of common solvents, including water. TEG12PH2 was prepared on multigram scale by the 12-way O-alkylation of tetrakis(3,4,5-trihydroxyphenyl)porphyrin using 2-(2-(2-methoxyethoxy)ethoxy)ethyl 4-toluenesulfonate as reaction solvent. The corresponding Zn(II) complex TEG12PZn was also prepared and studied. Its 1O2 QYs in the different solvents studied were found to be 0.86 (acetone), 0.59 (acetonitrile), 0.66 (chloroform), 0.85 (methanol), 0.45 (toluene) and 0.51 (water). TEG12PH2 can be considered a reliable and easy to implement omnisoluble reference compound for the estimation of the 1O2 generating activities of new materials, especially new porphyrinic compounds. | Daniel T. Payne; Jan Hynek; Jan Labuta; Jonathan P. Hill | Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Photochemistry (Org.); Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2021-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61540b199e38408c36442853/original/simple-nonionic-omnisoluble-tetraphenylporphyrin-for-relative-referencing-of-singlet-oxygen-quantum-yield.pdf |
64d4b6d769bfb8925ab22caa | 10.26434/chemrxiv-2023-gs41m | K-ion slides in Prussian Blue Analogues | We study the phenomenology of cooperative off-centering of K+ ions in potassiated Prussian blue analogues. The principal distortion mechanism by which this off-centering occurs is termed a `K-ion slide', and its origin is shown to lie in the interaction between local electrostatic dipoles that couple through a combination of electrostatics and elastic strain. Using synchrotron X-ray powder diffraction measurements, we determine the crystal structures of a range of low-vacancy K2M[Fe(CN)6] PBAs (M = Mn, Co, Fe, Ni, Cd) and establish an empirical link between composition, temperature, and slide-distortion magnitude. Our results reflect a common underlying physics responsible for K-ion slides and their evolution with temperature and composition. Monte Carlo simulations driven by a simple model of dipolar interactions and strain coupling reproduce the general features of the experimental phase behaviour. We discuss the implications of our study for optimising the performance of PBA K-ion battery cathode materials, and also its relevance to distortions in other, conceptually related, hybrid perovskites. | John Cattermull; Nikolaj Roth; Simon Cassidy; Mauro Pasta; Andrew Goodwin | Inorganic Chemistry; Solid State Chemistry; Materials Chemistry; Crystallography – Inorganic | CC BY NC 4.0 | CHEMRXIV | 2023-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d4b6d769bfb8925ab22caa/original/k-ion-slides-in-prussian-blue-analogues.pdf |
652fd98b87198ede0789f4ad | 10.26434/chemrxiv-2023-8m6b9 | Conformational Source of Comonomer Sequence-Dependent Copolymer Glass-Transition Temperatures | This brief review addresses the source of the dependence of copolymer glass transition temperatures (Tgps) on their comonomer sequences. Here we show that a comparison of the conformational entropies obtained from the Rotational Isomeric State (RIS) conformational models of the poly-A and poly-B homopolymers and their resultant poly-A/B co-polymers, i.e., ΔSconf = (XASA + XBSB) - SA/B (X = comonomer fraction), can be used to predict/understand the Tgps of copolymers. For copolymers with ΔSconf ~ 0, we expect their Tgps to follow Fox behavior and to depend only on copolymer composition, because of the similar conformational flexibilities of the A and B homo- and A/B-copolymers. When the conformational entropy ΔSconf is negative the A/B copolymer is assumed more flexible than the weighted sum of polymer-A and polymer-B conformational entropies, resulting in Tgps that are lower than expected from the Fox equation. Conversely, a positive ΔSconf suggests the copolymer’s lower flexibility, resulting in higher Tgps than expected from the Fox relation. We use the successful comparison of the observed dependence of numerous copolymer Tgps to demonstrate the validity of using their calculated RIS conformational entropies to predict their comonomer sequence dependencies. | Alan Tonelli; Jialong Shen | Polymer Science; Polymer chains | CC BY NC 4.0 | CHEMRXIV | 2023-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652fd98b87198ede0789f4ad/original/conformational-source-of-comonomer-sequence-dependent-copolymer-glass-transition-temperatures.pdf |
662ab303418a5379b0ba09f8 | 10.26434/chemrxiv-2023-n62vd-v2 | Comprehensive two-dimensional liquid chromatography – high-resolution mass spectrometry for complex protein digest analysis using parallel gradients | Despite the high gain in peak capacity, online comprehensive two-dimensional liquid chromatography coupled with high-resolution mass spectrometry (LC×LC-HRMS) has not yet been widely applied to the analysis of complex protein digests. One reason is the methods' reduced sensitivity that can be linked to the high flow rates of the second separation dimension (2D ). This results in higher dilution factors and the need for flow splitters to couple to ESI-MS. This study reports proof of principle results of the development of an RPLC×RPLC-HRMS using parallel-gradients (2D flow rate of 0.7 mL min-1) and its comparison to shifted gradient methods (2D of 1.4 mL min-1) for the analysis of complex digests using a QExactive-Plus MS. Shifted and parallel-gradients resulted in high surface coverage (SC) and effective peak capacity (SC of 0.6226 and 0.7439 and an effective peak capacity of 779 and 757 in 60 minutes). When applied to a cell line digest sample, parallel-gradients allowed higher sensitivity (e.g., average MS intensity increased by a factor of 3), allowing for a higher number of identifications (e.g., about 2600 vs 3900 peptides). In addition, reducing the modulation time to 10s significantly increased the number of MS/MS events that could be performed. When compared to a 1D-RPLC method, parallel RPLC×RPLC-HRMS methods offered higher separation performance (FHWH from 0.12 to 0.018 min) with limited sensitivity losses resulting in an increase of analyte identifications (e.g. about 6000 vs 7000 peptides). | Rick S. van den Hurk ; Bart Lagerwaard ; Nathan Terlouw; Mingzhe Sun; Job Tieleman; Anniek Verstegen; Saer Samanipour; Bob W.J. Pirok; Andrea Gargano | Analytical Chemistry; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662ab303418a5379b0ba09f8/original/comprehensive-two-dimensional-liquid-chromatography-high-resolution-mass-spectrometry-for-complex-protein-digest-analysis-using-parallel-gradients.pdf |
6139d65c656369336f26f151 | 10.26434/chemrxiv-2021-5568h | Polydopamine coated CdSe@CdS dot-in-rod heterostructures with Rhodium-based catalysts for stable photocatalytic NAD+ reduction | We report on a photocatalytic system consisting of CdSe@CdS nanorods, coated with a polydopamine (PDA) shell functionalized with molecular rhodium catalysts. The PDA shell was implemented to enhance photostability of the photosensitizer, to improve charge carrier separation and to offer multiple options for stable covalent functionalization, allowing for spatial proximity and efficient shuttling of charges between sensitizer and reaction center. The activity of the photocatalytic system was demonstrated by light-driven reduction of nicotinamide adenine dinucleotide (NAD+) to its reduced form NADH. This work shows that PDA coated nanostructures present an attractive platform for covalent attachment of reduction and oxidation reaction centers for photocatalytic applications. | Marcel Boecker; Mathias Micheel; Alexander K. Mengele; Christof Neumann; Tilmann Herberger ; Tommaso Marchesi D'Alvise; Bei Liu; Andreas Undisz; Sven Rau; Andrey Turchanin; Christopher V. Synatschke; Maria Wächtler; Tanja Weil | Catalysis; Polymer Science; Nanoscience; Nanocatalysis - Catalysts & Materials; Heterogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6139d65c656369336f26f151/original/polydopamine-coated-cd-se-cd-s-dot-in-rod-heterostructures-with-rhodium-based-catalysts-for-stable-photocatalytic-nad-reduction.pdf |
64e148ca00bbebf0e6775a1f | 10.26434/chemrxiv-2023-b8qn6-v2 | Comprehensive analysis of relaxation decays from high-resolution relaxometry | Relaxometry consists in measuring relaxation rates over orders of magnitude of magnetic fields to probe motions of complex systems. High-resolution relaxometry (HRR) experiments can be performed on conventional high-field NMR magnets equipped with a sample shuttle. During the experiment, the sample shuttle transfers the sample between the high-field magnetic center and a chosen position in the stray field for relaxation during a variable delay, thus using the stray field as a variable field. As the relaxation delay occurs outside of the probe, HRR experiments cannot rely on the control of cross-relaxation pathways, which is standard in high-field relaxation pulse sequences. Thus, decay rates are not pure relaxation rates, which may impair a reliable description of the dynamics. Previously, we took into account cross-relaxation effects in the analysis of high- resolution relaxometry data by applying a correction factor to relaxometry decay rates in order to estimate relaxation rates. These correction factors were obtained from the iterative simulation of the relaxation decay while the sample lies outside of the probe and a preceding analysis of relaxation rates which relies on the approximation of a priori multi-exponential decays by mono-exponential functions. However, an analysis protocol matching directly experimental and simulated relaxometry decays should be more self consistent. Here, we introduce Matching INtensities for the Optimization of Timescales and Amplitudes of motions Under Relaxometry (MINOTAUR), a framework for the analysis of high-resolution relaxometry that takes as input the intensity decays at all fields. This approach uses the full relaxation matrix to calculate intensity decays, allowing complex relaxation pathways to be taken into account. Therefore, it eliminates the need for a correction of decay rates and for fitting multi-exponential decays with mono-exponential functions. The MINOTAUR software is designed as a flexible framework where relaxation matrices and spectral density functions corresponding to various models of motions can be defined on a case-by-case basis. The agreement with our previous analyses of protein side-chain dynamics from carbon-13 relaxation is excellent, while providing a more robust analysis tool. We expect MINOTAUR to become the tool of choice for the analysis of high-resolution relaxometry. | Nicolas Bolik-Coulon; Milan Zachrdla; Guillaume Bouvignies; Philippe Pelupessy; Fabien Ferrage | Physical Chemistry; Biophysical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e148ca00bbebf0e6775a1f/original/comprehensive-analysis-of-relaxation-decays-from-high-resolution-relaxometry.pdf |
613eda3d27d90665ef85e626 | 10.26434/chemrxiv-2021-xr3x5 | Dipole Moment Calculations Using
Multiconfiguration Pair-Density Functional Theory and
Hybrid Multiconfiguration Pair-Density Functional Theory
| The dipole moment is the molecular property that most directly indicates molecular polarity. The accuracy of computed dipole moments depends strongly on the quality of the calculated electron density, and the breakdown of single-reference methods for strongly correlated systems can lead to poor predictions of the dipole moments in those cases. Here, we derive the analytical expression for obtaining the electric dipole moment by multiconfiguration pair density functional theory (MC-PDFT), and we assess the accuracy of MC-PDFT for predicting dipole moments at equilibrium and nonequilibrium geometries. We show that MC-PDFT dipole moment curves have reasonable behavior even for stretched geometries, and they significantly improve upon the CASSCF results by capturing more electron correlation. The analysis of a dataset consisting of 18 first-row transition metal diatomics and 6 main-group polyatomic molecules with multireference character suggests that MC-PDFT and its hybrid extension (HMC-PDFT) perform comparably to CASPT2 and MRCISD+Q methods and have a mean unsigned deviation of 0.2–0.3 D with respect to the best available dipole moment reference values. We explored the dependence of the predicted dipole moments upon the choice of the on-top density functional and active space, and we recommend the tPBE and hybrid tPBE0 on-top choices for the functionals combined with the moderate correlated participating orbital scheme for selecting the active space. With these choices, the mean unsigned deviations (in debyes) of the calculated equilibrium dipole moments from the best estimates are 0.77 for CASSCF, 0.29 for MC-PDFT, 0.24 for HMC-PDFT, 0.28 for CASPT2, and 0.25 for MRCISD+Q. These results are encouraging because the computational cost of MC-PDFT or HMC-PDFT is largely reduced compared to the CASPT2 and MRCISD+Q methods. | Aleksandr Lykhin; Donald Truhlar; Laura Gagliardi | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613eda3d27d90665ef85e626/original/dipole-moment-calculations-using-multiconfiguration-pair-density-functional-theory-and-hybrid-multiconfiguration-pair-density-functional-theory.pdf |
621cf1d8ce899b6b8aa71e58 | 10.26434/chemrxiv-2021-52kwx-v2 | Selective cellular probes for mammalian thioredoxin reductase TrxR1: rational design of RX1, a modular 1,2-thiaselenane redox probe | Cellular redox networks power a multitude of cellular processes, and are often dysregulated in pathologies including cancer and inflammatory diseases. Quantifying the turnover of the key players in redox homeostasis is crucial for understanding their physiological dynamics and for targeting them in pathologies. However, suitably selective probes for assessing specific redox enzyme activities in cells are lacking. We rationally developed the first chemical probes targeting the mammalian selenoprotein thioredoxin reductase (TrxR) while fully resisting other cellular thiols and oxidoreductases. We used a cyclic selenenylsulfide as a thermodynamically stable and kinetically reversible trigger, oriented to harness the chemistry of TrxR's unique selenolthiol active site, and integrated it into modular probes releasing arbitrary cargos upon reduction. The probes showed remarkable selenocysteine-dependent sensitivity to cytosolic TrxR1, against a panel of oxidoreductases. Lead probe RX1 also had excellent TrxR1-selective performance in cells, as cross-validated by TrxR1 knockout, selenium starvation, TrxR1 knock-in, and TrxRselective chemical inhibitors. Its background-free fluorogenicity enabled us to perform the first quantitative high-throughput live cell screen for TrxR1 inhibitors. This indicated that tempered SNAr electrophiles may be a more favorable drug class than classically-used electrophiles. The RX1 design is thus a robust, cellularly validated, high-performance modular system for mammalian TrxR1. This sets the stage for in vivo imaging TrxR1 activity in health and disease, and can also drive and reorient TrxR1-inhibitor drug design. The thermodynamic and kinetic considerations behind RX1's selectivity also outline paths towards rationally-designed probes for other key players in redox biology. | Lukas Zeisel; Jan G. Felber; Lena Poczka; Karoline Scholzen; Dorian Cheff; Martin S. Maier; Qing Cheng; Min Shen; Matt D. Hall; Elias S. J. Arnér; Julia Thorn-Seshold; Oliver Thorn-Seshold | Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Biochemistry; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2022-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621cf1d8ce899b6b8aa71e58/original/selective-cellular-probes-for-mammalian-thioredoxin-reductase-trx-r1-rational-design-of-rx1-a-modular-1-2-thiaselenane-redox-probe.pdf |
67c823d16dde43c90893a7e3 | 10.26434/chemrxiv-2025-x1zq1 | Substituent effects of fluorinated bambusurils on their anion transport | Anionophores are molecules that can transport ions across membranes. Several structural design criteria must be met for anionophores to be highly active. Fluorinated anionophores are usually more potent than their non-fluorinated analogues due to their higher lipophilicity and increased affinity for anions. Clear structure-activity relationships have been described for small and relatively simple anionophores. However, such studies are more challenging for large and macrocyclic anionophores, as their preparation is usually more complicated, limiting the number of compounds tested in anion transport studies.
Here we present a series of twelve macrocyclic bambusuril anion transporters to investigate how variations in fluorinated substituents affect their transport properties. Measurements of Cl−/HCO3− antiport activities in liposomes revealed links between parameters such as lipophilicity or substituent polarity and transport activity. For some bambusurils, an unusually large effect of the presence of cholesterol in the membrane on transport activity was found. Further studies showed that for very potent anion receptors, such as the bambusurils described here, the binding selectivity towards anions becomes more important than the absolute binding affinity to anions when considering anion exchange across the membrane.
| Matúš Chvojka; Vladimír Šindelář; Hennie Valkenier | Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2025-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c823d16dde43c90893a7e3/original/substituent-effects-of-fluorinated-bambusurils-on-their-anion-transport.pdf |
60c74dd3ee301c772bc7a399 | 10.26434/chemrxiv.12662561.v1 | Predicting Chemical Reaction Equilibrium in Dilute Solutions by Atomistic Simulation: Application to CO2 Reactive Absorption in Aqueous Primary Alkanolamine Solutions | We present a general atomistic simulation framework for efficient reactive equilibrium calculations in dilute solutions, and its application to CO2 reactive absorption in aqueous alkanolamine solutions. No experimental data of any kind for the
solvents is required and no empirical adjustments are required for its implementation. This hybrid methodology involves calculating the required reaction equilibrium
constants by combining high–level quantum chemical calculations of ideal–gas standard reaction Gibbs energies (∆G0
) with conventional free energy calculations for
transfer of the molecular species from the ideal gas to infinite dilution in the solvent (i.e, their solvation free energies). For the solvation free energy calculations,
we use explicit solvent molecular dynamics simulations with the General AMBER
Force Field (GAFF). The resulting equilibrium constants are then coupled with a
macroscopic Henry–Law–based ideal solution model to calculate the solution speciation and the CO2 partial pressure, PCO2
. We show results for seven primary
amines: monoethanolamine (MEA), 2–amino–2–methylpropanol (AMP), 1–amino–2–
propanol (1–AP), 2–amino–2–methyl–1,3–propanediol (AMPD), 2–aminopropane–1,3–
diol (SAPD), 2–(2–aminoethoxy)ethanol (2–AEE) or diglycolamine (DGA), and 2–
amino–1–propanol (2–AP). Experimental speciation and PCO2 data for some of these
is available, with which we validate our methodology. We predict new results for others
in cases when such data is unavailable, and provide explanations for the experimental
inability to detect carbamate species in some cases. Our results for the pK value of
the carbamate reversion reaction are within the chemical accuracy limit of 218.506/T
in comparison with experiment when such data exist, which at 298.15 K corresponds
to 0.73 pK units. We argue that the precision of our pK predictions in general is
comparable to that which can be obtained from conventional experimental methodologies for these quantities. Our results suggest that the presented molecular simulation
methodology may provide a robust and cost–efficient tool for solvent screening in the
design of post–combustion CO2 capture processes.<br /> | Javad Noroozi; William Smith | Computational Chemistry and Modeling; Theory - Computational; Thermodynamics (Chem. Eng.); Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74dd3ee301c772bc7a399/original/predicting-chemical-reaction-equilibrium-in-dilute-solutions-by-atomistic-simulation-application-to-co2-reactive-absorption-in-aqueous-primary-alkanolamine-solutions.pdf |
64ccfb32dfabaf06ffb276a8 | 10.26434/chemrxiv-2023-d3r4g | Fluorophosphoniums as Lewis acids in organometallic catalysis: application in cobalt-catalyzed carbonylation of β-lactones | Within the context of the development of phosphorus-based Lewis acids, we report herein the synthesis of four fluorophosphonium organic Lewis acids, with tetracarbonyl cobaltate as counter-anion: [R3PF]+[Co(CO)4]- (with R = o-Tol, Cy, iPr, and tBu). These novel ion pairs were fully characterized by NMR and IR spectroscopy, elemental analysis, and, for three of them, X-ray diffraction. The catalytic activities of these ion pairs were investigated for the carbonylation of β lactones to succinic anhydrides. [tBu3PFCo(CO)4] IV (3 mol%) afforded 91 % of succinic anhydride after 16 h at 80 °C, at a very mild pressure of 2 bar of carbon monoxide. To our knowledge, this work is the first report on using fluorophosphoniums as main-group Lewis acids in a transition metal-catalyzed reaction. | Marie-Hélène Pietraru; Louise Ponsard; Nicolas Lentz; Pierre Thuéry; Emmanuel Nicolas; Thibault Cantat | Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Main Group Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ccfb32dfabaf06ffb276a8/original/fluorophosphoniums-as-lewis-acids-in-organometallic-catalysis-application-in-cobalt-catalyzed-carbonylation-of-lactones.pdf |
6141926f27d906e30288cff1 | 10.26434/chemrxiv-2021-hz0qp | On the climate impacts of blue hydrogen production | Natural gas based hydrogen production with carbon capture and storage is referred to as blue hydrogen. If substantial amounts of CO2 from natural gas reforming are captured and permanently stored, such hydrogen could be a low-carbon energy carrier. However, recent research raises questions about the effective climate impacts of blue hydrogen from a life cycle perspective. Our analysis sheds light on the relevant issues and provides a balanced perspective on the impacts on climate change associated with blue hydrogen. We show that such impacts may indeed vary over large ranges and depend on only a few key parameters: the methane emission rate of the natural gas supply chain, the CO2 removal rate at the hydrogen production plant, and the global warming metric applied. State-of-the-art reforming with high CO2 capture rates combined with natural gas supply featuring low methane emissions does indeed allow for substantial reduction of greenhouse gas emissions compared to both conventional natural gas reforming and direct combustion of natural gas. Under such conditions, blue hydrogen is compatible with low-carbon economies and features climate change impacts in line with green hydrogen from electrolysis supplied with renewable electricity. However, neither current blue nor green hydrogen production pathways render fully “net-zero” hydrogen without additional carbon dioxide removal. | Christian Bauer; Karin Treyer; Cristina Antonini; Joule Bergerson; Matteo Gazzani; Emre Gencer; Jon Gibbins; Marco Mazzotti; Sean T. McCoy; Russell McKenna; Robert Pietzker; Arvind P. Ravikumar; Matteo C. Romano; Falko Ueckerdt; Jaap Vente; Mijndert van der Spek | Energy; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6141926f27d906e30288cff1/original/on-the-climate-impacts-of-blue-hydrogen-production.pdf |
60c73edabb8c1a4aa53d99c7 | 10.26434/chemrxiv.7137026.v1 | Unifying the Alkaline Hydrogen Evolution/oxidation Reactions Kinetics by Identifying the Roles of Hydroxyl-Water-Cation Adducts | Despite the fundamental and practical
significance of the hydrogen evolution and oxidation reactions (HER/HOR), their
kinetics in base remain unclear. Herein, we show that the alkaline HER/HOR
kinetics can be unified by the catalytic roles of the adsorbed hydroxyl (OH<sub>ad</sub>)-water-alkali
metal cation (AM<sup>+</sup>) adducts, on the basis of the observations that
enriching the OH<sub>ad</sub> abundance via surface Ni benefits the HER/HOR; increasing
the AM<sup>+</sup> concentration only promotes the HER while varying the
identity of AM<sup>+</sup> affects both HER/HOR. The presence of OH<sub>ad</sub>-(H<sub>2</sub>O)<sub>x</sub>-AM<sup>+</sup>
in the double layer region facilitates the OH<sub>ad</sub> removal into the bulk
forming OH<sup>-</sup>-(H<sub>2</sub>O)<sub>x</sub>-AM<sup>+</sup> <i>as per</i> the hard-soft acid-base (HSAB) theory,
thereby selectively promoting the HER. It can be detrimental to the HOR <i>as per</i> the bifunctional mechanism as the
AM<sup>+</sup> destabilizes the OH<sub>ad</sub>, which is further supported by the
CO oxidation results. This new notion may be important for alkaline
electrochemistry. | Ershuai Liu; Jingkun Li; Li Jiao; Huong Thi Thanh Doan; Zeyan Liu; Zipeng Zhao; Yu Huang; Kuzhikalail. M. Abraham; Sanjeev Mukerjee; Qingying Jia | Electrochemical Analysis; Electrochemistry; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73edabb8c1a4aa53d99c7/original/unifying-the-alkaline-hydrogen-evolution-oxidation-reactions-kinetics-by-identifying-the-roles-of-hydroxyl-water-cation-adducts.pdf |
64186595dab08ad68f69acbb | 10.26434/chemrxiv-2023-w7v23 | Spontaneous Emulsification: Elucidation of the Local Processes | Micro and/or Nano sized emulsions are formed when an organic liquid gently comes in contact with water in the presence of a surfactant, where no external agitation is required. Many years of research made it clear that the driving force for spontaneous emulsification arises from the differences of the chemical potentials of various components in the organic and aqueous phases, which triggers diffusion coupled hydrodynamic fluctuation. While extraordinary theoretical developments have taken place that attempted to describe these processes within the scopes of equilibrium and non-equilibrium thermodynamics, the local processes underlying the spontaneous emulsification, however, still remain elusive. In this research, we investigate the local processes that involve the transfer of surfactant as well as water from one phase to another (i.e. water to oil), which results in the formation of water-in-oil emulsion in the organic phase and, subsequently. Thes emulsions invert into oil-in-water emulsion, rather abruptly, as they cross the phase boundary. Studies based on UV spectroscopy and molecular dynamics indicate that these processes may involve explosive events and subsequent assembly of the fragments to other organized structures which are reminiscent of cusp catastrophe proposed earlier by Dickinson. These processes lead to either to a strong or a weak fluctuation of the component concentrations below the interface that also becomes evident in the fast (athermal) diffusion of the emulsion droplets from the interfacial region farther into the bulk water. These events can be arrested suitably with polymeric additives. | Monicka Kullappan; Wes Patel; Manoj Chaudhury | Physical Chemistry; Organic Chemistry; Chemical Engineering and Industrial Chemistry; Interfaces | CC BY 4.0 | CHEMRXIV | 2023-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64186595dab08ad68f69acbb/original/spontaneous-emulsification-elucidation-of-the-local-processes.pdf |
60c74b5b4c89191f7ead3421 | 10.26434/chemrxiv.12325844.v1 | Natural Compounds from Djiboutian Medicinal Plants as Inhibitors of COVID-19 by in Silico Investigations | The new coronavirus type SARS-Cov 2 (severe acute respiratory syndrome), which appeared in autumn 2019 in China, became a global pandemic in a few months. In this work, we looked for the potential anti SARS-Cov 2 of the compounds isolated from three Djiboutian medicinal plants namely Acacia seyal, Cymbopogon commutatus, and Indigofera caerulea. For this we carried out a docking with nine biomolecules, β-Sitosterol , Quercetin, Catechin, Lupeol, Rutin, Kaempferol, Gallic acid, Piperitone and Limonene on three target sites which are SARS-CoV-2 main protease (Mp), SARS-CoV-2 receptor binding domain (RBD) and human furin protease. These targets are chosen because of their role in the process of penetration of the virus into human cells and its multiplication. The phenolic compounds have a very good afinity on these three target sites with binding energies of up to -9.098 kcal/mol for rutin on SARS-CoV-2 Mp, much better than the two reference drugs hydroxychloroquine (-5.816 kcal / mol) and remdesivir (-7.194 kcal/mol). These natural compounds do not present toxicities and can be used pending In vitro and In vivo evaluations. | abdirahman elmi; S. al jawad sayem; Mohamed Ahmed; fatouma mohamed | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b5b4c89191f7ead3421/original/natural-compounds-from-djiboutian-medicinal-plants-as-inhibitors-of-covid-19-by-in-silico-investigations.pdf |
64e7f4223fdae147fac1c6e4 | 10.26434/chemrxiv-2023-d147w | Expansion of Bond Dissociation Prediction with Machine Learning to Medicinally and Environmentally Relevant Chemical Space | Bond dissociation energetics underpin the thermodynamics of chemical transformations where bonds are broken or formed and can also be used to predict reaction rates and selectivities. Current machine learning (ML) models to predict bond dissociation energy (BDE) are largely limited in their elemental coverage to hydrogen and the second-row elements. This has restricted the applicability of ML-derived BDE predictions, particularly for molecules of medicinal relevance, since the heteroatoms S, Cl, F, P, Br, and I are commonly found in approved pharmaceuticals. Atmospherically and environmentally relevant molecules containing multiple halogen atoms have been similarly inaccessible. In this study, we considerably expand the size, elemental composition, and bond types of an extensive BDE database and train a new ML BDE model that includes C, H, N, O, S, Cl, F, P, Br, and I. We curate a new quantum chemical dataset of 531,244 unique zero-point energy inclusive homolytic dissociations of organic compounds. We investigate accuracy for out-of-sample molecules and implement iterative training and testing cycles during model development to improve the model accuracy. Improvements in predictive accuracy were achieved for datasets of pharmaceutically relevant molecules containing multiple C(sp2)–halogen bonds from 5.7 to 0.8 kcal mol-1 and polyhaloalkyl compounds with multiple C(sp3)–halogen bonds from 2.7 to 1.2 kcal mol-1 through the targeted augmentation of training data by as little as eight additional molecules. Our updated and expanded model (ALFABET) achieves a mean absolute error of 0.6 kcal mol-1 for both enthalpies and free energies compared to the quantum chemical ground truth. The graph-based representations utilized here outperform traditional cheminformatics features such as radial fingerprints, and there is no discernible improvement in accuracy by including more expensive QM-derived parameters, such as optimized bond lengths. Finally, we illustrate high accuracy in external prediction tasks for large halogenated natural products, pharmaceutically-relevant halogenated molecules, atmospherically-important halocarbons, and polyfluoroalkyl substances related to environmental toxicity. | Shree Sowndarya Santhanalakkshmi Vejaykummar; Yeonjoon Kim; Seonah Kim; Peter St. John; Robert Paton | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e7f4223fdae147fac1c6e4/original/expansion-of-bond-dissociation-prediction-with-machine-learning-to-medicinally-and-environmentally-relevant-chemical-space.pdf |
60c73d4c567dfe5230ec35df | 10.26434/chemrxiv.5533066.v1 | Simulation-based characterization of electrolyte and small molecule diffusion in oriented mesoporous silica thin films | We developed a new workflow for simulating ion reaction-adsorption-diffusion in nanoporous silica-based materials that are resolved through electron microscopy. Firstly, we propose a matched filtering procedure to identify and segment unique porous regions of the material that will be subject to PDE simulation. Secondly, we perform reaction-adsorption-diffusion PDE simulations on representative material regions that are then applied to characterize the entire microscopy-resolved film surface. Using this model, we examine the capacity of a recently synthesized mesoporous film to tune small molecule permeation through modulating the material permeability, surface chemistry<br />including buffering and adsorption, as well as electrolyte composition. Specifically, we find that our proposed matched filtering approach reliably discriminates hexagonal close packed (HCP) porous regions (bulk) from characterized defect regions in transmission electron microscopy (EM) data for nanoporous silica films. Further, based on our implementation of a pH-/surface-chemistry dependent Poisson-Nernst-Planck (PNP) model that is consistent with existing experimental measurements of KCl and CaCl2 conductance, we characterize ion and 5(6)-Carboxyfluorescein (CF) dye permeability in silica-based nanoporous materials over a broad range of ionic strengths, pHs, and surface chemistries. Using this protocol, we probe conditions for selectively tuning small molecule permeability based on mesoporous film pore size, surface charge, ionic strength and surface reactions in the rapid-equilibrium limit. <br /><br /> | Bin Sun; Ryan Blood; Selcuk Atalay; Dylan Colli; Stephen E. Rankin; Barbara L. Knutson; Peter M. Kekenes-Huskey | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2017-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d4c567dfe5230ec35df/original/simulation-based-characterization-of-electrolyte-and-small-molecule-diffusion-in-oriented-mesoporous-silica-thin-films.pdf |
63195c27bc257bc31fded8e7 | 10.26434/chemrxiv-2022-k3dq1 | Metal-Free Covalent Organic Frameworks Containing Precise Heteroatoms for Efficient Oxygen Reduction Reaction | Heteroatom-doped carbon-based nanomaterials are one of the most promising metal-free electrocatalysts due to their high activity, low cost, long lifetime, and environmental friendliness. However, the precise atomic position is hard to tune; moreover, the specific role of those heteroatom species is still unclear. Herein, we report a series of metal-free benzotrithiophene-based covalent organic frameworks containing various heteroatoms (Se, S or O), BTT-COFs (named JUC-616, JUC-617, and JUC-618, respectively), and explore their oxygen reduction reaction (ORR) catalytic activity. Remarkably, JUC-616 involving precise Se atoms exhibits an onset potential of 1.02 V and half-wave potential of 0.78 V, which is the best among metal- and pyrolysis-free COF-based electrocatalysts reported so far. Furthermore, we demonstrate that the high ORR catalytic performance of JUC-616 can be attributed to the small free energy and overpotential by DFT calculations. This work thus promotes the promising potential of functionalized COFs with precise heteroatoms for electrocatalysts. | Qianrong Fang; Jiali Li; Ji Jia; Jinquan Suo; Cuiyan Li; Yusran Yusran; Hui Li; Valentin Valtchev; Shilun Qiu; xiaoming Liu | Catalysis; Polymer Science; Electrocatalysis; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63195c27bc257bc31fded8e7/original/metal-free-covalent-organic-frameworks-containing-precise-heteroatoms-for-efficient-oxygen-reduction-reaction.pdf |
62f3e9b8e78f70f41c36c7ca | 10.26434/chemrxiv-2022-4lhqb-v2 | Sensitivity analysis methodology for battery
degradation models | Accurate degradation models are crucial to battery design and management. However, the time and resources required to improve the accuracy of the model input factors that the output is sensitive to, which is essential for elucidating the inherent dominant mechanism in the model, remain a challenge. Here we present a sensitivity analysis of a pseudo-two-dimensional battery model coupled with a capacity fade model based on solid electrolyte interphase formation and the corresponding irreversible charge loss for Li-ion batteries. The proposed method is based on training an inexpensive differentiable surrogate Gaussian process regression model on observed input-output pairs and analysing the surrogate model to learn about the global and local sensitivities of the original system. With this method, the relevant global sensitive parameters can be identified, and an in-depth analysis of electrochemical phenomena such as the correlation between the thickness of the solid electrolyte interphase and the irreversible charge loss can be explored. This proposed method will provide key insight into how the sensitivity analysis of the physics-based degradation model must be conducted for effective integration into battery management systems. | Williams Agyei Appiah; Jonas Busk; Tejs Vegge; Arghya Bhowmik | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f3e9b8e78f70f41c36c7ca/original/sensitivity-analysis-methodology-for-battery-degradation-models.pdf |
6707815c51558a15efac616b | 10.26434/chemrxiv-2024-4bpkc | NMR and SPR Fragment-Based Screening Can Produce Novel High Affinity Small Molecule Hits Against Structured RNAs | Non-coding RNAs account for up to 98 % of the human transcriptome. It has become increasingly clear that non-coding RNAs play diverse and critical roles in many important cellular functions. Although modulation of non-coding RNAs using small molecules is a promising therapeutic strategy, there are relatively few well-characterised RNA-ligand structures. Therefore, the structure-interaction relationships of RNA-targeting small molecules remain underexplored. Here we present a fragment-based screening approach using biophysical assays to identify and evaluate fragments that bind to the theophylline RNA aptamer, which we use as a model system. We were able to identify high affinity fragment hits and generate models of RNA-ligand complexes using a combination of biophysical data and computational docking. Together, these provided insights into the RNA-fragment interactions that underpin binding. This approach demonstrates the feasibility of identifying high-affinity RNA-targeting small molecules with limited structural information. | Brooke Kwai; Indu Chandrashekaran; Biswaranjan Mohanty; Menachem Gunzburg; Bradley Doak; Ashish Sethi; Shubhadra Pillay; David Lok; Sean Harrison; Pedro Serrano; Elisa Barile; Martin Scanlon | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6707815c51558a15efac616b/original/nmr-and-spr-fragment-based-screening-can-produce-novel-high-affinity-small-molecule-hits-against-structured-rn-as.pdf |
60fb1cd5d03b3d03f20288be | 10.26434/chemrxiv-2021-w4sb3 | Fluorine labeling of ortho-phenylenes to facilitate conformational analysis | ¹H NMR spectroscopy is a powerful tool for the conformational analysis of ortho-phenylene foldamers in solution. However, as o-phenylenes are integrated into ever-more-complex systems, we are reaching the limits of what can be analyzed by ¹H- and ¹³C-based NMR techniques. Here, we explore fluorine labeling of o-phenylene oligomers for analysis by ¹⁹F NMR spectroscopy. Two series of fluorinated oligomers have been synthesized. Optimization of monomers for Suzuki coupling enables an efficient stepwise oligomer synthesis. The oligomers all adopt well-folded geometries in solution, as determined by ¹H NMR spectroscopy and X-ray crystallography. ¹⁹F NMR experiments complement these methods well. The resolved singlets of one-dimensional ¹⁹F{¹H} spectra are very useful for determining relative conformer populations. The additional information from two-dimensional ¹⁹F NMR spectra is also clearly valuable when making ¹H assignments. Comparison of ¹⁹F isotropic shielding predictions to experimental chemical shifts is not, however, currently sufficient by itself to establish o-phenylene geometries. | Viraj C. Kirinda; Gopi Nath Vemuri; Nicholas G. Kress; Kaitlyn M. Flynn; Nuwanthika Dilrukshi Kumarage; Briana R. Schrage; David L. Tierney; Christopher J. Ziegler; C. Scott Hartley | Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60fb1cd5d03b3d03f20288be/original/fluorine-labeling-of-ortho-phenylenes-to-facilitate-conformational-analysis.pdf |
633b81ef0e3c6a48e8327574 | 10.26434/chemrxiv-2022-41npn | Design of Class I/IV Bromodomain-Targeting Degraders for Chromatin Remodeling Complexes | Targeted protein degradation is an emerging technology that can be used for modulating the activity of epigenetic protein targets. Among bromodomain-containing proteins, a number of degraders for the BET family have been developed while non-BET bromodomains remain underexplored. Several of these proteins are subunits in chromatin remodeling complexes often associated with oncogenic roles. Here we describe the design of class I (BPTF and CECR2) and IV (BRD9) bromo-domain-targeting degraders based on two scaffolds derived from pyridazinone and pyrimidine-based heterocycles. We evalu-ate various exit vectors and linkers to identify analogues that demonstrate selectivity within these families. We further use an in-cell NanoBRET assay to demonstrate that these heterobifunctional molecules are cell-permeable, form ternary complexes, and can degrade nanoluciferase-bromodomain fusions. Finally, as a first example of a CECR2 degrader, we observe that our pyrimidine-based analogues degrade endogenous CECR2, while showing a smaller effect on BPTF levels. The pyridazinone-based compounds did not degrade BPTF when observed through western blotting, supporting a more challenging target for degradation and a goal for future optimization | Huda Zahid; Jeff Costello; Jennifer Kimbrough; Marisa Actis; Zoran Rankovic; William Pomerantz | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633b81ef0e3c6a48e8327574/original/design-of-class-i-iv-bromodomain-targeting-degraders-for-chromatin-remodeling-complexes.pdf |
60c755389abda285f4f8e2d1 | 10.26434/chemrxiv.13234289.v3 | Comparative Study of Deep Generative Models on Chemical Space Coverage (v18) | <p>In recent years, deep molecular generative models have emerged as novel methods for <i>de
novo</i> molecular design. Thanks to the rapid advance of deep learning techniques, deep learning architectures such as recurrent neural networks,
generative autoencoders, and adversarial networks, to give a few examples,
have been employed for constructing generative models. However, so far the metrics used to evaluate these
deep generative models are not discriminative enough to separate the performance of various
state-of-the-art generative models. This work presents a novel metric for evaluating
deep molecular generative models; this new metric is based on the chemical
space coverage of a reference database, and compares not only the molecular
structures, but also the ring systems and functional groups, reproduced from a
reference dataset of 1M structures. In this study, the performance of 7
different molecular generative models was compared by calculating their
structure and substructure coverage of the GDB-13 database while using a 1M
subset of GDB-13 for training. Our study shows that the performance of various
generative models varies significantly using the benchmarking metrics
introduced herein, such that generalization capability of the generative model
can be clearly differentiated. Additionally, the coverage of ring systems and
functional groups existing in GDB-13 was also compared between the models. Our
study provides a useful new metric
that can be used for evaluating and comparing generative models.</p> | Jie Zhang; Rocío Mercado; Ola Engkvist; Hongming Chen | Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755389abda285f4f8e2d1/original/comparative-study-of-deep-generative-models-on-chemical-space-coverage-v18.pdf |
62d44fd181efd055caaf67f9 | 10.26434/chemrxiv-2022-b0zq0 | Harnessing systematic protein-ligand interaction fingerprints for drug discovery | Determining protein-ligand interaction characteristics and mechanisms is critical in the drug discovery process. Here we review recent progress and successful applications of a systematic protein-ligand interaction fingerprint (IFP) approach for investigating proteome-wide protein-ligand interactions for drug development. Specifically, we review the use of this IFP approach for revealing polypharmacology across the whole kinome, predicting promising targets from which to design allosteric inhibitors and covalent kinase inhibitors, uncovering the binding mechanisms of drugs of interest, and demonstrating resistant mechanisms of specific drugs. Together, we demonstrate that the IFP strategy is efficient and practical for drug design research and development in the current era of big data. | Zheng Zhao; Philip E. Bourne | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d44fd181efd055caaf67f9/original/harnessing-systematic-protein-ligand-interaction-fingerprints-for-drug-discovery.pdf |
64269ea262fecd2a83bad695 | 10.26434/chemrxiv-2023-vv65f | Synthesis and Characterization of Iron oxide Nanoparticles with Thymoquinone | Nigella sativa is a medicinal plant used for its antimicrobial properties. Thymoquinone (TQ) being the lead component of this plant seeds, exerts antibacterial, antifungal and antioxidant activity. It has also shown promising activity against cancer and inflammation through different modes of action.
In recent developments for new applications in the field of medicine, nanotechnology has excelled as a very prominent and important field. Nanoparticles are generally in the dimension range of 1–100 nm. Iron oxide nanoparticles show enhanced antibacterial activity against gram-negative bacteria. The current research focuses on comparing the yield, stability and purity of thymoquinone synthesised iron oxide nanoparticles using different organic solvents, the benefits expressed by thymoquinone as a herbal drug and a novel approach to green synthesis of iron oxide nanoparticles with thymoquinone and testing for their stability, size and functional groups.
| Sheshadri S Temkar; Tarun M; Seema Tharannum ; Dinesh M S | Nanoscience; Nanofabrication; Nanostructured Materials - Nanoscience | CC BY 4.0 | CHEMRXIV | 2023-03-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64269ea262fecd2a83bad695/original/synthesis-and-characterization-of-iron-oxide-nanoparticles-with-thymoquinone.pdf |
619fb014a1292393444e06e1 | 10.26434/chemrxiv-2021-72q5b | Au(I) Catalyzed HF Transfer: Tandem Alkyne Hydrofluorination and Perfluoroarene Functionalisation | HF transfer reactions between organic substrates are an incredibly rare class of transformation. Such reactions require the development of new catalytic systems that can promote both defluorination and fluorination steps in a single reaction sequence. Herein, we report a novel catalytic protocol in which an equivalent of HF is generated from a perfluoroarene | nucleophile pair and transferred directly to an alkyne. The reaction is catalysed by [Au(IPr)NiPr2] (IPr = N,N’-1,3-Bis(2,6-diisopropylphenyl)imidazol-2-ylidene) and is 100 % atom efficient. HF transfer generates two useful products in the form of functionalised fluoroarenes and fluoroalkenes. Mechanistic studies (rate laws, KIEs, DFT calculations, competition experiments) are consistent with the Au(I) catalyst facilitating a catalytic network involving both concerted SNAr and hydrofluorination steps. The nature of the nucleophile impacts the turnover-limiting step. The cSNAr step is turnover-limiting for phenol-based nucleophiles while proteodeauration likely becomes turnover-limiting for aniline-based nucleophiles. The new approach removes the need for direct handling of HF reagents in hydrofluorination and offers new possibilities to manipulate the fluorine content of organic molecules through catalysis. | Daniel Mulryan; Jack Rodwell; Nicholas Phillips; Mark Crimmin | Organic Chemistry; Inorganic Chemistry; Catalysis; Organic Synthesis and Reactions; Kinetics and Mechanism - Inorganic Reactions; Homogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2021-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619fb014a1292393444e06e1/original/au-i-catalyzed-hf-transfer-tandem-alkyne-hydrofluorination-and-perfluoroarene-functionalisation.pdf |
66c91d13a4e53c48766cf76e | 10.26434/chemrxiv-2024-706kg-v2 | Accurate physics-based prediction of binding affinities of RNA and DNA targeting ligands | Accurate prediction of the affinity of ligand binding to nucleic acids represents a significant challenge for current computational approaches. This limitation has hindered the use of computational methods to develop small molecule drugs that modulate the activity of nucleic acids, including those associated with anticancer, antiviral and antibacterial effects. In recent years, significant scientific and technological advances as well as easier access to compute resources have contributed to free-energy perturbation (FEP) becoming one of the most consistently reliable approaches for predicting relative binding affinities of ligands to proteins. Nevertheless, FEP’s applicability to nucleic-acid targeting ligands has remained largely undetermined. In this work, we present a systematic assessment of the accuracy of FEP, as implemented in the FEP+ software and facilitated by improvements in the OPLS4 force field, in predicting relative binding free energies of congeneric series of ligands interacting with a variety of DNA/RNA systems. The study encompassed more than 100 ligands exhibiting diverse binding modes, some partially exposed and others deeply buried. Using a consistent simulation protocol, more than half of the predictions are within 1 kcal/mol of the experimentally measured values. Across the dataset, we report a combined average pairwise root-mean-square-error (RMSE) of 1.39 kcal/mol, which falls within one log unit of the experimentally measured dissociation constants. These results suggest that FEP+ has sufficient accuracy to guide the optimization of lead series in drug discovery programs targeting RNA and DNA. | Ara M. Abramyan; Anna Bochicchio; Chuanjie Wu; Wolfgang Damm; David R. Langley; Devleena Shivakumar; Dmitry Lupyan; Lingle Wang; Edward Harder; Eliud O. Oloo | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biophysics; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c91d13a4e53c48766cf76e/original/accurate-physics-based-prediction-of-binding-affinities-of-rna-and-dna-targeting-ligands.pdf |
67367d315a82cea2fa27cca1 | 10.26434/chemrxiv-2024-4zw7v | Ab initio molecular dynamics studies of Ethylene glycol partial oxidation on Co3O4 (001) surfaces | The catalytic oxidation of ethylene glycol (EG) on the Co3O4 (001) surface is investigated by ab initio molecular dynamics simulations in the presence of a water layer for the A- and B- terminations. In addition to the surface structure and composition, the chemical state of the aqueous environment plays a crucial role in the oxidation process. Specifically, it depends on the concentration of surface hydroxyl groups, which can act both as proton donors and acceptors. Reference surfaces, which are generated by bringing the unhydrogenated A- and B-terminated surfaces in contact with a stoichiometric water layer, show some spontaneous water dissociation, which produces a number of surface hydroxyl groups. On such an A-terminated reference surface, the EG molecule is barely reactive. This holds even in a more oxidative state. On the B-terminated surface, EG's decomposition into ethylenedioxy species occurs already in the reference state. Under the more oxidative hydrogen- deficient conditions obtained by removing 8 hydrogen atoms, the reaction proceeds to the formation of the two-electron oxidation product glycolaldehyde. Removal of altogether 16 hydrogen atoms facilitates the formation of four-electron oxidation products such as glycolic acid and glyoxal and the observation of a transient H2O2 species which subsequently evolves to form dioxygen. | Falonne B. S. Nkou; Stephane Kenmoe | Theoretical and Computational Chemistry; Catalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC 4.0 | CHEMRXIV | 2024-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67367d315a82cea2fa27cca1/original/ab-initio-molecular-dynamics-studies-of-ethylene-glycol-partial-oxidation-on-co3o4-001-surfaces.pdf |
60c749febdbb89694ca392c9 | 10.26434/chemrxiv.12136470.v1 | Network-Based Analysis of Fatal Comorbidities of COVID-19 and Potential Therapeutics | <p>Coronavirus disease 2019 (COVID-19) is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The case fatality rate is significantly higher in older patients and those with diabetes, cancer or cardiovascular disorders. The human proteins, angiotensin-converting enzyme 2 (ACE2) and basigin (BSG), are involved in high-confidence host-pathogen interactions with proteins from SARS-CoV-2. We applied the random walk with restart method on the human interactome to construct a significant sub-network around these two proteins. The protein-protein interaction sub-network captures the effects of viral invasion on fatal comorbidities through critical pathways. The ‘insulin resistance’, ‘AGE-RAGE signaling pathway in diabetic complications’ and ‘adipocytokine signaling pathway’ were found in all fatal comorbidities. The association of these critical pathways with aging and its related diseases explains the molecular basis of COVID-19 fatality. We further investigated the critical proteins and corresponding pathways, and identified drugs that have effects on these proteins/pathways based on gene expression studies. We particularly focused on drugs that significantly downregulate ACE2 along with other critical proteins identified by the network-based approach. Among them, COL-3 (also known as incyclinide) had earlier shown activity against acute lung injury and acute respiratory distress, while entinostat and mocetinostat have been investigated for non-small-cell lung cancer. We propose that these drugs can be repurposed for COVID-19. </p> | Broto Chakrabarty; Dibyajyoti Das; Gopalakrishnan Bulusu; Arijit Roy | Biochemistry; Bioinformatics and Computational Biology; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749febdbb89694ca392c9/original/network-based-analysis-of-fatal-comorbidities-of-covid-19-and-potential-therapeutics.pdf |
60c758c3ee301cdd89c7b7b6 | 10.26434/chemrxiv.14601168.v1 | Tuning Electronic Structure and Optical Properties of Li@cyclo[18]carbon Complex via Switching Doping Position of Lithium Atom | Doping
alkali metal atoms, especially lithium (Li), in nanocarbon materials has always
been considered as one of the most effective methods to improve the optical
properties of the system. In this theoretical work, we doped a Li atom into the
recently observed all-carboatomic molecule, cyclo[18]carbon (C<sub>18</sub>),
and finally obtained two stable configurations with Li inside and outside the
ring. The calculation results show that the energy barrier of transition
between the two Li@C<sub>18</sub> complexes is quite low, and thus the
conversion is easy to occur at ambient temperature. Importantly, the electronic
structure, absorption spectrum, and optical nonlinearity of the two configurations
are found to be significantly different, which indicates that the electronic
structure and optical properties of the Li@C<sub>18</sub> complex can be
effectively regulated by switching the location of the doped Li atom between
inside and outside the carbon ring. With the help of a variety of wave function
analysis techniques, the nature of the discrepancies in the properties of the Li@C<sub>18</sub>
complex with different configurations has been revealed in depth. The relevant
results of this work are expected to provide theoretical guidance for the
future development of cyclocarbon-based optical molecular switches. | Zeyu Liu; Xia Wang; Tian Lu; Aihua Yuan; Xiufen Yan | Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758c3ee301cdd89c7b7b6/original/tuning-electronic-structure-and-optical-properties-of-li-cyclo-18-carbon-complex-via-switching-doping-position-of-lithium-atom.pdf |
666fae055101a2ffa8bf62f3 | 10.26434/chemrxiv-2024-c8x0p-v2 | Nanoconfinement of Myoglobin and Green Fluorescent Protein in Metal-Organic Frameworks (MOFs): A Molecular Dynamics Study | The chemical and structural diversity, as well as the scope of applications of Metal-organic frameworks (MOF) have expanded over the last decade. In the biomedical domain, they have played a significant role acting as a bio-compatible host platform for delivering cargoes inside cells, including the immobilization of proteins within their pores. The proteins myoglobin and the green fluorescent protein (GFP) have been shown to form inclusion complexes in the isoreticular IRMOF series, i.e., within IRMOF-74-VII-oeg and IRMOF-74-IX, respectively, where -oeg is a short ethylene oxide oligomer. The present work studies these two inclusions using all-atom molecular dynamics simulations. We observe that both these inclusions are mainly governed by van der Waals interactions at the protein-MOF interface. The effect of confinement on myoglobin was found to be larger than that of GFP, due to the relatively smaller size difference between the former and its MOF host. The primary signature of the confinement was observed in the root mean squared fluctuations of the protein sidechains. Although experiments could not succeed in the inclusion of myoglobin in IRMOF-74-VII-hex (where -hex is the hexyl group), our simulations suggest that it could be facilely accommodated in the same, suggesting the possibility of kinetic contributions in the experimental observation. Overall, for both the proteins, the tertiary structures and hydration of the surfaces of the proteins were well maintained inside the MOF channels. | Oishika Jash; Sundaram Balasubramanian | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Thermodynamics (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666fae055101a2ffa8bf62f3/original/nanoconfinement-of-myoglobin-and-green-fluorescent-protein-in-metal-organic-frameworks-mo-fs-a-molecular-dynamics-study.pdf |
60c74a12f96a0070db287365 | 10.26434/chemrxiv.12149502.v1 | Squeezing Bi: PNP and P2N3 Pincer Complexes of Bismuth(III | We report the first application of a rigid <i>P<sub>2</sub>N<sub>3</sub></i> pincer ligand in p-block chemistry by preparing its bismuth complex. We also report the first example of bismuth complexes featuring a flexible <i>PNP</i> pincer ligand, which shows phase-dependent structural dynamics. Highly electrophilic, albeit thermally unstable, Bi(III) complexes of the <i>PNP</i> ligand were also prepared. <br /> | Marcus B. Kindervater; Toren Hynes; Katherine Marczenko; Saurabh Chitnis | Bonding; Coordination Chemistry (Inorg.); Main Group Chemistry (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a12f96a0070db287365/original/squeezing-bi-pnp-and-p2n3-pincer-complexes-of-bismuth-iii.pdf |
6613931a91aefa6ce11668b3 | 10.26434/chemrxiv-2024-b8wzs | A trimetallic bismuth-based allyl cation | The chemistry of low-valent bismuth compounds has recently unlocked new concepts in catalysis as well
as unique electronic structure fundamentals. In this work, we describe the synthesis and characterization of
a highly-reduced bismuth salt featuring a cationic core based on three contiguous Bi(I) centers. The triatomic
bismuth-based core holds an electronic situation that mimics the description of the archetypical carbonbased π-allyl cation. Structural, spectroscopic and theoretical analyses validate the unique π-delocalization
between the bismuth’s highly diffused 6p-orbitals, resulting in a 1.5 bond order between the Bi atoms. This
electronic situation places this complex as the heaviest and non-radioactive π-allyl cation of the periodic
table. Furthermore, we demonstrate that the newly synthesized complex is able to act as a synthon for the
transfer of a Bi(I) cation to forge other low-valent organobismuth complexes. | Davide Spinnato; Nils Nöthling; Markus Leutzsch; Maurice van Gastel; Lucas Wagner; Frank Neese; Josep Cornella | Organometallic Chemistry; Coordination Chemistry (Organomet.); Main Group Chemistry (Organomet.); Theory - Organometallic | CC BY 4.0 | CHEMRXIV | 2024-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6613931a91aefa6ce11668b3/original/a-trimetallic-bismuth-based-allyl-cation.pdf |
64f70707dd1a73847f3b916c | 10.26434/chemrxiv-2023-h5s4w | An exact and ubiquitous condition for solid-state deracemization in vitro and in nature | Solid-state deracemization refers to the amplification of an enantiomeric excess in suspensions of conglomerate-forming compounds, in the presence of racemization in solution. It is an attractive route to the manufacture of enantiopure products, and a possible pathway to the emergence of homochirality on Earth, which is linked to the origin of life. Numerous compounds are known to deracemize, including many of biological relevance, which suggests the existence of a general governing mechanism. Yet pinning down such mechanism has been difficult, controversial, and not conclusive. Here we use a simplified formulation of the classical population balance model of deracemization through temperature cycles that includes neither agglomeration, nor breakage, nor ripening, to prove an exact condition under which deracemization occurs: crystal dissolution must be faster than crystal growth. Such kinetic asymmetry is a fundamental principle of crystallization, which explains the general success of deracemization experiments in the literature. Our theoretical analysis allows predicting that deracemization occurs for any amplitude of the temperature cycles, however small, and even for random temperature fluctuations. Here we demonstrate through ad hoc experiments that these predictions are correct. Since the exact condition for deracemization is simple and ubiquitous, solid-state deracemization provides indeed both a technical route to enantiopure products and a natural pathway towards homochirality. | Leif-Thore Deck; Mercedeh Sadat Hosseinalipour; Marco Mazzotti | Physical Chemistry; Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Thermodynamics (Chem. Eng.); Materials Chemistry; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f70707dd1a73847f3b916c/original/an-exact-and-ubiquitous-condition-for-solid-state-deracemization-in-vitro-and-in-nature.pdf |
6268c09bef2ade68193ec677 | 10.26434/chemrxiv-2022-1xt5m | Gas impurity in calcination atmosphere governing electrochemical properties of LiNi0.8Mn0.1Co0.1O2 cathode material for lithium ion batteries
| In this work, we investigated the influence of gas impurity in oxygen as calcination gas on the electrochemical properties of high Ni LiNi0.8Mn0.1Co0.1O2 (NMC811) cathode materials. Among investigated gas compositions, the oxygen mixed with a small amount of argon (96% O2, 4% Ar) shows the same level of Li/Ni cation mixing as 100% O2 sample, with not only a very stable discharge capacity retention (89% at 200 cycles) but also higher C-rate capability (67% at 20C) compared to other samples. Despite well suppressed Li/Ni cation mixing, 100% O2 sample suffers from an over-oxidation of Ni and Co of the surface, leading to an increase of surface resistance, as a consequence, a fast capacity fade over cycling with lower C-rate capability compared to the material calcined under 96% O2/4% Ar. This result demonstrates that calcination gas composition plays a key role in determining the electrochemical properties of high Ni cathode materials, not only in terms of Li/Ni cation mixing in the bulk structure, but also the oxidation properties of Ni, Co at the surface. | Sanghoon Kim; Ronghui Wang; Guillaume de Verthamon; Francis Briand; Laurent Prost | Materials Science; Energy; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6268c09bef2ade68193ec677/original/gas-impurity-in-calcination-atmosphere-governing-electrochemical-properties-of-li-ni0-8mn0-1co0-1o2-cathode-material-for-lithium-ion-batteries.pdf |
60c75074ee301c7ed1c7a882 | 10.26434/chemrxiv.12919349.v2 | Ultrastrong Regulation Effect of Electric Field on Cyclo[18]carbon: Phenomenon and Essence | Cyclo[18]carbon has a very unique geometry and electronic structure. Based on quantum chemistry calculations, we found that external electric field (EEF) has an ultrastrong regulation effect on various aspects of the cyclo[18]carbon. The main findings are as follows: (1) The EEF evidently affects geometric structure of the cyclo[18]carbon, and the ring is greatly elongated when EEF exceeds 0.02 a.u. (2) The EEF causes a huge polarization in the charge distribution of the system, and large EEF can even make some in-plane pi electrons nearly detached from the system (3) Presence of EEF significantly reduces HOMO-LUMO gap (4) The EEF not only greatly changes the position and intensity of the original absorption peak of the cyclo[18]carbon in the ultraviolet region, but large EEF also leads to a new absorption band in the visible light range and thus makes the cyclo[18]carbon show color. We made an in-depth explanation and discussion of the above phenomena from the aspects of energy, electronic structure, and atomic force. Furthermore, we demonstrated that it is feasible to equivalently apply strong EEF on the cyclo[18]carbon via a purely chemical and thus a more easily achieve way, namely introducing divalent alkaline earth metal cation. This work is not only of scientific interest in the interplay between the EEF and the cyclo[18]carbon, but may also open a novel path to explore different applications of this unusual molecule. | Tian Lu; Qinxue Chen | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75074ee301c7ed1c7a882/original/ultrastrong-regulation-effect-of-electric-field-on-cyclo-18-carbon-phenomenon-and-essence.pdf |
6564ff0329a13c4d47215b97 | 10.26434/chemrxiv-2023-hc8jv-v3 | Molecular Gas Phase Conformational Ensembles | Abstract. Accurately determining the global minima of a molecular structure is important in diverse scientific fields, including drug design, materials science, and chemical synthesis. Conformational search engines serve as valuable tools for exploring the extensive conformational space of molecules and identifying energetically favorable conformations. In this study, we present a comparison of Auto3D, CREST, Balloon, and ETKDG (from RDKit), which are freely available conformational search engines, to evaluate their effectiveness in locating the global minima. These engines employ distinct methodologies, including machine learning (ML) potential-based, semiempirical, and force field (FF) based approaches. To validate these methods, we propose the use of collisional cross section (CCS) values obtained from ion mobility – mass spectrometry (IM-MS) studies. We hypothesize that experimental gas-phase CCS values can provide experimental evidence that we likely have the global minimum for a given molecule. To facilitate this effort, we used our gas-phase conformation library (GPCL) which currently consists of the full ensembles of 20 small molecules, which can be used by the community to validate any conformational search engine. Further members of the GPCL can be readily created for any molecule of interest using our standard workflow used to compute CCS values expanding the ability of the GPCL in validation exercises. These innovative validation techniques enhance our understanding of the conformational landscape and provide valuable insights into the performance of conformation generation engines. Our findings shed light on the strengths and limitations of each search engine, enabling informed decisions for their utilization in various scientific fields, where accurate molecular structure determination is crucial for understanding biological activity and designing targeted interventions. By facilitating the identification of reliable conformations, this study significantly contributes to enhancing the efficiency and accuracy of molecular structure determination, with a particular focus on metabolite structure elucidation. The findings of this research also provide valuable insights for developing effective workflows in predicting the structures of unknown compounds with high precision. | Susanta Das; Kenneth M. Merz, Jr. | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6564ff0329a13c4d47215b97/original/molecular-gas-phase-conformational-ensembles.pdf |
671ced4a98c8527d9e72249a | 10.26434/chemrxiv-2024-lrh78 | Determination of the experimental minimal formula of metal-organic frameworks | Metal-organic frameworks have emerged as one of the most promising classes of materials in the last decade with potential applications in many domains of science. However, the determination of their precise chemical composition has been often overlooked, although it is crucial for many advanced applications such as catalysis or drug delivery. Here, we propose a rigorous yet simple protocol for the accurate determination of a MOF's minimal formula. By integrating quantitative NMR and UV-Vis spectroscopy data alongside TGA analysis, we construct the complete minimal formula using MOF-808 as a model material. We show the critical influence of the MOF digestion method and of the NMR measurement parameters on the accuracy of the minimal formula. Furthermore, we provide a quantitative method for determining the amount of residual chloride that originates from the precursors used in MOF synthesis, which has been often ignored in minimal formulae determination. In order to help improve the reproducibility and accuracy of MOF applications, we introduce the concept of room temperature molar mass that can deviate significantly from the idealized molar mass. Although the determination of the MOF experimental minimal formula is often perceived as a complex and tedious task, the general methodology presented here is straightforward and can be achieved with very simple equations and procedures. | Jikson Pulparayil Mathew; Charlotte Simms; David E. Salazar Marcano; Evert Dhaene; Tatjana N. Parac-Vogt; Jonathan De Roo | Inorganic Chemistry; Organometallic Chemistry; Solid State Chemistry; Spectroscopy (Inorg.); Coordination Chemistry (Organomet.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671ced4a98c8527d9e72249a/original/determination-of-the-experimental-minimal-formula-of-metal-organic-frameworks.pdf |
60c7468bee301c3c37c79558 | 10.26434/chemrxiv.11302478.v1 | Magnetically Responsive Horseradish peroxidase@ZIF-8 for Biocatalysts | <div>Here, we studied a catalytically active and magnetically responsive porous bio-composite obtained from the synthesis of ZIF-8 in presence of iron oxide magnetic nanoparticles and horseradish peroxidase (HRP) enzyme as guest species. Using a one-pot approach in water the precursors of ZIF-8 (zinc acetate and 2-methylimidazole) spontaneously self-assembles around the guest species. We characterized the composite by means of XRD, SEM, FTIR, AFM, and CLSM. SAXS investigation of the kinetics of crystallization showed how the presence of the guest species can act as nucleation seeds. Moreover, we found that the bio-catalytic activity of the HRP/MNP@ZIF-8 biocomposite is 5 times higher than the analoguous composite without MNPs.</div> | Raffaele Ricco; Heinz Amenitsch; paolo falcaro | Catalysts; Composites; Hybrid Organic-Inorganic Materials; Magnetic Materials; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7468bee301c3c37c79558/original/magnetically-responsive-horseradish-peroxidase-zif-8-for-biocatalysts.pdf |
60c74a45702a9b3dd218b257 | 10.26434/chemrxiv.12174693.v1 | Dispersion State Phase Diagram of Citrate-Coated Metallic Nanoparticles in Saline Solutions | The fundamental interactions underlying citrate-mediated chemical stability of metal nanoparticles (NPs), and their surface characteristics dictating particle dispersion/aggregation in aqueous solutions, are largely unclear. Here, we used a newly developed theoretical model to estimate the stoichiometry of citrate molecules chemisorbed onto spherical metallic NPs and define the uncovered solvent-accessible surface area of the NP. Then, we exploited two-body free energy calculations and extended coarse-grained molecular dynamics simulations of citrate-capped metallic NPs in saline solutions to explore an experimentally relevant range of NP charge, as well as the electrolytic medium’s ionic strength, a known trigger for aggregation. In this way, we define dispersion state phase diagrams of citrate-capped metal nanocolloids. UV-vis spectroscopy experiments validated our predictions and extended our results to NPs up to 35 nm. Altogether, our results disclose a complex interplay between the particle size, its surface charge density, and the ionic strength of the medium, which ultimately clarifies how these variables impact colloidal stability.
<br /> | Sebastian Franco Ulloa; Giuseppina Tatulli; Sigbjørn Løland Bore; Mauro Moglianetti; Pier Paolo Pompa; Michele Cascella; Marco De Vivo | Aggregates and Assemblies; Biocompatible Materials; Coating Materials; Composites; Core-Shell Materials; Nanostructured Materials - Materials; Nanocatalysis - Catalysts & Materials; Nanodevices; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices; Supramolecular Chemistry (Inorg.); Bioengineering and Biotechnology; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Properties; Self-Assembly; Statistical Mechanics; Surface; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a45702a9b3dd218b257/original/dispersion-state-phase-diagram-of-citrate-coated-metallic-nanoparticles-in-saline-solutions.pdf |
60c748c2337d6c6b99e275d3 | 10.26434/chemrxiv.11965329.v1 | Bulk Fatigue Induced by Surface Reconstruction in Layered Ni-Rich Oxide Cathodes for Liion Batteries | <div><div><div><p>Ni-rich layered cathode materials are among the most promising candidates for high energy density Li-ion batteries. However, the low cobalt containing materials suffer from rapid degradation, the underlying mechanism of which is still poorly understood. We herein report a novel structure-drive degradation mechanism for the NMC811(LiNi0.8Mn0.1Co0.1O2) cathode, in which a proportion of the material exhibits a lowered accessible state-of-charge (SoC) at the end of charge after repetitive cycling, i.e. becomes fatigued. Ex-situ and operando long- duration high-resolution X-ray diffraction enabled by a laser-thinned coin cell design clearly shows the emergence of the fatigued phase and the increase in its population as the cycling progresses. We show that the fatigue degradation is a structure-driven process rather than originating solely due to kinetic limitations or inter-granular cracking. No bulk phase transformations or increase in Li/Ni antisite mixing were observed by diffraction; no significant change in the local structure or Li-ion mobility of the bulk were observed by 7Li solid-state NMR spectroscopy. Instead, we propose that the fatigue process is a result of the high interfacial lattice strain between the reconstructed surface and the bulk layered structure when the latter is at SoCs above a distinct threshold of ~75 %. This mechanism is expected to be universal to Ni-rich layer cathodes, and our findings provide a fundamental guide for designing effective approaches to mitigate such deleterious processes.</p></div></div></div> | Chao Xu; Katharina Marker; Juhan Lee; Amoghavarsha Mahadevegowda; Philip
J. Reeves; Sarah Day; Matthias F. Groh; Steffen Emge; Caterina Ducati; B. Layla Mehdi; Chiu C. Tang; Clare P. Grey | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748c2337d6c6b99e275d3/original/bulk-fatigue-induced-by-surface-reconstruction-in-layered-ni-rich-oxide-cathodes-for-liion-batteries.pdf |
60c740629abda26fe7f8bc8b | 10.26434/chemrxiv.7716590.v1 | Temperature-Dependent Electronic Structure of Bixbyite α-Mn2O3 and the Importance of a Subtle Structural Change on Oxygen Electrocatalysis | <div><div><div><p>α-Mn2O3 is an inexpensive Earth-abundant mineral that is used as an electrode material in various kinds of electrochemical devices. The complex bixbyite structure of α-Mn2O3, and its subtle orthorhombic → cubic phase transformation near room temperature has made it challenging to accurately determine its electronic proper- ties. We used high-resolution X-ray diffraction to study the temperature-dependent structures of phase-pure α-Mn2O3 prisms. Our measurements show a clear change in the crystal phase from orthorhombic → cubic between 293K and 300K. We input the Rietveld refined high-resolution crystal structures collected at various temperatures (273, 293, 300, 330K) directly into density functional theory (DFT) calculations to model their electronic properties. These calculations indicate that the orthorhombic phase α-Mn2O3 is a narrow bandgap semiconductor as expected. However, temper- atures higher than 300K transform the α-Mn2O3 into the cubic phase, causing the molecular orbitals of the Mn 3d and O 2p bands to overlap and mix covalently, mak- ing the material behave as a semimetal. This subtle change in crystal structure will affect the bulk conductivity of the material as well as Mn-O-Mn bond distances that influence the quality of its catalytic active sites for oxygen electrochemistry. Elec- trochemical oxygen evolution (OER) and oxygen reduction reaction (ORR) experi- ments performed at various temperatures (∼ 288K to 323K) using the same prepared electrode show a marked enhancement in both OER and ORR performance that is attributed to the higher activity of the cubic phase.</p></div></div></div> | Junais Mokkath; Maryam Jahan; Masahiko Tanaka; Satoshi Tominaka; Joel Henzie | Electrochemical Analysis; Computational Chemistry and Modeling; Theory - Computational; Electrocatalysis; Fuel Cells; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740629abda26fe7f8bc8b/original/temperature-dependent-electronic-structure-of-bixbyite-mn2o3-and-the-importance-of-a-subtle-structural-change-on-oxygen-electrocatalysis.pdf |
612c618f42198e6fe5678d44 | 10.26434/chemrxiv-2021-gntgt | The surface tension and interfacial composition of water/ethanol mixture | This study develops a model to fit the surface tension of the water/ethanol mixture for the complete composition range from 0 to 1. The theoretical framework complements Van Der Waals’s theory on the density gradient. The modelling results overcome the limitation of Gibbs adsorption isotherm, which completely ignores the composition of the interfacial layer. Furthermore, the model presents a new method to correctly calculate the composition of the interfacial layer for binary liquid mixture and surfactant solutions. | Chi Phan | Physical Chemistry; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612c618f42198e6fe5678d44/original/the-surface-tension-and-interfacial-composition-of-water-ethanol-mixture.pdf |
60c74802ee301c3980c797e6 | 10.26434/chemrxiv.11826678.v1 | Synthesis of Structurally Controlled, Highly Branched Polymethacrylates) by Radical Polymerization Through the Design of a Monomer Having Hierarchical Reactivity | The controlled synthesis of highly branched (HB) poly(methyl methacrylate) (PMMA) with a molecular weight of up to 88 × 10<sup>3 </sup>gmol and low dispersity (<i>Ð</i> < 2.0) was achieved by the radical copolymerization of vinyltelluride, H<sub>2</sub>C=CHTePh (<b>4cD</b>), and MMA in the presence of the organotellurium chain transfer agent <b>6cI</b> at 30 °C. Control of the branching structure was suggested by the Mark-Hauwink-Khun-Sakurada plots corresponding to samples in solution and trapped ion mobility spectroscopy-time of flight mass spectrometry in the gas phase. The mechanism of <b>4cD</b> for the structural control of HB-PMMA synthesis comes from the hierarchical reactivity of the C-Te bond of <b>4cD</b>, which serves as the branching point only after <b>4cD</b> reacts and is incorporated into the polymer chain. In contrast, copolymerization using previously reported vinyltellurides <b>4aA</b> (H<sub>2</sub>C=C(Me)TeMe) and <b>4aB</b> (H<sub>2</sub>C=C(Me)-CH=CHTeMe) could not control the branching structure due to the <i>b</i>-carbon fragmentation reaction from the intermediate radicals generated from <b>4aA</b> and <b>4bB</b>. The theoretical calculations suggest that the suppression of the undesired fragmentation reaction when using <b>4cD</b> is due to the acceleration of the desired propagation reaction forming a branched structure instead of decelerating the fragmentation reaction. Due to the versatility of radical polymerization, methacrylates with bulky substituents, such as <i>t</i>-butyl methacrylate, and polar functional groups, such as <i>N,N</i>-dimethylethyl methacrylate (DMAEM), were also used as monomers to afford structurally controlled corresponding HB polymers. These studies clearly open a new possibility for the use of HB polymers in macromolecular engineering. | Shigeru Yamago; Yangtian Lu | Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74802ee301c3980c797e6/original/synthesis-of-structurally-controlled-highly-branched-polymethacrylates-by-radical-polymerization-through-the-design-of-a-monomer-having-hierarchical-reactivity.pdf |
60c73d0c4c89190179ad1b25 | 10.26434/chemrxiv.14703531.v2 | Quantum Tunneling Mechanisms in Monolayer Graphene Modulated by Multiple Electrostatic Barriers | The transmission coefficient and electronic
conductance of a graphene monolayer in the presence of multi-electrostatic
barriers are theoretically investigated using the transfer matrix method (TMM).
The transmission coefficient, conductance, and Fano factor are evaluated as a
function of the number and width of the barriers, angle/energy of incidence, as
well as the applied potential at each barrier. We find that the transmission
coefficient presents a series of resonances that depends on the number and
widths of the barriers. Furthermore, we show that the resonant states can be
suppressed for larger incidence angles and barrier widths and tuned towards
lower energies. Consequently, the proposed structure can be used to fabricate
new optoelectronic devices based on (ON/OFF) states as tunable field-effect
transistors. | Hassen Dakhlaoui; Walid Belhadj; Bryan Wong | Carbon-based Materials; Nanostructured Materials - Materials; Optical Materials; Nanodevices; Nanofabrication; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Theory - Computational; Interfaces; Quantum Mechanics; Quasiparticles and Excitations; Structure; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0c4c89190179ad1b25/original/quantum-tunneling-mechanisms-in-monolayer-graphene-modulated-by-multiple-electrostatic-barriers.pdf |
60c744374c8919368ead2780 | 10.26434/chemrxiv.9761597.v1 | DeltaDelta Neural Networks for Lead Optimization of Small Molecule Potency | The capability to rank different potential drug molecules against a protein target for potency has always been a fundamental challenge in computational chemistry due to its importance in drug design. While several simulation-based methodologies exist, they are hard to use prospectively and thus predicting potency in lead optimization campaigns remains an open challenge. Here we present the first machine learning approach specifically tailored for ranking ranking congeneric series based on deep 3D-convolutional neural networks. Furthermore we prove its effectiveness by blindly testing it on datasets provided by Janssen, Pfizer and Biogen totalling over 3246 ligands and 13 targets as well as several well-known openly available sets, representing one the largest evaluations ever performed. We also performed online learning simulations of lead optimization using the approach in a predictive manner obtaining significant advantage over experimental choice. We believe that the evaluation performed in this study is strong evidence of the usefulness of a modern deep learning model in lead optimization pipelines against more expensive simulation-based alternatives. | Jose Jimenez-Luna; Laura Pérez-Benito; Gerard Martinez-Rosell; Simone Sciabola; Rubben Torella; Gary Tresadern; Gianni De Fabritiis | Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744374c8919368ead2780/original/delta-delta-neural-networks-for-lead-optimization-of-small-molecule-potency.pdf |
6772884d6dde43c908c7314c | 10.26434/chemrxiv-2024-tnx0l | Hetero[3.1.1]propellanes | [n.1.1]Propellanes are molecules featuring a carbon-carbon bond to which three rings are fused, two being cyclopropanes. [1.1.1] and [3.1.1]propellane are key precursors to small-ring bridged bicyclic hydrocarbons, motifs that have emerged as important building blocks in contemporary drug design. Due to their rigid frameworks and well-defined substituent vectors, these bicyclic hydrocarbons can serve as bioisosteres for disubstituted benzene rings, exhibiting improved metabolic stability compared to their aromatic parents, while also bringing benefits to solubility and other physicochemical properties. Unknown to date are [n.1.1]propellanes featuring heterocyclic rings, molecules that could enable the direct and rapid synthesis of a wide diversity of bridged bicyclic heterocycles, which should exhibit superior physicochemical profiles compared to their carbocyclic analogues while also introducing additional functionality for potential interactions with molecular targets. Here we report the unified synthesis of a family of heterocyclic [3.1.1]propellanes featuring oxygen, nitrogen and sulfur heteroatoms in the three-carbon bridge. The approaches we developed are necessarily distinct from the established route to carbocyclic propellanes, and utilise a common precursor that is conveniently assembled on multigram scale via a rhodium-catalysed cyclopropanation. We found that these hetero[3.1.1]propellanes are stable towards isolation and storage, but amenable to a range of radical ring-opening reactions, leading to bridgehead-disubstituted hetero-bicyclo[3.1.1]heptanes that cannot be accessed using alternative methods. Given the importance of heterocyclic scaffolds in pharmaceutical design, and the ever-growing popularity of rigid small ring building blocks, we expect these unprecedented hetero-propellanes will be of exceptional utility in drug discovery programmes | Rebecca Revie; Ayan Dasgupta; Yasmine Biddick; Kirsten Christensen; Russell Smith; Edward Anderson | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2024-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6772884d6dde43c908c7314c/original/hetero-3-1-1-propellanes.pdf |
61fac55dc0a86881213b2175 | 10.26434/chemrxiv-2022-c1jwr-v2 | SupraFit - An Open source Qt based fitting application to
determine stability constants from titration experiments | A novel application to determine stability constants from supramolecular titration experiments is
presented. The focus lies on NMR titration and ITC experiments for pure 1:1 systems, as well as
mixed 2:1/1:1, 1:1/1:2 and 2:1/1:1/1:2 systems. SupraFit provides global and local fitting and a
global search tool. Statistical methods are implemented and can be applied to analyse the results
of nonlinear regression. Monte Carlo simulations, combined with the percentile methods and F-Test
approaches to calculate confidence intervals are supported. The implemented statistical approaches
are illustrated and discussed on model functions. All methods are accessible through an intuitive
user interface, providing charts for all (kind of) data produced. SupraFit is written in C++, using
the Qt Toolkit for the Graphical User Interface (GUI) and the Eigen library for nonlinear regression
and is released under the GNU Public License (GPL). | Conrad Hübler | Physical Chemistry; Organic Chemistry; Analytical Chemistry; Physical Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2022-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61fac55dc0a86881213b2175/original/supra-fit-an-open-source-qt-based-fitting-application-to-determine-stability-constants-from-titration-experiments.pdf |
66fa4dfb51558a15ef905d19 | 10.26434/chemrxiv-2024-h4qlt | NETWORK ANALYSIS OF THE ORGANIC CHEMISTRY IN PATENTS,
LITERATURE, AND PHARMACEUTICAL INDUSTRY | Chemical reactions can be connected in large networks such as knowledge graphs. In this way, prior
work has been able to draw meaningful conclusions about the structures and properties of the included
organic chemistry. However, the research has focused on public sources of organic chemistry that
might lack the intricate details of the synthesis routes used in in-house drug discovery. In this work,
we expand on previous analyses to also include an in-house electronic lab notebook (ELN), such that
important differences between the network architectures can be investigated. Three chemical reaction
knowledge graphs were constructed from US Patent and Trademark Office (USPTO), Reaxys, and an
in-house ELN, respectively. The three knowledge graphs were compared. We found that the Reaxys
knowledge graph is the most interconnected, whereas the USPTO and ELN knowledge graphs appear
more arranged around a few central nodes. These differences might be attributed to the different
origins of the data in the three sources. | Thierry Kogej; Emma Svensson; Emma Rydholm; Tomas Bastys; Christos Kannas; Mikhail Kabeshov; Samuel Genheden; Ola Engkvist | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2024-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fa4dfb51558a15ef905d19/original/network-analysis-of-the-organic-chemistry-in-patents-literature-and-pharmaceutical-industry.pdf |
64de5b5101042bc1cc37933c | 10.26434/chemrxiv-2023-n8jsm-v2 | Bottom-up Atomistic Descriptions of Top-Down Macroscopic Measurements: Computational Benchmarks for Hammett Electronic Parameters | The ability to relate substituent electronic effects to chemical reactivity is a cornerstone of physical organic chemistry and Linear Free Energy Relationships. The computation of electronic parameters is increasingly attractive since they can be obtained rapidly for structures and substituents without available experimental data and can be applied beyond aromatic substituents. Nevertheless, the description of “top-down” macroscopic observables, such as Hammett parameters using a “bottom-up” computational approach, poses several challenges for the practitioner. We have examined and benchmarked the performance of various computational charge schemes and atomic properties, the locations of the atoms used to obtain these descriptors, and their correlation with empirical Hammett parameters and rate differences resulting from electronic effects. These seemingly small choices have a much more significant impact than previously imagined, which outweighs the level of theory or basis set used. We observe a wide range of performance across the different computational protocols and observe stark and surprising differences in the ability of computational parameters to capture para vs. meta-electronic effects. In general σm predictions fare much worse than σp. As a result, the choice of where to compute these descriptors – for the ring carbons or the attached H or other substituent atoms – affects their ability to capture experimental electronic differences. Density-based schemes, such as Hirshfeld charges, are more stable towards unphysical charge perturbations that result from nearby functional groups, and outperform all other computational descriptors, including several commonly used basis set based schemes such as Natural Population Analysis. Using attached atoms also improves the statistical correlations. We have obtained general linear relationships for the global prediction of experimental Hammett parameters from computed descriptors for use in statistical modeling studies. | Guilian Luchini; Robert Paton | Theoretical and Computational Chemistry; Organic Chemistry; Physical Organic Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64de5b5101042bc1cc37933c/original/bottom-up-atomistic-descriptions-of-top-down-macroscopic-measurements-computational-benchmarks-for-hammett-electronic-parameters.pdf |
67a6ca0d6dde43c90802a1ed | 10.26434/chemrxiv-2025-b7prh | Perovskite Catalysts for Pure-Water-Fed Anion-Exchange-Membrane Electrolyzer Anodes: Co-Design of Electrically Conductive Nanoparticle Cores and Active Surfaces | Anion-exchange-membrane water electrolyzers (AEMWEs) are a possible low-capital expense, efficient, and scalable hydrogen-production technology with inexpensive hardware, earth-abundant catalysts, and pure-water. However, pure-water-fed AEMWEs are still at an early stage of development and suffer from inferior performance compared to proton-exchange-membrane water electrolyzers (PEMWEs). One key challenge is to develop effective non-platinum group metal (non-PGM) anode catalysts and electrodes in pure-water-fed AEMWEs. We show how LaNiO3-based perovskite oxides can be tuned by co-substitution on both A- and B-sites to simultaneously maintain high metallic electrical conductivity along with controlled surface reconstruction to expose stable Co-based active catalyst. The optimized perovskite, Sr0.1La0.9Co0.5Ni0.5O3, yielded pure-water AEMWEs operating at 1.97 V at 2 A cm–2 at 70 oC with pure-water feed, thus illustrating the utility of the catalyst design principles. | Tingting Zhai; Hao Wang; Sarah Beaudoin; Ran Zhang; Minkyoung Kwak; Shujin Hou; Zhengxiao Guo; Shannon Boettcher | Energy | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a6ca0d6dde43c90802a1ed/original/perovskite-catalysts-for-pure-water-fed-anion-exchange-membrane-electrolyzer-anodes-co-design-of-electrically-conductive-nanoparticle-cores-and-active-surfaces.pdf |
60c7500e469df478def447cd | 10.26434/chemrxiv.12988478.v1 | On-surface Synthesis of [7]triangulene Quantum Ring via Antidot Engineering | The ability to engineer geometrically well-defined antidots in large triangulene homologues
allows for creating an entire family of triangulene quantum ring (TQR) structures with tunable high-spin
ground state and magnetic ordering, crucial for next-generation molecular spintronic devices. Herein, we
report the synthesis of an open-shell [7]triangulene quantum ring ([7]TQR) molecule on Au(111) through
the surface-assisted cyclodehydrogenation of a rationally-designed kekulene derivative. Bond-resolved
scanning tunneling microscopy (BR-STM) unambiguously imaged the molecular backbone of a single
[7]TQR with a triangular zigzag edge topology, which can be viewed as [7]triangulene decorated with a
coronene-like antidot in the molecular centre. Additionally, dI/dV mapping reveals that both inner and
outer zigzag edges contribute to the edge-localized and spin-polarized electronic states of [7]TQR. Both
experimental results and spin-polarized density functional theory calculations indicate that [7]TQR
retains its open-shell septuple ground-state (� = 3) on Au(111). This work demonstrates a new route for
the design of high-spin graphene quantum rings as the key components for future quantum devices. | Jie Su; Wei Fan; Pingo Mutombo; Xinnan Peng; Shaotang Song; Mykola Telychko; Pavel Jelinek; Jishan Wu; Jiong Lu | Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7500e469df478def447cd/original/on-surface-synthesis-of-7-triangulene-quantum-ring-via-antidot-engineering.pdf |
65bd9bf09138d2316150aceb | 10.26434/chemrxiv-2024-lqj0v | Enhanced Atrazine Degradation Using Laccase Immobilized on Arginine-Functionalized Boron Nitride Nanosheets | Fungal enzyme-mediated systems have been widely employed for the degradation of environmental contaminants. However, the use of free enzymes is limited by the rapid loss of their catalytic activity, stability, and reusability, which further restricts their catalytic performance. In this work, we developed an enzyme immobilization platform by elaborately anchoring the fungal laccase onto arginine-functionalized boron nitride nanosheets (BNNS-Arg@Lac). BNNS-Arg@Lac showcased enhanced stability against fluctuating pH values and temperatures, along with remarkable reusability across six consecutive cycles, outperforming free natural laccase (nlaccase). As a demonstration, a model pollutant of atrazine (ATR) was selected for proof-of-concept applications, given substantial environmental and public health concerns in agriculture runoff. By applying BNNS-Arg@Lac, the ATR degradation rate was nearly doubled that of nlaccase. Moreover, BNNS-Arg@Lac consistently demonstrated superior ATR degradation capabilities in synthetic agricultural wastewater and various mediator systems compared to nlaccase. Comprehensive product analysis unraveled distinct degradation pathways for BNNS-Arg@Lac and nlaccase, further elucidating the mechanism of the laccase-catalyzed ATR treatment. Overall, this research provides a foundation for the future development of enzymatic catalysts in tackling pollution problems and may unlock new potential for green and efficient environmental remediation and waste management strategies. | Yifan Gao; Minhao Xiao; Haiyuan Zou; Glenn Nurwono; David Zgonc; Junyoung O. Park; Jens Blotevogel; Chong Liu; Eric M.V. Hoek; Shaily Mahendra | Materials Science; Catalysis; Earth, Space, and Environmental Chemistry; Environmental Science; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2024-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bd9bf09138d2316150aceb/original/enhanced-atrazine-degradation-using-laccase-immobilized-on-arginine-functionalized-boron-nitride-nanosheets.pdf |
67893dbf6dde43c908d766c8 | 10.26434/chemrxiv-2025-fdcmb | The smart way of simultaneous scaling up and optimizing the synthesis of PGS for further rapid thermal cross-linking with the use of response surface methodology | Due to its very good biocompatibility, poly(glycerol sebacate) – PGS – is probably one of the most interesting synthetic biomaterials. This material passes several in vitro and in vivo tests with the use of quite a wide range of cells and animals. Nowadays, PGS is known as a good material for tissue engineering, drug delivery systems, surgical sealants, and other biomedical uses. Unfortunately, prepolymer synthesis and its subsequent cross-linking are usually time-consuming processes carried out at high temperatures, which is not beneficial from an economic and ecological point of view. This work describes a study of PGS prepolymer synthesis with the use of an acid catalyst in the Fischer mechanism. Mathematical methods were used to optimize and develop a fast and stable synthesis method, which allowed the obtaining of prepolymer in a short time without risk of gelation in the reactor. The proposed method could be easily used in industry. | Michał Wrzecionek; Bartłomiej Kryszak; Agnieszka Gadomska-Gajadhur | Materials Science; Polymer Science; Biodegradable Materials; Biopolymers; Polymerization (Polymers); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67893dbf6dde43c908d766c8/original/the-smart-way-of-simultaneous-scaling-up-and-optimizing-the-synthesis-of-pgs-for-further-rapid-thermal-cross-linking-with-the-use-of-response-surface-methodology.pdf |
60c7416c0f50db40b4395b01 | 10.26434/chemrxiv.7985300.v2 | Harnessing Applied Potential: The Anti-Markovnikov Hydrocarboxylation of Substituted Olefins | <div>The construction of carboxylic acid compounds in a selective fashion, from low value materials such as alkenes remains a long-standing challenge to synthetic chemists. In particular, anti-Markovnikov addition to styrenes are underdeveloped. Herein we report a new electrosynthetic approach to the selective hydrocarboxylation of substituted alkenes.</div> | Anas Alkayal; Volodymyr Tabas; Andrei V. Malkov; Benjamin Buckley | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry; Electrochemistry - Organometallic; Small Molecule Activation (Organomet.); Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7416c0f50db40b4395b01/original/harnessing-applied-potential-the-anti-markovnikov-hydrocarboxylation-of-substituted-olefins.pdf |
638a2c797b7c91020ce029df | 10.26434/chemrxiv-2022-1hc2j | Electronic structure of colloidal 2H-MoS2 mono- and bilayers determined by spectroelectrochemistry | We investigate the electronic structure of mono- and bilayers of colloidal 2H-MoS2 nanosheets synthesized by wet-chemistry using potential-modulated absorption spectroscopy (EMAS), differential pulse voltammetry (DPV) and electrochemical gating (ECG) measurements. We report the energetic positions of the conduction and valence band edges of the direct and indirect bandgap and observe strong bandgap renormalization effects, charge screening of the exciton as well as intrinsic n-doping of the as-synthesized material. We find two distinct transitions in the spectral regime associated with the C exciton, which overlap into a broad signal upon filling the conduction band. In contrast to the oxidation, the reduction of the nanosheets is largely reversible, enabling potential applications for reductive electrocatalysis. This work demonstrates that EMAS is a highly sensitive tool for determining the electronic structure of thin films with few nanometer thickness and that colloidal chemistry affords high-quality transition metal dichalcogenide nanosheets with an electronic structure comparable to that of exfoliated samples. | Kai Wurst; Onno Strolka; Jannika Lauth; Marcus Scheele | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Electrochemistry - Mechanisms, Theory & Study; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638a2c797b7c91020ce029df/original/electronic-structure-of-colloidal-2h-mo-s2-mono-and-bilayers-determined-by-spectroelectrochemistry.pdf |
67da38ba6dde43c9085d5857 | 10.26434/chemrxiv-2025-dtd2t | On Molecule Symmetry, Latent Heat, and Entropy | This paper suggested correlating the entropy with the geometric symmetry of the molecular orbits instead of the atomic mass distribution in a molecule. Employing the NIST thermodynamic parameters of substances at saturation, linear regressions of exothermic heat over T give ε_exo=B-(3+2A)/2 RT. B is the molar heat of liquefication, which equals the latent heat (∆H_v^Φ) at the boiling point. A reflects the molecule's symmetry; the more symmetric the molecular orbits, the smaller A. For example, the symmetry of inert gas atoms gives the operation number n = 1 in the theoretical frame of the geometric symmetry of atomic mass distribution. However, three p orbits give n = 7; correspondingly, A values of Ne, Ar, Kr, and Xe are 2.5518, 2.9104, 2.9140, and 2.9178. Similarly, a tetrahedron of C sp3 gives n = 8, CH4: A=2.9519. Hence, assuming that (3+2A)/2 R is the lost entropy, (n-2A)/2 R may be regarded as the residual in liquid. According to the above suggestion, CO is more symmetric than CO2. Moreover, the similarity in A between ethylene and ethane, propylene and propane, etc., implies that the C-C π bond should be rotatable rather than rigid. Helium-4 superfluid finds an increase in entropy as T decreases from 3.5 to 0.8 K. Clausius-Clapeyron equation was derived from ε_exo. | Henmei Ni | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Theory - Computational; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2025-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67da38ba6dde43c9085d5857/original/on-molecule-symmetry-latent-heat-and-entropy.pdf |
67d93be0fa469535b9a1c2e0 | 10.26434/chemrxiv-2025-jt4sg-v2 | Excitation Energy Transfer from Single Rare-Earth Upconversion Nanoparticles to Organic Conjugated Polymer Film: a Super-Resolved Microscopic Study | We have utilized an upconverting nanoparticle (UCNP) with thulium (Tm) ions as emitters and Ytterbium (Yb) ions as sensitizers (TmUCNP) for nanometric photoexcitation of a film of conjugated polymer, poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene] (MEH-PPV). The TmUCNPs surrounded by a thin layer of MEH-PPV were photoexcited at 976 nm using a continuous-wave (CW) near-infrared laser. The NIR light was selectively absorbed by the sensitizer of the TmUCNPs, leading to the formation of submillisecond-lifetime excited states of Tm ions in the UCNPs through stepwise multiphoton energy transfer between Yb and Tm. The visible emission from the Tm ions, coupled with their long excited-state lifetime, allowed for the production of locally excited states of the MEH-PPV through the excitation energy transfer (EET) from the individual TmUCNPs. This EET was confirmed by spectrally separated wide-field single-particle imaging and single-particle emission dynamics measurement with a hyperspectral confocal microscope. The spectrally separated wide-field images of the TmUCNPs and the MEH-PPV film, analyzed using a 2D localization method, provided a 2D spatial distribution of the emissive trap sites in the MEH-PPV surrounding individual TmUCNPs. From the 2D map of the emissive sites, the length of EET in the MEH-PPV solid was determined to be in the range from several to 50 nm. Thus, nanometric local photoexcitation using single UCNPs enabled direct evaluation of EET length in nano-space. | Syoji Ito; Hirotaka Kageyama; Takato Mizoguchi; Bhagya Lakshmi S. B.; Hikaru Sotome; Ali Eftekhari; Aude Bouchet; Michel Sliwa; Hiroshi Miyasaka | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d93be0fa469535b9a1c2e0/original/excitation-energy-transfer-from-single-rare-earth-upconversion-nanoparticles-to-organic-conjugated-polymer-film-a-super-resolved-microscopic-study.pdf |
66d05976f3f4b052907c0712 | 10.26434/chemrxiv-2024-b33q8 | The Roles of Hydroxyl Radicals and Superoxide in Oxidizing Aqueous Benzyl Alcohol under Ultrasound Irradiation. | The abatement of aromatic pollutants in water requires resource-intensive oxidation to nontoxic products by hydroxyl radicals (•OH). In this study, we elucidate the mechanisms of •OH-induced aromatic ring degradation by combining kinetic measurements, electron paramagnetic resonance spectroscopy, density functional theory (DFT) calculations, and kinetic modelling. We demonstrate that benzyl alcohol, a model aromatic compound, is oxidized by •OH radicals, generated by ultrasonic irradiation in an O2-rich environment, into aromatic compounds (benzaldehyde and phenol derivatives) and C1-C2 oxygenates (formic acid, glyoxal, and oxalic acid). Through pathways akin to atmospheric chemistry, these •OH radicals de-aromatize and fragment benzyl alcohol, producing 5-hydroxy-4-oxo-pentenal and other dicarbonyl products. Unique to the aqueous phase, however, superoxide (•O2–) is generated as a byproduct of •OH-benzyl alcohol reactions. •O2– acts as a potent nucleophile, oxidizing 5-hydroxy-4-oxo-pentenal into oxalic acid and C1 oxygenates via aldehyde and ketone intermediates. This process regenerates •O2– and does not consume •OH, thereby further degrading ring fragmentation products while preserving •OH to activate the refractory aromatic ring of benzyl alcohol. These nucleophilic •O2– reactions can therefore reduce the energy and chemical demands needed to degrade aromatic compounds, thus promoting the sustainable and scalable application of •OH-based oxidation processes in water treatment. | Ari F. Fischer; Teseer Bahry; Zhangyue Xie; Roberto Batista da Silva Junior; Kaicheng Qian; Renhong Li; James Kwan; François Jerome; Sabine Valange; Wen Liu; Prince N. Amaniampong; Tej S. Choksi | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Computational Chemistry and Modeling; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d05976f3f4b052907c0712/original/the-roles-of-hydroxyl-radicals-and-superoxide-in-oxidizing-aqueous-benzyl-alcohol-under-ultrasound-irradiation.pdf |
60c740610f50db6d81395944 | 10.26434/chemrxiv.7713632.v1 | Regio- and Diastereoselective Intermolecular [2+2] Cycloadditions Photocatalyzed by Quantum Dots | Here we show that colloidal quantum dots serve as visible-light
chromophores, photocatalysts, and resuable scaffolds for homo- and
hetero-intermolecular [2+2] photocycloadditions of 4-vinylbenzoic acid
derivatives, with >90% tunable regioselectivity and up to 98%
diastereoselectivity for the previously minor syn-cyclobutane products,
including the syn-heda-to-tail cyclobutane, which has never been
produced as the major product of a photochemical reaction. | Yishu Jiang; Chen Wang; Cameron Rogers; Mohamad S. Kodaimati; Emily Weiss | Nanocatalysis - Catalysts & Materials; Nanocatalysis - Reactions & Mechanisms; Photocatalysis; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740610f50db6d81395944/original/regio-and-diastereoselective-intermolecular-2-2-cycloadditions-photocatalyzed-by-quantum-dots.pdf |
60c742a7567dfe3775ec3f79 | 10.26434/chemrxiv.8320610.v1 | Certification of Matrix Reference Materials in Chemical Measurement: A New Basis for Adopting a Consensus Value Derived from a Proficiency Test | <p>ISO Guide 35 (2017) specifies conditions
for the certification of matrix reference materials via information from
proficiency tests. Many scientists involved in the provision of proficiency
tests for analytical chemistry have concluded that the Guide 35 conditions are <i>effectively</i> fulfilled by identifying
certified values with properly-derived consensus values. However, the claim
that such reference materials are ‘certified’ is likely to be challenged by
traditional metrologists. This paper proposes to move beyond this unresolved situation
to put certification <i>via</i> proficiency
testing on an unassailable footing. The proposal therefore is not a
questionable fulfilment of the Guide 35 conditions but an unrelated paradigm
for certification.</p> | Michael Thompson; Philip Potts; Peter Webb | Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742a7567dfe3775ec3f79/original/certification-of-matrix-reference-materials-in-chemical-measurement-a-new-basis-for-adopting-a-consensus-value-derived-from-a-proficiency-test.pdf |
60c7505ebb8c1a070c3dbaf2 | 10.26434/chemrxiv.13031144.v1 | Phosphate Ions Alter the Binding of Daptomycin to Living Cell Membranes | Advancements in antibiotic drug design are often hindered by missing information in how these small molecules interact with living cells. The antibiotic, daptomycin, has found clinical success, and emerging resistance, but a comprehensive picture of its mechanism of action has remained elusive. Using the surface-specific spectroscopy, second harmonic generation, we are able to quantitatively assess the binding of daptomycin to living cell membranes without the addition of exogenous labels. Our results reveal similar binding affinities for both gram-positive and gram-negative bacteria studied, including <i>E. coli</i>. More importantly, we show that phosphate ions influence the binding of daptomycin to the gram-positive bacterium <i>E. faecalis</i>. The role of environmental phosphate has not previously been considered in any proposed mechanism and its implications are expected to be important <i>in vivo</i>. | Lindsey Miller; Tessa Calhoun | Biophysical Chemistry; Interfaces; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7505ebb8c1a070c3dbaf2/original/phosphate-ions-alter-the-binding-of-daptomycin-to-living-cell-membranes.pdf |
639c529ae8047a17abeaf499 | 10.26434/chemrxiv-2022-hz6cb | On the role charge ordering in the dynamics of cluster formation in associated liquids | Abstract Liquids are archetypes of disordered systems, yet liquids of polar molecules are locally more ordered than non-polar molecules, due to the Coulomb interaction based charge ordering phenomenon. Hydrogen bonded liquids, such as water or alcohols, for example, represent a special type of polar liquids, in that they form labile clustered local structures. For water, in particular, hydrogen bonding and the related local tetrahedrality, play an important role in the various attempts to understand this liquid. However, labile structures imply dynamics, and it is not clear how it affects the understanding of this type of liquids from purely static point of view. Herein, we propose to reconsider hydrogen bonding as a charge ordering process. This perspective allows to demonstrate the insufficiencies of the analysis of the microscopic structure based solely on static pair correlation functions, and the need for dynamical correlation functions, both in real and reciprocal space. This extended analysis allows to recover several aspects of our understanding of hydrogen bonded liquids, but from a unified viewpoint. For water, it confirms the jump rotation picture found recently, and it allows to rationalize the contradicting pictures that arise when following the interpretations based on hydrogen bonding. For alcohols, it allows to understand the dynamical origin of the scattering pre-peak, which does not exist for water, despite the fact that both these liquids have very similar hydroxyl group chain clusters. The concept of charge ordering complemented by the analysis of dynamical correlation functions appear as a promising way to understand micro-heterogeneity in complex liquids and mixtures from kinetics point of view | Bernarda Lovrincevic; Martina Pozar; Ivo Jukic; Aurélien PERERA | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Self-Assembly; Statistical Mechanics | CC BY 4.0 | CHEMRXIV | 2022-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639c529ae8047a17abeaf499/original/on-the-role-charge-ordering-in-the-dynamics-of-cluster-formation-in-associated-liquids.pdf |
6632716f418a5379b02f35a0 | 10.26434/chemrxiv-2024-x8t26-v2 | A method for separating and quantifying organic and inorganic ice nucleating substances in atmospheric samples based on density gradient centrifugation | Ice nucleating substances (INSs) influence the properties and frequencies of ice and mixed-phase clouds in the atmosphere, and hence, climate and the hydrological cycle. INSs can be classified as inorganic (e.g., mineral dust, volcanic ash) or organic (e.g., bacterial cells, cell-free proteins). While the properties of both INS classes have been studied in the laboratory, the amounts in the atmosphere are still poorly constrained. Here, we demonstrate a new method for separating and quantifying inorganic and organic INSs. First, INS suspensions were separated into a high-density isolate containing inorganic INSs and a low-density isolate containing organic INSs using density gradient centrifugation, and then INSs were quantified in each isolate using a droplet freezing technique. Inorganic K-feldspar and organic Snomax INSs were used to test our method. The average K-feldspar INS recovery in the high-density isolate was 54%, with no evidence of K-feldspar INSs in the low-density isolate. The average Snomax INS recovery in the low-density isolate was 27%, with small amounts of Snomax contaminating the high-density isolate. A mixture of K-feldspar and Snomax was successfully separated, with recoveries comparable to those observed for K-feldspar and Snomax individually. Recoveries less than 100% can be explained by losses of INSs to vessel walls, accidental mixing of the different density layers during pipetting, and incomplete collection of material during pipetting. | Soleil E. Worthy; Lanxiadi Chen; Gurcharan K. Uppal; Yu Xi; Vakshan Varatharajah; Marie Line Torrijos; Anne Fuertes; Runqiu Song; Qianqian Zhang; Joyce Huang; Allan K. Bertram | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry | CC BY 4.0 | CHEMRXIV | 2024-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6632716f418a5379b02f35a0/original/a-method-for-separating-and-quantifying-organic-and-inorganic-ice-nucleating-substances-in-atmospheric-samples-based-on-density-gradient-centrifugation.pdf |
60c745fcf96a00d850286c80 | 10.26434/chemrxiv.10295129.v1 | A Bayesian Framework for Adsorption Energy Prediction on Bimetallic Alloy Catalysts | For high-throughput screening of materials for heterogeneous catalysis, scaling relations provides an efficient scheme to estimate the chemisorption energies of hydrogenated species. However, conditioning on a single descriptor ignores the model uncertainty and leads to sub optimal prediction of the chemisorption energy. In this paper, we extend the single descriptor linear scaling relation to a multi descriptor linear regression models to leverage the correlation between adsorption energy of any two pair of adsorbates. With a large dataset, we use Bayesian Information Criteria (BIC) as the model evidence to select the best linear regression model that are derived from non-informative priors. Furthermore, Gaussian Process Regression (GPR) based on the meaningful convolution of physical properties of the metal-adsorbate complex can be used to predict the baseline residual of the selected model. This integrated Bayesian model selection and Gaussian process regression, dubbed as residual learning, can achieve performance comparable to standard DFT error (0.1 eV) for most adsorbate system. For sparse and small datasets, we propose an ad hoc Bayesian Model Averaging (BMA) approach to make a robust prediction. With this Bayesian framework, we significantly reduce the model uncertainty and improve the prediction accuracy. The possibilities of the framework for high-throughput catalytic materials exploration in a realistic setting is illustrated using large and small sets of both dense and sparse simulated dataset generated from a public database of bimetallic alloys available in Catalysis-Hub.org. | Osman Mamun; Kirsten Winther; Jacob Boes; Thomas Bligaard | Theory - Computational; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745fcf96a00d850286c80/original/a-bayesian-framework-for-adsorption-energy-prediction-on-bimetallic-alloy-catalysts.pdf |
613a141942198eaeed7187ce | 10.26434/chemrxiv-2021-92x9d-v2 | Strain driven negative Poisson's ratio and extraordinary light-harvesting response of Penta-BCN monolayer | We report here, structural, dynamic, and mechanical stability in pentagonal boron carbon nitride (p-BCN) monolayer, a new member of direct bandgap two-dimensional (2D) semiconductor. The identified visible range bandgap with excellent mechanical strength allows it to be a promising candidate material in optoelectronics and nanomechanics. By employing density functional theory (DFT), we reveal a unique geometrical reconstruction with rigidity in B$ - $N and C$ - $N bond lengths with applied strain. These quasi-sp$ ^3$ hybridized short and strong covalent bonding and unique geometry support the monolayer to possess extraordinary mechanical response. Remarkably, the very rare, negative Poisson's ratio (NPR), with softening and hardening, mechanical anisotropy to isotropy is achieved with the application of a small value of strain. Similarly, the desired bandgap is manipulated by loading the biaxial strain. Most importantly, our predictions on p-BCN show excellent optical response such as good static dielectric constant and refractive index, strong optical absorption (up to 1.08$\times$10$ ^5 $ $ {cm}^{-1}$ in VR and 7.01$\times$10$ ^5 $ $ {cm}^{-1}$ in UV) with small energy loss and reflectance both appearing in visible and ultraviolet regions (UV). The desired optical response along with the blue and red shift is demonstrated by tailoring with tensile and compressive strain. Additionally, the predicted strong optical anisotropy provides it's application in polarized photodetection.
| Shambhu Bhandari Sharma; Ramchandra Bhatta; Rajendra Adhikari; Durga Paudyal | Materials Science; Elastic Materials; Materials Processing; Metamaterials | CC BY 4.0 | CHEMRXIV | 2021-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613a141942198eaeed7187ce/original/strain-driven-negative-poisson-s-ratio-and-extraordinary-light-harvesting-response-of-penta-bcn-monolayer.pdf |
61728a38d7e1ee03b82e8c7c | 10.26434/chemrxiv-2021-znd87 | Enantiomer stability of atropisomeric 1,5-disubstituted 1,2,3-triazoles | The synthesis and characterisation of axially chiral atropisomeric 1,5-disubstituted 1,2,3-triazoles is reported. Molecules designed to display restricted rotation about 1,2,3-triazole N-1-aryl or 1,2,3-triazole C-5-aryl bonds were investigated by physical and computational techniques. The barrier to 1,2,3-triazole N-1-aryl rotation was found to be higher than that for 1,2,3-triazole C-5-aryl rotation, confirming axial chirality stemming from restricted rotation about an N-1-aryl bond in a 1,5-disubstituted 1,2,3-triazole to be the most suitable for the development of an axial chirality triazole-based platform. | Fernanda Meloni; William Brittain; Louise Male; Cécile Le Duff; Benjamin Buckley; Andrew Leach; John Fossey | Theoretical and Computational Chemistry; Organic Chemistry; Stereochemistry; Theory - Computational; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61728a38d7e1ee03b82e8c7c/original/enantiomer-stability-of-atropisomeric-1-5-disubstituted-1-2-3-triazoles.pdf |
621c2e7cce899b1474a6a147 | 10.26434/chemrxiv-2022-h5v60 | Carbodefluorination via a carbene-initiated rearrangement strategy | The C–F bond cleavage and C–C bond formation (i.e., carbodefluorination) of readily accessible (per)fluoroalkyl groups constitutes an atom-economical and efficient route to partially fluorinated compounds. However, the selective mono-carbodefluorination of trifluoromethyl (CF3) groups remains a formidable challenge, due to the notorious inertness of C–F bond and the risk of over-defluorination arising from C–F bond strength decrease as the defluorination proceeds. Herein, we report a carbene-initiated rearrangement strategy for the carbodefluorination of fluoroalkyl ketones with β,γ-unsaturated alcohols. The reaction starts with formation of a silver carbene from a fluoroalkyl ketone N-triftosylhydrazone, followed by nucleophilic addition of a β,γ-unsaturated alcohol to form a key oxonium ylide intermediate, which triggers selective C–F bond cleavage by HF elimination and C–C bond formation through Claisen rearrangement of in situ generated difluorovinyl ether. This method described here is versatile and enables the conversion of fluoroalkyl ketones into skeletally and functionally diverse α-mono- and α,α-difluoro-γ,δ-unsaturated ketones. The reaction mechanism and the origin of chemoselectivity were established by experimental and computational approaches. Collectively, current strategy integrates successive C–F bond cleavage and C–C bond formation on a single molecule entity by an intramolecular cascade process, thereby offering significant advances over existing stepwise strategies in term of selectivity, efficiency, functional group tolerance, etc. | Linxuan Li; Xinyu Zhang; Yongquan Ning; Xiaolong Zhang; Binbin Liu; Zhansong Zhang; Paramasivam Sivaguru; Giuseppe Zanoni; Shuang Li; Edward A. Anderson; Xihe Bi | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621c2e7cce899b1474a6a147/original/carbodefluorination-via-a-carbene-initiated-rearrangement-strategy.pdf |
6477c18de64f843f411b0284 | 10.26434/chemrxiv-2023-hftx9 | Electron count and ligand composition influence the optical and chiroptical signatures of NIR-emissive DNA-stabilized silver nanoclusters | Near-infrared (NIR) emissive DNA-stabilized silver nanoclusters (AgN-DNAs) are promising fluorophores in the biological tissue transparency windows. Hundreds of NIR-emissive AgN-DNAs have been recently discovered, but their structure-property relationships remain poorly understood. Here, we investigate 19 different far-red and NIR emissive AgN-DNA species stabilized by 10-base DNA templates, including several well-studied emitters whose compositions and chiroptical properties have never been reported before. The molecular formula of each purified species is determined by high-resolution mass spectrometry and correlated to its optical absorbance, emission, and circular dichroism (CD) spectra. We find that AgN-DNAs emissive at the far red/NIR spectral border are either 6-electron clusters or 8-electron clusters. 8-electron AgN-DNAs are stabilized by two DNA oligomer copies, while three different ligand compositions are observed for 6-electron AgN-DNAs: two oligomer copies, three oligomer copies, or two oligomer copies with additional chlorido ligands. Distinct optical and chiroptical signatures correlate with ligand composition of 6-electron AgN-DNAs. AgN-DNAs with three oligomer ligands exhibit shorter Stokes shifts than AgN-DNAs with two oligomers, and the presence of chlorido ligands is correlated with increased Stokes shifts and significantly suppressed visible CD transitions. Nanocluster electron count also significantly influences electronic structure and optical properties, with 6-electron and 8-electron AgN-DNAs exhibiting distinct absorbance and CD spectral features. This study shows that the optical and chiroptical properties of NIR-emissive AgN-DNAs are highly sensitive to nanocluster composition and illustrates the diversity of structure-property relationships for NIR-emissive AgN-DNAs, which could be harnessed to precisely tune these emitters for bioimaging applications. | Rweetuparna Guha; Anna Gonzàlez-Rosell; Malak Rafik; Nery Arevalos; Benjamin Katz; Stacy Copp | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Clusters; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6477c18de64f843f411b0284/original/electron-count-and-ligand-composition-influence-the-optical-and-chiroptical-signatures-of-nir-emissive-dna-stabilized-silver-nanoclusters.pdf |
65116fddb927619fe7c86e00 | 10.26434/chemrxiv-2023-lhl0f-v2 | Coupled-Cluster Density-Based Many-Body Expansion | While CCSD(T) is often considered the ``gold standard'' of computational chemistry, the scaling of its computational cost as N^7 limits is applicability for large and complex molecular systems. In this work, we apply the density-based many-body expansion [Int. J. Quantum Chem. 2020, 120, e26228] in combination with CCSD(T). The accuracy of this approach is assessed for neutral, protonated, and deprotonated water hexamers as well as (H2O)16 and (H2O)17 clusters. For the neutral water clusters, we find that already with a density-based two-body expansion, we are able to approximate the supermolecular CCSD(T) energies within chemical accuracy (4 kJ/mol). This surpasses the accuracy that is achieved with a conventional, energy-based three-body expansion. We show that this accuracy can be maintained even when approximating the electron densities using Hartree-Fock instead of using coupled-cluster densities. The density-based many-body expansion thus offers a simple, resource efficient, and highly parallelizable approach that makes CCSD(T)-quality calculations feasible where they would otherwise be prohibitively expensive. | Kevin Focke; Christoph Jacob | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65116fddb927619fe7c86e00/original/coupled-cluster-density-based-many-body-expansion.pdf |
6644287891aefa6ce1093d5e | 10.26434/chemrxiv-2024-hn926 | Revealing the Molecular Origin of Driving Forces and Thermodynamic Barriers for Li+ Ion Transport to Electrode-Electrolyte Interfaces | Enhancing the power of lithium-ion batteries necessitates understanding the molecular processes governing Li+ ion transfer across the electrode-electrolyte interface. Here, employing enhanced sampling molecular dynamics simulations, we investigated the driving force and the thermodynamic barrier of Li+ ion adsorption onto Li0.5CoO2 (104) in LiClO4-, LiPF6-, and LiTFSI-based EC/EMC (3:7) electrolytes. The weaker cation-anion pairing in LiTFSI compared to LiClO4 was found to enhance the driving force for adsorption from -0.48 eV in LiClO4 to -1.26 eV in LiTFSI for an electrode-electrolyte interface with zero cation coverage, which was accompanied by an increased thermodynamic barrier from 0.33 eV in LiClO4 to 0.43 eV in LiTFSI at equilibrium surface coverage of Li+ ions. The hindered diffusivity of the solvent molecules in the electric double layer (EDL) at the electrode-electrolyte interface was the main contributor to the thermodynamic barrier for ion transport. The entropic component of the thermodynamic barrier was found to be more than one order of magnitude smaller for ClO4 compared to the TFSI-, which can be attributed to the presence of more ClO4 than TFSI- in EDL, causing more structural changes in EDL. The strong dependence of the entropic component of the thermodynamic barrier on the EDL structure enables its decoupling from the enthalpic components (e.g., ion-pairing that can be tuned independently) and thus can be used to control the kinetics of the interfacial transport. This work provides a fundamental understanding of the thermodynamic and kinetic parameters involved in Li+ ion adsorption, which is a crucial step in the performance of Li+ ion batteries. | Abhishek Aggarwal; Kiarash Gordiz; Artem Baskin; Daniele Vivona; Joakim Halldin Stenlid; John W. Lawson; Jeffrey C. Grossman; Yang Shao-Horn | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Energy Storage | CC BY NC 4.0 | CHEMRXIV | 2024-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6644287891aefa6ce1093d5e/original/revealing-the-molecular-origin-of-driving-forces-and-thermodynamic-barriers-for-li-ion-transport-to-electrode-electrolyte-interfaces.pdf |
60c753a6567dfe26a1ec5f4f | 10.26434/chemrxiv.13013936.v1 | An Orbital Exchange Calculation of Chemical Bonding in Metals | <p><a>This work calculates the chemical bonds in lithium
metal and beryllium metal </a>using the orbital exchange method, a
method that recognizes that the two electrons of a bonding pair cannot be
completely distinguished when their orbitals overlap to bond. Since in metals there is no preferred
bond direction, the symmetry axes of the lattice are chosen as the bonding
axes. The
calculations sum the primary, secondary and many tertiary bonds along these
axes. <a>The bond
length and bond energy results are in agreement with the observed values with
bond energies accurate to 0.2 eV or better and bond lengths to 0.02Å. </a> The bond lengths are found at the point where
the total bond overlap equals 1.0. </p><p> These results are compared with <a>the orbital exchange calculations of bonding in diamond, a
nonconductor, and graphite, a semiconductor</a>. An uncomplicated explanation for the
difference in electrical properties emerges.
The conductor, lithium metal, has a 2s bonding orbital which bonds
equally in both directions along all axes providing for the continuous flow of
electrons. The nonconductor, diamond,
has a directional s p hybrid type bonding orbital which bonds in one direction
along a single axis, preventing the flow of electrons from atom to atom. </p><p>
</p><p> </p><p></p> | Paul Merrithew | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753a6567dfe26a1ec5f4f/original/an-orbital-exchange-calculation-of-chemical-bonding-in-metals.pdf |
67c9a093fa469535b9306a17 | 10.26434/chemrxiv-2025-605xd | How repair proteins identify DNA damage in the nucleosome | The DNA base-excision repair (BER) pathway shares the second part of its enzymatic chain with the single-strand break (SSB) repair pathway. BER is initiated by a glycosylase, such as UDG, while SSBR is initiated by the multifunctional enzyme PARP1. The very early steps in the identification of the DNA damage are crucial to the correct initiation of the repair chains, and become even more complex when considering the realistic environment of damage to the DNA in the nucleosome. We performed molecular dynamics computer simulations of the interaction between the glycosylase UDG and a mutated uracil (as resulting from oxidative deamination of cytosine), and between the Zn1-Zn2 fragment of PARP1 and a simulated SSB. The model system is a whole nucleosome in which DNA damage is inserted at various typical positions along the 145-bp sequence. It is shown that damage recognition by the enzymes requires very strict conditions, unlikely to be matched by pure random search along the DNA. We propose that mechanical deformation of the DNA around the defective sites may help signaling the presence of the defect, accelerating the search process. | Safwen Ghediri; Parvathy A. P. Sarma; Vinnarasi Saravanan; Corinne Abbadie; Ralf Blossey; Fabrizio Cleri | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c9a093fa469535b9306a17/original/how-repair-proteins-identify-dna-damage-in-the-nucleosome.pdf |
644be0330d87b493e37120c9 | 10.26434/chemrxiv-2023-wbzpt | Simple lattice model explains equilibrium separation phenomena in glassy polymers | The Robeson bound is a theoretical limit that applies to kinetics-driven membrane separations of gas mixtures. However, this bound does not apply to sorption-driven membrane processes such as CO$_\text{2}$/N$_\text{2}$ separation, which lacks a theoretical explanation. As a result, we are uncertain about the factors that control the limiting behavior of sorption-driven separations. To address this issue, we employed a simple lattice model and dynamic mean field theory to examine the transport properties of disordered model structures, isolating sorption effects from purely kinetic effects. Our findings indicate that transport effects play a crucial role in sorption-driven processes, and perm-selectivity is consistently lower than sorption selectivity, which is an unattainable limit. We used basic geometric fragments of the structure to explain how transport effects emerge and manifest themselves in sorption-driven processes. | Tianmu Yuan; Maria Grazia De Angelis; Lev Sarkisov | Physical Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry; Thermodynamics (Chem. Eng.); Statistical Mechanics | CC BY 4.0 | CHEMRXIV | 2023-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644be0330d87b493e37120c9/original/simple-lattice-model-explains-equilibrium-separation-phenomena-in-glassy-polymers.pdf |
661670f391aefa6ce1406f4c | 10.26434/chemrxiv-2024-ws952 | 2D Hexagonal Assembly of a Dipolar Rotor with a Close Interval of 0.8 nm Using a Triptycene-Based Supramolecular Scaffold | Controlling the rotation of carbon-carbon bonds, which is ubiquitous in organic molecules, to create functionality has been a subject of interest for a long time. In this context, it would be interesting to explore whether cooperative and collective rotation could occur if dipolar molecular rotors were aligned close together while leaving adequate space for rotation. However, it is difficult to realize such structures as bulk assemblies, since molecules generally tend to assemble into a closest packing structure to maximize intermolecular forces. To tackle this question, we examined an approach using a supramolecular scaffold composed of a tripodal triptycene, which has been demonstrated to strongly promote the assembly of various molecular and polymer units into regular “2D hexagonal packing + 1D layer” structures. We found that a molecule (1) consisting of a dipolar 1,2-difluorobenzene rotor sandwiched by two 10-ethynyl-1,8,13-tridodecyloxy triptycenes, successfully self-assembles into the desired structure, where the rotor units align two-dimensionally at a close interval of approximately 0.8 nm while having a degree of freedom for rotational motion. Here we describe the self-assembly behavior of 1 in comparison with the general trend in molecular self-assembly, as well as the motility of the aligned rotors investigated using solid-state 19F-MAS NMR spectroscopy. | Takejiro Ogawa; Fumitaka Ishiwari; Fatin Hajjaj; Yoshiaki Shoji; Takashi Kajitani; Koji Yazawa; Takanori Fukushima | Physical Chemistry; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661670f391aefa6ce1406f4c/original/2d-hexagonal-assembly-of-a-dipolar-rotor-with-a-close-interval-of-0-8-nm-using-a-triptycene-based-supramolecular-scaffold.pdf |
63c0533ba5c35478009147e1 | 10.26434/chemrxiv-2023-fn3hf | N-Terminal Proline Editing for the Synthesis of Peptides with Mercaptoproline and Selenoproline: Mechanistic Insights Lead to Greater Efficiency in Proline Native Chemical Ligation
| Native chemical ligation (NCL) at proline has been limited by cost and synthetic access. In addition, prior examples of NCL using mercaptoproline have exhibited stalling of the reaction after thioester exchange, due to inefficient SN acyl transfer. Herein, we develop methods, using inexpensive Boc-4R-hydroxyproline, for the solid-phase synthesis of peptides containing N-terminal 4R-mercaptoproline and 4R-selenoproline. The synthesis proceeds via proline editing on the N-terminus of fully synthesized peptides on the solid phase, converting an N-terminal Boc-4R-hydroxyproline to the 4S-bromoproline, followed by SN2 reaction with potassium thioacetate or selenobenzoic acid. After cleavage from the resin and deprotection, peptides with functionalized N-terminal proline amino acids were obtained. NCL reactions with mercaptoproline proceeded slowly under standard NCL conditions, with the S-acyl transthioesterification intermediate observed as a major species. Computational investigations indicated that the bicyclic intermediates and transition states for SN acyl transfer are sufficiently low in energy (10-15 kcal mol–1 above starting material) that ring strain cannot explain slow SN acyl transfer. Instead, the bicyclic zwitterionic tetrahedral intermediate has a low barrier for reversion to the S-acyl intermediate, causing reversion to the thioester (reverse reaction) to occur preferentially over elimination to generate the amide (forward reaction). We hypothesized that a buffer capable of general acid and/or general base catalysis could promote SN acyl transfer, and thus achieve greater efficiency in proline NCL. In the presence of 2 M imidazole at pH 6.8, NCL with mercaptoproline proceeded efficiently to generate the peptide with a native amide bond. NCL with selenoproline also proceeded efficiently to generate the desired products when a thiophenol thioester was employed as a ligation partner. After desulfurization or deselenization, the products obtained were identical to those synthesized directly, confirming that the solid-phase proline editing reactions proceeded stereospecifically and without epimerization. | Brice Ludwig; Christina Forbes; Neal Zondlo | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Bioorganic Chemistry; Organic Synthesis and Reactions; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c0533ba5c35478009147e1/original/n-terminal-proline-editing-for-the-synthesis-of-peptides-with-mercaptoproline-and-selenoproline-mechanistic-insights-lead-to-greater-efficiency-in-proline-native-chemical-ligation.pdf |
620e85b64e899eb25f51704a | 10.26434/chemrxiv-2022-0z38x | Controlled CVD growth of highly <111>-oriented 3C-SiC | Highly <111>-oriented 3C-SiC coatings with distinct surface morphology consisting of hexagonally shaped pyramidal crystals were prepared by chemical vapor deposition (CVD) using silicon tetrachloride (SiCl4) and toluene (C7H8) at T ≤ 1250 ℃ and p = 10 kPa. In contrast, similar deposition conditions, using methane (CH4) as carbon precursor, resulted in randomly oriented 3C-SiC coatings with a cauliflower-like surface of SiC crystallites. No excess carbon was detected in the highly <111>-oriented 3C-SiC samples despite the use of aromatic hydrocarbons. The difference in the preferred growth orientation of the 3C-SiC coatings deposited using C7H8 and CH4 as carbon precursors is explained via quantum chemical calculations of binding energies on various crystal planes. The adsorption energy of C6H6 on the SiC (111) plane was 6 times higher than that on the (110) surface. On the other hand, the CH3 exhibited equally strong adsorption on both planes. This suggests that the highly <111>-oriented 3C-SiC growth in the C7H8 process, where both C6H6 and CH3 are considered the main active carbon-containing film forming species, is due to the highly preferred adsorption on (111) planes, while the lower surface energy of the (110) plane controls the growth orientation in the CH4 process, in which only CH3 contributes to the film deposition. | Jing-Jia Huang; Christian Militzer; Charles Wijayawardhana; Urban Forsberg; Lars Ojamäe; Henrik Pedersen | Physical Chemistry; Materials Science; Materials Processing; Thin Films; Surface; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620e85b64e899eb25f51704a/original/controlled-cvd-growth-of-highly-111-oriented-3c-si-c.pdf |
66cb0df3f3f4b052901317e3 | 10.26434/chemrxiv-2024-w97n8 | Protein Electronic Energy Transport Levels Derived from High-Sensitivity Near-UV and Constant Final State Yield Photoemission Spectroscopy | Proteins are attractive as functional components in molecular junctions. However, control-ling the electronic charge transport via proteins, held between two electrodes, requires in-formation on their frontier orbital energy level alignment relative to the electrodes’ Fermi level (EF), which normally requires studies of UV Photoemission Spectroscopy (UPS) with HeI excitation. Such excitation is problematic for proteins, which can denature under stand-ard measuring conditions. Here we use high-sensitivity soft UV photoemission spectroscopy (HS-UPS) combined with Constant Final State Yield Spectroscopy (CFS-YS) to get this in-formation for electrode/protein contacts. Monolayers of the redox protein Azurin, (Az) and its Apo-form on Au substrates, have HOMO onset energies, obtained from CFS-YS, differ by ~ 0.2 eV, showing crucial role of the Cu redox centre in the electron transport process. We find that combined HS-UPS / CFS-YS measurements agree with the Photoelectron Yield Spectroscopy (PYS), showing potential of the HS-UPS + CFS-YS as a powerful tool to char-acterize and map the energetics of a protein-electrode interfaces, which will aid optimizing design of devices with targeted electronic properties, as well as for novel applications. | Jerry Alfred Fereiro; Masaki Tomita; Tatyana Bendikov; Sudipta Bera; Israel Pecht; Mordechai Sheves; David Cahen; Hisao Ishii | Physical Chemistry; Materials Science; Nanoscience; Thin Films; Biophysical Chemistry; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cb0df3f3f4b052901317e3/original/protein-electronic-energy-transport-levels-derived-from-high-sensitivity-near-uv-and-constant-final-state-yield-photoemission-spectroscopy.pdf |
67877825fa469535b91929a1 | 10.26434/chemrxiv-2025-30hgs | Evolving Cyclopropenium Derivatives into High-Performance Bifunctional Organocatalysts towards Ring-Opening Alternating Copolymerization | Bifunctional catalysts, known for their superior activity and selectivity compared to binary systems, hold great promise for ring-opening copolymerization (ROCOP). Here, we present our recent advancements in developing high-performance bifunctional organocatalysts by integrating borane with triamino-cyclopropenium (TAC) derivatives. Specifically, we developed a bifunctional catalyst by conjugating 9-borabicyclo[3.3.1]nonane (9-BBN) with TAC-Cl through an optimized alkyl linker (TB-3). This catalyst exhibited outstanding performance in the controlled ROCOP of epoxides and anhydrides, demonstrating high activity, selectivity, and thermal stability, and outperforming both binary catalytic systems and quaternary ammonium-borane analogues. Notably, further transformation of the TAC moiety into its cyclopropenimine (CPI) derivative led to the creation of a cyclopropenimine-borane bifunctional organocatalyst (CPI-B). The strong yet dissociative intramolecular N-B coordination between the CPI and BBN units imparts remarkable air stability to CPI-B. Additionally, the N/B Lewis pair in CPI-B effectively activates protic initiators, enabling precise control over end-group functionality and polymer topology in ROCOP. These advancements significantly broaden the practical utility of CPI-B in polymer synthesis. | Cunluo Wu; Xinyuan Song; Qingqing Han; Ronglin Zhong; Xiaowu Wang; Zhibo Li; Yiliu Liu | Catalysis; Polymer Science; Polymerization (Polymers); Homogeneous Catalysis; Organocatalysis | CC BY NC 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67877825fa469535b91929a1/original/evolving-cyclopropenium-derivatives-into-high-performance-bifunctional-organocatalysts-towards-ring-opening-alternating-copolymerization.pdf |
655a517b6e0ec7777f470ebe | 10.26434/chemrxiv-2023-pfz5g | A Widespread, Diiron-dependent Diterpenoid Hydroxylase | This communication describes the discovery of a family of monooxygenases that selectively hydroxylate abundant abietane diterpenoids. Previous studies on abietic acid metabolism had implicated an unknown C(5) hydroxylase and herein we determine that this role is filled by DitZ. Structural and sequence analyses indicate that DitZ represents a new member of the Amidohydrolase-related Dinuclear Oxygenase (ADO) superfamily. Kinetic studies on multiple DitZ enzymes reflect highly efficient and selective C(5) hydroxylation of a range of diterpenoids using only O2 and a sacrificial reductant (sodium ascorbate) as co-reagents. These enzymatic reactions are promoted by a diiron cofactor that has access to multiple observable redox states. | Sarah Chen; Chang Liu; George Liu; Jonathan Rittle | Biological and Medicinal Chemistry; Inorganic Chemistry; Catalysis; Bioinorganic Chemistry; Biochemistry; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655a517b6e0ec7777f470ebe/original/a-widespread-diiron-dependent-diterpenoid-hydroxylase.pdf |
6114013d30231a6249081bb6 | 10.26434/chemrxiv-2021-ffx98 | A Study in Red: The Overlooked Role of Azo-Moieties in Polymeric Carbon Nitride Photocatalysts with Strongly Extended Optical Absorption | The unique optical and photoredox properties of heptazine-based polymeric carbon nitride (PCN) materials make them promising semiconductors for driving various productive photocatalytic conversions. However, their typical absorption onset at ca. 430-450 nm is still far from optimum for efficient sunlight harvesting. Despite many reports of successful attempts to extend the light absorption range of PCNs, the determination of the structural features responsible for the red shift of the light absorption edge beyond 450 nm has often been obstructed by the highly disordered structure of PCNs and/or low content of the moieties responsible for changes in optical and electronic properties. In this work, we implement a high-temperature (900 °C) treatment procedure for turning the conventional melamine-derived yellow PCN into a red carbon nitride. This approach preserves the typical PCN structure but incorporates a new functionality that promotes visible light absorption. A detailed characterization of the prepared material reveals that partial heptazine fragmentation accompanied by de-ammonification leads to the formation of azo-groups in the red PCN, a chromophore moiety whose role in shifting the optical absorption edge of PCNs has been overlooked so far. These azo moieties can be activated under visible-light (470 nm) for H2 evolution even without any additional co-catalyst, but are also responsible for enhanced charge-trapping and radiative recombination, as shown by spectroscopic studies. Our work thus highlights the importance of careful determination of structural features governing the complex interplay between the light absorption, charge separation and catalytic turnover in PCN-based polymers tailored for visible light-driven photocatalysis. | Dariusz Mitoraj; Igor Krivtsov; Chunyu Li; Ashwene Rajagopal; Changbin Im; Christiane Adler; Kerstin Köble; Olena Khainakova; Julian Hniopek; Christof Neumann; Andrey Turchanin; Ivan da Silva; Michael Schmitt; Robert Leiter; Tibor Lehnert; Jürgen Popp; Ute Kaiser; Timo Jacob; Carsten Streb; Benjamin Dietzek; Radim Beranek | Physical Chemistry; Catalysis; Heterogeneous Catalysis; Photocatalysis; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6114013d30231a6249081bb6/original/a-study-in-red-the-overlooked-role-of-azo-moieties-in-polymeric-carbon-nitride-photocatalysts-with-strongly-extended-optical-absorption.pdf |
6230fc1521e2d099eaa51ec7 | 10.26434/chemrxiv-2022-n236n-v3 | Towards a Mechanistic Model of Solid-Electrolyte Interphase Formation and Evolution in Lithium-ion Batteries | The formation of passivation films by interfacial reactions, though critical for applications ranging from advanced alloys to electrochemical energy storage, is often poorly understood. In this work, we explore the formation of an exemplar passivation film, the solid-electrolyte interphase (SEI), which is responsible for stabilizing lithium-ion batteries. Using stochastic simulations based on quantum chemical calculations and data-driven chemical reaction networks, we directly model competition between SEI products at a mechanistic level for the first time. Our results recover the Peled-like separation of the SEI into inorganic and organic domains resulting from rich reactive competition without fitting parameters to experimental inputs. By conducting accelerated simulations at elevated temperature, we track SEI evolution, confirming the postulated reduction of lithium ethylene monocarbonate to dilithium ethylene monocarbonate and H2. These findings furnish fundamental insights into the dynamics of SEI formation and illustrate a path forward towards a predictive understanding of electrochemical passivation. | Evan Walter Clark Spotte-Smith; Ronald L Kam; Daniel Barter; Xiaowei Xie; Tingzheng Hou; Shyam Dwaraknath; Samuel M Blau; Kristin Aslaug Persson | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Theory - Computational; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6230fc1521e2d099eaa51ec7/original/towards-a-mechanistic-model-of-solid-electrolyte-interphase-formation-and-evolution-in-lithium-ion-batteries.pdf |
60c74785ee301c7e9bc796f7 | 10.26434/chemrxiv.11691852.v1 | Carboxylated Chitosan Nanocrystals: Novel Synthetic Route and Application as Superior Support for Gold-Catalyzed Reactions | <p>Chitin nanocrystals (ChNCs) were
prepared by partial cleavage of glycosidic bonds in chitin with concurrent
oxidation of chitin C6 primary alcohols to produce carboxylate groups on the
surface of the ChNCs. Following alkaline deacetylation of the ChNCs in the
presence of NaBH<sub>4</sub> to inhibit “end-peeling” afforded chitosan
nanocrystals (ChsNCs) with a degree of deacetylation (DDA) >80%. Transmission
electron microscopy (TEM), X-ray diffraction (XRD) and Fourier-transform
Infrared (FTIR) spectroscopy were used to determine the morphology and
composition of these carboxylated ChNCs and ChsNCs. Subsequently, two methods were
used to deposit Au onto the nanocrystals, and the catalytic activities of the resulting
biomass-based nanocatalysts were tested for the 4-nitrophenol reduction and the
aldehyde-amine-alkyne (A<sup>3</sup>) coupling reaction. In particular, Au
nanoparticles over ChsNCs featured the highest turnover frequency value for the
4-nitrophenol reduction reported to date. Spectroscopic and imaging techniques confirmed
the importance of controlling precisely the redox state of Au as it is being
deposited to afford highly disperse active site on the bio-nano-support. </p> | Tony Jin; Davis Kurdyla; Sabahudin Hrapovic; Alfred Leung; Sophie Régnier; Yali Liu; Audrey Moores; Edmond Lam | Nanostructured Materials - Nanoscience; Nanocatalysis - Reactions & Mechanisms | CC BY NC 4.0 | CHEMRXIV | 2020-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74785ee301c7e9bc796f7/original/carboxylated-chitosan-nanocrystals-novel-synthetic-route-and-application-as-superior-support-for-gold-catalyzed-reactions.pdf |
620b6faabd05a030d9077c9a | 10.26434/chemrxiv-2022-rd73z-v2 | Neural ordinary differential equations and recurrent Neural Networks for Predicting the State of Health of Batteries | Battery management systems require efficient battery
prognostics so that failures can be prevented, and efficient operation
guaranteed. In this work, we develop new models based on neural networks and
ordinary differential equations (ODE) to forecast the state of health (SOH) of
batteries and predict their end of life (EOL). Governing differential equations
are discovered using measured capacities and voltage curves. In this context,
discoveries and predictions made with neural ODEs, augmented neural ODEs,
predictor-corrector recurrent ODEs are compared against established recurrent
neural network models, including long short-term memory and gated recurrent units. The ODE models show good
performance, achieving errors of 1% in SOH and 5% in EOL estimation when
predicting 30% of the remaining battery’s cycle life. Variable cycling
conditions and a range of prediction horizons are analyzed to evaluate the
models’ characteristics. The results obtained are extremely promising for
applications in SOH and EOL predictions. | Simona Pepe; Jiapeng Liu; Emanuele Quattrocchi; Francesco Ciucci | Theoretical and Computational Chemistry; Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620b6faabd05a030d9077c9a/original/neural-ordinary-differential-equations-and-recurrent-neural-networks-for-predicting-the-state-of-health-of-batteries.pdf |
622b7b0e835f774be6fe9c3d | 10.26434/chemrxiv-2022-k3j3f | Diversifying Amino Acids and Peptides via Deaminative Reductive Cross-Couplings Leveraging High-Throughput Experimentation | A deaminative reductive coupling of amino acid pyridinium salts with aryl bromides has been developed to enable efficient synthesis of noncanonical amino acids and diversification of peptides. This method transforms natural, commercially available lysine, ornithine, diaminobutanoic acid (DAB), and diaminopropanoic acid (DAP) to aryl alanines and homologated derivatives with varying chain lengths. Attractive features include scalability, tolerance of pharma-relevant (hetero)aryls and functional groups, applicability to both monomeric amino acid and short peptide substrates, and compatibility with biorthogonal handles useful for chemical biology. Furthermore, these cross-couplings can be conducted in microscale and nanoscale and are amenable to solid-phase peptide synthesis platforms. The success of this work relied on an academic/industry collaboration and high-throughput experimentation to identify complementary conditions that proved critical for achieving broad scope of aryl bromides and pyridinium substrates. | J. Cameron Twitty; Yun Hong; Bria Garcia; Stephanie Tsang; Jennie Liao; Danielle Schultz; Amelie Dion; Dipannita Kalyani; Mary Watson | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622b7b0e835f774be6fe9c3d/original/diversifying-amino-acids-and-peptides-via-deaminative-reductive-cross-couplings-leveraging-high-throughput-experimentation.pdf |
60c75634567dfe05ceec63f8 | 10.26434/chemrxiv.14206619.v1 | Cobalt Metal ALD: Understanding the Mechanism and Role of Zink Alkyl Precursors as Reductants for Low Resistivity Co Thin Films | In this work, we report a new and promising approach towards the atomic layer deposition (ALD) of metallic Co thin films. Utilizing the simple and known CoCl<sub>2</sub>(TMEDA) (TMEDA = N,N,N’,N’-tetramethylethylenediamine) precursor in combination with the intramolecularly stabilized Zn aminoalkyl compound Zn(DMP)<sub>2</sub> (DMP = dimethylaminopropyl) as auxiliary reducing agent, a thermal ALD process is developed that enables the deposition of Zn free Co thin films. ALD studies demonstrate the saturation behavior of both precursors, linearity in dependency of the applied number of cycles as well as investigations of the temperature dependency of film growth in a regime of 140 - 215 °C. While the process optimization is carried out on Si with native oxide, additional growth studies are conducted on Au and Pt substrates. This study is complemented by initial reactivity and suitability tests of several potential Zn alkyl reducing agents. For the CoCl<sub>2</sub>(TMEDA) - Zn(DMP)<sub>2</sub> combination, these findings allow to propose a series of elemental reaction steps hypothetically leading to pure Co film formation in the ALD process whose feasibility are probed by a set of DFT calculations. The DFT results show that for reactions of the precursors in the gas phase and on Co(111) substrate surfaces, a pathway involving C-C coupling and diamine formation through reductive elimination of an intermediate Co(II) alkyl species is preferred. Co thin films with an average thickness of 10 - 25 nm obtained from the process are subjected to thorough analysis comprising AFM, SEM, RBS/NRA as well as depth profiling XPS. Resistivity measurements for ~ 22 nm thick films grown on a defined SiO<sub>2</sub> insulator layer yield highly promising values in a range of 15 - 20 μΩ cm without any after treatment. | David Zanders; Ji Liu; Jorit Obenlüneschloß; Claudia Bock; Detlef Rogalla; Lukas Mai; Michael Nolan; Sean Barry; Anjana Devi | Thin Films; Kinetics and Mechanism - Inorganic Reactions; Theory - Inorganic; Computational Chemistry and Modeling; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75634567dfe05ceec63f8/original/cobalt-metal-ald-understanding-the-mechanism-and-role-of-zink-alkyl-precursors-as-reductants-for-low-resistivity-co-thin-films.pdf |
67451c77f9980725cfef0b3f | 10.26434/chemrxiv-2024-x00x1 | Acceleration with Interpretability: Surrogate Model Based Collective Variable for Enhanced Sampling | Most enhanced sampling methods facilitate the exploration of molecular free energy landscapes by applying a bias potential along a reduced dimensional collective variable (CV) space. The success of these methods depends on the ability of the CVs to follow the relevant slow modes of the system. Intuitive CVs, such as distances or contacts, often prove inadequate, particularly in biological systems involving many coupled degrees of freedom. Machine learning algorithms, especially neural networks (NN), can automate the process of CV discovery by combining a large number of molecular descriptors and often outperform intuitive CVs in sampling efficiency. However, their lack of interpretability and high cost of evaluation during trajectory propagation make NN-CVs difficult to apply to large biomolecular processes. Here, we introduce a surrogate model approach using lasso regression to express the output of a neural network as a linear combination of an automatically chosen subset of the input descriptors. We demonstrate successful applications of our surrogate model CVs in the enhanced sampling simulation of the conformational landscape of alanine dipeptide and chignolin mini-protein. In addition to providing mechanistic insights due to their explainable nature, the surrogate model CVs showed a negligible loss in efficiency and accuracy, compared to the NN-CVs, in reconstructing the underlying free energy surface. Moreover, due to their simplified functional forms, these CVs are better at extrapolating to unseen regions of the conformational space, e.g., saddle points. Surrogate model CVs are also less expensive to evaluate compared to their NN counterparts, making them suitable for enhanced sampling simulation of large and complex biomolecular processes. | Sompriya Chatterjee; Dhiman Ray | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67451c77f9980725cfef0b3f/original/acceleration-with-interpretability-surrogate-model-based-collective-variable-for-enhanced-sampling.pdf |
61e19decf81dfe872db862bd | 10.26434/chemrxiv-2022-nkj0n | From simple to complex crystal chemistry in the RE−Au−Tt systems (RE = La, Ce, Pr, Nd, Ho; Tt = Ge, Sn, Pb) | Polar intermetallics are an intriguing class of compounds with complex relationships between composition and structure that are not fully understood. This work reports a systematic study of the underexplored ternary composition space RE–Au–Tt (RE = La, Ce, Pr, Nd, Ho; Tt = Ge, Sn, Pb) to expand our knowledge of the intriguing chemistry and diversity achievable with these metallic constituents. These composition spaces are particularly interesting because of the potential to find Au-bearing, highly polar intermetallic compounds. The elements were first reacted through arc welding under an inert atmosphere followed by annealing at 850°C. X-ray diffraction of the products identified unreported eight compounds ranging from the simple NaTl-type compounds La1.5Au2Pb0.5, Nd2-xAu2Pbx, and Ho2-xAu2Snx, to the more structurally complex La5AuPb3 in the Hf5CuSn3-type structure and Pu3Pd4-type RE3Au3Ge (RE = La, Ce, Pr, Nd). First-principles electronic structure calculations revealed that a combination of Fermi surface-Brillouin zone interactions, electrostatic interactions, and delocalized metallic bonding contributes to the formation of these phases. These calculations show that a mixture of electrostatic and metallic bonding plays a dominant role in these phases. The RE–Au–Tt composition space remains full of potential for discovering materials with relevant magnetic and quantum properties, provided the crystal chemistry can be comprehended. | Sogol Lotfi; Roy Arrieta; Gordon Peterson; Pablo Delgado; Jakoah Brgoch | Theoretical and Computational Chemistry; Inorganic Chemistry; Solid State Chemistry; Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e19decf81dfe872db862bd/original/from-simple-to-complex-crystal-chemistry-in-the-re-au-tt-systems-re-la-ce-pr-nd-ho-tt-ge-sn-pb.pdf |
60c74329bdbb8911e3a385c4 | 10.26434/chemrxiv.8943878.v1 | Improvement of Oxidative Stability and Microbial Shelf Life of Vanilla Cake by Coconut Oil Meal and Sesame Oil Meal Phenolic Extracts | <p></p><p>Phenolic extracts of coconut oil meal (CME) and sesame oil meal (SME) were compared with synthetic antioxidants for the potential of improving shelf life of vanilla cake. CME maintained hexanal (product of chemical spoilage) levels below 0.3 mg/kg in cake up to 14 days. BHT- and SME-added cakes maintained hexanal levels below 2 mg/kg while control cake with no added antioxidants exceeded this level by day 14. Both CME and SME extended the microbial shelf life up to 13 days while control and BHT-added cake exceeded the maximum allowed colony count by day 7 and day 11 respectively. The results indicate that the onset of microbial spoilage of vanilla cake is faster than the chemical spoilage and addition of CME and SME extend both microbiological and chemical stability of cakes beyond day 7 during storage. Over 90% of the antioxidant activity of CME and SME retained after heating at 180 °C for 2 h. CME and SME are ideal thermally stable natural alternatives for synthetic antioxidants in vanilla cake. <br /></p><br /><p></p> | Chathuri Senanayake; Harshani Algama; Ruwani Wimalasekara; W. N. M. T. D. N. Weerakoon; Nimanthi Jayathilaka; Kapila Seneviratne | Food | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74329bdbb8911e3a385c4/original/improvement-of-oxidative-stability-and-microbial-shelf-life-of-vanilla-cake-by-coconut-oil-meal-and-sesame-oil-meal-phenolic-extracts.pdf |
Subsets and Splits
No saved queries yet
Save your SQL queries to embed, download, and access them later. Queries will appear here once saved.