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6507901eb338ec988aa89f88 | 10.26434/chemrxiv-2023-rr34z | Electron density mapping of boron clusters via convolutional neural networks to augment structure prediction algorithms | Determination and prediction of atomic cluster structures is an important endeavor in the field of nanoclusters and thereby in materials research. To a large extent the fundamental properties of a nanocluster including its chemical, optical, magnetic, mechanical and transport properties are mainly governed by the molecular structure it adopts. Traditionally, structure elucidation is achieved using quantum chemical (QC) calculations that are usually tedious and time consuming for large size clusters. Various structural search algorithms, implemented in software codes, have been reported in the literature. Although they tend to accelerate the structure exploration, they still require the aid of QC calculations of energies for structure evaluation. This makes the structure prediction process using these approaches a computationally expensive affair. In this paper, we report on the creation of a convolutional neural network model based on a machine learning, which can give relatively accurate energies for the ground state of nanoclusters from the total electron density on the fly and could thereby be utilized for aiding structure prediction algorithms. We have built up a dataset consisting of pure boron clusters for the purpose of training our model. | Pinaki Saha; Minh Tho Nguyen | Theoretical and Computational Chemistry; Materials Science; Nanoscience; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6507901eb338ec988aa89f88/original/electron-density-mapping-of-boron-clusters-via-convolutional-neural-networks-to-augment-structure-prediction-algorithms.pdf |
644194d1df78ec50151bf1e3 | 10.26434/chemrxiv-2023-n4pz9 | Computer-assisted discovery and rational synthesis of ternary oxides | Exploratory synthesis has been the main generator of new inorganic materials for decades. However, our Edisonian and bias-prone processes of synthetic exploration alone are no longer sufficient in an age that demands rapid advances in materials development. In this work, we demonstrate one of the first end-to-end attempts towards systematic, computer-aided discovery and laboratory synthesis of inorganic crystalline compounds as a modern alternative to purely exploratory synthesis. Our approach initializes materials discovery campaigns by autonomously mapping the synthetic feasibility of a chemical system using density functional theory with AI feedback. Following expert-driven down-selection of newly generated phases, we use solid-state synthesis and in situ characterization via hot-stage X-ray diffraction in order to realize new ternary oxide phases experimentally. We applied this strategy in six ternary transition-metal oxide chemistries previously considered well-explored, one of which culminated in the discovery of two novel phases of calcium ruthenates. Detailed characterization using room temperature X-ray powder diffraction, 4D-STEM and SQUID measurements identify the structure, composition and confirm distinct properties, including distinct defect concentrations, of one of the new phases formed in our experimental campaigns. While the discovery of a new material guided by AI and DFT theory represents a milestone, our procedure and results also highlight a number of critical gaps in the process that can inform future efforts towards the improvement of AI-coupled methodologies, which are discussed. | Joseph Montoya; Carolyn Grimley; Muratahan Aykol; Colin Ophus; Hadas Sternlicht; Benjamin H. Savitzky; Andrew M. Minor; Steven Torrisi; Jackson Goedjen; Ching-Chang Chung; Andrew Comstock; Shijing Sun | Theoretical and Computational Chemistry; Materials Science; Ceramics; Computational Chemistry and Modeling; Artificial Intelligence; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644194d1df78ec50151bf1e3/original/computer-assisted-discovery-and-rational-synthesis-of-ternary-oxides.pdf |
62e2affbadb01e94b2b01788 | 10.26434/chemrxiv-2022-7lwf0 | A comparative spectroscopic study revealing why the CO2 electroreduction selectivity switches from CO to HCOO- at Cu-Sn and Cu-In based catalysts | To address the challenge of selectivity towards single product in Cu-catalyzed electrochemical CO2 reduction, one strategy is to incorporate a second metal with the goal of tuning catalytic activity via synergy effects. In particular, catalysts based on Cu modified with post-transition metals (Sn or In) are known to reduce CO2 selectively to either CO or HCOO- depending on their composition. However, it remains unclear exactly which factors induce this switch in reaction pathways, and whether these two related bimetal combinations follow similar general structure-activity trends. To investigate these questions systematically, Cu-In and Cu-Sn bimetallic catalysts were synthesized across a range of composition ratios and studied in detail. Compositional and morphological control was achieved via a simple electrochemical synthesis approach. A combination of operando and quasi in-situ spectroscopic techniques, including X-ray photoelectron, X-ray absorption, and Raman spectroscopy, were used to observe the dynamic behaviors of the catalysts’ surface structure, composition, speciation, and local environment during CO2 electrolysis. The two systems exhibited similar selectivity dependency on their surface composition. Cu-rich catalysts produce mainly CO, while Cu-poor catalysts were found to mainly produce HCOO-. Despite these similarities, the speciation of Sn and In at the surface differed from each other, and were found to be strongly dependent on the applied potential and the catalyst composition. For Cu-rich compositions optimized for CO production (Cu85In15 and Cu85Sn15), indium was present predominantly in reduced metallic form (In0), whereas tin mainly existed as an oxidized species (Sn2/4+). Meanwhile, for the HCOO--selective compositions (Cu25In75 and Cu40Sn60), the indium exclusively exhibited In0 regardless of the applied potential, while the tin resembles was reduced to metallic (Sn0) only at most negative applied potential, which corresponds to the best HCOO- selectivity. Furthermore, while Cu40Sn60 enhances HCOO- selectivity by inhibiting H2 evolution, Cu25In75 improves the HCOO- selectivity at the expense of CO production. Due to these differences, we contend that identical mechanisms cannot be used to explain the behavior of these two bimetallic systems (Cu-In and Cu-Sn). Operando surface-enhanced Raman spectroscopy measurements provide direct evidence of the local alkalization and its impact on the dynamic transformation of oxidized Cu surface species (Cu2O/CuO) into a mixture of Cu(OH)2 and basic Cu carbonates (Cux(OH)y(CO3)y) rather than metallic Cu under CO2 electrolysis. This study provides novel insight into the origin of the switch in selectivity between CO and HCOO- pathways at Cu bimetallic catalysts and the nature of surface-active sites and key intermediates for both pathways. | Gumaa El-Nagar; Fan Yang; Sasho Stojkovikj ; Stefan Mebs ; Siddharth Gupta; Ibbi Ahmet; Holger Dau; Matthew Mayer | Physical Chemistry; Catalysis; Energy; Electrocatalysis; Interfaces | CC BY 4.0 | CHEMRXIV | 2022-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e2affbadb01e94b2b01788/original/a-comparative-spectroscopic-study-revealing-why-the-co2-electroreduction-selectivity-switches-from-co-to-hcoo-at-cu-sn-and-cu-in-based-catalysts.pdf |
60c75568702a9b244e18c6c9 | 10.26434/chemrxiv.14096049.v1 | Nanostructured Si-C Composites As High-Capacity Anode Material For All-Solid-State Lithium-Ion Batteries | <p>Silicon carbon void structures (Si-C) are
attractive anode materials for Lithium-ion batteries to cope with the volume
changes of silicon during cycling. In this study, Si-C with varying Si contents
(28 ‑ 37 %) are evaluated in all-solid-state batteries (ASSBs) for the first
time. The carbon matrix enables enhanced performance and lifetime of the Si-C
composites compared to bare silicon nanoparticles in half-cells even at high
loadings of up to 7.4 mAh cm<sup>-2</sup>. In full cells with nickel-rich NCM
(LiNi<sub>0.9</sub>Co<sub>0.05</sub>Mn<sub>0.05</sub>O<sub>2</sub>, 210 mAh g<sup>-1</sup>),
kinetic limitations in the anode lead to a lowered voltage plateau compared to
NCM half-cells. The solid electrolyte (Li<sub>6</sub>PS<sub>5</sub>Cl, 3 mS cm<sup>-1</sup>)
does not penetrate the Si-C void structure resulting in less side reactions and
higher initial coulombic efficiency compared to a liquid electrolyte (72.7 %
vs. 31.0 %). Investigating the influence of balancing of full cells using
3-electrode ASSB cells revealed a higher delithiation of the cathode as a
result of the higher cut-off voltage of the anode at high n/p ratios. During
galvanostatic cycling, full cells with either a low or rather high overbalancing
of the anode showed the highest capacity retention of up to 87.7 % after 50
cycles. </p> | Stephanie Poetke; Felix Hippauf; Anne Baasner; Susanne Dörfler; Holger Althues; Stefan Kaskel | Electrochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75568702a9b244e18c6c9/original/nanostructured-si-c-composites-as-high-capacity-anode-material-for-all-solid-state-lithium-ion-batteries.pdf |
66b36ace5101a2ffa8611f29 | 10.26434/chemrxiv-2023-f42kl-v2 | Ion mobility mass spectrometry unveils conformational effects of drug lead EPI-001 on the intrinsically disordered N-terminal domain of the Androgen Receptor | Intrinsically disordered proteins (IDPs) are important drug targets as they are key actors within cell signalling networks. Accordingly, their dysregulation is highly implicated in a range of disease states. However, the conformational plasticity of IDPs renders them challenging to characterise both experimentally and theoretically, which is a major bottleneck in the development of small molecule drugs that bind to IDPs and modulate how they behave. In relation to this, ion mobility mass spectrometry (IM-MS) is a useful tool in the investigation of IDPs, as it can reveal their conformational preferences when they are ionised from different conditions. It also has the potential to offer important insight to the drug discovery field as it can measure binding stoichiometry and unveil conformational shifts of IDPs exerted by the binding of small drug-like molecules, which will affect their associated pharmacology. In the current study, we have used IM-MS to investigate the effect of drug lead EPI-001 on the intrinsically disordered N-terminal domain of the Androgen Receptor (AR-NTD). Despite structural heterogeneity rendering the NTD a challenging region of the protein to drug, this domain is responsible for most, if not all, of the transcriptional activity. We quantify the stoichiometry of EPI-001 binding to various constructs that correspond to functional domains of the AR-NTD, and show that it binds to separate constructs containing transactivation unit (TAU)-1 and TAU-5, respectively, and that 1-2 molecules bind to a larger construct containing both sequences. We also identify a conformational shift upon EPI-001 binding to the TAU-5 containing construct, and only to a much lesser extent with TAU-1. This work provides novel insight on the interactions of EPI-001 with the AR-NTD, and the structural alterations that it exerts, and positions IM-MS as an informative tool that will enhance the tractability of IDPs, potentially leading to better therapies. | Ikhlas M. M. Ahmed; Adam Rofe; Martyn C. Henry; Eric West; Craig Jamieson; Iain J. McEwan; Rebecca Beveridge | Biological and Medicinal Chemistry; Analytical Chemistry; Mass Spectrometry; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b36ace5101a2ffa8611f29/original/ion-mobility-mass-spectrometry-unveils-conformational-effects-of-drug-lead-epi-001-on-the-intrinsically-disordered-n-terminal-domain-of-the-androgen-receptor.pdf |
655cdb45dbd7c8b54bb8168c | 10.26434/chemrxiv-2023-2w1pr | The influence of carbon on polytype and growth stability of epitaxial hexagonal boron nitride films and layers | Boron nitride (BN) is a promising two-dimensional material as well as a potential wide-bandgap semiconductor. Chemical vapor deposition (CVD) is commonly used to deposit single layers or thin films of BN, but the deposition process is insufficiently understood at an atomic scale. We study the CVD of BN using two boron precursors, the organoboranes, triethylborane and trimethylborane. Using high resolution (scanning) transmission electron microscopy and electron energy loss spectroscopy we show that hexagonal-BN (h-BN) nucleates and grows epitaxially for ~4 nm before it either polytype transforms to rhombohedral-BN (r-BN), turns to less ordered turbostratic-BN or is terminated by a layer of amorphous carbon. We propose that the carbon in the organoboranes deposits on the epitaxially growing h-BN surface and this either leads to the polytype transition to r-BN, the transition to less ordered BN growth or complete surface poisoning with carbon terminating BN growth. Our results question the use of organoboranes in CVD of epitaxial BN films, and the polytype stability of h-BN growing on graphene. | Sachin Sharma; Justinas Palisaitis; Ivan Ivanov; Per Persson; Henrik Pedersen; Hans Högberg | Materials Science; Nanoscience; Nanostructured Materials - Materials; Thin Films; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655cdb45dbd7c8b54bb8168c/original/the-influence-of-carbon-on-polytype-and-growth-stability-of-epitaxial-hexagonal-boron-nitride-films-and-layers.pdf |
612c29bc66dedd895bfef0ea | 10.26434/chemrxiv-2021-pls58 | Effective Carbon Number and Inter-Class Retention Time Conversion Enhances Lipid Identifications in Untargeted Clinical Lipidomics | Chromatography is often used as a method for reducing sample complexity prior to analysis by mass spectrometry, the use of retention time (RT) is becoming increasingly popular to add valuable supporting information in lipid identification.
The RT of lipids with the same headgroup in reverse-phase separation can be predicted using the effective carbon number (ECN) model. This model describes the effect of acyl chain length and degree of saturation on lipid RT, which increases predictably with acyl chain length and degree of saturation. Furthermore, we have found a robust correlation in the chromatographic separation of lipids with different headgroups that share the same fatty acid motive. By measuring a small number of lipids from each subclass it is possible to build a model that allows for the prediction of the RT of one lipid subclass based on another.
Here, we utilise ECN modelling and inter-class retention time conversion (IC-RTC) to build a glycerophospholipid RT library with 481 entries based on 136 MS/MS characterised lipid RTs from NIST SRM-1950 plasma and lipid standards.
The library was tested on a patient cohort undergoing coronary artery bypass grafting surgery (n=37). A total of 129 unique circulating glycerophospholipids were identified, of which, 57 (4 PC, 24 PE, 4 PG, 15 PI, 10 PS) were detected with IC-RTC, thereby demonstrating the utility of this technique for the identification of lipid species not found in commercial standards.
| Jake White; Paul Trim; Thalia Salagaras; Aaron Long; Peter Psaltis; Johan Verjans; Marten Snel | Analytical Chemistry; Mass Spectrometry; Separation Science | CC BY NC 4.0 | CHEMRXIV | 2021-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612c29bc66dedd895bfef0ea/original/effective-carbon-number-and-inter-class-retention-time-conversion-enhances-lipid-identifications-in-untargeted-clinical-lipidomics.pdf |
6645445321291e5d1d618977 | 10.26434/chemrxiv-2024-w1jls | Voltage Relaxation Characterization Methods in Lithium-Ion Batteries | This study evaluated three approaches for characterizing voltage relaxation in lithium-ion batteries: voltage vs. time, the derivative of voltage vs. time, and the second derivative of voltage vs. time. The first two are well-established approaches, whereas the third was never investigated, to our knowledge. To assess the potential of each approach, characterizations were performed on data with various depth-of-discharges, regimes, SOHs, temperatures, and chemistries. Findings indicate that the established approaches do not comprehensively characterize voltage relaxation whereas the novel approach demonstrated promise in providing a quantitative feature to compare relaxation behaviors. However, limitations persisted in its application due to its reliance on heavy filtering and inability to identify trends in capacity loss, preventing widespread application. | Alexa Fernando; Matthias Kuipers; Georg Angenendt; Kai-Philip Kairies; Matthieu Dubarry | Materials Science; Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6645445321291e5d1d618977/original/voltage-relaxation-characterization-methods-in-lithium-ion-batteries.pdf |
67123ad551558a15ef6e0249 | 10.26434/chemrxiv-2024-t7dtf | Topology optimization of porous electrodes for electrochemical flow reactors using the finite element method and triply periodic minimal surfaces | Porous electrodes are ubiquitous to electrochemical technologies for energy conversion and storage, where they play a set of critical roles in the performance and cost of the systems. While progress on electrode design has been mostly driven by experimentation which is time- and resource-intensive, predictive design algorithms such as topology optimization have the potential to accelerate and guide the design of porous electrodes. By setting a performance target (e.g. maximizing electrochemical power output, reducing pumping power), the computational framework iterates mathematically over multiple electrode structures to satisfy the target, finding the optimal structure in a predictive manner. Here, we present a high-performance topology optimization framework, integrated with multi-physics computational models of transport processes, to design optimal porous electrodes in two- or three-dimensional space for use in electrochemical flow cells. We find that the algorithms computes electrode geometries that enhance the electrochemical and hydraulic performance by up to 29% and 98%, respectively. The resulting optimized designs were translated into cellular architectures using triply periodic minimal surface (TPMS) structures and fabricated using stereolithography 3D printing to demonstrate the manufacturability of the generated structures. We hope that such framework can inspire manufacturing of porous electrodes and the method can be extended to other electrochemical systems. | Mojtaba Barzegari; Antoni Forner-Cuenca | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Fluid Mechanics; Transport Phenomena (Chem. Eng.) | CC BY 4.0 | CHEMRXIV | 2024-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67123ad551558a15ef6e0249/original/topology-optimization-of-porous-electrodes-for-electrochemical-flow-reactors-using-the-finite-element-method-and-triply-periodic-minimal-surfaces.pdf |
6502d4c599918fe537ee6b4b | 10.26434/chemrxiv-2023-rd5jj | Ring-Expansion and Desulfurisation of Thiophenes with an Aluminium(I) Reagent | Reactions of thiophene, 2-methylthiophene, 2-methoxythiophene, 2,3-dimethylthiophene, and benzothiophene with the aluminium(I) complex [{(ArNCMe)2CH}Al] (Ar = 2,6-di-isopropylphenyl) are reported. In all cases, carbon–sulfur bond activation and ring-expansion of the heterocycle is observed. For thiophene, we identify a reaction network for desulfurisation that includes an unusual second carbon–sulfur bond activation step. | Jacob McMullen; Andrew White; Mark Crimmin | Inorganic Chemistry; Organometallic Chemistry; Bond Activation; Main Group Chemistry (Organomet.); Reaction (Organomet.) | CC BY 4.0 | CHEMRXIV | 2023-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6502d4c599918fe537ee6b4b/original/ring-expansion-and-desulfurisation-of-thiophenes-with-an-aluminium-i-reagent.pdf |
664f5f1791aefa6ce1cedf60 | 10.26434/chemrxiv-2024-0qlff | Hydrazine-Catalyzed Ring-Opening Metathesis Polymerization of Cyclobutenes | Materials formed by the ring-opening metathesis polymerization (ROMP) of cyclic olefins are highly valued for industrial and academic applications but are difficult to prepare free of metal contaminants. Here we describe a highly efficient metal-free ROMP of cyclobutenes using hydrazine catalysis. Reactions can be initiated via in situ condensation of a [2.2.2]-bicyclic hydrazine catalyst with an aliphatic or aromatic aldehyde initiator. The polymerizations show living characteristics, achieving excellent control over molecular weight, low dispersity values, and high chain-end fidelity. Additionally, the hydrazine can be used in substoichiometric amounts relative to the aldehyde chain-end while maintaining good control over molecular weight and low dispersity values, indicating that a highly efficient chain transfer mechanism is occurring. | Julian Kellner-Rogers; Jesse Hsu; Ivan Keresztes; Brett Fors; Tristan Lambert | Organic Chemistry; Catalysis; Polymer Science; Organic Synthesis and Reactions; Polymerization (Polymers); Organocatalysis | CC BY 4.0 | CHEMRXIV | 2024-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664f5f1791aefa6ce1cedf60/original/hydrazine-catalyzed-ring-opening-metathesis-polymerization-of-cyclobutenes.pdf |
65a5f2b366c138172989ec34 | 10.26434/chemrxiv-2024-z5sr4 | Revisiting the Reactivity of the Dismissed Hydrogen Atom Transfer Catalyst Succinimide-N-oxyl | Phthalimide-N-oxyl (PINO) and related radicals are promising catalysts for C-H functionalization reactions. To date, only a small number of N-oxyl derivatives have demonstrated improved activities over PINO. We postulate that the lack of success in identifying superior catalysts is associated not only with challenges in the design and synthesis of new structures, but also the way catalysts are evaluated and utilized. Catalyst evaluation typically relies on the use of chemical oxidants to generate N-oxyl radicals from their parent N-hydroxy compounds. We put forth an example where a potential-controlled electrochemical analy-sis reveals that succinimide-N-oxyl (SINO) compares favorably to PINO as a hydrogen atom transfer catalyst – in contrast to previous claims based on other approaches. Furthermore, our efforts to understand the basis for the greater reactivity of SINO relative to PINO have shed further light on the interplay of thermodynamic and kinetic factors in these HAT reactions and sug-gest that transition state (TS) polarization is a particularly important consideration. This is illustrated by the essentially identi-cal reactivity of tetrachloro-PINO and SINO despite the significantly greater thermodynamic driving force in the reactions of the latter. Such measures of HAT TS polarization (i.e., proton affinity of the N-oxide anion) may be useful parameters in pre-dicting and/or rationalizing reactivity in addition to reaction energetics (i.e., O-H bond dissociation enthalpy of the N-OH moie-ty). Building on these insights, we report the design and initial characterization of a chlorinated SINO derivative that has signif-icantly greater reactivity as a HAT catalyst than either PINO or its chlorinated derivative. | Cheng Yang; Luke Farmer; Derek Pratt; Stephen Maldonado; Corey Stephenson | Organic Chemistry; Catalysis; Electrocatalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a5f2b366c138172989ec34/original/revisiting-the-reactivity-of-the-dismissed-hydrogen-atom-transfer-catalyst-succinimide-n-oxyl.pdf |
636284efca86b8f5dccdbfce | 10.26434/chemrxiv-2022-4nq1v | Synthesis of homo-metallic heavier analogues of cyclobutene and the cyclobutadiene dianion | The reduction of the boryl-substituted SnII bromide {(HCDippN)2B}Sn(IPrMe)Br with 1.5 equivalents of potassium graphite leads to the generation of the cyclic tetratin tetraboryl system K2[Sn4{B(NDippCH)2}4], a homo-metallic heavier analogue of the cyclobutadiene dianion. This system is non-aromatic as determined by Nucleus Independent Chemical Shift Calculations (NICS(0) = −0.28, NICS(1) = −3.17), with the primary contributing resonance structures shown by Natural Resonance Theory (NRT) to involve a Sn=Sn double bond and 1,2-localized negative charges. Abstraction of the K+ cations or oxidation lead to contraction or cleavage of the Sn4 unit, respectively, while protonation generates the neutral dihydride cis-1,2-Sn4{B(NDippCH)2}4H2 (a heavier homologue of cyclobutene) in a manner consistent with the predicted charge distribution in the [Sn4{B(NDippCH)2}4]2- dianion. | Xiongfei Zheng; Agamemnon Crumpton; Andrey Protchenko; Mathias Ellwanger; Andreas Heilmann; Simon Aldridge | Inorganic Chemistry; Bonding; Main Group Chemistry (Inorg.); Theory - Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636284efca86b8f5dccdbfce/original/synthesis-of-homo-metallic-heavier-analogues-of-cyclobutene-and-the-cyclobutadiene-dianion.pdf |
60c75629ee301cf7f8c7b2ca | 10.26434/chemrxiv.14199884.v1 | A New Library-Search Algorithm for Mixture Analysis Using DART-MS | This manuscript introduces a new library-search algorithm for identifying components of a mixture using in-source collision-induced dissociation (is-CID) mass spectra. The two-stage search, titled the Inverted Library-Search Algorithm (ILSA), identifies potential components in a mixture by first searching its low fragmentation mass spectrum for target peaks, assuming these peaks are protonated molecules, and then scoring each target peak with possible library matches using one of two schemes. Utility of the ILSA is demonstrated through several example searches of model mixtures of acetyl fentanyl, benzyl fentanyl, amphetamine and methamphetamine searched against a small library of select compounds and the NIST DART-MS Forensics library. Discussion of the search results and several open areas of research to further extend the method are provided. A prototype implementation of the ILSA is available at <a href="https://github.com/asm3-nist/DART-MS-DST">https://github.com/asm3-nist/DART-MS-DST</a>. | Arun Moorthy; Edward Sisco | Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75629ee301cf7f8c7b2ca/original/a-new-library-search-algorithm-for-mixture-analysis-using-dart-ms.pdf |
60f5e29f40c8bd258d972b34 | 10.26434/chemrxiv-2021-rwr0w | Machine Learning-Guided Discovery of 19F MRI Agents Enabled by Automated Copolymer Synthesis | Modern polymer science is plagued by the curse of multidimensionality; the large chemical space imposed by including combinations of monomers into a statistical copolymer overwhelms polymer synthesis and characterization technology and limits the ability to systematically study structure–property relationships. To tackle this challenge in the context of 19F MRI agents, we pursued a computer-guided materials discovery approach that combines synergistic innovations in automated flow synthesis and machine learning (ML) method development. A software controlled, continuous polymer synthesis platform was developed to enable iterative experimental–computational cycles that resulted in the synthesis of 397 unique copolymer compositions within a six-variable compositional space. The non-intuitive design criteria identified by ML, which was accomplished by exploring less than 0.9% of overall compositional space, upended conventional wisdom in the design of 19F MRI agents and lead to the identification of >10 copolymer compositions that outperformed state-of-the-art materials. | Marcus Reis; Filipp Gusev; Nicolas Taylor; Sang Hun Chung; Matthew Verber; Yueh Lee; Olexandr Isayev; Frank Leibfarth | Theoretical and Computational Chemistry; Polymer Science; Polymerization (Polymers); Machine Learning; Artificial Intelligence | CC BY NC 4.0 | CHEMRXIV | 2021-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f5e29f40c8bd258d972b34/original/machine-learning-guided-discovery-of-19f-mri-agents-enabled-by-automated-copolymer-synthesis.pdf |
63fbb74532cd591f12837824 | 10.26434/chemrxiv-2023-hcls5 | Replacing the BO in BODIPY: Unlocking the Path to SBIDIPY and BIDIPY Chromophores | Boron-based dipyrrin chromophores (BODIPY) have found widespread application over the last twenty years in fields as diverse as medicine and materials. Thus, several efforts have been placed to exchange boron with other elements, with the aim of developing materials with complementary luminescence properties. However, despite the attempts, the incorporation of other main-group elements in dipyrrin scaffolds remains still rare. We have successfully synthesized and characterized novel chromophores based on heavy pnictogens antimony and bismuth, SBIDIPY and BIDIPY. Solution stabilities have been investigated by VT-UV/Vis spectroscopy and the fluorescence emission studied and supported by computational analysis. We were also able to isolate for the first direct analog of BODIPY containing fluoride handles, which featured a strong intensity of fluorescence emission. | André Korzun; Stefano Crespi; Christopher Golz; Alessandro Bismuto | Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Inorg.); Main Group Chemistry (Inorg.); Main Group Chemistry (Organomet.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63fbb74532cd591f12837824/original/replacing-the-bo-in-bodipy-unlocking-the-path-to-sbidipy-and-bidipy-chromophores.pdf |
633466e92984c90f81702c35 | 10.26434/chemrxiv-2022-f8l14 | Surfactant-free colloidal syntheses of precious metal nanoparticles for improved catalysts
| Colloidal syntheses of nanomaterials offer multiple benefits to study, understand and optimize un-supported and supported catalysts. In particular, colloidal syntheses are relevant to synthetize (precious) metal nanoparticles. By separating the synthesis of the active phase nanoparticles from supporting steps, a deeper knowledge and a rational control on supported catalyst properties is gained. The effect of nanoparticle size, shape, composition, nature of support or metal loading on a support can be studied in more systematic ways. The fundamental knowledge gained paves the way for catalyst optimization by tuning the catalyst activity, selectivity, and stability. However, a major drawback is that most colloidal syntheses require the use of additives or surfactants, which are detrimental to most catalytic reactions since they typically block catalyst active sites. Surfactant removal typically adds complexity, can introduce a lack of reproducibility, is energy consuming, generates waste, and prevents the full exploitation of the many benefits of colloidal syntheses for catalysis. Several surfactant-free strategies to obtain stable colloidal nanoparticles are here reviewed. A focus is given to laser synthesis and processing of colloids (LSPC), solution plasma process (SPP), N,N-dimethylformamide (DMF), polyols, and recently reported mono-alcohols based syntheses. The relevance of these synthetic approaches for catalysis is detailed with a focus on heterogeneous catalysis and electro-catalysis. | Jonathan Quinson; Sebastian Kunz; Matthias Arenz | Catalysis; Nanoscience; Chemical Engineering and Industrial Chemistry; Nanocatalysis - Catalysts & Materials; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633466e92984c90f81702c35/original/surfactant-free-colloidal-syntheses-of-precious-metal-nanoparticles-for-improved-catalysts.pdf |
667972d45101a2ffa8636fb3 | 10.26434/chemrxiv-2024-cwphv | Dual Reactivity Mode of Vinyl Ethylene Carbonates with Anilines: A Catalyst-Controlled Chemodivergent Entry to N-Heterocycles and the Observation of Unusual Competing Pathways | A unique catalyst-controlled chemodivergent strategy to access 2-vinyl indolines and indole-2-acetates by overcoming the usual allylic reactivity of vinyl ethylene carbonates (VECs) via a tandem C-H/C-O bond activation sequence is disclosed herein. This methodology provides useful molecular scaffolds by following two distinct pathways in a highly step- and atom-economical manner. The pathway features a challenging beta-hydroxide elimination and in the Rh-catalyzed transformation, we have observed unusual competing pathways such as an oxidative insertion of MeOH into Rh(III) to give a putative Rh(V)-H intermediate. Mechanistic insights unveil a new reactivity mode of vinyl ethylene carbonates and open a new avenue for divergent catalysis. Post synthetic modification of the annulated products add additional advantage to the methodology. | Santosh Kumar Keshri; Manmohan Kapur | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Bond Activation; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667972d45101a2ffa8636fb3/original/dual-reactivity-mode-of-vinyl-ethylene-carbonates-with-anilines-a-catalyst-controlled-chemodivergent-entry-to-n-heterocycles-and-the-observation-of-unusual-competing-pathways.pdf |
65176ae9a69febde9ef2afc2 | 10.26434/chemrxiv-2023-mlmwv-v2 | The role of dynamics in heterogeneous catalysis: surface diffusivity and N2 decomposition on Fe(111) | The cleavage of the N2 triple bond on the Fe(111) surface is believed to be the rate limiting step of the famed Haber-Bosch ammonia catalysis. Using a combination of machine learning potentials and advanced simulation techniques, we study this important catalytic step as a function of temperature. We find that at low temperatures our results agree with the well-established picture. However, if we increase the temperature to reach operando conditions the surface undergoes a global dynamical change and the step structure of the Fe(111) surface is destroyed. The catalytic sites, traditionally associated with the Fe(111) surface appear and disappear continuously. Our simulations illuminate the danger of extrapolating low-temperature results to operando conditions and indicate that the catalytic activity can only be inferred from calculations that take dynamics fully into account. More than that, they show that it is the transition to this highly fluctuating interfacial environment that drives the catalytic process. | Luigi Bonati; Daniela Polino; Cristina Pizzolitto; Pierdomenico Biasi; Rene Eckert; Stephan Reitmeier; Robert Schlögl; Michele Parrinello | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Machine Learning; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65176ae9a69febde9ef2afc2/original/the-role-of-dynamics-in-heterogeneous-catalysis-surface-diffusivity-and-n2-decomposition-on-fe-111.pdf |
63dbffeca8f79476ca624f75 | 10.26434/chemrxiv-2022-0pv2d-v2 | Open-Source Chromatographic Data Analysis for Reaction Optimization and Screening | Automation and digitalization solutions in the field of small molecule synthesis face new challenges for chemical reaction analysis, especially in the field of high-performance liquid chromatography (HPLC). Chromatographic data remains locked in vendors hardware and software components, limiting their potential in automated workflows and data science applications. In this work, we present an open-source Python project called MOCCA for the analysis of HPLC-DAD (photodiode array detector) raw data. MOCCA provides a comprehensive set of data analysis features, including an automated peak deconvolution routine of known signals, even if overlapped with signals of unexpected impurities or side products. We highlight the broad applicability of MOCCA in four studies: (i) a simulation study to validate MOCCAs data analysis features; (ii) a reaction kinetics study on a Knoevenagel condensation reaction demonstrating MOCCAs peak deconvolution feature; (iii) a closed-loop optimization study for the alkylation of 2-pyridone without human control during data analysis; (iv) a well plate screening of categorical reaction parameters for a novel palladium-catalyzed cyanation of aryl halides employing O-protected cyanohydrins. By publishing MOCCA as a Python package with this work, we envision an open-source community project for chromatographic data analysis with the potential of further advancing its scope and capabilities. | Christian P. Haas; Maximilian Lübbesmeyer; Edward H. Jin; Matthew A. McDonald; Brent A. Koscher; Nicolas Guimond; Laura Di Rocco; Henning Kayser; Samuel Leweke; Sebastian Niedenführ; Rachel Nicholls; Emily Greeves; David M. Barber; Julius Hillenbrand; Giulio Volpin; Klavs F. Jensen | Organic Chemistry; Analytical Chemistry; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Analytical Chemistry - General; Chemoinformatics | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63dbffeca8f79476ca624f75/original/open-source-chromatographic-data-analysis-for-reaction-optimization-and-screening.pdf |
650894e4b6ab98a41caefad2 | 10.26434/chemrxiv-2023-kb74z | Catalytic Behavior of K-doped Fe/MgO Catalysts for Ammonia Synthesis Under Mild Reaction Conditions | An important part of realizing a carbon-neutral society using ammonia will be the development of an inexpensive yet efficient catalyst for ammonia synthesis under mild reaction conditions (<400 °C, <10 MPa). Here, we report Fe/K(3)/MgO, fabricated via an impregnation method, as a highly active catalyst for ammonia synthesis under mild reaction conditions (350 °C, 1.0 MPa). At the mentioned conditions, the activity of Fe/K(3)/MgO (17.5 mmol h−1 gcat−1) was greater than that of a commercial fused iron catalyst (8.6 mmol h−1 gcat−1) currently used in the Haber–Bosch process. K doping was found to increase the dispersion and turnover frequency of Fe in our Fe/K(3)/MgO catalyst. In addition, increasing the pressure to 3.0 MPa at the same temperature led to a significant improvement of the ammonia synthesis rate to 29.6 mmol h−1 gcat−1, which was much higher than that of two more expensive, benchmark Ru-based catalysts, which are also potential alternative catalysts. A kinetics analysis revealed that the addition of K dramatically enhanced the ammonia synthesis activity at ≥300 °C by changing the main adsorbed species from NH to N which can significantly accelerate dissociative adsorption of nitrogen as the rate limiting step in ammonia synthesis. | Kohei Era; Katsutoshi Sato; Shin-ichiro Miyahara; Takahiro Naito; Kanishka De Silva; Saeid Akrami; Hiroshi Yamada; Takaaki Toriyama; Tomokazu Yamamoto; Yasukazu Murakami; Ken-ichi Aika; Koji Inazu; Katsutoshi Nagaoka | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650894e4b6ab98a41caefad2/original/catalytic-behavior-of-k-doped-fe-mg-o-catalysts-for-ammonia-synthesis-under-mild-reaction-conditions.pdf |
629b1d4d82f9564eeacfff5b | 10.26434/chemrxiv-2022-f9ms2 | Tuning Selectivity in the Direct Conversion of Methane to Methanol: Bimetallic Synergistic Effects on the Cleavage of C-H and O-H Bonds over NiCu/CeO2 Catalysts | The efficient activation of methane and simultaneous water dissociation are crucial in many catalytic reactions on oxide-supported transition metal catalysts. On very low-loaded Ni/CeO2 surfaces, methane easily fully decomposes, CH4 -> C + 4H, and water dissociates, H2O-> OH + H. However, in important reactions such as the direct oxidation of methane to methanol (MTM), where complex interplay exists between reactants (CH4, O2), it is desirable to avoid the complete dehydrogenation of methane to carbon. Remarkably, the barrier for the activation of CH bonds in CHx (x= 1-3) species on Ni/CeO2 surfaces can be manipulated by adding Cu, forming bimetallic NiCu clusters, whereas the ease for cleavage of OH bonds in water, is not affected by ensemble effects, as obtained from density functional theory-based calculations. CH4 activation occurs only on Ni sites and H2O activation on both Ni and Cu sites. The MTM reaction pathway for the example of the Ni3Cu1/CeO2 model catalyst predict higher selectivity and a lower activation barrier for methanol production, compared with that for Ni4-CeO2. These findings point toward a possible strategy to design active and stable catalysts which can be employed for methane activation and conversions. | Pablo G. Lustemberg; Sanjaya D. Senanayake; José A. Rodriguez; M. Verónica Ganduglia-Pirovano | Theoretical and Computational Chemistry; Catalysis; Theory - Computational; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629b1d4d82f9564eeacfff5b/original/tuning-selectivity-in-the-direct-conversion-of-methane-to-methanol-bimetallic-synergistic-effects-on-the-cleavage-of-c-h-and-o-h-bonds-over-ni-cu-ce-o2-catalysts.pdf |
60c73d47469df47cd0f42692 | 10.26434/chemrxiv.5525572.v1 | Understanding and Breaking Scaling Relations in Single-Site Catalysis: Methane-to-methanol Conversion by Fe(IV)=O | <p>Computational high-throughput
screening is an essential tool for catalyst design, limited primarily by the
efficiency with which accurate predictions can be made. In bulk heterogeneous
catalysis, linear free energy relationships (LFERs)
have been extensively developed to relate elementary step activation energies,
and thus overall catalytic activity, back to the adsorption energies of key intermediates,
dramatically reducing the computational cost of screening. The applicability of
these LFERs to single-site catalysts remains unclear, owing to the directional,
covalent metal-ligand bonds and the broader chemical space of accessible ligand
scaffolds. Through a computational screen of nearly 500 model Fe(II) complexes
for CH<sub>4</sub> hydroxylation, we observe that 1) tuning ligand field
strength yields LFERs by comparably shifting energetics of the metal 3<i>d</i> levels that govern stability of
different intermediates and 2) distortion of the metal coordination geometry breaks
these LFERs by increasing the splitting between the <i>d</i><sub>xz</sub>/<i>d</i><sub>yz</sub>
and <i>d</i><sub>z</sub><sup>2</sup> metal states
that govern reactivity. Thus, in single site catalysts, low Brønsted-Evans-Polanyi
slopes for oxo formation, which would limit peak turnover frequency achievable
through ligand field tuning alone, can be overcome through structural
distortions achievable in experimentally characterized compounds. Observations
from this screen also motivate the placement of strong HB donors in
targeted positions as a scaffold-agnostic strategy for further activity
improvement. More generally, our findings motivate broader variation of
coordination geometries in reactivity studies with single-site catalysts.</p> | Terry Gani; Heather Janine Kulik | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2017-10-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d47469df47cd0f42692/original/understanding-and-breaking-scaling-relations-in-single-site-catalysis-methane-to-methanol-conversion-by-fe-iv-o.pdf |
60c75655f96a0008fb288a94 | 10.26434/chemrxiv.14229413.v1 | Animal Species Identification of Meat Using MALDI-TOF Mass Spectrometry | <p>We describe the animal species identification of meat using MALDI-TOF
mass spectroscopy including the development and validation of a reliable
method, qualified for use in the accredited official food-control laboratory.</p>
<p>Previous publications had shown the potential of MALDI-TOF MS for animal
species differentiation of several kind of food, including meat. Our aim was to
establish a rapid and reliable method by means of a simplified sample
preparation without prior tryptic digest, an existing popular MALDI system, an
independent extensive reference database, and an adequate validation concept.
In contrast to the previous works, we consequently use the MALDI user platform
“MALDI-UP” to give other food control laboratories the possibility of
exchanging reference and validation spectra.<br /></p> | Jörg Rau; Ekkehard Hiller; Annegret Männig; Martin Dyk; Olivera Wenninger; Philipp Stoll; Gudrun Wibbelt; Pat Schreiter | Mass Spectrometry; Food | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75655f96a0008fb288a94/original/animal-species-identification-of-meat-using-maldi-tof-mass-spectrometry.pdf |
6331df3c08470075068a62b0 | 10.26434/chemrxiv-2022-3tjl1 | A Four-Step Biocatalytic and Organocatalytic Cascade for Single-Flask Production of Dinitroalkanes from Alcohols in Aqueous Buffer | Dinitroalkanes are powerful synthetic building blocks because of the versatility of the 1,3-dinitro motif. Here, we show that dinitroalkanes can be synthesized from alcohol substrates using a combination of biocatalysis and organocatalysis in a single-flask process. Alcohol oxidase oxidizes alcohol substrates to an intermediate aldehyde, which is sequentially converted to a nitroalcohol, then a nitroalkene, and finally, to a 1,3-dinitroalkane with a combination of phosphate buffer and lysine catalysis. Simultaneous addition of all reagents gives a maximal yield of 52%, whereas staggering the introduction of the amino acid catalyst and nitromethane substrate boosts the yield to 71% with near-quantitative conversion. Taken together, this work shows that biocatalysed oxidation can be coupled to multi-step catalytic cascades to expand the types of products available from bioprocesses. | Kelsey N. Stewart; Kendyll G. Hawkins; Dylan W. Domaille | Organic Chemistry; Catalysis; Biocatalysis; Organocatalysis | CC BY NC 4.0 | CHEMRXIV | 2022-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6331df3c08470075068a62b0/original/a-four-step-biocatalytic-and-organocatalytic-cascade-for-single-flask-production-of-dinitroalkanes-from-alcohols-in-aqueous-buffer.pdf |
60c742a8702a9bd64218a4b2 | 10.26434/chemrxiv.8323406.v1 | Photochemical Strain-Release Driven Cyclobutylation of C(sp3)-Centered Radicals | Our manuscript describes a photoredox-catalyzed decarboxylative radical addition approach to functionalized cyclobutanes. The reaction involves an unprecedented formal Giese-type addition of C(<i>sp</i><sup>3</sup>)-centered radicals to highly strained bicyclo[1.1.0]butanes. The mild photoredox conditions, which make use of a readily available and bench stable phenyl sulfonyl bicyclo[1.1.0]butane, proved to be amenable to a diverse range of α-amino and α-oxy carboxylic acids, providing a concise access to 1,3-disubstituted cyclobutanes. Furthermore, kinetic studies and DFT calculations unveiled mechanistic details on bicyclo[1.1.0]butane reactivity relative to the corresponding olefin system. | Guillaume Ernouf; Egor Chirkin; Lydia Rhyman; Ponnadurai Ramasami; Jean-Christophe Cintrat | Photochemistry (Org.); Theory - Computational; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742a8702a9bd64218a4b2/original/photochemical-strain-release-driven-cyclobutylation-of-c-sp3-centered-radicals.pdf |
60c74f410f50dbc28b397388 | 10.26434/chemrxiv.12871571.v1 | A Double Bond with Weak σ- and Strong π-Interactions Is Still a Double Bond | A critical analysis of single π-Interactions | Cina Foroutan-Nejad | Bonding; Coordination Chemistry (Inorg.); Theory - Inorganic; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f410f50dbc28b397388/original/a-double-bond-with-weak-and-strong-interactions-is-still-a-double-bond.pdf |
611ceb125322c1fe13045523 | 10.26434/chemrxiv-2021-dvkpb | Multi-Wavelength Photopolymerization of Stable Poly(Catecholamines)-DNA Origami Nanostructures | Orthogonality is pivotal yet chemically challenging in the bottom-up synthesis of multicomponent nanostructures. Here, we leverage the fidelity of the DNA origami technique to install a multi wavelength responsive photopolymerization system with nanometer resolution. By precisely immobilizing various photosensitizers on the origami template, which are only activated at their respective peak wavelength, we can control sequential polymerization processes. In particular, the triggered photosensitizers generate reactive oxygen species that in turn initiate the polymerization of the catecholamines dopamine and norepinephrine. We imprint polymeric layers at designated positions on DNA origami, which modifies the polyanionic nature of the DNA objects, thus, promoting their uptake into living cells while preserving their integrity. Our herein proposed methodology provides a rapid platform to access complex 3D nanostructures by customizing material and biological interfaces. | Pia Winterwerber; Colette J. Whitfield; David Y. W. Ng; Tanja Weil | Materials Science; Nanoscience; Biological Materials; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611ceb125322c1fe13045523/original/multi-wavelength-photopolymerization-of-stable-poly-catecholamines-dna-origami-nanostructures.pdf |
63a216b2dadddcb60195aecf | 10.26434/chemrxiv-2022-btz77 | Graph neural networks and molecular docking as two complementary approaches for virtual screening: a case study on Cruzain | The idea behind virtual screening is to first test compounds computationally in order to reduce the number of compounds that need to be screened experimentally, thus reducing the time and cost of physical experiments. Molecular docking is the most popular virtual screening technique, it predicts the binding of candidate compounds to the protein target by modeling the interactions at the binding pocket. Despite being widely used, docking accuracy is often low due to the difficulty of modeling inherently complex biological systems. On the other hand, state of the art deep neural networks, like Graph Convolutional Networks (GCNs) are able to capture the complex non-linear relationships between structural and biological data, but they lack the interpretability of structure-based modeling. In this work we took advantage of the activity data from a quantitative High Throughput Screen (HTS) of ~200K compounds against Cruzain (Cz) to retrospectively evaluate the ability of a docking algorithm and a Graph Convolutional Network for prioritizing the active compounds from the dataset. We then propose strategies to combine both techniques in a single virtual screening pipeline in order to exploit their orthogonal benefits. By plugging in the atomic embeddings learned by the GCN into the docking algorithm by means of pharmacophoric restraints, docking ability to retrieve the active ligands was enhanced. Moreover, by applying the GCN as a pre-docking filter, the compound’s library was enriched in active molecules and subsequent docking of the filtered library achieved significantly higher hit rates. This work aims to be a proof of concept of the usefulness of combination strategies involving deep learning and classical molecular docking techniques, in the context of drug discovery.
| Adriano Martin Luchi; José Leonardo Gomez Chávez ; Roxana Noelia Villafañe; Germán Andrés Conti ; Ernesto Rafael Pérez; Emilio Angelina; Nélida María Peruchena | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a216b2dadddcb60195aecf/original/graph-neural-networks-and-molecular-docking-as-two-complementary-approaches-for-virtual-screening-a-case-study-on-cruzain.pdf |
6292d372eac79aabfe9e07b4 | 10.26434/chemrxiv-2021-q4375-v3 | Pushing steric limits in osmium(IV) tetraaryl complexes | Investigations into the reactivity, properties, and applications of osmium(IV) tetraaryl complexes have been hampered by their low yielding syntheses from volatile and toxic OsO4 (typically ≤34%). Here we show that known air-stable M(aryl)4 compounds (M = Os, Ru; aryl = 2-tolyl, 2,5-xylyl) can be prepared in ≤73% yields using new, less hazardous (Oct4N)2[MX6] precursors (M = Os, Ru; X = Cl, Br). This approach also facilitates the preparation of Os(mesityl)4 (Os3) for the first time, a complex comprising bulky 2,6-dimethyl substituted aryl ligands, albeit in low yield (5%). To better understand these yield extremes, we track, by synthesizing two additional new complexes with different 2-substituted σ-aryl ligands, a clear relationship between the yields of Os(aryl)4 and ligand steric bulk. Single-crystal X-ray structures of these compounds indicate that the observed yield trend reflects the ease of accommodating aryl substituents into an open pocket that lies directly opposite each M-aryl coordination site. We perform variable-temperature 1H NMR studies of Os3, utilize a "tetrahedricity" metric to assess geometric distortion in Ru(aryl)4 and Os(aryl)4 materials, and calculate cone angle and percentage buried volume metrics to further illustrate and help quantify 𝜎-aryl ligand steric properties. Solution cyclic voltammograms of Os(aryl)4 show that the potentials of their reversible 1−/0 and 0/1+ redox features can be fine-tuned by varying aryl substituents, and that Os3 exhibits an additional 1+/2+ redox event not previously observed in this class of compounds. Taken together, this work helps to advance the potential application of these relatively underexplored organometallic complexes in established and emerging areas of molecular materials science, such as extended molecular frameworks and self-assembled monolayers, where analogous tetraphenylmethane and silane species (M = C, Si) have been frequently targeted. | Joseph Parr; Clarissa Olivar; Thomas Saal; Ralf Haiges; Michael Inkpen | Inorganic Chemistry; Organometallic Chemistry; Organometallic Compounds; Electrochemistry - Organometallic; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6292d372eac79aabfe9e07b4/original/pushing-steric-limits-in-osmium-iv-tetraaryl-complexes.pdf |
60c75085f96a00c20c287e64 | 10.26434/chemrxiv.12925550.v2 | Themis: A Software to Assess Association Free Energies via Direct Estimative of Partition Functions | <div>We present the program <i>Themis</i> - a computer implementation of a standard statistical mechanics framework to compute free energies, average energies and entropic contributions for association processes of two atom-based structures. The partition functions are computed analytically using a discrete grid in the phase space, whose size and degree of coarseness can be controlled to allow efficient calculations and to achieve the desired level of accuracy. With this strategy, applications ranging from molecular recognition, chiral discrimination, surface adsorption and even the interactions involving molecules in electronic excited states can be handled.</div> | Felippe Colombari; Asdrubal Lozada-Blanco; Kalil Bernardino; Weverson Gomes; André Farias de Moura | Computational Chemistry and Modeling; Theory - Computational; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75085f96a00c20c287e64/original/themis-a-software-to-assess-association-free-energies-via-direct-estimative-of-partition-functions.pdf |
60c74870ee301c9d76c7987e | 10.26434/chemrxiv.11845584.v2 | Complex Relationship Between Signal Intensity Properties in Magnetic Particle Imaging (MPI) and Iron Oxide Nanoparticle Degradation | Magnetic particle imaging (MPI) is an exciting new biomedical imaging technology that uses superparamagnetic nanoparticles as an imaging tracer. MPI is touted as a quantitative imaging modality but MPI signal properties have never been characterized for nanoparticles undergoing biodegradation. Here we characterize the nature of the MPI signal properties as a function of degradation of various magnetic particle formulations. We show that MPI signal properties can increase or decrease as a function of nanoparticle formulation and chemical environment and that long-term in vitro experiments only roughly approximate long-term in vivo MPI signal properties. Data are supported by electron microscopy of nanoparticle degradation. Knowledge of MPI signal property changes during nanoparticle degradation will be critical in design and interpretation of all MPI experiments. Further, we demonstrate for the first time, an environmentally sensitive MPI contrast mechanism opening the door to smart contrast paradigms in MPI.<br /> | Julia Guzy; Shatadru Chakravarty; Foster Buchanan; Haoran Chen; Jeffrey M. Gaudet; Jeremy Hix; Christiane L. Mallett; Erik Shapiro | Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74870ee301c9d76c7987e/original/complex-relationship-between-signal-intensity-properties-in-magnetic-particle-imaging-mpi-and-iron-oxide-nanoparticle-degradation.pdf |
675d52617be152b1d0f2eeab | 10.26434/chemrxiv-2024-947bt | Exploring MII-CDI Adducts: 1,3 H-Shift, N(I) Compounds and Guanidinate-Type Ligands | In this study, we report our recent findings on the synthesis and reactivity of a novel 1,2,3-triazolin-5-imine type mesoionic imine-carbodiimide (MII-CDI) adduct. Unlike reported reactions of N-heterocyclic imines (NHI) with CDI, these zwitterionic compounds undergo a spontaneous 1,3 H-shift, resulting in guanidine-type compounds. The MII-CDI adduct serves as a valuable synthon for the synthesis of mesoionic carbene-acyclic diamino carbene (MIC-ADC)-based nitreone (N(I)) compounds. We have conducted a detailed investigation into the electronic properties, chemical reactivity, and electrochemical behaviour of this nitreone (N(I)). Additionally, the potential of these MII-CDI adducts as guanidinate ligands is explored. Our investigations here display the distinct reactivities of MII in contrast to their NHI congeners. | Alok Mahata; Richard Rudolph; Robert R. M. Walter; Nicolas Neuman; Biprajit Sarkar | Organic Chemistry; Inorganic Chemistry; Organometallic Chemistry; Organometallic Compounds; Ligands (Organomet.); Main Group Chemistry (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2024-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675d52617be152b1d0f2eeab/original/exploring-mii-cdi-adducts-1-3-h-shift-n-i-compounds-and-guanidinate-type-ligands.pdf |
60c749d94c89191550ad3135 | 10.26434/chemrxiv.12116136.v1 | Generating Ampicillin-Level Antimicrobial Peptides with Activity-Aware Generative Adversarial Networks | <p>Antimicrobial peptides are a potential solution to the threat of multidrug-resistant bacterial pathogens. Recently, deep generative models including generative adversarial networks (GANs) have been shown to be capable of designing new antimicrobial peptides. Intuitively, a GAN controls the probability distribution of generated sequences to cover active peptides as much as possible. This paper presents a peptide-specialized model called PepGAN that takes the balance between covering active peptides and</p><p>dodging non-active peptides. As a result, PepGAN has superior statistical fidelity with respect to physicochemical descriptors including charge, hydrophobicity and weight. Top six peptides were synthesized and one of them was confirmed to be highly antimicrobial. The minimum inhibitory concentration was 3.1μg/mL, indicating that the peptide is twice as strong as ampicillin.</p> | Andrejs Tucs; Duy Phuoc Tran; Akiko Yumoto; Yoshihiro Ito; Takanori Uzawa; Koji Tsuda | Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749d94c89191550ad3135/original/generating-ampicillin-level-antimicrobial-peptides-with-activity-aware-generative-adversarial-networks.pdf |
65e1d28fe9ebbb4db9a79a29 | 10.26434/chemrxiv-2024-26354 | Suppression of Salt Precipitation in Membrane Electrode Assembly Electrolyzers for CO2 reduction reactions by Intermittent Supply of Alkali Metal Cations | The electrolysis of CO2 into value-added products holds great potential for closing the carbon cycle. A membrane electrode assembly (MEA) that uses solid polymer electrolytes is a critical technology for enhancing the energy efficiency for the CO2 reduction reaction (CO2RR) because a thin electrolyte layer can effectively reduce the ohmic resistance. The stable operation of the CO2RR in MEA-based cells with an anion-exchange membrane (AEM), however, is hindered by the accumulation of bicarbonate salts, which are derived from alkali-metal cations in anolytes, on the cathode side. Therefore, for stable operation of CO2 electrolysis using an MEA-based cell, the amount of alkali-metal cations needs to be reduced. However, the minimal amount of alkali-metal cations required to operate the reaction system has not been elucidated. Quantitative analysis of the amount of alkali-metal cations transported from the anode to the cathode is essential to obtain the insight into the necessary amount for the operation. In this study, we conducted a quantitative evaluation of the correlation between the production of high-value C2+ compounds, such as ethylene and ethanol, and the transported alkali-metal cations. As a result, although the presence of transported alkali-metal cations on the cathode surface significantly contributes to the generation of C2+ compounds, the rate of K+ ion transport did not match the selectivity of C2+. This result suggests a continuous supply of high amount of K+ to the cathode surface is not required for C2+ formation. On the basis of these findings, we achieved a faradaic efficiency (FE) and a partial current density for C2+ of 77% and 230 mA cm−2, respectively, even after switching the anode solution from 0.1 M KHCO3 to a dilute K+ solution (<7 mM) in an MEA-based cell using AEM and Cu nanoparticles as the cathode catalyst. These values of FE and partial current density were almost identical to those when 0.1 M KHCO3 was continuously supplied as the anode solution. Based on this insight, we successfully improved the durability of the system against salt precipitation. The FE for ethylene remained constant for as long as 60 h at 150 mA cm−2 when continuously flowing 0.1 M KHCO3 as anolyte. However, the FE suddenly decreased after 60 h due to the cessation of CO2 gas flow, caused by salt precipitation in the cathode flow channel. On the contrary, by intermittently supplying 0.1 M KHCO3, we confirmed that the amount of visible K+ salt in the cathode flow field remained negligible even after more than 90 hours of stable operation. | Shintaro Kato; Shotaro Ito; Shoko Nakahata; Ryo Kurihara; Takashi Harada; Shuji Nakanishi; Kazuhide Kamiya | Physical Chemistry; Energy; Fuels - Energy Science; Electrochemistry - Mechanisms, Theory & Study; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e1d28fe9ebbb4db9a79a29/original/suppression-of-salt-precipitation-in-membrane-electrode-assembly-electrolyzers-for-co2-reduction-reactions-by-intermittent-supply-of-alkali-metal-cations.pdf |
64b6848cb605c6803bed39a2 | 10.26434/chemrxiv-2023-n48g3 | Expanding Bioactive Fragment Space with the Generated Database GDB-13s | Identifying innovative drug-like small molecules is critically important in medicinal chemistry to address new targets and overcome limitations of classical molecular series. By deconstructing molecules into ring fragments (RFs, ring and ring-adjacent atoms) and acyclic fragments (AFs, only acyclic atoms), we find that molecules in public databases of drug-like compounds (ZINC, PubChem) and natural products (COCONUT) mostly consist of RFs and AFs up to 13 atoms, and that many RFs and AFs are enriched in bioactive compared to inactive molecules in ChEMBL. We then search the 28,246,012 RFs and 2,640,023 AFs in the generated database GDB-13s (99,394,177 molecules up to 13 atoms following simple functional group and ring strain criteria) for subsets resembling ChEMBL bioactive RFs and AFs. Many of these RFs and AFs are structurally simple, have favorable synthetic accessibility scores, and represent opportunities for synthetic chemistry to contribute to drug innovation in the context of fragment-based drug discovery. | Ye Buehler; Jean-Louis Reymond | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2023-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b6848cb605c6803bed39a2/original/expanding-bioactive-fragment-space-with-the-generated-database-gdb-13s.pdf |
65666495cf8b3c3cd759427a | 10.26434/chemrxiv-2023-7v4v4 | Long-lasting Cross-linked PLGA-Inspired Nanoparticles
from One-pot Nanopolymerization of Precisely Sequenced
Short Oligolactoglycolic Acid Dimethacrylates
| Poly(lactic-co-glycolic acid) (PLGA) is a widely utilized polymer for biomedical applications due to its biocompatibility and degradability in vivo. Traditional methods of fabrication of drug-loaded nanoparticles (NPs) employ the random sequence form of linear PLGA to yield non-crosslinked polymeric NPs that form when the polymer nanoprecipitates out of solution. Given the large-scale use of PLGA-based polymeric drug delivery systems to date, it is crucial to be able to control the ratio and sequence of lactic and glycolic components in the overall drug delivery system, which in turn can impact factors such as stability, drug loading, drug release and degradability. In this work, we present a novel PLGA-inspired NP polymerization technique, which allows the formation of NPs via the cross-linking of precisely sequenced short oligolactoglycolic acid dimethacrylates (OLGADMAs). Following the synthesis of a range of OLGADMAs we successfully generated a library of NPs via this rapid and surfactant-free nanopolymerization method, which permits the simultaneous NP formation and encapsulation of drugs such as dexamethasone. Our results indicate that NPs produced through this nanopolymerization technique with precisely controlled sequences exhibit heightened stability compared to conventionally sequenced and non-sequence controlled PLGA, as evidenced by minimal pH changes over a five-week span. This improved stability is attributed to simultaneous crosslinking and co-polymerization of the OLGADMAs. Moreover, the long-acting NPs demonstrated minimal cytotoxicity and uniform cellular uptake in vitro. We conclude that the ability to precisely regulate the sequence of short PLGA-inspired monomers and employ a unique in situ nanopolymerizing reaction results in exceptionally stable NPs for sustained drug delivery and opens exciting possibilities for the development of a range of long-lasting drug delivery systems with programmable structure and function. | Luka Blagojevic; Nazila Kamaly | Organic Chemistry; Materials Science; Nanoscience; Controlled-Release Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65666495cf8b3c3cd759427a/original/long-lasting-cross-linked-plga-inspired-nanoparticles-from-one-pot-nanopolymerization-of-precisely-sequenced-short-oligolactoglycolic-acid-dimethacrylates.pdf |
6447cd64e4bbbe4bbf3a906b | 10.26434/chemrxiv-2022-mw2lr-v4 | Low-temperature electrochemical ammonia synthesis: measurement reliability and comparison to Haber-Bosch in terms of energy efficiency | Recently several studies paved a way to nearly 100% selectivity of the electrochemical ammonia synthesis (EAS), which had been identified earlier as a main challenge. These results motivated us to benchmark the energy efficiency (EE) of EAS against the Haber-Bosch process. We present a method to calculate EE of EAS, which can be used by a broader audience. EAS studies historically suffered from reliability issues, and to avoid benchmarking of false-positive results, we established a method to calculate a reliability indicator to assess the measurement reliability of a published work. We used the indicator to evaluate the studies published in 2020, 2021 and 2022. We calculated the EE of EAS for works that were assessed as reliable with our indicator. We identified and discussed several promising systems and strategies enabling higher selectivity and EE. The EE of some aqueous EAS reports are up to 55%, and non-aqueous are below 15%. | Fateme Rezai; Søren Læsaa; Nihat Ege Sahin; Jacopo Catalano; Emil Dražević | Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6447cd64e4bbbe4bbf3a906b/original/low-temperature-electrochemical-ammonia-synthesis-measurement-reliability-and-comparison-to-haber-bosch-in-terms-of-energy-efficiency.pdf |
60c73f9f469df45f0af42b17 | 10.26434/chemrxiv.7450898.v1 | An introduction to digital microfluidic concepts in chemistry using a macroscopic droplet generator | <div><div><div><div><div><div><p>This activity introduces digital microfluidics and the usage of aqueous droplets as independent chemical microreactors for reaction kinetics studies. Students build their own droplet generator from common macroscopic glassware and connecting parts, to create trains of millimetric droplets in which a redox reaction takes place. The activity allows working on reaction kinetics, hydrodynamics at low Reynolds number and image analysis at a macroscopic scale.</p></div></div></div></div></div></div> | Clotilde Vié; Jacques Fattaccioli; philippe jacq | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f9f469df45f0af42b17/original/an-introduction-to-digital-microfluidic-concepts-in-chemistry-using-a-macroscopic-droplet-generator.pdf |
668775805101a2ffa871a56c | 10.26434/chemrxiv-2024-w8fps-v2 | Multi-modal conditioning for metal-organic frameworks generation using 3D modeling techniques | The design of porous materials with user-desired properties has been a great interest for the last few decades. However, the flexibility of target properties has been highly limited, and targeting multiple properties of diverse modalities simultaneously has been scarcely explored. Furthermore, although deep generative models have opened a new paradigm in materials generation, their incorporation into porous materials such as metal-organic frameworks (MOFs) has not been satisfactory due to their structural complexity. In this work, we introduce MOFFUSION, a latent diffusion model that addresses the aforementioned challenges. Signed distance functions (SDFs) were employed for the input representation of MOFs, marking their first usage in representing porous materials for generative models. Using the suitability of SDFs in describing complicated pore structures, MOFFUSION exhibited exceptional generation performance, and demonstrated its versatile capability of conditional generation with handling diverse modalities of data, including numeric, categorical, text data, and their combinations. | Junkil Park; Youhan Lee; Jihan Kim | Theoretical and Computational Chemistry; Materials Science; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC 4.0 | CHEMRXIV | 2024-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668775805101a2ffa871a56c/original/multi-modal-conditioning-for-metal-organic-frameworks-generation-using-3d-modeling-techniques.pdf |
67500afef9980725cfff5e22 | 10.26434/chemrxiv-2024-x89jw-v2 | Elucidation of the Nano-sized Molecular Structure of Methylaluminoxane using Synchrotron X-ray Total Scattering | Methylaluminoxane (MAO) is commonly employed to activate molecular pre-catalysts in polyolefin synthesis, both indus-trially and in the laboratory. Despite the extensive use of this compound, the ambiguity related to its structure hampers the understanding of its structure–function relationship. The current study therefore employed synchrotron X-ray total scattering to elucidate the nano-sized molecular structure of MAO. The MAO samples, which were prepared using various synthetic protocols, exhibited consistent X-ray scattering patterns and atomic pair distribution function curves, indicating similar molecular structures. However, the scattering intensity in the small-angle region revealed differences in the high-er-order structures. A fitting study performed using 172 molecular models showed that small molecule and tube models were inadequate to reproduce the experimental results, whereas cage and sheet models provided comparably better fits. The sheet model was found to be consistent with the observed molecular weight and the molecular weight distribution, in addition to accounting for the intensity in the small-angle scattering region. These results align with recent crystallo-graphic findings reported in Science, where a stacked sheet model successfully reproduced an experimental X-ray dif-fraction pattern. Ultimately, determination of the structural motif of MAO is expected to be beneficial to systematic re-search and development using this compound. | Toru Wada; Toshiaki Taniike | Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67500afef9980725cfff5e22/original/elucidation-of-the-nano-sized-molecular-structure-of-methylaluminoxane-using-synchrotron-x-ray-total-scattering.pdf |
60c74b59bdbb8928b3a39588 | 10.26434/chemrxiv.12324875.v1 | Synthesis and Photochemical Properties of Re(I) Tricarbonyl Complexes Bound to Thione and Thiazole-2-ylidene Ligands | <p>Three Re(I) tricarbonyl complexes,
with general formulation Re(N^L)(CO)<sub>3</sub>X
(where N^L is a bidentate ligand containing a pyridine functionalized in the
position 2 with a thione or a thiazol-2-ylidene group and X is either chloro or
bromo) were synthesized and their reactivity explored in terms of
solvent-dependent ligand substitution, both in the ground and excited states.
When dissolved in acetonitrile, the complexes bound to the thione ligand underwent
ligand exchange with the solvent resulting in the formation of Re(NCMe)<sub>2</sub>(CO)<sub>3</sub>X.
The exchange was found to be reversible, and the starting complex was reformed
upon removal of the solvent. On the other hand, the complexes appeared inert in
dichloromethane or acetone. Conversely, the complex bound to the
thiazole-2-ylidene ligand did not display any ligand exchange reaction in the
dark, but underwent photoactivated ligand substitution when excited to its
lowest metal-to-ligand charge transfer manifold. Photolysis of this complex in
acetonitrile generated multiple products, including Re(I) tricarbonyl and dicarbonyl
solvato-complexes as well as free thiazole-2-ylidene ligand.</p> | Matthew Stout; Brian Skelton; Alexandre N. Sobolev; Paolo Raiteri; Massimiliano Massi; Peter Simpson | Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b59bdbb8928b3a39588/original/synthesis-and-photochemical-properties-of-re-i-tricarbonyl-complexes-bound-to-thione-and-thiazole-2-ylidene-ligands.pdf |
636aa393c4c8799aeb223a10 | 10.26434/chemrxiv-2022-14kg2 | Mechanism of plasmon-induced catalysis of thiols and the impact of reaction conditions | Plasmon-induced catalysis of the thiols 4-aminothiophenol (ATP) and 4-nitrothiophenol (NTP) has been investigated in numerous studies. Currently, two reaction pathways are discussed in the literature, one leading to dimerization to 4,4’-dimercaptoazobenzene (DMAB), and the other, depending on experimental conditions, resulting in a monomer commonly assigned to ATP. In this joint experimental-theoretical study, we disentangle the involved photo-/plasmon-mediated reaction mechanisms by thorough control of the reaction conditions, particularly the involved surface-enhanced Raman scattering (SERS) substrates. The Raman spectra experimentally and strongly suggest that the formation of a new stable intermediate plays a crucial role. Tracking the reaction with time-dependent SERS experiments allows us to build the connection between the dimer (DMAB) and monomer pathways and to propose potential reaction pathways for different environmental conditions. Furthermore, theoretical modelling addressing the excited-states properties of key intermediates involved in both reaction pathways and the respective thermodynamics allows to investigate the underlying reaction mechanism in more detail – complementing the spectroscopic results. | Xiaobin Yao; Sadaf Ehtesabi; Christiane Höppener; Tanja Deckert-Gaudig; Henrik Schneidewind; Stephan Kupfer; Stefanie Gräfe; Volker Deckert | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636aa393c4c8799aeb223a10/original/mechanism-of-plasmon-induced-catalysis-of-thiols-and-the-impact-of-reaction-conditions.pdf |
67ac6be8fa469535b9010996 | 10.26434/chemrxiv-2025-grk3r | Room Temperature Dinitrogen Cleavage and Hydrogenation with Organometallic Complexes of Uranium | The conversion of atmospheric nitrogen into ammonia is not just a crucial reaction for sustaining life on Earth; it is a pivotal cornerstone for our planet's future. The Haber-Bosch process, although a well-established method utilizing hydrogen and nitrogen, demands an extensive industrial infrastructure, limiting its accessibility and flexibility. Innovative technologies that harness hydrogen from renewable resources, combined with decarbonized electricity and nitrogen from the ambient air, are imperative to address the pressing need for sustainable ammonia production. The chemistry of molecular catalysts, whether supported or unsupported, offers numerous advantages. In this context, we present groundbreaking findings on the reactivity of dinitrogen with an organometallic uranium complex featuring the Cpttt ligand (Cpttt = 1,2,4-tris(tert-butyl)cyclopentadienyl). This complex demonstrates the ability to cleave and hydrogenate dinitrogen with notable kinetics at ambient temperature and pressure. Most notably, redox assistance from the hydrocarbon ligand is crucial to this reaction, highlighting the promise of such complexes as viable candidates for ammonia synthesis technologies. | Angus Shephard; Lucie Pedussaut; Linda De Marchi; Luca Demonti; Thayalan Rajeshkumar; Nicolas Casaretto; Laurent Maron; Grégory Danoun; Thomas Simler; Gregory Nocton | Inorganic Chemistry; Organometallic Chemistry; Energy; Lanthanides and Actinides; Coordination Chemistry (Organomet.); Ligands (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ac6be8fa469535b9010996/original/room-temperature-dinitrogen-cleavage-and-hydrogenation-with-organometallic-complexes-of-uranium.pdf |
60c74574567dfe9a5fec446f | 10.26434/chemrxiv.10022858.v1 | Stereocontrolled Synthesis of Melokhanine E via an Intramolecular Formal [3+2] Cycloaddition | <p>A convergent sequence to access the indole alkaloid melokhanine E in 12-steps (8-step longest linear sequence) and an 11% overall yield is reported. The approach utilizes two cyclopropane moieties as reactive precursors to a 1,3-dipole and imine species to enable stereoselective construction of the core scaffold through a formal [3+2] cycloaddition. The natural product was evaluated for its antimicrobial activity based on isolation reports; however, no activity was observed. The reported efforts serve as a synthetic platform to prepare an array of alkaloids bearing this core structural motif.</p> | Joshua Pierce; Anna Cholewczynski; Peyton Williams | Natural Products; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74574567dfe9a5fec446f/original/stereocontrolled-synthesis-of-melokhanine-e-via-an-intramolecular-formal-3-2-cycloaddition.pdf |
60c750bf702a9be02118be2e | 10.26434/chemrxiv.12813443.v2 | Molybdenum Trioxide on Anatase TiO2(101) - Formation of Monodispersed (MoO3)1 Monomers from Oligomeric (MoO3)n Clusters | <p>Complex oxide systems with hierarchical order are of
critical importance in material science and catalysis. Despite their immense
potential, their design and synthesis are rather difficult. In this study we
demonstrate how the deposition of small oligomeric (MoO<sub>3</sub>)<sub>1-6</sub> clusters,
which can be formed by the sublimation of MoO<sub>3</sub> powders,
leads to the formation of locally ordered layers of (MoO<sub>3</sub>)<sub>1</sub> monomers
on anatase TiO<sub>2</sub>(101). Using both high-resolution imaging and
theoretical calculations, we show that at room temperature, such oligomers
undergo spontaneous dissociation to their monomeric units. In initial stages of
the deposition, this is reflected by the observation of one to six
neighboring (MoO<sub>3</sub>)<sub>1</sub> monomers that parallel the size
distribution of the oligomers. A transient mobility of such oligomers on both
bare TiO<sub>2</sub>(101) and (MoO<sub>3</sub>)<sub>1</sub> covered
areas is key to the formation of a complete layer with a saturation coverage of
one (MoO<sub>3</sub>)<sub>1</sub> per two undercoordinated surface Ti
sites. We further show that such layers are stable to 500 K, making them highly
suitable for a broad range of applications. </p> | Nassar Doudin; Gregory Collinge; Pradeep Kumar Gurunathan; Mal Soon Lee; Vassiliki-Alexandra Glezakou; Roger Rousseau; Zdenek Dohnálek | Catalysts; Acid Catalysis; Base Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750bf702a9be02118be2e/original/molybdenum-trioxide-on-anatase-ti-o2-101-formation-of-monodispersed-mo-o3-1-monomers-from-oligomeric-mo-o3-n-clusters.pdf |
60c75904469df41c3bf457c7 | 10.26434/chemrxiv.14633295.v1 | Elucidation of Charge Contribution in Iridium-Chelated Hydrogen-Bonding Systems | <p>We present two iridium complexes 1H+ and 2H+ 9 that contain cationic ligands to extend the knowledge
10 of charge-assisted hydrogen bonding (CAHB), which counts among the strongest non-covalent
11 bonding interactions. Upon protonation, both complexes were converted into new hydrogen-bonding
12 arrays with various selectivity for respective H-bonding partners. This study compares the association
13 strengths of four hydrogen-bonding co-systems, emphasizing the roles of CAHB in supramolecular
systems. We determined that the cationic charge in these systems contributed up to 2.7 kJ mol-1 14 in the
15 H-bonding complexation processes<br /></p> | Barbora Balonova; Barry Blight | Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75904469df41c3bf457c7/original/elucidation-of-charge-contribution-in-iridium-chelated-hydrogen-bonding-systems.pdf |
674888317be152b1d03a974e | 10.26434/chemrxiv-2024-cgnhq-v2 | Continuous photo-flow synthesis of heterohelicenes | Heterohelicenes continue to attract interest for their potential applications as organic chiral materials. To keep up with the demand for novel heterohelicene structures, expedient and scaleable synthetic procedures are required. We report a ‘Mallory’ photocyclisation methodology in continuous flow for the synthesis of thia-, oxa- and azahelicenes. This procedure has been sucessfully scaled-up to 9.8 mmol and can be applied to an iterative modular synthesis. | Katherine Lyon; Chenyu Pan; Shainthavaan Sathiyalingam; Yang Wu; Jochen R. Brandt | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674888317be152b1d03a974e/original/continuous-photo-flow-synthesis-of-heterohelicenes.pdf |
62913087f89e5d4e6ee8828d | 10.26434/chemrxiv-2022-zl7l6 | Long-term stability of ferri-/ferrocyanide as an electroactive component for redox flow battery applications: On the origin of apparent capacity fade | We assess the suitability of potassium ferri-/ferrocyanide as an electroactive species for long-term utilization in aqueous organic redox flow batteries. A series of electrochemical and chemical characterization experiments was performed to distinguish between structural decomposition and apparent capacity fade of ferri-/ferrocyanide solutions used in the capacity-limiting side of a flow battery. Our results indicate that, in contrast with previous reports, no structural decomposition of ferri-/ferrocyanide occurs at tested pH values as high as 14 in the dark or in diffuse indoor light. Instead, an apparent capacity fade takes place due to an electroless reduction of ferricyanide to ferrocyanide, via electroless oxygen evolution reaction. We find that this parasitic process can be further exacerbated by carbon electrodes, with apparent capacity fade rates at pH 14 increasing with an increased ratio of carbon electrode surface area to total amount of ferricyanide in solution. Based on these results, we report a set of operating conditions that enables the cycling of alkaline ferri-/ferrocyanide electrolytes, and demonstrate how apparent capacity fade rates can be engineered by the initial cell setup. If protected from direct exposure to light, the chemical stability of ferri-/ferrocyanide anions allows for their practical deployment as electroactive species in long duration energy storage applications. | Eric Fell; Diana De Porcellinis; Yan Jing; Valeria Gutierrez-Venegas; Roy Gordon; Sergio Granados-Focil; Michael Aziz | Inorganic Chemistry; Energy; Electrochemistry; Energy Storage; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62913087f89e5d4e6ee8828d/original/long-term-stability-of-ferri-ferrocyanide-as-an-electroactive-component-for-redox-flow-battery-applications-on-the-origin-of-apparent-capacity-fade.pdf |
617952328acf7e2d39d0bd3c | 10.26434/chemrxiv-2021-zv6f1-v2 | Perplexity-based molecule ranking and bias estimation of chemical language models | Chemical language models (CLMs) can be employed to design molecules with desired properties. CLMs generate new chemical structures in the form of textual representations, such as the simplified molecular input line entry systems (SMILES) strings, in a rule-free manner. However, the quality of these de novo generated molecules is difficult to assess a priori. In this study, we apply the perplexity metric to determine the degree to which the molecules generated by a CLM match the desired design objectives. This model-intrinsic score allows identifying and ranking the most promising molecular designs based on the probabilities learned by the CLM. Using perplexity to compare “greedy” (beam search) with “explorative” (multinomial sampling) methods for SMILES generation, certain advantages of multinomial sampling become apparent. Additionally, perplexity scoring is performed to identify undesired model biases introduced during model training and allows the development of a new ranking system to remove those undesired biases. | Michael Moret; Francesca Grisoni; Paul Katzberger; Gisbert Schneider | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2021-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617952328acf7e2d39d0bd3c/original/perplexity-based-molecule-ranking-and-bias-estimation-of-chemical-language-models.pdf |
6603e6d2e9ebbb4db9aa029d | 10.26434/chemrxiv-2024-qbhkv | Studying the degradation of bulk PTFE into microparticles via SP ICP-MS: A systematically developed method for the detection of F-containing particles | Fluoropolymers, such as polytetrafluoroethylene (PTFE), have unique properties, which enable versatile applications in industry and make them useful for various consumer products. However, it is known that these polymers degrade over time and form small particles with possible implications for environment and health. Building on previous reports for the detection of Fluorine (F) via inductively coupled plasma-tandem mass spectrometry (ICP-MS/MS) using a Barium-based modifier, this study presents a design of experiments approach (DoE), which optimised plasma parameters, ion optics, mass filtering and collision/reaction cell conditions systematically. The resulting method was capable to detect micro-scaled PTFE particles and to determine number concentrations as well as size distributions. Validation was carried out in two steps: First, micro-scaled PTFE standards were characterised via microscopy and Raman spectroscopy and second, carbon-selective single particle (SP) ICP-MS was employed to corroborate results obtained via the F-selective method.
The developed method has a high utility to characterise the degradation of bulk PTFE into microplastics, which was demonstrated in an environmentally focussed proof-of-concept study. Here, bulk PTFE material was stirred in simulated seawater under UV-light illumination for 6 days. After this incubation period a microplastic number concentration of 2.35 x 105 F-based particles per gram immersed bulk PTFE was detected. PTFE particles had a mean mass and size of 28 pg and 2.7 µm, respectively.
| Raquel Gonzalez de Vega; Thebny Thaíse Moro; Bernhard Grüner; Tatiane de Andrade Maranhão; Maximilian Huber; Natalia Ivleva; Etienne Skrzypek; Jörg Feldmann; David Clases | Analytical Chemistry; Environmental Analysis; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6603e6d2e9ebbb4db9aa029d/original/studying-the-degradation-of-bulk-ptfe-into-microparticles-via-sp-icp-ms-a-systematically-developed-method-for-the-detection-of-f-containing-particles.pdf |
634a5084de2a2174b2a60019 | 10.26434/chemrxiv-2022-g40k5 | Why are Aromatic Additives Effective in Asymmetric Organocatalysis? | The presence of an aromatic additive has been seen to enhance, often significantly, the yield and enantioselectivityof the desired product in asymmetric organocatalysis.Considering their success across a dizzying range of organocatalysts and organic transformations, it would seem unlikely that a common principleexists by which they function.However, the current investigations with DFT reveal that such a general principle indeed does exist: thearomatic additivesandwiches itself, through hydrogen bonding and π•••π stacking, between theorganocatalyst coordinatedelectrophile and nucleophile. This is seen to occur for a wide range of experimentally reported systems.That such complex formation leads to enhanced stereoselectivity isthen demonstrated for two cases: the cinchona alkaloid complex (BzCPD), catalysing thiocyanation(2-naphthol additive employed), as well as for the L-pipecolicacidcatalyst (2,4-dinitrophenol additive employed), catalysingtheasymmetric nitroaldol reaction.These findings are likely to have a significant impact on the field of asymmetric organocatalysis. | Subhrashis Banerjee; Kumar Vanka | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Computational Chemistry and Modeling; Homogeneous Catalysis; Organocatalysis | CC BY 4.0 | CHEMRXIV | 2022-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634a5084de2a2174b2a60019/original/why-are-aromatic-additives-effective-in-asymmetric-organocatalysis.pdf |
6585705be9ebbb4db97d9675 | 10.26434/chemrxiv-2024-165mp | In vivo polymer mechanochemistry with polynucleotides | Polymer mechanochemistry utilizes mechanical force to activate latent functionalities in macromolecules and widely relies on ultrasonication techniques. Although ultrasound is a clinically established modality, fundamental constraints of frequency and power intensity have prohibited the application of the polymer mechanochemistry principles in a biomedical context up to now. Here, a universal polynucleotide framework is presented that allows the binding and release of therapeutic oligonucleotides, both DNA- and RNA-based, as cargo by biocompatible imaging ultrasound. It is shown that the high molar mass, colloidal assembly, and a distinct mechanochemical mechanism enable the force-induced release of cargo and subsequent activation of biological function in vitro and in vivo. Thereby, an avenue for the exploration of biological questions and therapeutics development steered by mechanical force is uncovered. | Aman Ishaqat; Johannes Hahmann; Cheng Lin; Chuanjiang He; Khosrow Rahimi; Rostislav Vinokur; Robert Göstl; Matthias Bartneck; Andreas Herrmann | Polymer Science; Biopolymers; Drug delivery systems; Hydrogels | CC BY NC 4.0 | CHEMRXIV | 2024-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6585705be9ebbb4db97d9675/original/in-vivo-polymer-mechanochemistry-with-polynucleotides.pdf |
646b0447fb40f6b3eef8dccd | 10.26434/chemrxiv-2023-35txk | PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent | We introduce PyConSolv, a freely available python package that automates the generation of conformers of metal and non-metal containing complexes in explicit solvent, through classical molecular dynamics simulations. Using a streamlined workflow and interfacing with widely used computational chemistry software, PyConSolv is an all-in-one tool for the generation of conformers in any solvent. Input requirements are minimal, only the geometry of the structure and the desired solvent in xyz (XMOL) format are needed. The package can also account for charged systems, by including arbitrary counterions in the simulation. A bonded model parametrization is performed automatically, utilizing the AmberTools, ORCA, and Multiwfn software packages. PyConSolv provides a selection of pre-parametrized solvents and counterions for use in classical molecular dynamics simulations. We show the applicability of our package on a number of (transition-metal-containing) systems. The software is provided open-source and free of charge. | Radu A. Talmazan; Maren Podewitz | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646b0447fb40f6b3eef8dccd/original/py-con-solv-a-python-package-for-conformer-generation-of-metal-containing-systems-in-explicit-solvent.pdf |
60c74ce3469df43cbdf44199 | 10.26434/chemrxiv.12556160.v1 | Synthesis of Atomically Precise Single-Crystalline Ru2-Based Coordination Polymers | Methods to incorporate kinetically inert metal nodes and highly basic ligands into single-crystalline metal-organic frameworks (MOFs) are scarce, which prevents synthesis and systematic variation of many potential heterogeneous catalyst materials. Here we demonstrate that metallopolymerization of kinetically inert Ru<sub>2</sub> metallomonomers via labile Ag–N bonds provides access to a family of atomically precise single-crystalline Ru<sub>2</sub>-based coordination polymers with varied network topology and primary coordination sphere. | Wen-Yang Gao; Gerard Van Trieste; David Powers | Catalysts; Hybrid Organic-Inorganic Materials; Coordination Chemistry (Inorg.); Organometallic Compounds; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ce3469df43cbdf44199/original/synthesis-of-atomically-precise-single-crystalline-ru2-based-coordination-polymers.pdf |
63349d91e61502f26f2a09c0 | 10.26434/chemrxiv-2022-kxdzr | The binding affinity of monoalkyl phosphinic acid ligands towards nanocrystal surfaces | We recently introduced monoalkyl phosphinic acids as a ligand class for nanocrystal synthesis. Their metal salts have interesting reactivity differences with respect to metal carboxylates and phosphonates, and provide cleaner work-up compared to phosphonates. However, there is little known about the surface chemistry of nanocrystals with monoalkyl phosphinate ligands. Here, we probe the relative binding affinity of monoalkyl phosphinate ligands with respect to other X-type ligands. We perform competitive ligand exchange reactions with carboxylate and phosphonate ligands at the surface of HfO2, CdSe, and ZnS nanocrystals. We monitor the ligand shell composition by solution 1H and 31P NMR spectroscopy. Using a monoalkyl phosphinic acid with an ether functionality, we gain an additional NMR signature, apart from the typical alkene resonance in oleic acid and oleylphosphonic acid. We find that carboxylate ligands are easily exchanged upon exposure to monoalkyl phosphinic acids, whereas an equilibrium is reached between monoalkyl phosphinates and phosphonates, slightly in the favour of phosphonate (K = 2). Phosphinic acids have thus an intermediate binding affinity between carboxylic acids and phosphonic acids for all nanocrystals studied. These results enable the sophisticated use of monoalkyl phosphinic acids for nanocrystal synthesis and for post-synthetic surface engineering. | Evert Dhaene; Simon Coppenolle; Loren Deblock; Klaartje De Buysser; Jonathan De Roo | Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Ligands (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63349d91e61502f26f2a09c0/original/the-binding-affinity-of-monoalkyl-phosphinic-acid-ligands-towards-nanocrystal-surfaces.pdf |
63277af9e665bd2c8f097ae4 | 10.26434/chemrxiv-2022-cf28j | PRODUCTION AND CHARACTERIZATION OF BIODIESEL FROM CASTOR SEED OIL USING COCOA POD ASH AS A CATALYST | A major problem retarding the commercialization of biodiesel is the derivation of catalysts and feedstock from high-cost materials. Hence, in order to mitigate such challenge, the following objective is being put forward: to extract and characterize castor oil, synthesize and characterize cocoa pod ash as the base catalyst before and after use, and apply the base catalyst for biodiesel production. The cocoa pods were thermally treated at 600 ℃ for 35 minutes in a muffle furnace, then it was sieved to obtain ash that is uniform in size distribution. The yield of castor oil extracted was 42 %. Also, the catalyst synthesized was found to possess good features that are capable of transesterifying the extracted oil. Afterward, the castor oil was used for the production of biodiesel with the aid of cocoa pod ash as a catalyst under the reaction conditions, 88 % yield of biodiesel was obtained. Characterization methods such as XRD, SEM, and FTIR were performed on the catalyst to confirm the presence of the active sites. The physico-chemical properties of the castor oil produced are consistent with literature values. | Olahanmi Olatayo; Sunday Ogunniyi ; Oladimeji Olaluwoye | Chemical Engineering and Industrial Chemistry; Petrochemicals | CC BY 4.0 | CHEMRXIV | 2022-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63277af9e665bd2c8f097ae4/original/production-and-characterization-of-biodiesel-from-castor-seed-oil-using-cocoa-pod-ash-as-a-catalyst.pdf |
636a84ab80c9bf01cc8d95f9 | 10.26434/chemrxiv-2022-8cd9w-v2 | Generality-Oriented Optimization of Enantioselective Aminoxyl Radical Catalysis | Catalytic enantioselective methods that are general over a broad range of substrates facilitate application in synthetic discovery and development settings; however, truly general catalysts for asymmetric synthesis are rare. Herein, we report a strategy for the oxidative desymmetrization of meso-1,4 diols predicated on a non-traditional optimization protocol utilizing a panel of screening substrates rather than a singular model substrate. Critical to this approach was rational modulation of a peptide sequence incorporating a novel, aminoxyl-based catalytic residue. A general catalyst emerged, providing high selectivity in delivery of enantioenriched lactones across a broad range of diols. | Jonas Rein; Soren Rozema; Olivia Langner; Samson Zacate; Melissa Hardy; Juno Siu; Brandon Mercado; Matthew Sigman; Scott Miller; Song Lin | Organic Chemistry; Catalysis; Stereochemistry; Electrocatalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636a84ab80c9bf01cc8d95f9/original/generality-oriented-optimization-of-enantioselective-aminoxyl-radical-catalysis.pdf |
63f8e46832cd591f126c248e | 10.26434/chemrxiv-2023-jd57g | Simulation-guided engineering of split GFPs with efficient beta-strand photodissociation | Green fluorescent proteins (GFPs) are ubiquitous for protein tagging and live-cell imaging. Split-
GFPs are widely used to study protein-protein interactions by fusing proteins of interest to split
GFP fragments that create a fluorophore upon complementation. Complementation is typically
irreversible, and controlled dissociation of the fragments would be desirable. The quantum
efficiency of light-induced photodissociation of split GFPs is low, with extensive mutagenesis and
screening using traditional protein engineering approaches proving difficult to implement. To
reduce the search space, key states in the dissociation process were modeled by combining classical
and QM/MM molecular dynamics and enhanced sampling methods, enabling the rational design
and engineering of split GFPs with up to 20-fold faster photodissociation rates using non-intuitive
amino acid changes. This demonstrates the feasibility of modeling complex molecular processes
using state-of-the-art computational methods, and the potential of integrating computational
methods to increase the success rate in protein engineering projects. | Yasmin Shamsudin; Alice R. Walker; Chey M. Jones; Todd J. Martinez; Steven G. Boxer | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Bioengineering and Biotechnology; Computational Chemistry and Modeling; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f8e46832cd591f126c248e/original/simulation-guided-engineering-of-split-gf-ps-with-efficient-beta-strand-photodissociation.pdf |
66cf7669a4e53c4876ea96a7 | 10.26434/chemrxiv-2024-xtcbp | DFT Study of the Arbuzov Reaction Mechanism between Ethyl Halogenides and Trimethoxyphosphine | The mechanism of the reaction between ethyl chloride or ethyl bromide with trimethoxyphosphine in a non-polar (ε = 1) and polar medium (methanol, ε = 32.7) was studied within the density functional theory (DFT) using MOLPRO program. It was shown that the reaction occurs in 2 stages: first, a nucleophilic attack of the carbon atom by phosphorus occurs, followed by the interaction of methyl of one of the methoxy groups with the halide. The limiting stage in all cases is the second stage of the reaction, the barrier of which is approximately 1.5 times higher than the barrier of the first. The reaction barriers are lower for the reaction of ethyl bromide, while the stabilization energies of the intermediate complexes and products are almost the same for chloride and bromide. Temperature in general has little effect on the reaction profile, with the exception of entropic destabilization of the initial complex. At the same time, the usage of a polar solvent accelerates the reaction process, lowering the barriers and stabilizing the intermediates, and can be recommended for carrying out the reaction. | Anastasia Filippova; Maria Syzgantseva; Alexander Galitsin; Olga Syzgantseva | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cf7669a4e53c4876ea96a7/original/dft-study-of-the-arbuzov-reaction-mechanism-between-ethyl-halogenides-and-trimethoxyphosphine.pdf |
665c881791aefa6ce19cfddd | 10.26434/chemrxiv-2024-1xhm0 | Correlating Enzymatic Reactivity for Different Substrates using Transferable Data-Driven Collective Variables | Machine learning is transforming the investigation of complex biological processes. In enzymatic catalysis, one significant challenge is identifying the reactive conformations of the enzyme:substrate complex where the substrate assumes a precise arrangement in the active site necessary to initiate a reaction. Here, we applied machine learning techniques to address this challenge, focusing on human pancreatic α-amylase, a crucial enzyme in type-II diabetes treatment. Using machine learning-based collective variables, we correlated the probability of being in a reactive conformation with the experimental catalytic activity of several malto-oligosaccharide substrates. Our findings demonstrate a remarkable transferability of these collective variables across various compounds, significantly streamlining the modeling process and reducing both computational demand and manual intervention in setting up simulations for new substrates. This approach not only advances our understanding of enzymatic processes but also holds substantial potential for accelerating drug discovery by enabling rapid and accurate evaluation of drug efficacy across different generations of inhibitors. | Sudip Das ; Umberto Raucci; Rui P.P. Neves ; Maria J. Ramos; Michele Parrinello | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Computational Chemistry and Modeling; Machine Learning; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665c881791aefa6ce19cfddd/original/correlating-enzymatic-reactivity-for-different-substrates-using-transferable-data-driven-collective-variables.pdf |
67210679f9980725cf4609c9 | 10.26434/chemrxiv-2024-h0g2d-v2 | Photoemission Spectroscopy of Organic Molecules Using Plane-Wave/Pseudopoential Density Functional Theory: A Comprehensive Computational Protocol for Isolated Molecules, Molecular Aggregates and Periodic Systems | The possibility to perform low-pressure gas-phase photoemission experiments has allowed the exploration at molecular scale of the complex correlation between electronic and structural properties of the matter. A significant advantage in the removal of the interference of the surrounding at low-pressure is also the easier correlation of the experimental results with theoretical ab-initio simulations. In the context of core ionization, the development of accurate methods for calculating inner-shell binding energies (BEs) offers a dual benefit. Firstly, it aids significantly in interpreting experimental data, helping to assign the contributions of all non-equivalent atoms, even in unresolved features arising from a molecular structure. Secondly, it allows for the anticipation of experimental results by accurately predicting spectral lines. In this context, we have developed and extensively tested a computational protocol based on plane- wave/pseudopotential density functional theory (PW-DFT) to predict X-ray photoemission spectra (XPS) in molecules and molecular aggregates. This protocol is based on a ∆SCF approach and has been tested comparing the present theoretical results with experimental XPS spectra collected from several molecular systems in gas phase, ranging from benzene derivates to biomolecules. Our calculations have been performed using semilocal and global/range-separated hybrid density functionals, containing increasing fractions of Hartree-Fock exact exchange (EXX). Specifically, PBE, B3LYP (20 % EXX), HSE (range separated with 25 % EXX at short range) and BH&HLYP (50 % EXX) have been used for the assessment of the computational protocol. Equation-of-motion coupled-cluster with single and double excitations (EOM-CCSD) has been employed as reference theoretical method for comparison. Regarding XPS, our PW-DFT approach demonstrated to be generally accurate and robust even using semilocal DFT, and to be also suitable for application to very large molecular systems and organic thin films deposited on inorganic surfaces. A proof of concept of a robust machine learning (ML) model for the prediction of C1s BEs in isolated organic molecules has been developed and it is discussed. We also present an early-stage verification of the efficiency of the density functionals introduced above for predicting valence-shell ionization spectra. Preliminary data suggest in this case of BH&HLYP as a promising alternative to EOM-CCSD. | Francesco Porcelli; Emanuela Colasante; Francesco Filippone; Giuseppe Mattioli | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Machine Learning; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67210679f9980725cf4609c9/original/photoemission-spectroscopy-of-organic-molecules-using-plane-wave-pseudopoential-density-functional-theory-a-comprehensive-computational-protocol-for-isolated-molecules-molecular-aggregates-and-periodic-systems.pdf |
60c7435dbdbb899beaa38626 | 10.26434/chemrxiv.8217362.v2 | Car-Parrinello Monitor for More Robust Born-Oppenheimer Molecular Dynamics | <p>Born-Oppenheimer molecular dynamics (BOMD) is a promising simulation method for exploring the possible reaction pathways of a chemical system, but one significant challenge is the increased difficulty of converging the self-consistent field (SCF) calculation that often accompanies the breaking and forming of chemical bonds.</p><p>To address this challenge, we developed an enhancement to the BOMD simulation method called the Car-Parrinello monitor (CPMonitor) that uses Car-Parrinello molecular dynamics (CPMD) to recover from SCF convergence failures.</p><p>CPMonitor works by detecting SCF convergence failures in BOMD and switching to a CPMD Hamiltonian to propagate through the region of configuration space where the SCF calculation is unable to converge, then switching back to BOMD when good convergence behavior is re-established.</p><p>We present a series of simulation studies that use CPMonitor, including detailed studies of the thermodynamic and dynamical properties of simple systems, as well as <i>ab initio</i> nanoreactor simulations containing transition metal atoms that were previously not possible to simulate using standard BOMD methods.</p><p>Our studies show that CPMonitor can make BOMD simulations robust to SCF convergence difficulties and improve simulation performance and stability in reaction discovery applications.</p><div><br /></div> | Lee-Ping Wang; Chenchen Song | Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7435dbdbb899beaa38626/original/car-parrinello-monitor-for-more-robust-born-oppenheimer-molecular-dynamics.pdf |
6746d0b95a82cea2fa0da633 | 10.26434/chemrxiv-2024-7x9sm | Understanding and optimizing Li substitution in P2-type Sodium Layered Oxides for Sodium-Ion Batteries | In the quest for novel cathode materials for Na-ion batteries, we studied a family of Li-substituted P2 layered oxides with nominal stoichiometry Na5/6LiyNi5/12-3y/2Mn7/12+y/2O2 (y = 2/18, 3/18, 4/18, 5/18). We explored the consequences of Li substitution, as well as the challenge of elevating the Na content in the pristine materials through solid-state synthesis. By in situ temperature-resolved x-ray diffraction (XRD) we observed the synthesis process, clearly showing the formation of an intermediate Li2MnO3 structure with increasing Li content. Structurally, honeycomb ordering is observed in all samples, while we show that Li induces the loss of Na+/vacancy ordering hence it leads to more disordered Na positions. Electrochemically, this family of materials exhibits an increasing trend of polarized hysteresis in the first cycle, suggesting the contribution of oxygen redox. We coupled semi-simultaneous operando x-ray absorption near edge structure (XANES) and XRD to appreciate the structural evolution and redox behavior during this process. We verified that Li in the transition metal site eliminates phase transitions at high voltage and modifies the activation of O-redox. As confirmed by our XANES analysis and by Density Functional Theory calculations, the Li-free sample already surprisingly show anionic redox despite the residual availability of Ni-redox, due to the peculiar density of states dominated by Ni-O hybridized states at high state of charge. On the other hand, Li-containing samples have O non-bonding states that lead to increasing O-redox contribution as expected due to the limited Ni content. One composition (Na0.745(6)Li0.164(4)Ni0.238(1)Mn0.599(3)O2) proves to have the lowest proportion of O-redox among all samples, coupled with reduced phase transitions, disordered occupancy of Na sites, and small volume change during cycling (4.8%). This material hence delivers the best balance of cycling stability (∼92% after 100 cycles in half cells), capacity (> 100 mAh/g) and rate capability. Determining this optimal compositional range is a promising starting point for further development of P2 layered oxides as cathode materials for Na-ion batteries and can be generalized to other families of Na-based layered oxides with redox-inactive dopants. | Mingfeng Xu; Giovanni Gammaitoni; Michael Häfner; Eduardo Villalobos-Portillo; Carlo Marini; Matteo Bianchini | Inorganic Chemistry; Energy; Electrochemistry; Energy Storage; Materials Chemistry; Crystallography – Inorganic | CC BY NC 4.0 | CHEMRXIV | 2024-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6746d0b95a82cea2fa0da633/original/understanding-and-optimizing-li-substitution-in-p2-type-sodium-layered-oxides-for-sodium-ion-batteries.pdf |
6704fe3112ff75c3a1d70558 | 10.26434/chemrxiv-2024-p93db-v2 | Nature of Reactive Sites in TS-1 from 15N solid-state NMR and Ti K-edge X-Ray Absorption Spectroscopic Signatures upon Pyridine Adsorption | Ti-containing zeotypes, notably titanosilicalite-1 (TS-1), are prominent examples of heterogeneous catalysts that have found applications in selective oxidation processes with hydrogen peroxide. Despite extensive characterization studies including using various probe molecules to interrogate the nature and the local environment of Ti sites, their detailed structure (as well as reactivity) remains elusive. Here, we demonstrate that using low temperature 15N magic angle spinning (MAS) ssNMR spectroscopy of adsorbed pyridine on TS-1 combined with Ti K-edge XANES on a range of samples (dehydrated, hydrated, contacted with H2O2 and pyridine) provides unique information regarding the Ti sites, highlighting their reactivity and dynamic nature. While dehydrated TS-1 shows only Lewis acid sites, the presence of H2O generates Brønsted acid sites, whose amount correlate with water loading. Moreover, the methodology – based on 15N ssNMR and Ti K-edge XANES – applied to a library of samples with various Ti-loadings and absence of extraframework TiO2 also enables quantification of the amount of Lewis acid sites and to establish a structure-activity descriptor (ratio of pyridine adsorbed on silanols vs. titanium). Complementary analysis including computational modelling reveals that the reaction of Ti sites with H2O generates an acidic bridging silanol Ti-(OH)-Si, upon hydrolysis of one Ti-O-Si linkage, where Ti expands its coordination from four to pentacoordinated according to XAS. | Lukas Lätsch; Christoph J. Kaul; Alexander V. Yakimov; Rhaínna McEntee; Trees De Baerdemaeker; Andrei-Nicolae Parvulescu; Karsten Seidel; J. Henrique Teles; Christophe Copéret | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6704fe3112ff75c3a1d70558/original/nature-of-reactive-sites-in-ts-1-from-15n-solid-state-nmr-and-ti-k-edge-x-ray-absorption-spectroscopic-signatures-upon-pyridine-adsorption.pdf |
645cb7cef2112b41e95e6839 | 10.26434/chemrxiv-2022-zrbgt-v3 | Double glass transitions in single-component homogeneous liquids due to intramolecular vitrification | On supercooling a liquid, the viscosity rises rapidly until at the glass transition it vitrifies into an amorphous solid accompanied by a steep drop in the heat capacity. Therefore, a pure homogeneous liquid is not expected to display more than one glass transition. Here we show that a family of homogeneous non-polymeric liquids—titanium tetraalkoxides—do exhibit two calorimetric glass transitions of comparable magnitude, one of which is the conventional glass transition associated with dynamic arrest of the bulk liquid properties, while the other is associated with the freezing out of intramolecular degrees of freedom. Such intramolecular vitrification is likely to be found in molecules in which low-frequency terahertz intramolecular motion is strongly coupled to the surrounding liquid. | Ben Russell; Mario González-Jiménez; Nikita Tukachev; Laure-Anne Hayes; Tajrian Chowdhury; Uroš Javornik; Gregor Mali; Manlio Tassieri; Joy Farnaby; Hans Senn; Klaas Wynne | Physical Chemistry; Materials Science; Inorganic Chemistry; Physical and Chemical Properties; Structure; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645cb7cef2112b41e95e6839/original/double-glass-transitions-in-single-component-homogeneous-liquids-due-to-intramolecular-vitrification.pdf |
60c75444ee301cddf5c7af25 | 10.26434/chemrxiv.13635284.v1 | Crosslinked Carbon Nano Dots Membranes for Organic Solvent Nanofiltration | We report a facile synthesis strategy of a membrane active
layer consisting of crosslinked carbon nano dots through a layer-by-layer
process and the application of these membranes in organic solvent
nanofiltration. The synthesized membrane is stable in organic solvents for a
long duration, displays tight molecular weight cut off, and fluoresces under UV
light, allowing one to capture mechanical failure. | Mahsa Abbaszadeh; Andrew Atkinson; Kevin Trinh; Santanu Kundu | Carbon-based Materials; Materials Processing; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75444ee301cddf5c7af25/original/crosslinked-carbon-nano-dots-membranes-for-organic-solvent-nanofiltration.pdf |
60dc0fde2962504c41e5c35a | 10.26434/chemrxiv-2021-bpv0c | Using Active Learning to Develop Machine Learning Models for Reaction Yield Prediction | Computer aided synthesis planning is a rapidly growing field for suggesting synthetic routes for molecules of interest. The methods used are usually dependent on access to large datasets for training, but with a finite experimental budget there are limitations on how much data can be obtained from experiments. Active learning, which has been used in recent studies with success, is a strategy to identify which data points impact model accuracy the most. However, little has been done to explore the robustness of the methods predicting reaction yield. This study aims to investigate the influence of machine learning algorithms and the number of initial data points on reaction yield prediction for two public high-throughput experimentation datasets. Our results show that active learning based on output margin reached a pre-defined accuracy (AUROC) faster than using passive learning. Feature importance analysis of the trained machine learning models suggested active learning had larger influence on the model accuracy when only a few features were important for the model prediction. | Simon Viet Johansson; Hampus Gummesson Svensson; Esben Bjerrum; Alexander Schliep; Morteza Haghir Chehreghani; Christian Tyrchan; Ola Engkvist | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2021-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60dc0fde2962504c41e5c35a/original/using-active-learning-to-develop-machine-learning-models-for-reaction-yield-prediction.pdf |
60c73e59567dfecf1fec37e4 | 10.26434/chemrxiv.6954908.v1 | Prediction of Chemical Reactions Using Statistical Models of Chemical Knowledge | Is chemistry discoverable or can it only be invented? – this is the question of a computer scientist and a philosopher of science when looking at application of artificial intelligence methods for developing new chemical entities and new chemical transformations. This study confirms that, at least today, chemistry is, in part, discoverable from past history of chemical research – the accumulated chemical data contains hidden rules of chemistry, which can be exploited to discover new reaction pathways. This is shown using a stochastic block model approach, trained on chemical reaction data obtained from Reaxys®. | Philipp-Maximilian Jacob; Alexei Lapkin | Organic Synthesis and Reactions; Machine Learning; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2018-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e59567dfecf1fec37e4/original/prediction-of-chemical-reactions-using-statistical-models-of-chemical-knowledge.pdf |
666355a012188379d8945c88 | 10.26434/chemrxiv-2024-1pt7b | In-line Thermal Desorption and Dielectric Barrier Discharge Ionization for Rapid Mass Spectrometry Detection of Explosives | Thermal desorption (TD) of wipe-based samples was coupled with an in-line dielectric barrier discharge ionization (DBDI) source and rugged compact time-of-flight mass spectrometer (MS) for the detection of explosives, propellants, and post-blast debris. The chromatography-free TD-DBDI-MS platform enabled rapid and sensitive detection of organic nitramine, nitrate ester, and nitroaromatic explosives, as well as black powder and black powder substitute propellants. Parametric investigations characterized the response to TD temperature, and optimized DBDI voltage, aerodynamically assisted entrainment, and fragmentation through in-source collision induced dissociation (isCID). Excess nitrate generated by the DBDI source yielded predominantly nitrate-adduct formation. Sub-nanogram sensitivities were demonstrated for all explosives investigated, except for nitroglycerin, specifically due to its volatility. Further, most analytes/explosives exhibited tens of picogram sensitivities. The platform also demonstrated the detection of propellant and military explosives from post-blast debris. The TD-DBDI-MS system performed well without the need for aerodynamically assisted entrainment (and the associated rough pump), which along with requiring no additional gasses (i.e., N2 ¬or He) or solvents, aid in potential field deployment. The ease of TD-DBDI attachment and removal added trace solid or liquid residue detection to the rugged mass spectrometer, designed primarily for analysis of volatile organic and inorganic compounds. | Thomas P Forbes; Elizabeth Robinson; Edward Sisco; Abigail Koss | Analytical Chemistry; Analytical Apparatus; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666355a012188379d8945c88/original/in-line-thermal-desorption-and-dielectric-barrier-discharge-ionization-for-rapid-mass-spectrometry-detection-of-explosives.pdf |
60c7574d0f50db531f398249 | 10.26434/chemrxiv.13604504.v2 | A Single Residue on the WPD-Loop Affects the pH Dependency of Catalysis in Protein Tyrosine Phosphatases | <p>Catalysis by protein tyrosine phosphatases (PTPs) relies on the motion of a flexible protein loop (the WPD-loop) that carries a residue acting as a general acid/base catalyst during the PTP-catalyzed reaction. The orthogonal substitutions of a non-catalytic residue in the WPD-loops of YopH and PTP1B results in shifted pH-rate profiles, from an altered kinetic p<i>K</i><sub>a</sub> of the nucleophilic cysteine. Compared to WT, the G352T YopH variant has a broadened pH-rate profile, similar activity at optimal pH, but significantly higher activity at low pH. Changes in the corresponding PTP1B T177G variant are more modest and in the opposite direction, with a narrowed pH profile and less activity in the most acidic range. Crystal structures of the variants show no structural perturbations, but suggest an increased preference for the WPD-loop closed conformation. Computational analysis confirms a shift in loop conformational equilibrium in favor of the closed conformation, arising from a combination of increased stability of the closed state and destabilization of the loop-open state. Simulations identify the origins of this population shift, revealing differences in the flexibility of the WPD-loop and neighboring regions. Our results demonstrate that changes to the pH dependency of catalysis by PTPs can result from small changes in amino acid composition in their WPD-loops affecting only loop dynamics and conformational equilibrium. The perturbation of kinetic p<i>K</i><sub>a</sub> values of catalytic residues by non-chemical processes affords a means for nature to alter an enzyme’s pH dependency by a less disruptive path than altering electrostatic networks around catalytic residues themselves. </p> | Ruidan Shen; Rory Crean; Sean Johnson; Shina Caroline Lynn Kamerlin; Alvan C. Hengge | Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7574d0f50db531f398249/original/a-single-residue-on-the-wpd-loop-affects-the-p-h-dependency-of-catalysis-in-protein-tyrosine-phosphatases.pdf |
6763791181d2151a022a86e2 | 10.26434/chemrxiv-2024-h73fg | Photocatalytic Branched Allylic C-H Oxygenation of Terminal Alkenes with Free Oxygen-Based Nucleophiles | Allylic ethers are important functional motifs widespread in bioactive molecules and natural products and serve as versatile synthetic intermediates for value-added target molecules. Therefore, developing general and direct methods to allylic ethers from feedstocks is highly desirable. Direct cross-coupling of alkenes with free alcohols by allylic C-H functionalization under mild conditions represents the most ideal way for the synthesis of branched allylic ethers. Herein, a dual catalysis of visible-light and cobaloxime enables allylic C-H direct oxygenation of alkenes with alcohols to afford branched allylic ethers has been developed. Notably, exclusive regio- and chemoselective mono-etherification of C-H bond to give branched allylic ethers with primary, secondary, and tertiary free alcohols. Moreover, other oxygen-based nucleophiles, such as carboxylate and cyclic 1,3-diketones, are also compatible in the reaction, providing a mild and robust allylic oxygenation of more steric hindered C-H from easily available alkenes. | Yu-Feng Ren; Jin-Kui Chen; Wei Shu | Organic Chemistry; Catalysis | CC BY 4.0 | CHEMRXIV | 2024-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6763791181d2151a022a86e2/original/photocatalytic-branched-allylic-c-h-oxygenation-of-terminal-alkenes-with-free-oxygen-based-nucleophiles.pdf |
61b990f9f52bc457f8c0fd2c | 10.26434/chemrxiv-2021-27lw3 | Frequency-selective Heteronuclear Correlation (FS-HETCOR) Experiments in Solid-State NMR | Heteronuclear correlation (HETCOR) is critical to obtain structural information in solid-state nuclear magnetic resonance (NMR). We propose novel frequency-selective Heteronuclear correlation (FS-HETCOR) experiments to selectively enhance the inter-atomic correlations of interest. FS-HETCOR relies on heteronuclear selective phase-optimized recoupling (SPRx), which is frequency-selective in heteronuclear recouping without using selective pulses. Compared to regular HETCOR, FS-HETCOR selectively enhances the desired heteronuclear correlations by a factor of up to 5 and suppresses the unwanted ones to 10% as demonstrated in 1H-19F and 1H-13C experiments under fast magic-angle spinning (MAS). Moreover, FS-HETCOR can theoretically be applied at arbitrary MAS rates by utilizing various SPRx schemes. We believe that the method will enhance the ability of solid-state NMR to probe heteronuclear structural information. | Zhengfeng Zhang; Yongchao Su; Jun Yang | Physical Chemistry; Analytical Chemistry; Analytical Chemistry - General; Spectroscopy (Anal. Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b990f9f52bc457f8c0fd2c/original/frequency-selective-heteronuclear-correlation-fs-hetcor-experiments-in-solid-state-nmr.pdf |
60c7453cf96a002c5c286b69 | 10.26434/chemrxiv.9989102.v1 | The Catalytic Acid-Base in GH109 Resides in a Conserved GGHGG Loop and Allows for Comparable α-Retaining and β-Inverting Activity in an N-Acetylgalactosaminidase from Akkermansia Muciniphila | The study describes the first glycoside hydrolase that exhibits comparable levels of activity on α- and β-linked saccharide substrates. This enzyme, assigned into GH109, is encoded by the genome of the human gut symbiont Akkermansia muciniphila that is a model primary degrader of the heavily O-glycosylated mucin glycoprotein that coats the epithelial enterocytes.The elusive catalytic acid/base catalyst in GH109 enzymes is identified as a histidine that is presented by a flexible loop that positions it for catalysis on both α- and β-substrates. This dual activity may be an evolutionary adaptation to extend the range of substrates targeted by a single non-canonical NAD+-dependant GH. <br /> | David Teze; Bashar Shuoker; Evan Kirk Chaberski; Ruth Sonja Kunstmann; Folmer Fredslund; Günther H.J. Peters; Eva Nordberg Karlsson; Ditte Hededam Welner; Maher Abou Hachem | Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7453cf96a002c5c286b69/original/the-catalytic-acid-base-in-gh109-resides-in-a-conserved-gghgg-loop-and-allows-for-comparable-retaining-and-inverting-activity-in-an-n-acetylgalactosaminidase-from-akkermansia-muciniphila.pdf |
62b35c4c7da6ce793f1bd0fb | 10.26434/chemrxiv-2022-m6x53 | Emergence of layered nanoscale mesh networks through intrinsic molecular confinement self-assembly | Block copolymer self-assembly is a powerful tool for 2D nanofabrication; however, its extension to complex 3D network structures, which would be useful for a range of applications, is limited. Here, we report a simple method to generate unprecedented 3D mesh morphologies through intrinsic molecular confinement self-assembly. We designed triblock bottlebrush polymers with two Janus domains: one perpendicular and one parallel to the polymer backbone. The former enforces a lamellar superstructure that intrinsically confines the intra-layer self-assembly of the latter, giving rise to a mesh-like monoclinic M15 network substructure with excellent long-range order. Dissipative particle dynamics simulations show that the spatial constraints exerted on the polymer backbone drive the emergence of M15, as well as a tetragonal T131 in the strong segregation regime. This work demonstrates intrinsic molecular confinement as a path to bottom-up assembly of new geometrical phases of soft matter, extending the capabilities of block copolymer nanofabrication. | Zehao Sun; Runze Liu; Tingyu Su; Hejin Huang; Ken Kawamoto; Ruiqi Liang; Bin Liu; Mingjiang Zhong; Alfredo Alexander-Katz; Caroline A. Ross; Jeremiah A. Johnson | Materials Science; Polymer Science; Nanoscience; Nanostructured Materials - Materials; Polymer morphology | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b35c4c7da6ce793f1bd0fb/original/emergence-of-layered-nanoscale-mesh-networks-through-intrinsic-molecular-confinement-self-assembly.pdf |
62025795a6fb4def254ebbde | 10.26434/chemrxiv-2022-j2zkd | Oxygen tolerant RAFT polymerisation initiated by living bacteria | Living organisms can synthesize a wide range of macromolecules from a small set of natural building blocks, yet there is potential for even greater materials diversity by exploiting biochemical processes to convert unnatural feedstocks into new abiotic polymers. Ultimately the synthesis of these polymers in situ might aid the coupling of organisms with synthetic matrices, and the generation of biohybrids or engineered living materials. The key step in biohybrid materials preparation is to harness the relevant biological pathways to produce synthetic polymers with predictable molar masses and defined architectures under ambient conditions. Accordingly, we report an aqueous, oxygen-tolerant RAFT polymerization platform based on a modified Fenton reaction which is initiated by Cupriavidus metallidurans CH34, a bacterial species with iron reducing capabilities. We show the synthesis of a range of water-soluble polymers under normoxic conditions, with control over the molar mass distribution, and also the production of block copolymer nanoparticles via polymerization-induced self-assembly. Finally, we highlight the benefits of using a bacterial initiation system by recycling the cells for multiple polymerisations. Overall, our method represents a highly versatile approach to producing well-defined polymeric materials within a hybrid natural-synthetic polymerization platform and in engineered living materials with properties beyond those of biotic macromolecules. | Cara Moloney; Mechelle R Bennett; Francesco Catrambone; Federico Turco; Katalin Kovacs; Phillip J Hill; Cameron Alexander; Frankie J Rawson; Pratik Gurnani | Polymer Science; Biopolymers | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62025795a6fb4def254ebbde/original/oxygen-tolerant-raft-polymerisation-initiated-by-living-bacteria.pdf |
64edd62b3fdae147fa119bbc | 10.26434/chemrxiv-2023-gr260 | Ion Transport and Inhibitor Binding by human NHE1: Insights from Molecular Dynamics Simulations and Free Energy Calculations | The human Na+/H+ exchanger one (hNHE1) plays a crucial role in maintaining intracellular pH by regulating the electroneutral exchange of a single intracellular H+ for one extracellular Na+ across the plasma membrane. Understanding the molecular mechanisms governing ion transport and the binding of inhibitors is of importance in the development of anticancer therapeutics targeting hNHE1. In this context, we performed molecular dynamics (MD) simulations based on the recent cryo-electron microscopy (cryo-EM) structures of outward and inward-facing conformations of hNHE1. These simulations allowed us to explore the dynamics of the protein, examine the ion- translocation pore and confirm that Asp267 is the ion-binding residue. Our free energy calculations suggest that Na+ and K+ bind similarly at the ion-binding site. Consequently, Na+ over K+ selectivity cannot be solely explained by differences in ion binding. Our MD simulations involving hNHE1 inhibitors (cariporide and amiloride analogues), showed maintained stable interactions with Asp267 and Glu346. Our study highlights the importance of the salt bridge between the positively charged acylguanidine moiety and Asp267, which appears to play a role in the competitive inhibitory mechanism for this class of inhibitors. Our computational study provides a detailed mechanistic interpretation of experimental data and serves the basis of future structure-based inhibitor design. | Nehad El Salamouni; Benjamin Buckley; Richmond Lee; Marie Ranson; Michael Kelso; Haibo Yu | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biophysics; Computational Chemistry and Modeling; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2023-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64edd62b3fdae147fa119bbc/original/ion-transport-and-inhibitor-binding-by-human-nhe1-insights-from-molecular-dynamics-simulations-and-free-energy-calculations.pdf |
6586b38766c1381729de7ddd | 10.26434/chemrxiv-2023-x6d2t | Real-time Monitoring of Photoinduced pH-jumps by In Situ Rapid-scan EPR Spectroscopy | This work represents the first demonstration of a light-induced pH-switchable process monitored by in situ rapid-scan (RS) electron paramagnetic resonance (EPR) spectroscopy on the millisecond timescale. Here, we investigate the protonation state of an imidazoline type raical as pH sensor under visible light irradiation of a merocyanine photoacid in bulk solution. The results highlight the utility of photoacids in combination with pH-sensitive spin probes as an effective tool for real-time investigation of biochemical mechanisms regulated by changes of the pH value. | Florian Johannsen; Lara Williams; Man Him Chak; Malte Drescher | Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6586b38766c1381729de7ddd/original/real-time-monitoring-of-photoinduced-p-h-jumps-by-in-situ-rapid-scan-epr-spectroscopy.pdf |
66cfee10a4e53c4876f2ce7f | 10.26434/chemrxiv-2024-x1824 | In Silico Screening of P,N-Ligands Facilitates Optimization of Au(III)-Mediated S-Arylation | Metal-mediated cysteine S-arylation is an emerging bioconjugation technique due to its high chemoselectivity, rapid kinetics, and aqueous compatibility. We have previously demonstrated that by altering the sterics of the ligand and aryl groups of an Au(III) oxidative addition complex, one can modulate the kinetics of the bimolecular coordination and induce rate constants up to 16,600 M^−1s^−1. To further enhance the rate of coordination, density functional theory (DFT) calculations were performed to investigate the steric properties of the P,N-ligated Au(III) oxidative addition complex as well as the thermodynamics of the S-arylation reaction. This allowed for the accelerated screening of 13 new Au(III) oxidative addition complexes. Three of the more sterically available, synthetically accessible P,N-ligands were synthesized, incorporated into Au(I) and Au(III) complexes, and their rates determined experimentally. The comprehensive mechanistic insights from the DFT calculations led to the development of new reagents with bimolecular coordination rate constants as fast as 20,200 M^−1s^−1. Further experimental characterization of these reagents’ efficacy as S-arylation reagents led to a proposed switch in selectivity-determining step for the fastest reagent, which was further confirmed by profiling the reductive elimination kinetics. This work provides a concise workflow for the screening of metal-mediated cysteine S-arylation reagents and new fundamental insights into the coordination chemistry behavior of Au(III) systems. | Joseph Treacy; James Tilden; Elaine Chao; Zihuan Fu; Alexander Spokoyny; Kendall Houk; Heather Maynard | Theoretical and Computational Chemistry; Organic Chemistry; Organometallic Chemistry; Physical Organic Chemistry; Kinetics and Mechanism - Organometallic Reactions; Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cfee10a4e53c4876f2ce7f/original/in-silico-screening-of-p-n-ligands-facilitates-optimization-of-au-iii-mediated-s-arylation.pdf |
60c745ebee301c9839c793f5 | 10.26434/chemrxiv.9031346.v3 | Native Defects and their Doping Response in the Lithium Solid Electrolyte Li7La3Zr2O12 | <p>The Li-stuffed garnets Li<sub><i>x</i></sub>M<sub>2</sub>M<sub>3</sub>′O<sub>12</sub> are promising Li-ion solid electrolytes with potential use in solid-state batteries. One strategy for optimising ionic conductivities in these materials is to tune lithium stoichiometries through aliovalent doping, which is often assumed to produce proportionate numbers of charge compensating Li vacancies. The native defect chemistry of the Li-stuffed garnets, and their response to doping, however, are not well understood, and it is unknown to what degree a simple vacancy-compensation model is valid. Here, we report hybrid density-functional–theory calculations of a broad range of native defects in the prototypical Li-garnet Li<sub>7</sub>La<sub>3</sub>Zr<sub>2</sub>O<sub>12</sub>. We calculate equilibrium defect concentrations as a function of synthesis conditions, and model the response of these defect populations to extrinsic doping. We predict a rich defect chemistry that includes Li and O vacancies and interstitials, and significant numbers of cation-antisite defects. Under reducing conditions, O vacancies act as colour-centres by trapping electrons. We find that supervalent (donor) doping does not produce charge compensating Li vacancies under all synthesis conditions; under Li-rich / Zr-poor conditions the dominant compensating defects are Li<sub>Zr</sub> antisites, and Li stoichiometries strongly deviate from those predicted by simple “vacancy compensation” models.<br /></p> | Alex Squires; David Scanlon; Benjamin Morgan | Ceramics; Theory - Inorganic; Computational Chemistry and Modeling; Energy Storage; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745ebee301c9839c793f5/original/native-defects-and-their-doping-response-in-the-lithium-solid-electrolyte-li7la3zr2o12.pdf |
60c74e0d0f50db8d0e397142 | 10.26434/chemrxiv.12593381.v3 | Modeling the Ternary Chalcogenide Na2MoSe4 from First-Principles | In the ongoing pursuit of inorganic compounds suitable for solid-state devices, transition metal
chalcogenides have received heightened attention due to their physical and chemical properties.
Recently, alkali-ion transition metal chalcogenides have been explored as promising candidates to
be applied in optoelectronics, photovoltaics and energy storage devices. In this work, we present
a comprehensive theoretical study of sodium molybdenum selenide (Na<sub>2</sub>MoSe<sub>4</sub>). First-principles
computations were performed on a set of hypothetical crystal structures to determine the ground
state and electronic properties of Na<sub>2</sub>MoSe<sub>4</sub>. We find that the equilibrium structure of Na<sub>2</sub>MoSe<sub>4</sub>
is a simple orthorhombic (<i>oP</i>) lattice, with space group Pnma, as evidenced by thermodynamics.
Electronic structure computations reveal that three phases are semiconducting, while one (<i>cF</i>) is
metallic. Relativistic effects and Coulomb interaction of localized electrons were assessed for the
<i>oP</i> phase, and found to have a negligible influence on the band strucutre. Finally, meta-GGA
computations were performed to model the band structure of primitive orthorhombic Na<sub>2</sub>MoSe<sub>4</sub>
at a predictive level. We employ the Tran-Blaha modified Becke-Johnson potential to demonstrate
that <i>oP</i> Na2MoSe4 is a semiconductor with a direct bandgap of 0.53 eV at the <b>Γ</b> point. Our
results provide a foundation for future studies concerned with the modeling of inorganic and hybrid
organic-inorganic materials chemically analogous to Na<sub>2</sub>MoSe<sub>4</sub>.<br /> | Etienne Palos; Armando Reyes-Serrato; Gabriel Alonso-Nuñez; J. Guerrero Sánchez | Solid State Chemistry; Theory - Inorganic; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e0d0f50db8d0e397142/original/modeling-the-ternary-chalcogenide-na2mo-se4-from-first-principles.pdf |
628a9abfa42e9c51274a147d | 10.26434/chemrxiv-2022-r0xbx | MPACT: An Advanced Informatics Tool for Metabolomics and Data Visualization of Specialized Metabolites from Complex Microbial Samples | Untargeted metabolomics is a powerful tool for investigating chemistry of complex biological systems but its utility is compromised by the presence of uninformative features and the limited efficiency of currently available prioritization tools. More effective filtering and prioritization tools are required to address the challenges of large untargeted metabolomics datasets. Here, we introduce MPACT (Metabolomics Peak Analysis Computational Tool), a new mass spectrometry data analysis platform employing filtering based on multiple modalities, statistical techniques incorporating multilevel replication, and interactive data visualization. We demonstrate application of MPACT to uncover hidden effects of the rare earth element (REE) cerium on tunicate-associated bacterium Streptomyces sp. PTY087I2. Using this method, we have identified key autoregulators, siderophores. and a suite of structurally diversified granaticins, culminating in characterization of two thiolated compounds including a new cysteine derivative, granaticin C, and granaticin D, recently described as mycothiogranaticin A. MPACT is readily adaptable to investigation of other systems. | Robert Samples; Sara Puckett; Marcy Balunas | Biological and Medicinal Chemistry; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628a9abfa42e9c51274a147d/original/mpact-an-advanced-informatics-tool-for-metabolomics-and-data-visualization-of-specialized-metabolites-from-complex-microbial-samples.pdf |
60c75669842e6514a8db44dd | 10.26434/chemrxiv.14237690.v1 | Iron(II) Complexes Featuring a Redox-Active Dihydrazonopyrrole Ligand | <div>Nature uses control of the secondary coordination sphere</div><div>to facilitate an astounding variety of transformations. Similarly, synthetic chemists have found metal-ligand cooperativity to be a powerful strategy for designing complexes that can mediate challenging reactivity. In particular, this strategy has been used to facilitate two electron reactions with first row transition metals that</div><div>more typically engage in one electron redox processes. While NNN pincer ligands feature prominently in this area, examples which can potentially engage in both proton and electron transfer are less common. Dihydrazonopyrrole (DHP) ligands have been isolated in a variety of redox and protonation states when complexed to Ni. However, the redox-state of this ligand scaffold is less obvious when</div><div>complexed to metal centers with more accessible redox couples. Here, we synthesize a new series of Fe-DHP complexes in two distinct oxidation states. Detailed characterization supports that the redox chemistry</div><div>in this set is still primarily ligand based. Finally, these</div><div>complexes exist as 5-coordinate species with an open coordination site offering the possibility of enhanced reactivity.</div> | Kate Jesse; Mu-Chieh Chang; Alexander S. Filatov; John Anderson | Ligands (Inorg.); Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.); Coordination Chemistry (Organomet.); Ligand Design; Ligands (Organomet.); Transition Metal Complexes (Organomet.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75669842e6514a8db44dd/original/iron-ii-complexes-featuring-a-redox-active-dihydrazonopyrrole-ligand.pdf |
6318f812bc257badbede9014 | 10.26434/chemrxiv-2022-1874n | Free Radical-based Sequencing for Native Top-Down Mass Spectrometry | ABSTRACT: Native top-down proteomics allows for both proteoform identification and high-order structure characteri-zation for cellular protein complexes. Unfortunately, tandem MS-based fragmentation efficiencies for such targets are low due to an increase in analyte ion mass and the low ion charge states that characterize native MS data. Multiple fragmenta-tion methods can be integrated in order to increase protein complex sequence coverage, but this typically requires use of specialized hardware and software. Free-radical initiated peptide sequencing (FRIPS) enables access to charge-remote and electron-based fragmentation channels within the context of conventional CID experiments. Here, we optimize FRIPS la-belling for native top-down sequencing experiments. Our labelling approach is able to access intact complexes with TEMPO-based FRIPS reagents without significant protein denaturation or assembly disruption. By combining CID and FRIPS datasets, we observed sequence coverage improvements as large as 50% for protein complexes ranging from 36 kDa to 106 kDa. Fragment ion production in these experiments was increased by as much as 102%. In general, our results indicate that TEMPO-based FRIPS reagents have the potential to dramatically increase sequence coverage obtained in na-tive top-down experiments. | Carolina Rojas Ramirez; Rayan Murtada; Jinshan Gao; Brandon Ruotolo | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6318f812bc257badbede9014/original/free-radical-based-sequencing-for-native-top-down-mass-spectrometry.pdf |
60c74faf567dfe45c8ec5720 | 10.26434/chemrxiv.12931484.v1 | Decarboxylative Amination: Diazirines as Single and Double Electrophilic Nitrogen Transfer Reagents | <p>The ubiquity of nitrogen-containing small molecules in medicine necessitates the continued search for improved methods for C–N bond formation. Electrophilic amination often requires a disparate toolkit of reagents whose selection depends on the specific structure and functionality of the substrate to be aminated. Further, many of these reagents are challenging to handle, engage in undesired side reactions, and function only within a narrow scope. Here we report the use of diazirines as practical reagents for the decarboxylative amination of simple and complex redox-active esters. The diaziridines thus produced are readily diversifiable to amines, hydrazines, and nitrogen-containing heterocycles in one step. The reaction has also been applied in fluorous phase synthesis with a perfluorinated diazirine.</p> | Preeti P. Chandrachud; Lukasz Wojtas; Justin Lopchuk | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74faf567dfe45c8ec5720/original/decarboxylative-amination-diazirines-as-single-and-double-electrophilic-nitrogen-transfer-reagents.pdf |
675eb3547be152b1d00b6ce5 | 10.26434/chemrxiv-2024-f3tc4 | Synthesis of Substituted N -Benzylidene- N' -(2,4
dinitrophenyl)hydrazine and their Acidochromic Behaviour | Substituted 2,4-dinitrophenylhydrazone Schiff bases were efficiently synthesized
using microwave-induced organic reaction enhancement techniques. Different spectral techniques
UV–Visible, Fourier transform infrared (FTIR), and 1HNMR) were used to analyze the prepared
compounds (1a–1c). The hydrazone Schiff bases showed obvious acidochromic properties. The
acidochromic behavior of substituted 2,4-dinitrophenylhydrazone Schiff bases were investigated
by doping HCl in 3 different polar protic and aprotic solvent systems. The hyperchromic shift was
observed in all three compounds in polar protic and aprotic solvent systems. In contrast to protic
solvent, the hypsochromic shift was observed with an isosbestic point for all three compounds in
polar aprotic solvent systems. These spectral changes can be attributed to successive protonation
of the –C=N-chromophore. In order to probe this assumption, theoretical calculation was carried
out using TD/DFT/ B3LYP/6-311+G(d,p) level of theory with different solvent system. For
comparison the unprotonated and the protonated structure of UV–Vis spectra between
computational and experimental findings were also performed. These results are in good
agreement with the experimental data. | Ariful Islam; Md Kabidur Rahman; Md Mizanur Rahman Badal; Md Khabir Uddin; Md Maniruzzaman; Md Abu Yousuf | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675eb3547be152b1d00b6ce5/original/synthesis-of-substituted-n-benzylidene-n-2-4-dinitrophenyl-hydrazine-and-their-acidochromic-behaviour.pdf |
613081028e38a3bd644709da | 10.26434/chemrxiv-2021-jnpgl | MolAR: Bringing Chemical Structures to Life with
Augmented Reality and Machine Learning | Visualizing three-dimensional molecular structures is crucial to understanding and predicting their chemical behavior. Existing visualization software, however, can be cumbersome to use, and, for many, hand-drawn skeletal structures remain the preferred method of chemical communication. Although convenient, the static, two-dimensional nature of these drawings can be misleading in conveying the molecule’s 3D structure, not to mention that dynamic movement is completely disregarded. Here, we combine machine learning and augmented reality (AR) to develop MolAR, an immersive mobile application for visualizing molecules in real-world scenes. The application uses deep learning to recognize hand-drawn hydrocarbons structures which it converts into interactive 3D molecules in AR. Users can also “hunt” for chemicals in food and drink to uncover molecules in their real-life environment. A variety of interesting molecules are pre-loaded into the application, and users can visualize molecules in PubChem by providing their name or SMILES string and proteins in the Protein Data Bank by providing their PDB ID. MolAR was designed to be used in both research and education settings, providing an almost barrierless platform to visualize and interact with 3D molecular structures in a uniquely immersive way. | Sukolsak Sakshuwong; Hayley Weir; Umberto Raucci; Todd J. Martínez | Chemical Education; Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613081028e38a3bd644709da/original/mol-ar-bringing-chemical-structures-to-life-with-augmented-reality-and-machine-learning.pdf |
660f5f2891aefa6ce1d257e5 | 10.26434/chemrxiv-2024-ms4fs-v2 | On the thermodynamic feasibility of acid-base equilibria | Most undergraduate Organic chemistry textbooks contain a section on the general acid-base equilibria, strength of acids and bases, and predicting the equilibrium position of acid-base reactions (1-3). The students are taught to qualitatively predict the directions of these reactions using only the acid/base strengths or acid/base constants (pKa/pKb) without elaborating how or why they work. For example, statements like ‘stronger acids/bases tend to move towards weaker forms’ are not good explanations (1-3). Moreover, finding an answer in Analytical and Physical chemistry textbooks specific to this question is challenging (4-6). The simple thermodynamic framework put forward here can easily explain why these predictions work and allow one to quantify the direction of acid-base reactions. | Gayan Senavirathne | Chemical Education | CC BY 4.0 | CHEMRXIV | 2024-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660f5f2891aefa6ce1d257e5/original/on-the-thermodynamic-feasibility-of-acid-base-equilibria.pdf |
65c62d3d66c138172949876d | 10.26434/chemrxiv-2024-wdm73 | Silk Composite-based Multifunctional Pellets for Controlled Drug Release toward Advanced Wound Care | Chronic wounds pose a significant challenge in clinical settings due to their high risk of infections (by a mixed population of bacterial strains) and persistent inflammation. In this scenario, personalized treatment options are crucial but are limited by the complex fabrication techniques of the existing products. To this end, calcium sulfate hemihydrate (CSH)-based cement offers rapid fabrication but lacks other essential properties for promoting healing. To overcome this, herein tannic acid (TA) was added to create a multifunctional drug delivery platform. Nonetheless, direct loading of TA led to burst release, rendering it inefficient for long-term applications. Therefore, we aimed to engineer a complex of TA with silk fibroin (SF) to achieve sustained release. In this study, a multifunctional silk/bioceramic composite-based cement was developed, intended for use in point-of-care settings. The cement was cast into pellets for further evaluation. Compared to neat pellets, the composite pellets exhibited a 7.5-fold increase in antioxidant activity and prolonged antibacterial efficacy (up to 13 days). Moreover, the implantation of the pellets showed no hallmarks of local or systemic toxicity in a rodent model. The developed multifunctional composite cement proves to be a promising solution for the personalized treatment of chronic wounds designed for application in point-of-care settings. | Sushma Indrakumar; Sriram Gugulothu; Akshat Joshi; Tapan Dash; Vivek Mishra; Bharat Tandon; Kaushik Chatterjee | Materials Science; Biocompatible Materials | CC BY NC 4.0 | CHEMRXIV | 2024-02-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c62d3d66c138172949876d/original/silk-composite-based-multifunctional-pellets-for-controlled-drug-release-toward-advanced-wound-care.pdf |
60c75777f96a00570c288c85 | 10.26434/chemrxiv.14400953.v1 | How to Manipulate Through-Space Conjugation and Clusterolumi-nescence of Simple AIEgens with Isolated Phenyl Rings? | <a>Apart from the
traditional through-bond conjugation (TBC), through-space conjugation (TSC) is
gradually proved as another important interaction in photophysical processes,
especially for the recent observation of clusteroluminescence from
nonconjugated molecules. </a>Herein, <a>simple
and nonconjugated triphenylmethane (TPM) and its derivatives with
electron-donating and electron-withdrawing groups were synthesized</a>, and
their photophysical properties were systematically studied. <a>TPM was characterized with visible clusteroluminescence due
to the intramolecular TSC. Experimental and theoretical results showed that the
introduction of electron-donating groups into TPM could </a><a>red-shift </a>the wavelength and increase the efficiency of
clusteroluminescence simultaneously, due to the increased electronic density
and stabilization of TSC. However, TPM derivatives with electron-withdrawing
groups showed inefficient or even quenched clusteroluminescence caused by the
vigorous excited-state intramolecular motion and intermolecular photoinduced
electron transfer process. This work provides a reliable strategy to manipulate
TSC and clusteroluminescence. | Jianyu Zhang; lianrui hu; Kaihua Zhang; Junkai LIU; Xingguang Li; Haoran Wang; Zhaoyu Wang; Herman H.-Y. Sung; ian duncan williams; Zebing Zeng; Jacky W. Y. Lam; Haoke Zhang; Ben Zhong Tang | Quantum Computing; Clusters; Physical and Chemical Properties; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75777f96a00570c288c85/original/how-to-manipulate-through-space-conjugation-and-clusterolumi-nescence-of-simple-ai-egens-with-isolated-phenyl-rings.pdf |
60c748f34c8919b56bad2fe6 | 10.26434/chemrxiv.12003786.v1 | New Code for DNA Nucleotide Sequences | DNA nucleotides consist of the complementary base pairs of Adenine-Thymine (A-T) and Cytosine-Guanine (C-G) that encode as a sequence for genes, and encode for an upstream initiation site that enables transcription. Recently, this lab has shown that steroid hormones are structurally symmetric with each of the four DNA nucleotide pairs and through an ionic binding process may enable gene transcription. Here, a new code is developed for DNA nucleotide sequences that relates to the initiation site for gene transcription. The structural code consists of the orientation of steroid molecules in binding to DNA nucleotides and the class of steroid molecules that form an intermolecular hydrogen bond with an available functional group of Thymine. This later class thereby describes a steroid hormone-DNA nucleotide-ion complex with three hydrogen bonds for A-T and T-A, which thereby matches the three internal hydrogen bonds associated with C-G and G-C. The code consists of two binary vectors to characterize the four configurations of DNA nucleotides and is shown to be consistent with known regulatory elements of DNA sequences associated with gene transcription, including the TATA box and the E-Box, along with other promoters. In addition, the code, which is bijective, is applied to analyze the DNA sequence associated with SARS-CoV-2 to identify regions with relevant structural characteristics. | Charles Schaper | Biochemistry; Bioinformatics and Computational Biology; Biophysics; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748f34c8919b56bad2fe6/original/new-code-for-dna-nucleotide-sequences.pdf |
60c7498cf96a00cb5428729b | 10.26434/chemrxiv.11231153.v2 | Superionic Lithium Intercalation through 2 nm x 2 nm Columns in the Crystallographic Shear Phase Nb18W8O69 | <p>Nb<sub>18</sub>W<sub>8</sub>O<sub>69</sub> (9Nb<sub>2</sub>O<sub>5</sub>×8WO<sub>3</sub>) is the tungsten-rich end-member of the Wadsley–Roth crystallographic shear (<i>cs</i>) structures within the Nb<sub>2</sub>O<sub>5</sub>–WO<sub>3</sub> series. It has the largest block size of any known, stable Wadsley–Roth phase, comprising 5 x 5 units of corner-shared MO<sub>6</sub> octahedra between the shear planes, giving rise to 2 nm x 2 nm blocks. Rapid lithium intercalation is observed in this new candidate battery material and <sup>7</sup>Li pulsed field gradient nuclear magnetic resonance spectroscopy – measured in a battery electrode for the first time at room temperature – reveals superionic lithium conductivity with Li diffusivities at 298 K predominantly between 10<sup>–10</sup> and 10<sup>–12</sup> m<sup>2</sup>·s<sup>–1</sup>. In addition to its promising rate capability, Nb<sub>18</sub>W<sub>8</sub>O<sub>69</sub> adds a piece to the larger picture of our understanding of high-performance Wadsley–Roth complex metal oxides.</p> | Kent Griffith; Clare P. Grey | Electrochemistry; Solid State Chemistry; Spectroscopy (Inorg.); Energy Storage | CC BY 4.0 | CHEMRXIV | 2020-03-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7498cf96a00cb5428729b/original/superionic-lithium-intercalation-through-2-nm-x-2-nm-columns-in-the-crystallographic-shear-phase-nb18w8o69.pdf |
60c73f61469df4684df42ac5 | 10.26434/chemrxiv.7332764.v1 | Hundreds of Unrecognized Halogenated Contaminants Discovered in Polar Bear Blood | <p>Exposure of polar bears (<i>Ursus maritimus</i>) to persistent organic
pollutants was discovered in the 1970s, but recent evidence suggests the
presence of unknown toxic chemicals in their blood. Protein and phospholipid
depleted serum was stirred with polyethersulfone capillaries to extract a broad
range of analytes, and nontarget mass spectrometry with “fragmentation
flagging” was used for detection. Hundreds of analytes were discovered
belonging to 13 classes, including novel polychlorinated biphenyl (PCB)
metabolites and many fluorinated or chlorinated substances not previously
detected. All analytes were detected in the oldest (mid-1980s) archived polar
bear serum from Hudson Bay and Beaufort Sea, and all fluorinated classes showed
increasing trends. A mouse experiment confirmed the novel PCB metabolites,
suggesting that these could be widespread in mammals. Historical exposure and
toxic risk has been underestimated, and emerging contaminants pose uncertain
risks to this threatened species<br /></p><br /> | Yanna Liu; Evan S. Richardson; Andrew E. Derocher; Nicholas J. Lunn; Hans-Joachim Lehmler; Xueshu Li; Yifeng Zhang; Julia Yue Cui; Lihua Cheng; Jonathan W. Martin | Environmental Science; Environmental Analysis; Mass Spectrometry; Environmental biology | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f61469df4684df42ac5/original/hundreds-of-unrecognized-halogenated-contaminants-discovered-in-polar-bear-blood.pdf |
60c754adee301c4e65c7afd7 | 10.26434/chemrxiv.13710097.v1 | Strategic Design of Catalytic Lysine-Targeting Reversible Covalent BCR-ABL Inhibitors | Targeted covalent
inhibitors have re-emerged as validated drugs to overcome acquired resistance
in cancer treatment. Herein, by using a carbonyl boronic acid warhead, we
report the structure-based design of BCR-ABL inhibitors via reversible covalent
targeting of the catalytic lysine with improved single-digit nanomolar potency
against both wild-type and mutant ABL kinases, especially ABL<sup>T315I</sup>
bearing the gatekeeper residue mutation. We show that, by using techniques
including mass spectrometry, time-dependent biochemical assays and X-ray
crystallography, the evolutionarily conserved lysine can be targeted
selectively. Furthermore, we show that the selectivity depends largely on molecular
recognition of the non-covalent pharmacophore in this class of inhibitors,
probably due to the moderate reactivity of the warhead. We report the first
co-crystal structures of covalent inhibitor-ABL kinase domain complexes,
providing insights into the interaction of this warhead with the catalytic
lysine. We also employed label-free mass spectrometry to evaluate potential
off-targets of our compounds at proteome-wide level in different cancer cell
lines. | David Quach; Guanghui Tang; Jothi Anantharajan; Nithya Baburajendran; Anders Poulsen; John Wee; Priya Retna; Rong Li; Boping Liu; Doris Tee; Perlyn Kwek; Joma Joy; Wan-Qi Yang; Chong-Jing Zhang; Klement Foo; Thomas Keller; Shao Yao | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754adee301c4e65c7afd7/original/strategic-design-of-catalytic-lysine-targeting-reversible-covalent-bcr-abl-inhibitors.pdf |
64065a840e6a36fabad8a14a | 10.26434/chemrxiv-2023-sxb07 | NMR AS A TOOL FOR COMPOUND IDENTIFICATION IN MIXTURES | Natural products and metabolomics are intrinsically linked by the efforts of analyzing complex mixtures for compound annotation. Although most of the studies that aims for compound identification in mixtures use MS as the main analysis technique, NMR has complementary advances that are worth exploring for enhanced structure confidence. This review intends to showcase a portfolio of the main tools available for compound identification using NMR. COLMAR, SMART-NMR, MADByTE, and NMRfilter are presented using examples collected with real samples from the perspective of a natural products chemist. | Ricardo Moreira Borges; Gabriela de Assis Ferreira; Mariana Martins Campos; Andrew Magno Teixeira; Fernanda das Neves Costa; Fernanda Oliveira das Chagas; Maxwell Colonna | Analytical Chemistry | CC BY 4.0 | CHEMRXIV | 2023-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64065a840e6a36fabad8a14a/original/nmr-as-a-tool-for-compound-identification-in-mixtures.pdf |
63a2c483e8047a13c9f0c177 | 10.26434/chemrxiv-2022-g9lqd | The Radiative Surface Hopping (RSH) algorithm: capturing fluorescence events in molecular systems within a semi-classical Non-Adiabatic Molecular Dynamics framework | In this article, we present the Radiative Surface Hopping (RSH) algorithm which enables to model fluores- cence within a semi-classical Non-Adiabatic Molecular Dynamics framework. The algorithm has been tested for the photodeactivation dynamics of trans-4-Dimethylamino-4’-cyanostilbene (DCS). By treating on equal footing radiative and non-radiative processes, our method allows to attain a complete molecular movie of the excited-state deactivation. Our dynamics rely on a semiempirical quantum mechanical/molecular mechanical (QM/MM) Hamiltonian and has been run for hundreds of picoseconds, both in the gas phase and in isopropyl ether. The proposed approach successfully captures the first fluorescence processes occurring in DCS and it suc- ceeds in reproducing the experimental fluorescence lifetime and quantum yield, especially in the polar solvent. The analysis of the geometrical features of the emissive species during the dynamics discards the hypothesis of a twisted intramolecular charge transfer (TICT) state to be responsible for the dual emission observed experimen- tally in some polar solvents. In a nutshell, our method opens the way for theoretical studies on early-fluorescence events occurring up to hundreds of picoseconds in molecular systems. | Manuel Pérez-Escribano; Joanna Jankowska; Giovanni Granucci; Daniel Escudero | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2022-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a2c483e8047a13c9f0c177/original/the-radiative-surface-hopping-rsh-algorithm-capturing-fluorescence-events-in-molecular-systems-within-a-semi-classical-non-adiabatic-molecular-dynamics-framework.pdf |
6777b7e16dde43c90828b5f5 | 10.26434/chemrxiv-2025-qhh28-v2 | Techno-economic Impact of Incineration-Based Waste to Energy Generation Technology in Bangladesh: A Short Review and A Case Study | This study evaluates the feasibility of a municipal solid waste incineration-based power generation system in Dhaka, Bangladesh, addressing critical issues of waste management and energy deficits driven by rapid urbanization. A 10 MW waste-to-energy facility operating at 22.5% efficiency was analyzed using key economic metrics, including Net Present Value (NPV), Payback Period, Internal Rate of Return (IRR), Modified Internal Rate of Return (MIRR), Levelized Cost of Energy (LCOE), and Levelized Cost of Waste (LCOW). The analysis reveals an NPV of $4.99 million, an IRR exceeding 10%, and a payback period of 11.06 years, indicating economic viability. Additionally, the plant is projected to reduce annual CO2 emissions by 0.045 million tons, contributing to environmental sustainability. The findings demonstrate that waste-to-energy technology offers a viable solution for mitigating urban waste challenges while enhancing energy security, providing a sustainable pathway for Dhaka’s development and a model for similar urban context. | Mohammad Masrur Hossain; Tanvir Shahriar ; Md. Navid Inan ; M. Ahsan Habib; M. Hasanuzzaman; Mohammad Mehran Hossain | Energy | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6777b7e16dde43c90828b5f5/original/techno-economic-impact-of-incineration-based-waste-to-energy-generation-technology-in-bangladesh-a-short-review-and-a-case-study.pdf |
674a8c057be152b1d06f29c4 | 10.26434/chemrxiv-2024-srjwx | Nuclear Quantum Effects Across Chemical Space | Nuclear quantum effects (NQEs) are important in many physical and chemical processes--particularly those involving lighter nuclei or occurring at low temperatures. Nevertheless, NQEs have been carefully quantified in few systems, such as water, and their importance is rarely considered. Here, using path-integral molecular dynamics, we critically examine NQEs for a range of molecular properties (e.g., density, thermal expansion coefficients, isothermal compressibility, static dielectric constant, and the heat of vaporization) across 87 molecular liquids. We discover substantial NQEs in this broad chemical space, with molar volumes exhibiting differences of up to 5% between classical and quantum treatments; similar magnitudes are revealed in equilibrium isotope effects from deuteration. Using machine learning, we identify that four molecular properties that are readily known or easily computed with classical simulations—density, molar mass, hydrogen density, and thermal expansion coefficient—are strong predictors of NQEs. Further data-driven analysis reveals how molecular factors, such as branching and heteroatom composition, influence intermolecular interactions and fluid stability and thereby affect observed NQEs. This work offers new insights into the relationship between NQEs and molecular chemistry and refines expectations for when rigorous treatment of NQEs is necessary. | Michael Webb; Baris Ugur | Physical Chemistry; Materials Science; Earth, Space, and Environmental Chemistry; Physical and Chemical Properties; Thermodynamics (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674a8c057be152b1d06f29c4/original/nuclear-quantum-effects-across-chemical-space.pdf |
6675674601103d79c5c48527 | 10.26434/chemrxiv-2024-dkzt7 | Nucleo-SAFARI: Automated Identification of Fragment Ions in Top-Down MS/MS Spectra of Nucleic Acids | Recent progress in top-down mass spectrometry analysis of progressively larger nucleic acids has enabled in-depth characterization of intact, modified RNA molecules. Development of methods for desalting and MS/MS fragmentation allows rapid acquisition of high-quality top-down MS/MS spectra of nucleic acids up to 100 nt, which has spurred the need for development of software approaches to identify and validate nucleic acid fragment ions. We have implemented an R-based approach to aid in analysis of MS/MS spectra of nucleic acids based on fragment ions observed directly in the m/z domain. This program, entitled Shiny Application for Fragment Assignment by Relative Isotopes (Nucleo-SAFARI), utilizes the Shiny HTML framework for deployment of a user-friendly application for automated annotation of top-down MS/MS spectra of nucleic acids recorded on Orbitrap mass spectrometer platforms. This approach proceeds through in silico generation of fragment ions and their isotopic distributions, followed by algorithmic assessment of the experimental isotopic distributions. Nucleo-SAFARI is available for download at: https://github.com/mblanzillotti/Nucleo-SAFARI. | Michael Lanzillotti; Jennifer Brodbelt | Analytical Chemistry; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2024-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6675674601103d79c5c48527/original/nucleo-safari-automated-identification-of-fragment-ions-in-top-down-ms-ms-spectra-of-nucleic-acids.pdf |
64ff2914b338ec988a4a6274 | 10.26434/chemrxiv-2023-9djz2-v2 | Redox-Based Defect Detection in Packed DNA: Insights from Hybrid Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations | The impact of an 8-oxoguanine (8oxoG) defect on the redox properties of DNA within the Nucleosome Core Particle (NCP) was investigated employing hybrid Quantum Mechanical/Molecular Mechanics (QM/MM) molecular dynamics simulations of native and 8oxoG-containing NCP systems with an explicit representation of a biologically relevant environment. Two distinct NCP positions with varying solvent accessibility were considered for 8oxoG insertion. In both cases, it is found that the presence of 8oxoG drastically decreases the redox free energy of oxidation, by roughly 1 eV, very similar to what was recently reported for free native and 8oxoG-containing DNA. In contrast, the effect of 8oxoG on the reorganization free energy is even smaller for packed DNA (decrease of 0.13 eV and 0.01 eV for defect-free and defect-containing systems respectively) compared to the one of free DNA (0.25 eV), consistent with the increased rigidity of the NCP as compared to free DNA. Furthermore, the presence of an 8oxoG defect does not yield any significant changes in packed DNA structure. Such a conclusion favors the idea that also in the case of chromatin, defect-induced changes in DNA redox chemistry can be exploited to detect damaged bases via DNA mediated hole transfer. | Murat Kılıç; Polydefkis Diamantis; Sophia K. Johnson; Oliver Toth; Ursula Rothlisberger | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ff2914b338ec988a4a6274/original/redox-based-defect-detection-in-packed-dna-insights-from-hybrid-quantum-mechanical-molecular-mechanics-molecular-dynamics-simulations.pdf |
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