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60c74640ee301c24abc794a6
|
10.26434/chemrxiv.11247284.v1
|
Intra- and Intermolecular Interception of a Photochemically Generated Terminal Uranium Nitride
|
<p>The photochemically generated synthesis of a terminal uranium nitride species is here reported and an examination of its intra- and intermolecular chemistry is presented. Treatment of the U(III) complex L<sup>Ar</sup>UI(DME) ((L<sup>Ar</sup>)<sup>2-</sup>= 2,2”-bis(Dippanilide)-<i>p</i>-terphenyl; Dipp = 2,6-diisopropylphenyl) with LiNIm<sup>Dipp </sup>((NIm<sup>Dipp</sup>)<sup>–</sup>= 1,3-bis(Dipp)-imidaozolin-2-iminato) generates the sterically congested 3<i>N</i>-coordinate compound L<sup>Ar</sup>U(NIm<sup>Dipp</sup>) (<b>1</b>). Complex <b>1</b>reacts with 1 equiv of Ph<sub>3</sub>CN<sub>3</sub>to give the U(IV) azide L<sup>Ar</sup>U(N<sub>3</sub>)(NIm<sup>Dipp</sup>) (<b>2</b>). Structural analysis of <b>2</b>reveals inequivalent N<sub>α</sub>-N<sub>β</sub>> N<sub>β</sub>-N<sub>γ</sub>distances indicative of an activated azide moiety predisposed to N<sub>2</sub>loss. Room-temperature photolysis of benzene solutions of <b>2</b>affords the U(IV) amide (<i>N</i>-L<sup>Ar</sup>)U(NIm<sup>Dipp</sup>) (<b>3</b>) via intramolecular <i>N</i>-atom insertion into the benzylic C-H bond of a pendant isopropyl group of the (L<sup>Ar</sup>)<sup>2- </sup>ligand. The formation of <b>3</b>occurs as a result of the intramolecular interception of the intermediately generated, terminal uranium nitride (L<sup>Ar</sup>)U(N)(NIm<sup>Dipp</sup>) (<b>3’</b>). Evidence for the formation of <b>3’</b>is further bolstered by its intermolecular capture, accomplished by photolyzing solutions of <b>2</b>in the presence of an isocyanide or PMe<sub>3</sub>to give (L<sup>Ar</sup>)U[NCN(C<sub>6</sub>H<sub>3</sub>Me<sub>2</sub>)](NIm<sup>Dipp</sup>) (<b>5</b>) and (<i>N</i>,<i>C</i>-L<sup>Ar</sup>*)U(N=PMe<sub>3</sub>)(NIm<sup>Dipp</sup>) (<b>6</b>), respectively. These results expand upon the limited reactivity studies of terminal uranium-nitride moieties and provide new insights into their chemical properties. </p>
|
Munendra Yadav; Alejandro
J. Metta-Magaña; Skye Fortier
|
Lanthanides and Actinides
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-12-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74640ee301c24abc794a6/original/intra-and-intermolecular-interception-of-a-photochemically-generated-terminal-uranium-nitride.pdf
|
6632ffd791aefa6ce1ebd68a
|
10.26434/chemrxiv-2024-2w9ph
|
Bipolar membrane capacitive deionization for the selective capture of lithium ions from brines and conversion to lithium hydroxide
|
Meeting the increasing demand for lithium in vehicle electrification and renewable energy storage requires innovations in lithium-ion (Li+) separations. Traditional solar evaporation methods for lithium recovery are slow and consume tremendous volumes of water and secondary chemicals (acids and bases). This study introduces a bipolar membrane capacitive deionization (BPM-CDI) unit for direct lithium extraction (DLE) and LiOH production without the external addition of acids and bases. Utilizing de-lithiated lithium-iron-phosphate (LFP) coated carbon cloth electrodes, the BPM-CDI unit demonstrates selective Li+ capture over competing ions. Molecular dynamics (MD) simulations and H-cell experiments elucidate pH inversion mechanisms during Li+ release, yielding LiOH. The BPM-CDI platform efficiently removes Li+ from synthetic brines featuring 8x higher Mg2+ concentrations (200 ppm Mg2+) and 26x higher Na+ concentrations (682 ppm Na+), achieving a LiOH concentration of 36 ppm after 8 cycles of recirculation. Post-mortem analysis confirms electrode integrity and stability. BPM-CDI integrated with selective electrodes is a promising electrochemical separation-reactor platform for lithium recovery while producing LiOH.
|
Tanmay Kulkarni; Aliya Muhammad I Al Dhamen; Xiaoliu Zhang; Chan-Wen Chiu; Hanrui Zhang; Feifei Shi; Revati Kumar; Christopher Arges
|
Materials Science; Energy; Chemical Engineering and Industrial Chemistry; Materials Processing
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6632ffd791aefa6ce1ebd68a/original/bipolar-membrane-capacitive-deionization-for-the-selective-capture-of-lithium-ions-from-brines-and-conversion-to-lithium-hydroxide.pdf
|
662a773291aefa6ce16b2277
|
10.26434/chemrxiv-2024-gtdz8
|
Dynamic Implications of Non-Covalent Interactions in Amphiphilic Single-Chain Polymer Nanoparticles
|
Single-chain polymer nanoparticles (SCNPs) combine the chemical diversity of synthetic polymers with the intricate structure of biopolymers, generating versatile biomimetic materials. The mobility of polymer chain segments at length scales similar to secondary structural elements in proteins are critical to SCNP structure and thus function. However, the influence of non-covalent interactions used to form SCNPs (e.g., hydrogen-bonding and biomimetic secondary-like structure) on these conformational dynamics is challenging to quantitatively assess. To isolate the effects of non-covalent interactions on SCNP structure and conformational dynamics, we synthesized a series of amphiphilic copolymers containing dimethylacrylamide and monomers capable of forming these different interactions: 1) di(phenylalanine) acrylamide that forms intramolecular β-sheet-like crosslinks, 2) phenylalanine acrylamide that forms hydrogen-bonds, but lacks a defined local structure, and 3) benzyl acrylamide that has lowest propensity for hydrogen-bonding. Each SCNP formed folded structures comparable to those of intrinsically disordered proteins, as observed by size exclusion chromatography and Small Angle Neutron Scattering. The dynamics of these polymers, as characterized by a combination of dynamic light scattering and Neutron Spin Echo spectroscopy, was well described using the Zimm with internal friction (ZIF) model, high-lighting the role of each non-covalent interaction to additively restrict the internal relaxations of SCNPs. These results demonstrate the utility of local scale interactions to control SCNP polymer dynamics, guiding the design of functional biomimetic materials with refined binding sites and tunable kinetics.
|
Peter Dykeman-Bermingham; Laura-Roxana Stingaciu; Changwoo Do; Abigail Knight
|
Polymer Science; Biopolymers; Polymer morphology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-04-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662a773291aefa6ce16b2277/original/dynamic-implications-of-non-covalent-interactions-in-amphiphilic-single-chain-polymer-nanoparticles.pdf
|
60c73e99ee301c91acc7876b
|
10.26434/chemrxiv.7046495.v1
|
DNA Origami Nanoplate-Based Emulsion with Designed Nanopore Function
|
Bio-inspired functional microcapsules stabilised with surfactants, copolymers, and nano/microparticles have attracted much attention in many fields from physical/chemical science to artificial cell engineering. Although the particle-stabilized microcapsules have advantages for their stability and rich ways for functionalisation such as surface chemical modifications and shape control of particles, versatile methods for their designable functionalisation are desired to expand their possibilities. Here, we report a DNA-based microcapsule composed of a water-in-oil microdroplet stabilised with amphiphilised DNA origami nanoplates. By utilising function programmability achieved by DNA nanotechnology, the DNA nanoplates were designed as a nanopore device for ion transportation as well as the interface stabiliser. Microscopic observations showed that the microcapsule formed by amphiphilic DNA nanoplates accumulated at the oil-water interface. Ion current measurements demonstrated that pores in the nanoplates functioned as ion channels. These findings provide a general strategy for programmable designing of microcapsules for engineering artificial cells and molecular robots.<br />
|
Daisuke Ishikawa; Yuki Suzuki; Chikako Kurokawa; Masayuki Ohara; Misato Tsuchiya; Masamune Morita; Miho Yanagisawa; Masayuki Endo; Ryuji Kawano; Masahiro Takinoue
|
Biopolymers; Nanostructured Materials - Nanoscience; Interfaces; Self-Assembly
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-09-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e99ee301c91acc7876b/original/dna-origami-nanoplate-based-emulsion-with-designed-nanopore-function.pdf
|
60c75896702a9b9b7b18cd5a
|
10.26434/chemrxiv.13513731.v2
|
4n+2=6n?
|
We propose a unique scheme to manipulate in a coordinated way chemically or mechanically topological, aromatic, electronic, and magnetic (conventional or non-conventional) properties of various nanographenes simultaneously, based on the elimination of empty peripheral rings in This could be very useful for nanoelectronics and spintronics applications. <br />
|
Aristides Zdetsis
|
Carbon-based Materials; Thin Films; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75896702a9b9b7b18cd5a/original/4n-2-6n.pdf
|
669e89ddc9c6a5c07a895c36
|
10.26434/chemrxiv-2024-tm7n6-v2
|
fragSMILES: a Chemical String Notation for Advanced Fragment and Chirality Representation
|
Generative models have revolutionized de novo drug design, allowing to produce molecules on-demand with desired physicochemical and pharmacological properties. String based molecular representations, such as SMILES (Simplified Molecular Input Line Entry System) strings and SELFIES (Self-Referencing Embedded Strings), have played a pivotal role in the success of generative approaches, thanks to their capacity to encode atom- and bond- information and ease-of-generation. However, such ‘atom-level’ string representations have certain limitations, in terms of capturing information on chirality, and synthetic accessibility of the corresponding designs.
In this paper, we present fragSMILES, a novel fragment-based molecular representation in the form of string. fragSMILES encode fragments in a ‘chemically-meaningful’ way via a novel graph-reduction approach, allowing to obtain an efficient, interpretable, and expressive molecular representation, which also avoids fragment redundancy. fragSMILES advances the state-of-the-art of fragment-based representations, by reporting fragments and their ‘breaking’ bonds independently, without fragment redundancy. Moreover, fragSMILES also embeds information of molecular chirality, thereby overcoming known limitations of existing string notations. When compared with SMILES and SELFIES for de novo design, the fragSMILES notation showed its promise in generating molecules with desirable biochemical and scaffolds properties.
|
Fabrizio Mastrolorito; Fulvio Ciriaco; Maria Vittoria Togo; Nicola Gambacorta; Daniela Trisciuzzi; Cosimo Damiano Altomare; Nicola Amoroso; Francesca Grisoni; Orazio Nicolotti
|
Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669e89ddc9c6a5c07a895c36/original/frag-smiles-a-chemical-string-notation-for-advanced-fragment-and-chirality-representation.pdf
|
60c75973bb8c1a553d3dcc02
|
10.26434/chemrxiv.14697234.v1
|
Concentration and Composition Dependent Aggregation of Pluronic- and Poly-(2-Oxazolin)-Efavirenz Formulations in Biorelevant Media
|
Interactions of intestinal fluids with polymer excipients, drugs and their formulations are not fully understood. Here, diffusion ordered spectroscopy (DOSY) and nuclear Overhauser effect spectroscopy (NOESY), complemented by cryo-TEM were employed to address this. Efavirenz as model drug, the triblock copolymers Pluronic F-127 (PF127) and poly(2-oxazolin) based pMeOx-b-pPrOzi-b-pMeOx (pOx/pOzi) and their respective formulations were studied in simulated fed-state intestinal fluid (FeSSIF). For the individual polymers, the bile interfering nature of PF127 was confirmed and pure pOx/pOzi was newly classified as non-interfering. A different and more complex behaviour was observed if EFV was involved. The formulations showed multi-facetted concentration and composition dependent aggregation. This demonstrates that separate evaluation of polymers or drugs in biorelevant media is not sufficient and their mixtures need to be carefully studied.<br />
|
Sebastian Endres; Emil Karaev; Simon Hanio; Jonas Schlauersbach; Christian Kraft; Tim Rasmussen; Robert Luxenhofer; Bettina Böttcher; Lorenz Meinel; Ann-Christin Pöppler
|
Aggregates and Assemblies; Drug delivery systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75973bb8c1a553d3dcc02/original/concentration-and-composition-dependent-aggregation-of-pluronic-and-poly-2-oxazolin-efavirenz-formulations-in-biorelevant-media.pdf
|
67b6e90afa469535b920d329
|
10.26434/chemrxiv-2025-xzvw4
|
Discrete Element Method Model of An Extrusion Process with Recirculation for Dry Manufacturing of Lithium-Ion Battery Electrodes
|
In this article, we report a computational modeling study to enhance the understanding of the solvent-free extrusion process employed to produce filaments for the 3D printing of lithium-ion battery electrodes. Our study is supported by a newly developed dynamic 3D-resolved numerical model capable of simulating the extrusion process, including material recirculation within the extruder. This model describes the extrusion process at the mesoscale through a granular approach based on the discrete element method. Our model accounts for the main features of the twin-screw extruder, allowing the simulation of several recirculation cycles and extrusion of active material, carbon additive, and binder mixtures. We discuss how different electrode material formulations, material injection sequences, twin-screw rotation speeds, and residence time in the extruder barrel affect the microstructure and particle distribution of the extruded filament. Finally, we calculate parameters including the porosity, tortuosity factor, effective diffusivity and electrical conductivity of the filament microstructures.
|
Pei Sun; Paul Vigneaux; Alejandro A. Franco
|
Energy; Energy Storage
|
CC BY 4.0
|
CHEMRXIV
|
2025-02-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b6e90afa469535b920d329/original/discrete-element-method-model-of-an-extrusion-process-with-recirculation-for-dry-manufacturing-of-lithium-ion-battery-electrodes.pdf
|
60c73e15702a9b1775189cc1
|
10.26434/chemrxiv.6394925.v1
|
The Hidden Transition Paths During the Unfolding of Individual Peptides with a Confined Nanopore
|
A fundamental question in peptide folding/unfolding
is how the peptide fleets through a set of transition states which dominate the
dynamics of biomolecular folding path. Owing to their rapid duration and sub-nm
structure difference, however, they have always been oversimplified because of
limited instrumental resolution.<sup>1-3</sup> Moreover, the most experiments
indicate a single fold pathway while the simulations suggest peptides owns the
preference in multiple pathways. <a></a><a></a><a>Using the electrochemical confined effect of a solid-state
nanopore, we measured the multiple transit paths of peptide inside nanopores. </a>Combining with Markov chain modelling, this
new single-molecule technique is applied to clarify the 5 transition paths of
the <a>β-hairpin </a>peptide which shows 4 nonequilibrium
fluctuating stages. These results enable experimental access to previously
obscured peptide dynamics which are essential to understand the misfolding in
peptides. The statistical analysis of each peptide from high throughput shows
that 78.5% of the peptide adopts the Pathways I during their folding/unfolding
in a nanopore while 21.5% of the peptide undergoes the hidden folding/unfolding
of transit Pathways II-IV. The frequency of the ionic fluctuation
reveals a harmonic structure difference of the <a>metastable</a>
peptide. Our results suggest the folding/unfolding of β-hairpin undergo four
major structure vibrations which agree well with the theoretical expectation.
These measurements provide a first look at the critical experiment picture of
the mechanical folding/unfolding of a peptide, opening exciting avenues for the
high <a></a><a>throughput</a> investigation of transition paths.
|
Yi-Lun Ying; Shao-Chuang Liu; Xin Shi; Wei-hua Li; Yong-jing Wan; Yi-Tao Long
|
Biochemical Analysis; Electrochemical Analysis; Biochemistry; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-05-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e15702a9b1775189cc1/original/the-hidden-transition-paths-during-the-unfolding-of-individual-peptides-with-a-confined-nanopore.pdf
|
660b0d509138d23161e7dbe7
|
10.26434/chemrxiv-2022-crzzq-v2
|
Amphiphilic salts as single-component, solvent-free, lithium electrolytes
|
Electrolytes with enhanced thermal stability are sought for next-generation lithium batteries. In this work, we discuss the synthesis, thermal properties, morphology, and ionic conductivity of single-component, solvent-free electrolytes composed of lithium salts with amphiphilic anions. These salts exhibit nanoscale phase segregation between the ionic domains and aliphatic tails of the amphiphilic anions. It is found that for a series of lithium salts with a decane tail, the ionic conductivity is correlated with ion pair binding energy. The ionic conductivity is highest for the decane tailed salt with the –sulfonyl(trifluoromethanesulfonyl)imide head group (LiC10TFSI) at 5.6 × 10-7 S/cm at 70 °C, with salts with – sulfonyl(phenylsulfonyl)imide and –sulfonylazanide anions exhibiting lower conductivity. A salt with an octadecane tail and TFSI headgroup (LiC18TFSI) has further improved ionic conductivity, 10 to 1000 times higher depending on the temperature and 3.6 × 10-5 S/cm at 70 °C. LiC18TFSI is a smectic ionic liquid crystal at intermediate temperatures as confirmed through X-ray scattering experiments and molecular dynamics simulations, whereas LiC10TFSI is suspected to be a disordered ionic liquid at the measurement conditions, highlighting the importance of ionic aggregate morphology on bulk ionic conductivity of electrolytes with ion clusters.
|
Jiacheng Liu; Marvin Diaz-Segura; A. Scott Manning; Lingyu Yang; Sunil Upadhyay; Jonathan Whitmer; Jennifer Schaefer
|
Materials Science; Energy; Liquid Crystals; Energy Storage; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-04-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660b0d509138d23161e7dbe7/original/amphiphilic-salts-as-single-component-solvent-free-lithium-electrolytes.pdf
|
60c74bed337d6c5a81e27b6d
|
10.26434/chemrxiv.12401306.v1
|
Decoding the Proteome of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) for Cell-Penetrating Peptides Involved in Pathogenesis or Applicable as Drug Delivery Vectors
|
Synthetic or natural-derived cell penetrating peptides (CPPs) are vastly investigated as tools for the intracellular delivery of membrane-impermeable molecules. As viruses are obligate intracellular parasites, viral originated CPPs have been considered as suitable shuttling vectors for cargo transportation. A total of 310 CPPs were identified in the proteome of SARS-CoV-2. SCV2-CPPs span the regions involved in replication, protein-nucleotide and protein-protein interaction, protein-metal ion interaction, and stabilization of homo/hetero-oligomers. Computational analyses showed that the most optimal SCV2-CPP candidates as vectors for drug delivery are SCV2-CPP118, SCV2-CPP119, SCV2-CPP122, and SCV2-CPP129 of NSP12. Conclusively, the workflow of this study provides a platform for profound screening of viral proteomes as a rich source of bio-therapeutics or drug delivery carriers. <br />
|
Shiva Hemmati; Yasaman Behzadipour; Mahdi Haddad
|
Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bed337d6c5a81e27b6d/original/decoding-the-proteome-of-severe-acute-respiratory-syndrome-coronavirus-2-sars-co-v-2-for-cell-penetrating-peptides-involved-in-pathogenesis-or-applicable-as-drug-delivery-vectors.pdf
|
67900b5d81d2151a023022ec
|
10.26434/chemrxiv-2025-1pnxw
|
Artificial Intelligence Driven Prediction of Aqueous Solubility of Drug Molecules Using Molecular Descriptors and Optimized ANN Architectures
|
Accurate prediction of aqueous solubility (logS) is a cornerstone of drug development, influencing bioavailability, pharmacokinetics, and therapeutic efficacy. Traditional models, such as ESOL, often exhibit limited accuracy across diverse chemical datasets, whereas Artificial Neural Networks (ANNs) offer a robust alternative by capturing complex non-linear relationships in molecular descriptors derived from SMILES representations. This study evaluates the performance of various ANN architectures against baseline models, including Random Forest (RF) and Linear Regression (LR), demonstrating the superior accuracy of ANNs, which achieved the lowest mean error and most consistent error distribution. Nonetheless, model performance was influenced by the logS range and architectural complexity, with deeper networks prone to overfitting and simpler architectures susceptible to underfitting. These findings position ANNs as powerful tools for solubility prediction, underscoring the importance of balanced model design and expanded datasets to enhance generalization. AI-driven approaches offer transformative potential to accelerate drug discovery, reduce costs, and optimize therapeutic outcomes.
|
Taddeo Simon; Adriel Doppico Hidalgo; Yulianna Velina; Subhojit Majumdar
|
Theoretical and Computational Chemistry; Chemical Education; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67900b5d81d2151a023022ec/original/artificial-intelligence-driven-prediction-of-aqueous-solubility-of-drug-molecules-using-molecular-descriptors-and-optimized-ann-architectures.pdf
|
61e674f180719d9c501331a2
|
10.26434/chemrxiv-2022-7fv49
|
Efficient CPU and GPU implementations of multicenter integrals over long-range operators using Cartesian Gaussian functions
|
We present a library for evaluating multicenter integrals over
polarization operators of the form $x^{m_x} y^{m_y} z^{m_z} r^{-k} C(r)$ using Cartesian Gaussian basis functions. $m_x, m_y, m_z \geq 0$, $k > 2$ are integers, while the cutoff function, $C(r)=(1 - e^{-\alpha r^2})^q$, with $\alpha \in \mathbb{R}_{+}$ and certain integer values of $q$ ensures the existence of the integrals. The formulation developed by P. Schwerdtfeger and H. Silberbach [Phys. Rev. A 37, 2834 (1988)] is implemented in an efficient and stable way taking into account a recent fix in one of the equations. A cheap upper bound is presented that allows negligible integrals to be prescreened. The correctness of the analytical integrals was verified by numerical integration. The library provides separate codes for serial CPU and parallel GPU architectures and can be wrapped into a python module.
|
Alexander Humeniuk; William Glover
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics
|
CC BY 4.0
|
CHEMRXIV
|
2022-01-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e674f180719d9c501331a2/original/efficient-cpu-and-gpu-implementations-of-multicenter-integrals-over-long-range-operators-using-cartesian-gaussian-functions.pdf
|
63629e70aa27841f1756fad5
|
10.26434/chemrxiv-2022-znvj7
|
A Taguchi Design of Experiments Approach for Untargeted Metabolomics Sample Preparation Optimization
|
Metabolomics commonly uses analytical techniques such as nuclear magnetic resonance (NMR) and liquid chromatography coupled to mass spectrometry (LC-MS) to quantify and identify metabolites associated with biological variation. Metabolome coverage from untargeted LC-MS studies relies heavily on the pre-analytical protocols used (e.g., homogenization and extraction). Chosen protocols impact which metabolites are successfully measured, which in turn impacts biological conclusions. Furthermore, different homogenization and extraction parameters produce significant variability in metabolome coverage, sample reproducibility, and extraction efficiency. There is a need for an efficient and systematic approach to optimize matrix-specific sample preparation parameters. Herein we describe a Taguchi design of experiments (DOE) approach for matrix-specific sample preparation optimization using model organism Caenorhabditis elegans. To demonstrate this methodology we optimized: i) extraction solvent, ii) volume, iii) extraction time, and iv) LC reconstitution solvent for a sequential non-polar and polar extraction, and confirmed our optimized results using NMR spectroscopy. DOE is rarely used in metabolomics, yet it provides a systematic path forward for optimizing multiple sample preparation parameters while keeping the number of experiments, labor, and costs necessarily low. Altogether, the Taguchi DOE method is an adaptable and scalable method well-fit for the diversity of current and future hypotheses studied using untargeted metabolomics.
|
Brianna M. Garcia; Goncalo J. Gouveia; Amanda O. Shaver; Ricardo M. Borges; I. Jonathan Amster; Arthur S. Edison; Franklin E. Leach III
|
Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry; Spectroscopy (Anal. Chem.)
|
CC BY 4.0
|
CHEMRXIV
|
2022-11-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63629e70aa27841f1756fad5/original/a-taguchi-design-of-experiments-approach-for-untargeted-metabolomics-sample-preparation-optimization.pdf
|
60c73dd4567dfefb56ec370b
|
10.26434/chemrxiv.6159143.v1
|
DLSCORE: A Deep Learning Model for Predicting Protein-Ligand Binding Affinities
|
<p>In recent years, the cheminformatics community has seen an increased success with machine learning-based scoring functions for estimating binding affinities and pose predictions. The prediction of protein-ligand binding affinities is crucial for drug discovery research. Many physics-based scoring functions have been developed over the years. Lately, machine learning approaches are proven to boost the performance of traditional scoring functions. In this study, a novel deep learning based scoring function (DLSCORE) was developed and trained on the refined PDBBind v.2016 dataset using 348 BINding ANAlyzer (BINANA) descriptors. The neural networks of the DLSCORE model have different number of fully connected hidden layers. Our model, an ensemble of 10 networks, yielded a Pearson R2 of 0.82, a Spearman Rho R2 of 0.90, Kendall Tau R2 of 0.74, an RMSE of 1.15 kcal=mol, and an MAE of 0.86 kcal=mol for our test set. This software is available on Github at https://github.com/sirimullalab/dlscore.git</p><p><br /></p>
|
Mahmudulla Hassan; Daniel Castaneda Mogollon; Olac Fuentes; suman sirimulla
|
Chemical Biology; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Theory - Computational; Machine Learning
|
CC BY NC 4.0
|
CHEMRXIV
|
2018-04-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd4567dfefb56ec370b/original/dlscore-a-deep-learning-model-for-predicting-protein-ligand-binding-affinities.pdf
|
67d745e181d2151a02a03235
|
10.26434/chemrxiv-2025-93c25
|
Addressing sustainability challenges in peptide synthesis
with flow chemistry and machine learning
|
In the era of peptide therapeutics, solid phase peptide synthesis is becoming increasingly important in the pharmaceutical industry and related research. However, the high cost and the large amount of toxic waste generated during production overshadow the current technology, requiring the reduction of excess reagents and the replacement of the solvents used. Advances have been made to replace N,N-dimethylformamide with moderate success. Here, we report a recyclable anisole/dimethyl sulfoxide based and carefully tuned solvent system that is compatible with flow chemistry and outperforms DMF. By exploring the solvent parameter space, we have selected several mixtures, tested their swelling ability, amino acid solubility, coupling efficiency, and Fmoc-cleaving capacity, and found the Anisole/DMSO (17:3) mixture to be ideal for coupling. By adjusting the flow parameters, racemization was reduced to <2% in the case of His, and <1% for Cys. Several mixtures were screened for optimal Fmoc-cleavage, selected to cover the solvent parameter space uniformly. To test the selected solvent mixtures for aspartimide formation, and Fmoc-cleavage efficiency, both scorpion toxin II (VKDGYI) and JR10-mer (WFTTLISTIM) challenging sequences were synthesized and new correlations between reaction rates and solvent parameters were found. Further parameter optimizations were performed using a machine learning algorithm (Bayesian optimization) to reduce aspartimide formation and maximize Fmoc-deprotection. With the final parameters obtained, the Aib-ACP (10-mer), the glucagon like peptide 1 (GLP-1, 30-mer) and bovine pancreatic trypsin inhibitor (BPTI, 58-mer) polypeptides were synthesized with high efficiency and synthetic speed (12 min/cycle). The method is ideal for high temperature synthetic approaches. Based on sustainability metrics, the applied synthetic flow chemistry protocol, with the greener solvent mixture (Anisole/DMSO) performs outstandingly well compared to traditional methods and to state-of-the-art synthesizers.
|
Kristóf Ferentzi; Viktor Farkas; András Perczel
|
Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Biochemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2025-03-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d745e181d2151a02a03235/original/addressing-sustainability-challenges-in-peptide-synthesis-with-flow-chemistry-and-machine-learning.pdf
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6658a86391aefa6ce16450be
|
10.26434/chemrxiv-2024-lnwsb
|
Ultrasmall HgTe quantum dots with high photoluminescent quantum yields in the near and shortwave infrared
|
We demonstrate a low temperature synthesis of ultrasmall HgTe quantum dots with superlative optical properties in the near and shortwave infrared. The tunable cold-injection synthesis produces 1.7 to 2.3 nm diameter nanocrystals, with photoluminescence maxima ranging from 900-1180 nm. and a full width half max of ~100 nm (~130 meV). The synthesized quantum dots display extraordinarily high photoluminescence quantum yields (PLQY) ranging from 80-95% based on both relative and absolute methods. Furthermore, samples retain their high quantum yields (~60%) in the solid state, allowing for first of their kind photoluminescence imaging and blinking studies of HgTe QDs. The facile synthesis allows for the isolation of small photostable HgTe quantum dots and which can provide valuable insight into the extremes of quantum confinement.
|
Belle Coffey; Elise Skytte; Tasnim Ahmed; Eugenia Vasileiadou; Eric Yu Lin; Ash Sueh Hua; Elijah Cook; Stephanie Tenney; Ellen Sletten; Justin Caram
|
Physical Chemistry; Nanoscience; Clusters; Solution Chemistry; Spectroscopy (Physical Chem.); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6658a86391aefa6ce16450be/original/ultrasmall-hg-te-quantum-dots-with-high-photoluminescent-quantum-yields-in-the-near-and-shortwave-infrared.pdf
|
67b8786e6dde43c908daa077
|
10.26434/chemrxiv-2025-nszrb
|
Structure-Activity Relationships and Design of Focused Libraries Tailored for Staphylococcus aureus Inhibition
|
Staphylococcus aureus is a bacterium classified among the ESKAPE pathogens, which are anticipated to pose a significant global health emergency in the coming decades. The FabI enzyme, present in both Gram-positive and Gram-negative bacteria, is a key enzyme involved in fatty acid synthesis II (FAS-II). In this study, we utilized transformation rules to expand the chemical space from the most potent S. aureus FabI inhibitors. Three newly generated focused libraries, named INDDS, DIADS, and PYRDS, encompassed 172,026 compounds. These compounds were ranked based on structural similarity and predicted pIC50 values obtained from machine learning models. This approach allowed to prioritize compounds in each focused library targeting S. aureus FabI. We analyzed the pharmacological properties and chemical space diversity of the S. aureus FabI inhibitors to gather relevant insights and support the prioritization of compounds for further study. The three newly generated libraries are freely available at https://github.com/DIFACQUIM/S.aureus_inhibitors
|
Alberto Marbán-González; José L. Medina-Franco
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2025-02-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b8786e6dde43c908daa077/original/structure-activity-relationships-and-design-of-focused-libraries-tailored-for-staphylococcus-aureus-inhibition.pdf
|
6604ae2fe9ebbb4db9b7d490
|
10.26434/chemrxiv-2024-k94kx
|
Molybdenum Catalysts based on Salan Ligands for the
Deoxydehydration Reaction
|
Dioxomolybdenum complexes based on salan ligands have been evaluated for their potential in catalyzing the deoxydehydration (DODH) reaction. The DODH reaction is a formal reduction that converts vicinal diols into olefins using an oxometal catalyst and a sacrificial reductant. The reaction holds enormous potential in transforming biomass-derived molecules into platform chemicals. This study evaluated 20 molybdenum complexes supported by salan ligands in the DODH reaction with the goal of establishing structure-activity relationships. Catalyst screenings were performed using styrene glycol as a model substrate and 1-10 mol% loading of the molybdenum complexes at 170 oC producing styrene in up to 54% yield. Aliphatic diols and meso-/R,R-hydrobenzoin were also converted to the corresponding alkenes in moderate to good yields that are comparable to previously reported molybdenum catalysts. A bio-derived glycol, (+)−diethyltartrate, could be converted to the alkene product (diethyl fumarate) in >98% yield using 10 mol% catalyst. A high yield of diethyl fumarate (78%) was also obtained with Na2SO3 (cheap, readily available, and benign) as reductant. Quite significantly, a 42% yield of diethyl fumarate was also obtained at a 1 mol% catalyst loading which represents a turnover number (TON) of 42; this is one of highest activity in a DODH reaction observed with molybdenum catalysts. The catalytic studies along with preliminary kinetic investigations reveal significant ligand effects: sterically bulky ortho-substituents and electron-withdrawing para-substituents on the phenol arms were found to enhance catalytic activity while a rigid phenyl as well as an ethylene backbone featuring a tertiary amine were observed to impede catalysis.
|
Nathan Wagner; Wei-Chien Tang; Jonathan Wagner; Binh Nguyen; Jamie Lam; Skyler Gibbons-Stovall; Andrea Matias; Stephenie Martinez; Tristhan Trieu-Tran; Garrit Clabaugh; Christine Navarro; Ibrahim Abboud; Francis Flores; Kenneth Nicholas; Alex John
|
Inorganic Chemistry; Catalysis; Organometallic Chemistry; Ligands (Inorg.); Transition Metal Complexes (Inorg.); Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6604ae2fe9ebbb4db9b7d490/original/molybdenum-catalysts-based-on-salan-ligands-for-the-deoxydehydration-reaction.pdf
|
60c73d97f96a002966285dfc
|
10.26434/chemrxiv.6015848.v1
|
Revitalizing the Concept of Bond Order Through Delocalization Measures in Real Space
|
Ab initio quantum chemistry is an independent source of information supplying an ever widening group of experimental chemists. However, bridging the gap between these ab initio data and chemical insight remains a challenge. In particular, there is a need for a bond order index that characterizes novel bonding patterns in a reliable manner, while recovering the familiar effects occurring in well-known bonds. In this article, through a large body of calculations, we show how the delocalization index derived from Quantum Chemical Topology (QCT) serves as such a bond order. This index is defined in a parameter-free, intuitive and consistent manner, and with little qualitative dependency on the level of theory used. The delocalization index is also able to detect the subtler bonding effects that underpin most practical organic and inorganic chemistry. We explore and connect the properties of this index and open the door for its extensive usage in the understanding and discovery of novel chemistry.
|
Carlos Outeiral; Mark Vincent; Ángel Martín Pendás; Paul L. A. Popelier
|
Quantum Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-03-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d97f96a002966285dfc/original/revitalizing-the-concept-of-bond-order-through-delocalization-measures-in-real-space.pdf
|
661e758391aefa6ce1ad82e6
|
10.26434/chemrxiv-2024-swz2p-v2
|
Predicting Colloidal Interaction Parameters from Small Angle X-Ray Scattering Curves using Artificial Neural Networks and Markov Chain Monte Carlo Sampling
|
Small Angle X-Ray Scattering (SAXS) is a characterization technique which allows for the study of colloidal interactions by fitting the structure factor of the SAXS profile for a selected model and closure relation. However, the applicability of this approach is constrained by the limited number of existing models which can be fitted analytically, as well as the narrow operating range for which the models are valid. In this work, we demonstrate a proof-of-concept for using an artificial neural network (ANN) trained on small-angle x-ray scattering (SAXS) curves obtained from Monte Carlo (MC) simulations to predict values of the effective macroion valency (Zeff) and the Debye length (κ) for a given SAXS profile. This ANN, which was trained on 200,000 simulated SAXS curves, was able to predict values of Zeff and κ for a test set containing 25,000 simulated SAXS curves with ±20% accuracy to the ground truth values. Subsequently, an ANN was used as a surrogate model in a Markov Chain Monte Carlo sampling algorithm to obtain maximum a posteriori (MAP), associated confidence intervals estimates and details of correlations of Zeff and κ for an experimentally obtained SAXS profile.
|
Kelvin Wong; Qi Runzhang; Yang Ye; Luo Zhi; Stefan Guldin; Keith Butler
|
Physical Chemistry; Materials Science; Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-04-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661e758391aefa6ce1ad82e6/original/predicting-colloidal-interaction-parameters-from-small-angle-x-ray-scattering-curves-using-artificial-neural-networks-and-markov-chain-monte-carlo-sampling.pdf
|
60c74c0b0f50db6a25396d93
|
10.26434/chemrxiv.12417701.v1
|
Mild Deprotection of Dithioacetals by TMSCl / NaI Association in CH3CN
|
<p><a>We showed for the first
time, the fundamental role<b> </b>of CH<sub>3</sub>CN associated to TMSCl/NaI
combination to deprotect S,S-ethylene- and S,S-propylene-ketals into ketones.
Indeed, if the TMSCl/NaI association leads to the reduction of
dithioketals in CH<sub>2</sub>Cl<sub>2</sub>, we have demonstrated that this
association can be used to deprotect a large variety of various dithioketals
into ketones in CH<sub>3</sub>CN. Otherwise, under mild experimental
conditions, O,O-acetals as well as O,S-oxathianes were cleanly deprotected with
high yields. It is also possible to easily regenerate the carbonyl function of
various hydrazones and imines using this novel protocol. We believe that this metal-free
process is a good alternative to other known methodologies used to deprotect
dithioketals into ketones.<b></b></a></p><table></table><br />
|
Olivier Provot; Yunxin Yao; Guangkuan Zhao; Abdallah Hamze; Mouad Alami
|
Organic Synthesis and Reactions
|
CC BY 4.0
|
CHEMRXIV
|
2020-06-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c0b0f50db6a25396d93/original/mild-deprotection-of-dithioacetals-by-tms-cl-na-i-association-in-ch3cn.pdf
|
6112e9c042d16534d03d71ce
|
10.26434/chemrxiv-2021-25t0l
|
Photodeposited polyamorphous CuOx
hole-transport layers in organic photovoltaics
|
Hole-selective charge transport layers are an important part of modern thin-film electronics, serving to direct electron flow and prevent leakage current. Crystalline metal-oxide
hole-transport layers (HTLs) such as NiO and CuOx exhibit high performance and stability. However they are traditionally not amenable to scalable and sustainable solution-processing techniques. Conversely, amorphous metal oxides are much more readily prepared by lowtemperature solution processing methods but often lack the charge transport properties of crystalline semiconductors. Herein we report the fabrication of amorphous a-CuOx thin films from commercially available starting material using a simple UV-based thin-film deposition method. Subsequent thermal annealing of the a-CuOx induces an amorphous-to-amorphous phase transition resulting in p-type semiconducting behavior. The resulting thin films were used as HTLs in organic photovoltaic devices with power conversion efficiencies
comparable to those fabricated with PEDOT:PSS.
|
Nicholas Randell; Renaud Miclette Lamarche; Francesco Tintori; Roman Chernikov; Gregory Welch; Simon Trudel
|
Physical Chemistry; Materials Science; Materials Processing; Nanostructured Materials - Materials; Thin Films; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-08-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6112e9c042d16534d03d71ce/original/photodeposited-polyamorphous-cu-ox-hole-transport-layers-in-organic-photovoltaics.pdf
|
63a1bc8004902a564809f2ec
|
10.26434/chemrxiv-2022-9dpd6
|
Sequential dual-curing of electron-deficient olefins and alcohols relying on oxa-Michael addition and anionic polymerization
|
Herein we propose the preparation of crosslinked polymers from off-stoichiometric oxa-Michael formulations proceeding via a self-limiting base catalyzed reaction between difunctional Michael acceptors and substoichiometric amounts of diols followed by anionic polymerization of the remaining vinyl groups. The properties of the resulting polymers can easily be tuned by varying the amount of diols.
|
Susanne M. Fischer; Viktor Schallert; Johanna M. Uher; Christian Slugovc
|
Organic Chemistry; Polymer Science
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-12-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a1bc8004902a564809f2ec/original/sequential-dual-curing-of-electron-deficient-olefins-and-alcohols-relying-on-oxa-michael-addition-and-anionic-polymerization.pdf
|
60c74c95567dfe01a6ec516b
|
10.26434/chemrxiv.12465299.v1
|
Iterative Experimental Design Based on Active Machine Learning Reduces the Experimental Burden Associated with Reaction Screening
|
High-throughput reaction screening has emerged as a useful means of rapidly identifying the influence of key reaction variables on reaction outcomes. We show that active machine learning can further this objective by eliminating dependence on complete screens through iterative selection of maximally informative experiments from the subset of all possible experiments in the domain. To demonstrate our approach, we conduct retrospective analyses of the preexisting results of high-throughput reaction screening experiments. We compare the test set errors of models trained on actively-selected reactions to models trained on reactions selected at random from the same domain. We find that the degree to which models trained on actively-selected data outperform models trained on randomly-selected data depends on the domain being modeled, with it being possible to achieve very low test set errors when the dataset is heavily skewed in favor of low- or zero-yielding reactions. Our results confirm that the active learning algorithm is a useful experiment planning tool that can change the reaction screening paradigm, by allowing discovery and process chemists to focus their reaction screening efforts on the generation of a small amount of high-quality data.
|
Natalie Eyke; William H. Green; Klavs F. Jensen
|
Organic Synthesis and Reactions; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c95567dfe01a6ec516b/original/iterative-experimental-design-based-on-active-machine-learning-reduces-the-experimental-burden-associated-with-reaction-screening.pdf
|
60c74c7c702a9b1f0518b6ab
|
10.26434/chemrxiv.12490688.v1
|
Diisobutylene Maleic Acid Copolymer (DIBMA) Lipid Particle: A “Stealth” Membrane Mimetic for Neutron Scattering
|
Diisobutylene maleic acid (DIBMA) has been shown to solubilize and purify membrane proteins from a native lipid bilayer into nanodiscs without the need for a detergent. To explore DIBMA lipid particles as a suitable membrane mimetic system for neutron scattering studies of membrane proteins, we measured and determined the contrast matching point of DIBMA to be ~12% (v/v) D2O—similar to that of most protiated lipid molecules, but distinct from that of regular protiated proteins, providing a natural contrast for separating neutron scattering signals. Using SANS contrast variation, we demonstrated that the scattering from the whole lipid particle can be annihilated. Further, the lipid part of the particle shows a well-defined discoidal shape with DIBMA contrast matched. These results demonstrate that the DIBMA lipid particle is an outstanding “stealth” membrane mimetic for membrane proteins.<br />
|
Rong Guo; Jacob Sumner; Shuo Qian
|
Biochemistry; Biophysics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c7c702a9b1f0518b6ab/original/diisobutylene-maleic-acid-copolymer-dibma-lipid-particle-a-stealth-membrane-mimetic-for-neutron-scattering.pdf
|
60c74aebbdbb8905c7a39480
|
10.26434/chemrxiv.12271874.v1
|
Photodegradable Tissue-Adhesive Hydrogels
|
Hydrogels for wound management and tissue gluing have
to adhere to tissue for a given time scale and then disappear, either by
removal from the skin or by slow degradation in applications inside the body. Advanced
wound management materials also envision the encapsulation of therapeutic drugs
or cells to support the natural healing process. The design of hydrogels that
can fulfill all these properties with minimal chemical complexity, a stringent
condition to favor transfer into a real medical device, is challenging. Herein,
we present a hydrogel design with moderate structural complexity that fulfills a
number of relevant properties for wound dressing: it can form in situ and encapsulate
cells, it can adhere to tissue, and it can be degraded on demand by light
exposure under cytocompatible conditions. The hydrogels are based on starPEG
macromers terminated with catechol groups as crosslinking units and contain intercalated
photocleavable triazole nitrobenzyl groups. Hydrogels are formed under mild
conditions (HEPES buffer with 9-18 mM of sodium periodate as oxidant) and are
compatible with encapsulated cells. Upon light-irradiation, the cleavage of the
nitrobenzyl group mediates depolymerization, which enables on-demand release of
cells or debonding from tissue. The molecular design and obtained properties
are interesting for the development of advanced wound dressings and cell
therapies, and expand the range of functionality of current alternatives.
|
Maria Villou; Julieta Paez; Aránzazu del Campo
|
Biocompatible Materials; Hydrogels
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74aebbdbb8905c7a39480/original/photodegradable-tissue-adhesive-hydrogels.pdf
|
61efd55771868d17a3bdf7f5
|
10.26434/chemrxiv-2022-d7mcg
|
Potential response of single successive constant-current-driven electrolytic hydrogen bubbles spatially separated from the electrode
|
In gas-evolving electrolytic processes, the presence of bubbles can heavily alter the mass transport of gaseous products and can induce severe overpotential penalties at the electrode through the action of bubble coverage (hyperpolarization) and electrolyte constriction (Ohmic shielding). However, bubble formation can also alleviate the overpotential by lowering the concentration of dissolved gas in the vicinity of the electrode.
In this study, we investigate the latter by considering the growth of successive hydrogen bubbles driven by a constant current in alkaline-water electrolysis and their impact on the half-cell potential in the absence of hyperpolarization. The bubbles nucleate on a hydrophobic cavity surrounded by a ring microelectrode which remains free of bubble coverage.
The dynamics of bubble growth does not adhere to one particular scaling law in time, but undergoes a smooth transition from pressure-driven towards supply-limited growth.
The contributions of the different bubble-induced phenomena leading to the rich behaviour of the periodic fluctuations of the overpotential are identified throughout the different stages of the bubble lifetime, and the influence of bubble size and applied current on the concentration and Ohmic overpotential components is quantified.
We find that the efficiency of gas absorption, and hence the concentration-lowering effect, increases with increasing bubble size and also with increasing current. However, the concentration-lowering effect is always eventually countered and overcome by the effect of Ohmic shielding as the bubble size outgrows and eclipses the electrode ring beneath.
|
Akash Raman; Pablo Peñas; Devaraj van der Meer; Detlef Lohse; Han Gardeniers; David Fernández Rivas
|
Catalysis; Energy; Electrocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-01-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61efd55771868d17a3bdf7f5/original/potential-response-of-single-successive-constant-current-driven-electrolytic-hydrogen-bubbles-spatially-separated-from-the-electrode.pdf
|
63ac72f3e8047a066ef8888a
|
10.26434/chemrxiv-2022-f83g0
|
Quantum-Classical Transition Analogy of Diffusion-Mobility Relation for Organic Semiconductors
|
We propose the quantum-classical transition analogy for Einstein’s diffusion-mobility (D/μ) relation to reveal the electron hole dynamics in both the degenerate and nondegenerate molecular solids. Here, one to one variation between differential entropy and chemical potential (Δη/Δhs) is the proposed analogy, which unifies quantum and classical transport. The degeneracy stabilization energy on D/μ decides whether the transport is quantum or classical; accordingly, the transformation occurs in the Navamani-Shockley diode equation.
|
K. NAVAMANI
|
Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Theory - Computational; Quantum Mechanics; Transport phenomena (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-12-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ac72f3e8047a066ef8888a/original/quantum-classical-transition-analogy-of-diffusion-mobility-relation-for-organic-semiconductors.pdf
|
60c74372567dfecd99ec4108
|
10.26434/chemrxiv.9120953.v1
|
Pressing Induced Caking: A General Strategy to Scale-Span Molecular Self-Assembled Materials
|
We report that under mechanical pressure, caking of the precipitated
molecular self-assemblies may lead to bulk supramolecular films. Massive
fabrication of supramolecular films becomes possible using a simple household
noodle machine. The film can be endowed diversified functions by depositing
various functional ingredients via co-precipitation.
|
Yun Yan; Hongjun Jin; Mengqing Xie; Wenkai Wang; Lingxiang Jiang; Wenying Chang; Yue Sun; Limin Xu; Shihao Zang; Jianbing Huang; Lei Jiang
|
Aggregates and Assemblies; Materials Processing; Nanostructured Materials - Materials; Thin Films
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-07-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74372567dfecd99ec4108/original/pressing-induced-caking-a-general-strategy-to-scale-span-molecular-self-assembled-materials.pdf
|
645db842f2112b41e9696fe4
|
10.26434/chemrxiv-2023-zn6rm
|
Integrated Optics Polarized Light and Evanescent Wave Surface-Enhanced Raman Scattering to detect ligand Interactions at nanoparticle surfaces
|
The orientation of sensing molecules on the surface of biosensors is crucial for effective interaction with target analytes, and Raman spectroscopy is a versatile and non-invasive technique used to study molecular configurations at the sub-nanoscale level. This study explores the sensing abilities of an integrated optics construct called an Optical Chemical Bench (OCB) for the detection of molecular orientation, ion binding, and nanoparticle binding. The OCB consists of plasmonic gold-silver nanoparticles bound to the surface of a multimode slab waveguide. This design offers controlled plasmonic excitation in both position and polarization, increasing the interfacial mean square electric field relative to the incident field, and allowing for polarization-dependent surface-enhanced Raman scattering (SERS) on a chip. The experiments gave insight into how the TE and TM polarization modes interact with adsorbates that are built up as hierarchical structures on the OCB, providing an inexpensive yet effective molecular probing technology at the interface.
|
Xining Chen; Mark Andrews
|
Physical Chemistry; Nanoscience; Interfaces; Optics; Surface; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-05-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645db842f2112b41e9696fe4/original/integrated-optics-polarized-light-and-evanescent-wave-surface-enhanced-raman-scattering-to-detect-ligand-interactions-at-nanoparticle-surfaces.pdf
|
64e6aa103fdae147faaf7187
|
10.26434/chemrxiv-2023-cg4zv
|
Deciphering the selectivity of CBL-B inhibitors using all-atom molecular dynamics and machine learning
|
We employ a combination of accelerated molecular dynamics and machine learning techniques to unravel the dynamic characteristics of CBL-B and C-CBL, and how their configurational changes conferring the binding affinity and selectivity of their ligands. We demonstrate that the activity and selectivity against CBL-B and C stem from subtle structural disparities within their binding pockets, and dissociation pathways. Our predictive model for dissociation rate constants (koff) demonstrates a moderate correlation with experimental IC50 values, effectively aligning with two available experimental koff values. Moreover, the binding free energies calculated using MM/GBSA highlight the ΔG distinction between CBL-B and C-CBL. By employing a regression strategy on dissociation trajectories, we identified key amino acids in binding pocket and along the dissociation path responsible for activity and selectivity. These amino acids are statistically significant in achieving activity and selectivity and correspond to the primary structural discrepancies between CBL-B and C-CBL. Through microsecond-scale replica exchange molecular dynamics coupled with generative model of molecular generation and ensemble docking, we accomplish comprehensive simulations of the complete apo-holo-apo transformation cycle. This approach provides an enabling first-in-class drug design technology based on apo-to-holo structure transformation.
|
Feng Zhou; Haolin Du; Weiqiang Fu; Yang Wang; yingsheng zhang
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Biophysics; Computational Chemistry and Modeling
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-08-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e6aa103fdae147faaf7187/original/deciphering-the-selectivity-of-cbl-b-inhibitors-using-all-atom-molecular-dynamics-and-machine-learning.pdf
|
675088967be152b1d0f1e7ff
|
10.26434/chemrxiv-2024-slrc0
|
When Carbon Monoxide goes “Upside Down”: Vibrational Signatures of CO at NaCl(100) from Ab Initio Molecular Dynamics
|
CO adsorbed on NaCl(100) is a model system for surface science showing a rich variety of interesting phenomena. It features several adsorption phases like tilted / antiparallel or perpendicular / upright, very long vibrational lifetimes of the CO internal stretch (IS) mode, anharmonicity-driven vibrational energy pooling, “C-bound” vs. “O-bound” adsorption, and heavy-atom gateway tunneling during CO inversion at low temperatures. Typically, these features and phenomena are experimentally probed by stationary and time-resolved vibrational spectra, exhibiting characteristic differences between the various adsorption modes and phases. To gain atom- and time-resolved insight into vibrational response of CO molecules on NaCl(100), vibrational density of states (VDOS), Infrared (IR) and Vibrational Sum Frequency (VSF) spectra are computed from Velocity Velocity Correlation Functions (VVCFs) by Ab Initio Molecular Dynamics (AIMD) for various coverages, temperatures and phases. In agreement with experiments, we find that increasing CO (“C-bound”) coverages as well as CO inversion lead to redshifts of the CO IS mode. We predict more diffuse spectra at T = 300 K compared to 30 K, reflecting the disorder of adsorbates and monolayer instability at room temperature. Analyzing molecularly decomposed and internal VDOS curves as well as computed non-linear correlation matrices give further insight into the complex molecular dynamics underlying the vibrational spectra, notably for the low-frequency regime where frustrated rotations, translations and intermolecular motions come into play. On a methodological side, we also test and discuss some intricate details of how to compute IR and VSF response using a modified formulation of the VVCF methods [Ohto et al., J. Chem. Phys., 2015, 143, 124702], by including time and angle-dependent dipole and polarizability derivatives as well as intermolecular couplings by cross correlations. Their effect on computed vibrational spectra is studied. These findings provide a detailed, microscopic insight into the picosecond vibrational spectra and dynamics of CO on NaCl(100), highlighting the effects of temperature, coverage, and changes in adsorbate orientation.
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Shreya Sinha; Alec M. Wodtke; Peter Saalfrank
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Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational
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CC BY NC 4.0
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CHEMRXIV
|
2024-12-09
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675088967be152b1d0f1e7ff/original/when-carbon-monoxide-goes-upside-down-vibrational-signatures-of-co-at-na-cl-100-from-ab-initio-molecular-dynamics.pdf
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61a4c7e1a1292354e4525ff0
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10.26434/chemrxiv-2021-2cctp
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Microbial fermentation of polyethylene terephthalate (PET) plastic waste for the production of chemicals and electricity
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Ideonella sakaiensis (I. sakaiensis) can grow on polyethylene terephthalate (PET) as the sole carbon and energy source. Previous work has shown that conversion of the hydrolysis products terephthalic acid (TPA) and ethylene glycol (EG) under aerobic conditions released carbon dioxide and water while yielding adenosine triphosphate (ATP) through oxidative phosphorylation. This study demonstrates that under anaerobic conditions I. sakaiensis ferments PET to the feedstock chemicals acetate and ethanol while co-producing ATP by substrate-level phosphorylation. In addition to PET, maltose, EG, and ethanol can also serve as fermenting substrates. Co-culturing of I. sakaiensis with electrogenic Geobacter sulfurreducens produced electricity from PET or EG. This newly identified plastic fermentation process by I. sakaiensis provides a novel biosynthetic route to produce high-value chemicals and electricity from plastic waste streams.
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Shafeer Kalathil; Melanie Miller; Erwin reisner
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Biological and Medicinal Chemistry; Catalysis; Polymer Science; Chemical Biology; Microbiology; Biocatalysis
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CC BY 4.0
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CHEMRXIV
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2021-11-30
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a4c7e1a1292354e4525ff0/original/microbial-fermentation-of-polyethylene-terephthalate-pet-plastic-waste-for-the-production-of-chemicals-and-electricity.pdf
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60c73f80bb8c1a6b783d9b80
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10.26434/chemrxiv.7388318.v1
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Encoding Metal-Cation Arrangements in Metal-Organic Frameworks for Programming the Composition of Electrocatalytically Active Multi-Metal Oxides
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In the present contribution, we report how through the use of metal-organic frameworks (MOFs) composed of addressable combinations of up to four different metal elements it is possible to program the composition of multi-metal oxides, which are not attainable by other synthetic methodologies. Thus, due to the ability to distribute multiple metal cations at specific locations in the MOF secondary building units it is possible to code and transfer selected metal ratios to multi-metal oxides with novel, desired compositions through a simple calcination process. The demonstration of an enhancement in the electrocatalytic activity of new oxides by pre-adjusting the metal ratios is here reported for the oxygen reduction reaction, for which activity values comparable to commercial Pt/C catalysts are reached, while showing long stability and methanol tolerance.
|
Celia Castillo-Blas; María de las Nieves López-Salas; María C. Gutiérrez; Inés Puente-Orench; Enrique Gutiérrez-Puebla; María Luisa Ferrer; María Ángeles Monge; Felipe Gándara
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Catalysts; Hybrid Organic-Inorganic Materials; Coordination Chemistry (Inorg.); Solid State Chemistry; Electrocatalysis; Heterogeneous Catalysis
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CC BY NC ND 4.0
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CHEMRXIV
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1970-01-01
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f80bb8c1a6b783d9b80/original/encoding-metal-cation-arrangements-in-metal-organic-frameworks-for-programming-the-composition-of-electrocatalytically-active-multi-metal-oxides.pdf
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61e9c172f2bef721a1a8ca2d
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10.26434/chemrxiv-2022-gcq4k
|
Electrocatalytic Oxidation of Dinitrogen to Nitric Acid via Direct Ten–Electron Transfer Using Manganese Phthalocyanine
|
Ammonia produced through the energy intensive Haber–Bosch process, undergoes catalytic oxidation for the manufacture of commercial nitric acid in the age–old Ostwald process. This two–step energetically non–viable industrial process demands the quest of an alternative single step electrocatalysis from the last century. The quest ends up in optimism when we unravel a ten–electron pathway associated with electrochemical dinitrogen oxidation reaction (N2OR) to nitric acid by manganese phthalocyanine (MnPc) hierarchical nano–structures (HNs) at STP. The catalyst delivers nitric acid yield of 720 µmol h–1 g–1cat @ 1.9 V vs. RHE and F.E. of 17.32 % @ 1.7 V vs. RHE in 0.05 M HCl. The local co–ordination environment (Mn–N4) during electrocatalysis process is ensured by the XAFS study. DFT based calculations express that the Mn site of MnPc is the main active center for nitrogen adsorption for N2OR, suppressing the OER.
|
Uttam Ghorai; Ashadul Adalder; Sourav Paul; Biswajit Ghorai; Samadhan Kapse; Ranjit Thapa; Abharana N
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Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Electrocatalysis; Heterogeneous Catalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-01-21
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e9c172f2bef721a1a8ca2d/original/electrocatalytic-oxidation-of-dinitrogen-to-nitric-acid-via-direct-ten-electron-transfer-using-manganese-phthalocyanine.pdf
|
66053fee66c13817290cb1ee
|
10.26434/chemrxiv-2024-4lt9w
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Computational Predictive and Electrochemical Detection of Metabolites (CP-EDM) of Piperine
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In this article we introduce a proof of concept strategy: Computational Predictive and Electrochemical Detection of Metabolites (CP-EDM) to expedite the discovery of drug metabolites. The use of a bioactive natural product, piperine, that has a well curated metabolite profile but has an unpredictable computational metabolism (Biotransformer v3.0) was selected. We developed an electrochemical reaction to oxidise piperine into a range of metabolites, which were detected by LC-MS. In turn, a series of chemically plausible metabolites were predicted based on ion-fragmentation patterns. These metabolites were docked into the active site of CYP3A4 using Autodock4.2 From the clustered low-energy profile of piperine in the active site it can be inferred that the most likely metabolic position of piperine (based on intermolecular distances to the Fe-oxo active site) is the benzo[d][1,3]dioxole motif. The metabolic profile was confirmed by literature comparison and the electrochemical reaction delivered plausible metabolites vide infra. Thus, demonstrating the power of the hyphenated technique of tandem electrochemical detection and computational evaluation of binding poses. Taken together, we outline a novel approach where diverse data sources are combined to predict and confirm a metabolic outcome for a bioactive structure.
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Ridho Asra; Ana P.R. Povinelli; Gabriel Zazeri; Alan M. Jones
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Theoretical and Computational Chemistry; Organic Chemistry; Analytical Chemistry; Natural Products; Electrochemical Analysis; Computational Chemistry and Modeling
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CC BY 4.0
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CHEMRXIV
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2024-03-29
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66053fee66c13817290cb1ee/original/computational-predictive-and-electrochemical-detection-of-metabolites-cp-edm-of-piperine.pdf
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613ad8a527d906f624838c7a
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10.26434/chemrxiv-2021-4d5f4-v2
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Hydrogen evolution reaction on Co-Ni core-shell nanoclusters in different sizes: A DFT investigation from geometric structures to electronic structures
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Nanoclusters have broad prospects in the application of hydrogen evolution reaction (HER) electrocatalysis. Its high specific surface area, surface geometry effect, electronic properties, and quantum size effect often make the nanoclusters have higher activity than ordinary electrocatalytic materials. However, it is still challenging to design and regulate nanoclusters and make them have better HER performance. In this work, through first-principles calculation from geometric structures to electronic structures, we try to understand the basic physical and chemical properties and HER performance of nanoclusters composed of transition metals Co and Ni. We optimize the electronic structure and promote effective charge transfer by adjusting the size of nanoclusters and constructing core-shell alloying. First-principles studies reveal that the geometric size and electronic structures of Co-Ni nanoclusters can significantly affect the performance of the hydrogen evolution reaction. We found that Co@Ni12 (|ΔGH*|=0.01eV) shows the best HER performance. The Gibbs free energy of hydrogen adsorption of Co-Ni nanoclusters is positively related to the size of the clusters, and the ΔGH* can be adjusted within a certain range by changing the electronic structures of the clusters. Our research helps to understand and design high-efficiency nanocluster electrocatalysts, paving the way for the rational design and synthesis of advanced electrocatalysts for HER.
|
Hengyue Xu
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Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Theory - Computational; Electrochemistry - Mechanisms, Theory & Study; Physical and Chemical Properties
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-09-13
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613ad8a527d906f624838c7a/original/hydrogen-evolution-reaction-on-co-ni-core-shell-nanoclusters-in-different-sizes-a-dft-investigation-from-geometric-structures-to-electronic-structures.pdf
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668226abc9c6a5c07adaca3e
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10.26434/chemrxiv-2024-7rpw5
|
N-Heterocyclic Silylene-Copper(I)-Aryl Complex: Multitasking Cu(I) Synthon
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In this work, we have prepared [PhC{N(tBu)}2SiN(SiMe3)2] (1) coordinated organocopper(I) complexes (2 and 3) and utilized them as a useful synthon for the aryl group transfer and cleavage of a variety of homolytic and heterolytic bonds. Complex 2 was used as a mesityl transfer reagent in the C–C cross-coupling reaction that led to the formation of the coupled products in excellent yields. Further, we have demonstrated the reaction of 2 with compounds having B–B and Se–Se bonds, which led to the formation of dimeric µ-boryl bound Cu(I) complex (6) and a new class of unprecedented NHSi-supported copper-selenides (8 and 9). Finally, this new synthetic methodology smoothly afforded several elusive NHSi-copper amide complexes (10-14).
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Moushakhi Ghosh; Kumar Gaurav; Prakash Panwaria; Srinu Tothadi; SHABANA KHAN
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Inorganic Chemistry; Main Group Chemistry (Inorg.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-07-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668226abc9c6a5c07adaca3e/original/n-heterocyclic-silylene-copper-i-aryl-complex-multitasking-cu-i-synthon.pdf
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628fbd1f9a0ad54b2a14ff83
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10.26434/chemrxiv-2021-1v37x-v2
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Linker Redox Mediated Control of Morphology and Properties in Semiconducting Iron-Semiquinoid Coordination Polymers
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The emergence of conductive 2D, and less commonly 3D, coordination polymers (CPs) and metal–organic frameworks (MOFs) promises novel applications in chemical sensing, energy storage, optoelectronics, thermoelectrics, and spintronics. While classic CPs and MOFs now have relatively sophisticated synthetic parameters to control morphology, crystallinity, and phase purity, similar parameters are not thoroughly understood for electronically more complex materials. In particular, many linkers used in conducting CPs have multiple accessible redox states and the relationship between starting linker oxidation state and final material structure and properties is not well understood. Here we report a new 3D semiconducting coordination polymer, Fe5(C6O6)3, which is composed of hexagonal Fe2(C6O6)3 layers which are bridged by additional Fe ions. This material, which is a fusion of 2D Fe-semiquinoid materials and recently reported 3D cubic Fex(C6O6)y materials, is obtained by using a different initial redox-state of the C6O6 linker. The material displays high electrical conductivity (0.02 S cm–1), broad electronic transitions in the visible to middle-infrared region, promising thermoelectric behavior (S2σ = 4.2×10–9 W m–1 K–2), and strong antiferromagnetic interactions even at room temperature. The unique structure and properties of
this material illustrates that controlling the oxidation states of redox-active components in conducting CPs can be a “presynthetic” strategy to carefully tune material topologies, properties, and functionalities in contrast to more commonly encountered post-synthetic modifications.
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Lei Wang; Robert Papoular; Noah Horwitz; Jiaze Xie; Arup Sarkar; Dario Campisi; Norman Zhao; Baorui Cheng; Tengzhou Ma; Alexander Filatov; Laura Gagliardi; John Anderson
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Inorganic Chemistry; Coordination Chemistry (Inorg.); Magnetism; Crystallography – Inorganic
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-05-27
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628fbd1f9a0ad54b2a14ff83/original/linker-redox-mediated-control-of-morphology-and-properties-in-semiconducting-iron-semiquinoid-coordination-polymers.pdf
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672ce0967be152b1d0572794
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10.26434/chemrxiv-2024-ln3pk-v2
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Deep Learning Assisted Proton Pure Shift NMR Spectroscopy
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Nuclear magnetic resonance spectroscopy (NMR) plays a key role for the analysis of a plethora of molecules, including natural products and drug-like organic molecules. For such cases 1H NMR spectra have proven imperative because of their high sensitivity. However, these spectra are complicated by complex multiplet patterns that, although important for the analysis, lead to substantial overlap. Here we show a deep-learning approach, which transforms spin-echo modulated 1H NMR spectra into highly sensitive and high-resolution singlet NMR spectra, that is, virtual homonuclear decoupled pure shift spectra. The approach was evaluated on experimental NMR spectra of complex organic compounds, where it outperforms current methods. The method also predicts uncertainties of the transformation and therefore allows for quantifications. We believe that our approach will provide significant advantages when characterizing low sensitivity samples, where no signals are observed in traditional pure-shift spectra and strong overlaps are hampering analysis from conventional spectra.
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Veera Mohana Rao Kakita; D. Flemming Hansen
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Theoretical and Computational Chemistry; Artificial Intelligence
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CC BY 4.0
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CHEMRXIV
|
2024-11-08
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672ce0967be152b1d0572794/original/deep-learning-assisted-proton-pure-shift-nmr-spectroscopy.pdf
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60c7466b0f50dba1a4396435
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10.26434/chemrxiv.9985079.v2
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Benchmarking Electronic Structure Methods for Accurate Fixed-Charge Electrostatic Models
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<p>The accuracy of classical molecular mechanics (MM) force fields used for condensed phase molecular simulations depends strongly on the accuracy of modeling nonbonded interactions between atoms, such as electrostatic interactions. Some popular fixed-charge MM force fields use partial atomic charges derived from gas phase electronic structure calculations using the Hartree-Fock method with the relatively small 6-31G* basis set (HF/6-31G*). It is generally believed that HF/6-31G* generates fortuitously overpolarized electron distributions, as would be expected in the higher dielectric environment of the condensed phase. Using a benchmark set of 47 molecules we show that HF/6-31G* overpolarizes molecules by just under 10% on average with respect to experimental gas phase dipole moments. The overpolarization of this method/basis set combination varies significantly though and, in some cases, even leads to molecular dipole moments that are lower than experimental gas phase measurements. We further demonstrate that using computationally inexpensive density functional theory (DFT) methods, together with appropriate augmented basis sets and a continuum solvent model, can yield molecular dipole moments that are both more strongly and more uniformly overpolarized. These data suggest that these methods – or ones similar to them – should be adopted for the derivation of accurate partial atomic charges for next-generation MM force fields.<br /></p>
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Alex Zhou; Michael Schauperl; Paul Nerenberg
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Computational Chemistry and Modeling
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CC BY 4.0
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CHEMRXIV
|
2019-11-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7466b0f50dba1a4396435/original/benchmarking-electronic-structure-methods-for-accurate-fixed-charge-electrostatic-models.pdf
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67802965fa469535b95e119f
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10.26434/chemrxiv-2025-t38ql
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An Electrochemical Strategy for Chalcogenation of closo-Dodecaborate (B12H12)2– Anion
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Advancements in thermal neutron generation technologies within clinical environments have led to a renewed interest in developing boron-containing compounds for boron neutron capture therapy (BNCT). Previous syntheses of several key boron cluster-based therapeutics with clinical relevance are low-yielding and have complicated workup procedures. Using electrolytic methods, we report the in situ oxidation of pseudohalides, –SCN and –SeCN, to synthesize pseudohalogenated products, B12H11YCN2– (Y = S or Se). Further, these compounds can be reduced to their respective thiol or selenol, BSH or BSeH, which are exceedingly nucleophilic and able to form zwitterionic sulfonium and selenonium compounds using alkyl-based electrophiles. The newly reported preparation of BSH and BSeH provides an efficient and convenient route to the preparation of key chalcogenated boron cluster building blocks for the biomedical and materials science communities.
|
Tyler Kerr; Yessica Nelson; Nick Bernier; Alexander Spokoyny
|
Biological and Medicinal Chemistry; Inorganic Chemistry; Bonding; Electrochemistry; Main Group Chemistry (Inorg.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2025-01-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67802965fa469535b95e119f/original/an-electrochemical-strategy-for-chalcogenation-of-closo-dodecaborate-b12h12-2-anion.pdf
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60c7563e702a9b42c718c898
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10.26434/chemrxiv.14219450.v1
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Uncovering Halide Mixing and Octahedral Dynamics in Vacancy-Ordered Double Perovskites by Multinuclear Magnetic Resonance Spectroscopy
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Vacancy-ordered double perovskites Cs<sub>2</sub>SnX<sub>6</sub> (X = Cl, Br, I) have emerged as promising lead-free and ambient-stable materials for photovoltaic and optoelectronic applications. To advance these promising materials, it is crucial to determine the correlations between physical properties and their local structure and dynamics. Solid-state NMR spectroscopy of multiple NMR-active nuclei (<sup>133</sup>Cs, <sup>119</sup>Sn and <sup>35</sup>Cl) in these cesium tin(IV) halides has been used to decode the structure, which plays a key role in the materials’ optical properties. The <sup>119</sup>Sn NMR chemical shifts span approximately 4000 ppm and the <sup>119</sup>Sn spin-lattice relaxation times span three orders of magnitude when the halogen goes from chlorine to iodine in these diamagnetic compounds. Moreover, ultrawideline <sup>35</sup>Cl NMR spectroscopy for Cs<sub>2</sub>SnCl<sub>6</sub> indicates an axially symmetric chlorine electric field gradient tensor with a large quadrupolar coupling constant of <i>ca.</i> 32 MHz, suggesting a chlorine that is directly attached to Sn(IV) ions. Variable temperature <sup>119</sup>Sn spin lattice relaxation time measurements uncover the presence of hidden dynamics of octahedral SnI<sub>6</sub> units in Cs<sub>2</sub>SnI<sub>6</sub> with a low activation energy barrier of 12.45 kJ/mol (0.129 eV). We further show that complete mixed-halide solid solutions of Cs<sub>2</sub>SnCl<sub>x</sub>Br<sub>6−x</sub> and Cs<sub>2</sub>SnBr<sub>x</sub>I<sub>6−x</sub> (0 ≤ x ≤ 6) form at any halogen compositional ratio. <sup>119</sup>Sn and <sup>133</sup>Cs NMR spectroscopy resolve the unique local SnCl<i><sub>n</sub></i>Br<sub>6−<i>n</i></sub>and SnBr<i><sub>n</sub></i>I<sub>6−<i>n</i></sub> (<i>n</i> = 0−6) octahedral and CsBr<i><sub>m</sub></i>I<sub>12−<i>m</i></sub> (<i>m</i> = 0−12) cuboctahedral environments in the mixed-halide samples. The experimentally observed <sup>119</sup>Sn NMR results are consistent with magnetic shielding parameters obtained by density functional theory computations to verify random halogen distribution in mixed-halide analogues. Finally, we demonstrate the difference in the local structures and optical absorption properties of Cs<sub>2</sub>SnI<sub>6</sub> samples prepared by solvent-assisted and solvent-free synthesis routes.
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Abhoy Karmakar; Srija Mukhopadhyay; Pierre Gachod; Arturo Gomez; Guy Bernard; Alex Brown; Vladimir Michaelis
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Photovoltaics; Spectroscopy (Physical Chem.); Structure; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-03-16
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7563e702a9b42c718c898/original/uncovering-halide-mixing-and-octahedral-dynamics-in-vacancy-ordered-double-perovskites-by-multinuclear-magnetic-resonance-spectroscopy.pdf
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636cc2c48e0d35eb3f1551ac
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10.26434/chemrxiv-2022-mqbgv
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Scalable, Wasteless, and Energy-Efficient Diastereoselective Electrocatalytic Hydrogenation of Cyclic Ketones Using Proton-Exchange Membrane Reactor
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We report the diastereoselective electrocatalytic hydrogenation of cyclic ketones using a proton-exchange membrane (PEM) reactor. Adsorbed monoatomic hydrogen species (Hads) generated from protons at the triple-phase boundary of the cathode were found to reduce the C=O bond of cyclic ketones with high diastereoselectivity; cis-selectivity as high as 94% was achieved under the optimal conditions using a Rh catalyst. Operando infrared (IR) spectroscopy enabled the direct observation of adsorbed ketones involved in the reaction. We also demonstrated the 5 g-scale electrolysis of 4-tert-butylcyclohexanone by combining the hydrogenation process with water oxidation as an anodic reaction. This reaction successfully produced cis-4-tert-butylcyclohexanol, which is 52 times more expensive than the starting material based on commercial prices, using only electric energy and water as reagents and, importantly, without H2 gas. This research demonstrates the potential of PEM reactors as reliable, robust, and green systems for the electrochemical production of fine chemicals.
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Yugo Shimizu; Atsushi Fukazawa; Tomohiro Suzuki; Junko N. Kondo; Naoki Shida; Mahito Atobe
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Organic Chemistry; Catalysis; Energy; Organic Synthesis and Reactions; Electrocatalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-11-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636cc2c48e0d35eb3f1551ac/original/scalable-wasteless-and-energy-efficient-diastereoselective-electrocatalytic-hydrogenation-of-cyclic-ketones-using-proton-exchange-membrane-reactor.pdf
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60c74803bdbb892a14a38ee1
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10.26434/chemrxiv.11829576.v1
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Precise Identification and Characterization of Catalytically Active Sites on the Surface of γ-Alumina
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<p>γ-alumina is one of the oldest and most important commercial catalytic materials with high surface area and stability. These attributes enabled its use as the first commercial large-scale heterogeneous catalyst for ethanol dehydration. Despite progress in materials characterization and over a hundred years of active research, the nature of the specific sites on the surface of γ-alumina which are responsible for its unique catalytic properties has remained obscure and controversial. Herein, we identify for the first time using combined infrared spectroscopy, electron microscopy and solid-state nuclear magnetic resonance measurements that the octahedral amphoteric (O)<sub>5</sub>Al(VI)-OH sites on the massively restructured (110) facets on typical rhombus-platelet γ-alumina as well as (100) segments of irrational surfaces (invariably always present in all γ-alumina samples) are largely responsible for its unique catalytic activity. Such (O)<sub>5</sub>Al(VI)-OH sites are also present on macroscopically defined (100) facets γ-alumina of different, more elongated/rod-like geometry. They anchor organometallic fragments and isolated metal atoms. The exact mechanism by which these sites lose -OH group upon thermal dehydroxylation is clarified, resulting in coordinatively unsaturated penta-coordinate Al<sup>+3</sup>O<sub>5</sub> sites that can activate nitrogen. These coordinatively unsaturated Al penta-coordinate sites demonstrate new chemistry, producing the first well-defined thermally stable Al-carbonyl complexes. Our findings reunite and successfully clarify the contradictory findings in the literature over the last century, illuminating the true nature and the relationship between the catalytically active and coordinatively unsaturated Al sites on the surface of γ-alumina.</p>
|
Konstantin Khivantsev; Nicholas
R. Jaegers; Ja-Hun Kwak; János Szanyi; Libor Kovarik
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Catalysts; Nanocatalysis - Catalysts & Materials; Spectroscopy (Inorg.); Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Catalysis; Spectroscopy (Physical Chem.); Surface
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-02-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74803bdbb892a14a38ee1/original/precise-identification-and-characterization-of-catalytically-active-sites-on-the-surface-of-alumina.pdf
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60c758350f50db9aa13983ef
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10.26434/chemrxiv.14524977.v1
|
A Theoretical Approach to Demystify the Role of Copper Salts and O2 in the Mechanism of C-N Bond Cleavage and Nitrogen Transfer
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<b>C≡N bond scission accomplished by protonation, reductive cleavage and metathesis techniques are well-known to execute nitrogen transfer reactions. Herein, we have conducted an extensive computational study, using DFT and molecular dynamics simulations, to unravel the mechanistic pathways traversed in CuCN and CuBr<sub>2</sub> promoted splitting of coordinated cyanide anion under a dioxygen atmosphere, which enables nitrogen transfer to various aldehydes. Our detailed electronic structure analysis using <i>ab initio</i> multi-reference CASSCF calculations reveal that both the promoters facilitate radical pathways, in agreement with the experimental findings. This is a unique instance of oxygen activation initiated by single electron transfer from the nitrile carbon, while the major driving force is the operation of the Cu<sup>II/I </sup>redox cycle. Our study reveals that the copper salts act as the “electron pool” in this unique nitrogen transfer reaction forming aryl nitrile from aryl aldehydes.</b><br />
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Boyli Ghosh; Ambar Banerjee; Lisa Roy; Rounak Nath; Rabindra Nath Manna Manna; Ankan Paul
|
Computational Chemistry and Modeling; Theory - Computational
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CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758350f50db9aa13983ef/original/a-theoretical-approach-to-demystify-the-role-of-copper-salts-and-o2-in-the-mechanism-of-c-n-bond-cleavage-and-nitrogen-transfer.pdf
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60c748740f50db48c5396792
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10.26434/chemrxiv.11910768.v1
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N-Rich Electron Acceptor: Triplet Harvesting in Multichromophoric Pyridoquinoxaline and Pyridopyrazine-Based Organic Emitters
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<p></p><p>Control of nonradiative deactivation of triplet states
and tuning the singlet-triplet energy gap (ΔE<sub>ST</sub>) are the major
challenges to develop materials exhibiting thermally activated delayed
fluorescence (TADF) and room temperature phosphorescence (RTP). Herein, we
propose a new class of multichromophoric tridonor-acceptor (D<sub>3</sub>-A)
compounds with rigid and flexible π-spacer
having N-rich pyridoquinoxaline (PQ) and pyridopyrazine (PZ) acceptor core,
respectively. The molecule with carbazole (Cz) donors at <i>meta</i> to
quinoxaline (QX) nitrogen of rigid PQ core exhibits TADF. Whereas, the
variation of the linkage position of Cz to PQ as well as twisted and flexible PZ
core show predominantly RTP due to relatively higher singlet-triplet energy gap
(ΔE<sub>ST</sub>). Increasing the donor strength with phenoxazine (PO) in PZ
system leads to simultaneous TADF and RTP. Further, we demonstrate the
promising scope of all-organic triplet harvesting
materials in solid-state security encryption.</p><br /><p></p>
|
BAHADUR SK; Samarth Sharma; Anto James; Subhankar Kundu; Abhijit Patra
|
Optical Materials; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-02-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748740f50db48c5396792/original/n-rich-electron-acceptor-triplet-harvesting-in-multichromophoric-pyridoquinoxaline-and-pyridopyrazine-based-organic-emitters.pdf
|
61670e747d3da50c42f692b9
|
10.26434/chemrxiv-2021-h3tqz
|
Putting MicroED to the Test: An Account of the Evaluation of 30 Diverse Pharmaceutical Compounds
|
The application of microcrystal electron diffraction (microED) to a variety of pharmaceutical compounds is reported. The examples and work detailed showcase the utility of microED as a routine technique for the rapid collection, analysis, and generation of structural data on a number of pharmaceutically relevant compounds, requiring minimal sample preparation and often without the need for time-consuming vitrification and cryo transfer processes. The development of a scripted data processing workflow allowed for simultaneous collection and processing of electron diffraction data, further expediting structural analysis of fifteen compounds.
|
Jessica E. Burch; Austin G. Smith; Seb Caille; Shawn D. Walker; Ryan Wurz; Victor J. Cee; Jose Rodriguez; D. Gostovic; Kyle Quasdorf; Hosea M. Nelson
|
Biological and Medicinal Chemistry; Organic Chemistry; Process Chemistry; Stereochemistry; Crystallography – Organic
|
CC BY NC 4.0
|
CHEMRXIV
|
2021-10-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61670e747d3da50c42f692b9/original/putting-micro-ed-to-the-test-an-account-of-the-evaluation-of-30-diverse-pharmaceutical-compounds.pdf
|
611e3ec8ded28a727483f36a
|
10.26434/chemrxiv-2021-j9v6d
|
Sustainability assessment of biodiesel produced from Jatropha curcas using life cycle assessment approach
|
Transport sector in India is heavily dependent on fossil fuels and ~75% of the demand is met by import. National Biofuel Policy, 2009 focused on production of biodiesel from non-edible oil seeds. We assessed the sustainability of biodiesel produced from Jatropha curcas, using the life cycle assessment approach. India specific inventory data for biodiesel production was collected by extensive literature review. GaBi software was used to model the life cycle of biodiesel. The environmental impacts are compared for different blends of biodiesel with reference to diesel in four impact categories: Global Warming Potential, Acidification Potential, Eutrophication Potential, and Human Toxicity Potential. Using the biodiesel may reduce the global warming potential by 64.6% as compared to fossil diesel; while eutrophication potential, acidification potential, and human toxicity potential impacts may increase by 61.3%, 36.5%, and 52.5% respectively. A trade-off between impact categories is seen for biodiesel. Sensitivity analysis was done to identify most sensitive parameters in biodiesel life cycle. Use of electricity, life cycle span of Jatropha, seed yield, methanol, urea fertilizer, NOx emission factor, and steam are found to be highly sensitive in biodiesel life cycle. Scenario analysis was done to analyse the effect of change in seed yield, life span, and emission intensity of Indian electricity grid. Even low yield of Jatropha provides reduction in global warming potential (~27.7%) but in other impact categories significant increase is expected. Impacts could be further minimized if the emissions from grid are minimized in future.
|
Vijay Thakur; Munish Chandel
|
Energy; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science; Wastes; Fuels - Energy Science
|
CC BY 4.0
|
CHEMRXIV
|
2021-08-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611e3ec8ded28a727483f36a/original/sustainability-assessment-of-biodiesel-produced-from-jatropha-curcas-using-life-cycle-assessment-approach.pdf
|
669160b601103d79c5d5bdb0
|
10.26434/chemrxiv-2024-5v5s8
|
Automated Multicolumn Screening Workflow in Ultra-High Pressure Hydrophilic Interaction Chromatography for Streamlined Method Development of Polar Analytes
|
The pharmaceutical industry is rapidly advancing toward new drug modalities, necessitating the development of advanced analytical strategies for effective, meaningful, and reliable assays. Hydrophilic Interaction Chromatography (HILIC) is a powerful technique for the analysis of polar analytes. Despite being a well-established technique, HILIC method development can be laborious owing to the multiple factors that affect the separation mechanism, such as the selection of stationary phase chemistry, mobile phase eluents, and optimization of column equilibration time. Herein, we introduce a new automated multicolumn and multi-eluent screening workflow that streamlines the development of new HILIC assays, circumventing the existing tedious ‘hit-or-miss’ approach. A total of 12 complementary columns packed with sub-2 µm fully porous and 2.7 µm superficially porous particles operated on readily available ultra-high pressure liquid chromatography (UHPLC) instrumentation across a diverse set of commercially available polar stationary phases were investigated. Different mobile phases with pH ranging from pH 3 to 9 were evaluated using different organic modifier. The gradient and column re-equilibration were judiciously set to ensure a reliable assay screening framework yielding straightforward separation conditions for subsequent optimization and method deployment in fast-paced laboratory settings. This UHPLC screening system is coupled with a diode array and charged aerosol detectors (DAD and CAD) to ensure versatile detection for a variety of compounds. This fast-screening platform lays the foundation for a convenient generic workflow, accelerating the pace of HILIC method development and transfer across both academic and industrial sectors.
|
Mohamed Hemida; Rodell Barrientos; Andrew Singh; Gioacchino Luca Losacco; Heather Wang; Davy Guillarme; Eli Larson; Wei Xu; Emmanuel Appiah-Amponsah; Erik Regalado
|
Analytical Chemistry; Analytical Chemistry - General; Separation Science; High-throughput Screening
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669160b601103d79c5d5bdb0/original/automated-multicolumn-screening-workflow-in-ultra-high-pressure-hydrophilic-interaction-chromatography-for-streamlined-method-development-of-polar-analytes.pdf
|
65f07b189138d231615141fd
|
10.26434/chemrxiv-2024-m08kw
|
Mucus-Inspired Self-Healing Hydrogels: A Protective Barrier for Cells against Viral Infection
|
Mucus is a dynamic biological hydrogel, composed primarily of the glycoprotein mucin, exhibits unique biophysical properties and forms a barrier protecting cells against a broad spectrum of viruses. Here we developed a polyglycerol sulfate-based dendronized mucin-inspired copolymer (MICP-1) with ~10 % repeating units of activated disulfide as cross-linking sites. Cryo-EM analysis of MICP-1 reveals an elongated single-chain fiber morphology. MICP-1 shows potential inhibitory activity against many viruses such as HSV-1 and SARS-CoV-2 (including variants such as Delta and Omicron). MICP-1 produces hydrogels with viscoelastic properties similar to healthy human sputum and with tuneable microstructures using linear and branched PEG-thiol as cross-linkers. Single particle tracking microrheology, EPR and Cryo-SEM were used to characterize the network structures. The synthesized hydrogels exhibit self-healing properties, along with viscoelastic properties that are tuneable through reduction. a transwell assay was used to investigate the hydrogel’s protective properties against viral infection against HSV-1. Live-cell microscopy confirmed that these hydrogels can protect underlying cells from infection by trapping the virus, due to both network morphology and anionic multivalent effects. Overall, our novel mucin-inspired copolymer generates mucus-mimetic hydrogels on a multi-gram scale. These hydrogels can be used as a models for disulfide-rich airway mucus research, and as biomaterials.
|
Raju Bej; Corey Alfred Stevens ; Chuanxiong Nie ; Kai Ludwig; George Degen ; Yannic Kerkhoff ; Marina Pigaleva; Julia M. Adler; Nicole A. Bustos; Taylor M. Page; Jakob Trimpert; Stephan Block; Benedikt B. Kaufer; Katharina Ribbeck; Rainer Haag
|
Materials Science; Polymer Science; Biological Materials; Biodegradable Materials; Hydrogels; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-03-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f07b189138d231615141fd/original/mucus-inspired-self-healing-hydrogels-a-protective-barrier-for-cells-against-viral-infection.pdf
|
64c90480658ec5f7e58ebc14
|
10.26434/chemrxiv-2023-j2d3h-v3
|
Functionalizing DNA Origami by Triplex-Directed Site-Specific Photo- Crosslinking
|
Here we present a universal method to introduce functionality and improve the structural integrity of DNA origami in a one-pot reaction. Our strategy involves adding nucleotide sequences to adjacent staple strands so that, upon origami assembly, the add-on sequences form short hairpin duplexes targetable by psoralen-labelled triplex-forming oligonucleotides (pso-TFOs) bearing other functionality. Subsequent irradiation with UVA light generates psoralen adducts with one or both hairpin staples leading to site-specific attachment of the pso-TFO to the origami with >80% efficiency. Bis-adduct formation between strands in proximal hairpins further tethers the TFO to the structure and generates ‘super-staples’ that improve the structural integrity of the complex. We also show that crosslinking reduces the sensitivity of the functionalized origami to thermal denaturation and disassembly by T7 RNA polymerase. Our strategy is scalable and cost-effective as it works with existing DNA origami structures, does not require scaffold redesign, and can be achieved with just one psoralen- modified oligonucleotide. It is also non-damaging to the origami scaffold, as well as to introduced fluorescent functionalities.
|
Shantam Kalra; Amber Donnelly; Nishtha Singh; Daniel Matthews; Rafael del Villar-Guerra; Victoria Bemmer; Cyril Dominguez; Natalie Allcock; Dmitry Cherny; Andrey Revyakin; David Rusling
|
Nanoscience; Nanostructured Materials - Nanoscience
|
CC BY 4.0
|
CHEMRXIV
|
2023-08-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c90480658ec5f7e58ebc14/original/functionalizing-dna-origami-by-triplex-directed-site-specific-photo-crosslinking.pdf
|
60c74edd567dfe0dd6ec559b
|
10.26434/chemrxiv.12814793.v1
|
Parallel Quantum Computation of Vibrational Dynamics
|
The vibrational dynamics in a linear triatomic molecule is emulated by a quantum
information processing device operating in parallel. The quantum device is an ensemble of
semiconducting quantum dot dimers addressed and probed by ultrafast laser pulses in the
visible frequency range at room temperature. A realistic assessment of the inherent noise due
to the inevitable size dispersion of colloidal quantum dots is taken into account and limits the
time available for computation. At the short times considered only the electronic states of the
quantum dots respond to the excitation. We show how up to 82 = 64 quantum logic variables
can be realistically measured and used to process information. This is achieved by addressing
the lowest and second excited electronic states of the quantum dots. With a narrower laser
bandwidth (= longer pulse) only the lower band of excited states can be coherently addressed
enabling 42 = 16 logic variables. Already this is sufficient to emulate both energy transfer
between the two oscillators and coherent motions in the vibrating molecule.
|
Ksenia Komarova; Hugo Gattuso; Raphael D. Levine; Francoise Remacle
|
Quantum Computing
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74edd567dfe0dd6ec559b/original/parallel-quantum-computation-of-vibrational-dynamics.pdf
|
6528fb808bab5d2055429a70
|
10.26434/chemrxiv-2023-6hngt-v2
|
Accelerating antibiotic discovery by leveraging machine learning models: Application to identify novel inorganic complexes
|
The expanded prevalence of resistant bacteria and the inherent challenges of complicated infections highlight the urgent need to develop credible antibiotic options. Through conventional screening approaches, the discovery of new antibiotics has proven to be challenging. Anti-infective drugs, including antibacterials, antivirals, antifungals, and antiparasitics, have become less effective due to the spread of drug resistance. In this work we help define the design of next-generation antibiotic analogs based on metal complexes. The primary direction is based on the application of artificial intelligence (AI) methods, which demonstrated superior ability in tackling resistance in Gram-positive and Gram-negative bacteria, including multidrug-resistant strains. The bottleneck of the existing AI approaches relies on the structure similarities of the current antibiotics. The question of discovering and developing new unconventional antibiotic classes has challenged preconceptions about the scope and applicability of the existing methods. Herein, we developed a machine learning approach that predicts the minimum inhibitory concentration (MIC) of Re-complexes towards two S. aureus strains (ATCC 43300 - MRSA and ATCC 25923 - MSSA). Multi-layer Perceptron (MLP) was tailored with the structure features of the Re-complexes to develop the prediction model. Although our approach is demonstrated with a specific example, based on the rhenium carbonyl complexes, the predictive model can be readily adjusted to other candidate metal complexes. The model emphasizes applying a developed approach in the de novo design of a metal-based antibiotic with targeted activity against a challenging pathogen.
|
Miroslava Nedyalkova; Gözde Demirci; Youri Cortat; Kevin Schindler; Fatlinda Rhamani; Aleksandar Pavic; Fabio Zobi; Marco Lattuada
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Inorganic Chemistry; Microbiology; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6528fb808bab5d2055429a70/original/accelerating-antibiotic-discovery-by-leveraging-machine-learning-models-application-to-identify-novel-inorganic-complexes.pdf
|
644b3f3480f4b75b533d9c4f
|
10.26434/chemrxiv-2023-8w6tf-v2
|
Mechanistic Studies on Rh-Catalyzed Ligand-Controlled Chemoselective Hydrothiolation of Cyclopropenes
|
Recently, it has been reported that Rh-catalyzed ligand-controlled hydrothiolation of cyclopropenes leads to cyclopropyl or allylic sulfides with high regiocontrol. However, there has yet to be any previous research investigating the detailed mechanism of this reaction. Therefore, density functional theory calculations were performed to provide mechanistic insight into the hydrothiolation of cyclopropenes. The study results show that when L5 is the ligand, cyclopropyl sulfide 3 is the main product, and reductive elimination is the rate-determining step. However, allylic sulfide 4 becomes the primary product when L8 is employed. The reaction follows the carbene formation pathway instead of the initially proposed cyclopropene π bond activation pathway. The chemoselectivity is determined by the competition with Rh−Cγ insertion and reductive elimination. When L5 as the ligand, the origin of the chemoselectivity can be attributed to the electronic effect, steric hindrance effect, and C–H…π interaction. Additionally, the distortion/interaction analysis shows that the allylic sulfide originated predominantly due to the lower distortion energy of the substrate fragment in the reductive elimination transition state under the L8 ligand.
|
Dingyi Tang; Zhizheng Chen; Xiaoxi Su; Shuanglin Qu
|
Organometallic Chemistry; Theory - Organometallic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644b3f3480f4b75b533d9c4f/original/mechanistic-studies-on-rh-catalyzed-ligand-controlled-chemoselective-hydrothiolation-of-cyclopropenes.pdf
|
63c526503af97307c56a70a1
|
10.26434/chemrxiv-2023-sxd5h
|
Size and Composition Dependent Electronic, Structural and Optical Properties of Transition Metal Dichalcogenide Nanoflakes
|
Nanoparticles and nanostructures of two-dimensional semiconductors are being explored for their potential in photocatalysis, opto-electronics, and energy harvesting applications. Herein, we investigate the size and compo- sition dependence of electronic, structural, and optical properties of triangular transition metal dichalcogenide (MX2, M=Mo, W and X=S, Se, Te) nanoflakes. Structural optimizations reveal that, while all flakes undergo dimerization of X atoms along each edge, in large WS2 flakes the edge S form trimers. All flakes are found to be metallic with dominant contributions to the conducting states from the edges. Our time-dependent density functional theory-based calculations find both surface (2D) and edge (1D) plasmonic exictations at low ener- gies in all small flakes. However, only Se containing flakes are found to support edge plasmons at all sizes. The corresponding plasmon peaks exhibit a red-shift with flake size as expected from quantum confinement effects. Supported by induced charge-density and potential analyses, transition contribution maps as well as trends in generalized plasmonicity indices of the excitations, these findings assume significance given the role of plasmonic nanostructures in the aforementioned applications.
|
Paresh Rout; Vignesh Balaji; Nesta Benno; Shalini Tomar; Varadharajan Srinivasan
|
Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-01-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c526503af97307c56a70a1/original/size-and-composition-dependent-electronic-structural-and-optical-properties-of-transition-metal-dichalcogenide-nanoflakes.pdf
|
60c751e4842e65131ddb3c46
|
10.26434/chemrxiv.13224830.v1
|
A Tailored Phosphoaspartate Probe Unravels CprR as a Response Regulator in Pseudomonas Aeruginosa Interkingdom Signaling
|
Pseudomonas aeruginosa is a difficult-to-treat Gram-negative bacterial
pathogen causing life-threatening infections. Adaptive resistance (AR)
to cationic peptide antibiotics such as polymyxin B impairs the
therapeutic success. This self-protection is mediated by two component
systems (TCS) consisting of a membrane-bound histidine kinase and an
intracellular response regulator (RR). As phosphorylation of the key RR
aspartate residue is transient during signaling and hydrolytically
unstable, the study of these systems is challenging. Therefore, we
applied a tailored reverse polarity chemical proteomic strategy to
capture this transient modification and read-out RR phosphorylation in
complex proteomes using a nucleophilic probe. An ideal trapping
methodology was developed with a recombinant RR demonstrating the
importance of fine-tuned acidic pH values to facilitate the attack on
the aspartate carbonyl C-atom and prevent unproductive hydrolysis.
Analysis of Bacillus subtilis and P. aeruginosa proteomes revealed the
detection of multiple phosphoaspartate sites, which closely resembled
the conserved RR sequence motif. With this validated strategy we
dissected the signaling of dynorphin A, a human peptide stress hormone,
which is sensed by P. aeruginosa to mediate AR. Intriguingly, our
methodology identified CprR as an unprecedented RR in dynorphin A
interkingdom signaling.
|
Patrick Allihn; Mathias
W. Hackl; Christina Ludwig; Stephan M. Hacker; Stephan A. Sieber
|
Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-11-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751e4842e65131ddb3c46/original/a-tailored-phosphoaspartate-probe-unravels-cpr-r-as-a-response-regulator-in-pseudomonas-aeruginosa-interkingdom-signaling.pdf
|
60c746f0567dfec02cec4712
|
10.26434/chemrxiv.11406546.v1
|
Selenolysine: A New Tool for Traceless Isopeptide Bond Formation
|
<p>Despite their biological importance, post-translationally modified proteins are notoriously difficult to produce in a homogeneous fashion using conventional expression systems. Chemical protein synthesis or semi-synthesis offers a solution to this problem; however, traditional strategies often rely on sulfur-based chemistry that is incompatible with the presence of multiple cysteine residues in the target protein. To overcome these limitations, we present the design and synthesis of γ-selenolysine, a selenol-containing form of the commonly modified proteinogenic amino acid, lysine. The utility of γ-selenolysine is demonstrated with the traceless ligation of the small ubiquitin-like modifier protein, SUMO-1, to a peptide segment of human glucokinase. The resulting polypeptide is poised for native chemical ligation and selective deselenization in the presence of unprotected cysteine residues. Selenolysine’s straightforward synthesis and incorporation into synthetic peptides marks it as a universal handle for conjugating any ubiquitin-like modifying protein to its target.</p>
|
Rebecca Notis Dardashti; Shailesh Kumar; Shawn
M. Sternisha; Post Sai Reddy; Brian G. Miller; Norman Metanis
|
Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-12-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746f0567dfec02cec4712/original/selenolysine-a-new-tool-for-traceless-isopeptide-bond-formation.pdf
|
65273b53bda59ceb9a60f921
|
10.26434/chemrxiv-2023-vs1db
|
Systematic Evolution of High-affinity ssDNA Sequence to Carbon Nanotube
|
Single-walled carbon nanotubes (SWCNTs) have gained significant interest for their potential in biomedicine and nanoelectronics; particularly, the functionalization of SWCNTs with single-stranded DNA (ssDNA) enables precise control of SWCNT alignment and the development of optical and electronic biosensors. Our study addresses gaps in understanding by employing high-throughput systematic evolution, enriching high-affinity ssDNA sequences from a vast random library. We identify specific base compositions and patterns that govern the binding affinity between ssDNA and SWCNTs. Molecular dynamics simulation validates the stable ssDNA conformation on SWCNT and reveal the pivotal role of hydrogen bonds in this interaction. Additionally, we demonstrate machine learning's capacity to accurately distinguish high-affinity ssDNA sequences, providing an accessible model on a dedicated webpage (http://service.k-medai.com/ssdna4cnt). These findings open new avenues for high-affinity ssDNA-SWCNT constructs for enduring and sensitive molecular detection across diverse scientific disciplines.
|
Dakyeon Lee; Jaekang Lee; Woojin Kim; Yeongjoo Suh; Jiwoo Park; Sungjee Kim; YongJoo Kim; Sunyoung Kwon; Sanghwa Jeong
|
Physical Chemistry; Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65273b53bda59ceb9a60f921/original/systematic-evolution-of-high-affinity-ss-dna-sequence-to-carbon-nanotube.pdf
|
67559cf1085116a133c1a824
|
10.26434/chemrxiv-2024-7xxzg-v2
|
Enzyme enhancement through computational stability design targeting NMR-determined catalytic hotspots
|
Enzymes are the quintessential green catalysts, but realizing their full potential for biotechnology typically requires improvement of their biomolecular properties. Catalysis enhancement, however, is often accompanied by impaired stability. Here, we show how the interplay between activity and stability in enzyme optimization can be efficiently addressed by coupling two recently proposed methodologies for guiding directed evolution. We first identify catalytic hotspots from chemical shift perturbations induced by transition-state-analogue binding and then use computational/phylogenetic design (FuncLib) to predict stabilizing combinations of mutations at sets of such hotspots. We test this approach on a previously designed de novo Kemp eliminase, which is already highly optimized in terms of both activity and stability. Most tested variants displayed substantially increased denaturation temperatures and purification yields. Notably, our most efficient engineered variant shows a ~3-fold enhancement in activity (kcat 1700 s-1, kcat/KM 4.3·105 M-1s-1) from an already heavily optimized starting variant, resulting in the most proficient proton-abstraction Kemp eliminase designed to date, with a catalytic efficiency on a par with naturally occurring enzymes. Molecular simulations pinpoint the origin of this catalytic enhancement as being due to the progressive elimination of a catalytically inefficient substrate conformation that is present in the original design. Remarkably, interaction network analysis identifies a significant fraction of catalytic hot-spots, thus providing a computational tool which we show to be useful even for natural-enzyme engineering. Overall, our work showcases the power of dynamically guided enzyme engineering as a design principle for obtaining novel biocatalysts with tailored physicochemical properties, towards even anthropogenic reactions.
|
Luis I. Gutierrez-Rus; Eva Vos; David Pantoja-Uceda; Gyula Hoffka; Jose Gutierrez-Cardenas; Mariano Ortega-Muñoz; Valeria A. Risso; Maria Angeles Jimenez; Shina Caroline Lynn Kamerlin; Jose M. Sanchez Ruiz
|
Biological and Medicinal Chemistry; Catalysis; Biochemistry; Bioengineering and Biotechnology; Bioinformatics and Computational Biology
|
CC BY 4.0
|
CHEMRXIV
|
2024-12-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67559cf1085116a133c1a824/original/enzyme-enhancement-through-computational-stability-design-targeting-nmr-determined-catalytic-hotspots.pdf
|
60c74c06842e652962db324c
|
10.26434/chemrxiv.10049846.v5
|
Effect of Droplet Size and Counterions on the Spatial Distribution of Ions
|
<div>Charged droplets have become a new environment for accelerating chemical reactions by orders of magnitude relative to their bulk analogues. Nevertheless the reaction mechanisms still remain unknown. Here we investigate the ion spatial distributions and surface charge in aqueous droplets with diameters in the range of 5 nm to 16 nm with and without counterions using molecular dynamics. The charge carriers are Na, and Cl ions ions. We demonstrate the convergence of ion spatial distributions. Scaling of the ion distributions reveals underlying universal behavior. The convergence allows one to extrapolate the simulation results from nanoscopic dimensions to larger ones, which are still inaccessible to atomistic modeling.</div><div>The surface excess charge and electric field are also computed. We find that the surface excess charge layer in the presence of Na and Cl ions is approximately 1.5 nm-1.7 nm thick and that approximately 55%-33 % (from smaller to larger droplets) of the total number of ions reside in this layer. For the first time droplet sizes that are accessible to experimental scrutiny are modeled atomistically. </div>
|
Victor Kwan; Styliani Consta
|
Clusters; Interfaces; Solution Chemistry; Structure
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c06842e652962db324c/original/effect-of-droplet-size-and-counterions-on-the-spatial-distribution-of-ions.pdf
|
60c742f29abda2fdb8f8c0f4
|
10.26434/chemrxiv.8865056.v1
|
Constant Potential, Electrochemically Active Boundary Conditions for Electrochemical Simulation
|
This manuscript presents a theoretical model for simulating molecular dynamics at electrode-electrolyte interfaces. The novelty of the model is that it combines a method for simulating constant potential electrodes and a method for simulating stochastic interfacial charge transfer. We combine these methods to simulate model electrochemical systems under driven conditions, where charge is flowing across the electrode-electrolyte interface. The manuscript describes the theoretical formalism and applies it to a model battery system. We highlight the ability of the model to support the formation of electrical double-layers and to provide microscopic physical insight the results of potential jump experiments.
|
Kaitlyn Dwelle; Adam Willard
|
Electrochemistry - Mechanisms, Theory & Study
|
CC BY NC ND 4.0
|
CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742f29abda2fdb8f8c0f4/original/constant-potential-electrochemically-active-boundary-conditions-for-electrochemical-simulation.pdf
|
60c73d8d842e65c34fdb17a1
|
10.26434/chemrxiv.5844267.v1
|
A Versatile AuNP Synthetic Platform for Decoupled Control of Size and Surface Composition
|
While a plethora of protocols exist for the synthesis of sub-10 nm gold nanoparticles (AuNPs), the independent control over size and surface composition remains restricted. This poses a particular challenge for systematic studies of AuNP structure-function relationships and optimization of crucial design parameters. To this end, we report on a modular 2-step approach based on the synthesis of AuNPs in oleylamine (OAm) followed by the subsequent functionalization with target thiol ligands. The synthesis of OAm-capped AuNPs enables fine tuning of the core size in the range of 2–7nm by varying the reaction temperature. The subsequent thiol-for-OAm ligand-exchange allows a reliable generation of thiol-capped AuNPs with target surface functionality. The compatibility of this approach with a vast library of thiol ligands provides detailed control of mixed ligand composition and solubility in a wide range of solvents ranging from water to hexane. This decoupled control over the AuNP core and ligand shell provides a powerful toolbox for the methodical screening of optimal design parameters and facile preparation of AuNPs with target properties.
|
Ye Yang; Luis A. Serrano; Stefan Guldin
|
Nanostructured Materials - Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-02-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d8d842e65c34fdb17a1/original/a-versatile-au-np-synthetic-platform-for-decoupled-control-of-size-and-surface-composition.pdf
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640b40edb5d5dbe9e80a251f
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10.26434/chemrxiv-2023-6dzf5
|
Zinc Bromide: A General Mediator for the Ionothermal Synthesis of Microporous Polymers via Cyclotrimerization Reactions
|
Conjugated microporous polymers (CMPs) are porous organic materials that display (semi)conducting behavior due to their highly -conjugated structures, making them promising next-generation materials for applications requiring both electrical conductivity and porosity. Currently, most CMPs and related porous aromatic frameworks (PAFs) are prepared using expensive transition metals (e.g., Pd), significantly increasing the costs associated with their synthesis. Lewis acid-mediated cyclotrimerization reactions of methyl ketones and nitriles represent promising and green alternative methods for CMP and PAF synthesis. Herein, we demonstrate that the generality of the solvent-free cyclotrimerization reactions is significantly improved by using ZnBr2 instead of ZnCl2 as the ionothermal medium. Specifically, we show that 1,4-diacetylbenzene (DAB), 4,4-diacetylbiphenyl (DABP), 2,7-diacetylfluorene (DAF), 1,3,5-triacetylbenzene (TAB), tetrakis(4-acetylphenyl)methane (TAPM), and 1,4-dicyanobenzene (DCNB) can be polymerized in molten ZnBr2 to produce highly conjugated and microporous materials, as confirmed by 77 K N2 adsorption measurements, IR, and solid-state NMR. These findings support that ZnBr2 is an excellent Lewis acid mediator and medium for the ionothermal synthesis of porous organic materials.
|
Jaehwan Kim; Minh Le; Makayla Spicer; Casandra Moisanu; Suzi Pugh; Phillip Milner
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Materials Science; Polymer Science; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-03-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640b40edb5d5dbe9e80a251f/original/zinc-bromide-a-general-mediator-for-the-ionothermal-synthesis-of-microporous-polymers-via-cyclotrimerization-reactions.pdf
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60c73e96bdbb899b0ba37e60
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10.26434/chemrxiv.7011548.v1
|
Enantioselective Multi-Component Cyclopropane Synthesis Enabled by Cu-Catalyzed Cyclopropene Carbometallation with Organoboron Reagent
|
Deployment of organoboron in lieu of the strongly basic <br />organometallic reagents as carbon source in Cu-catalyzed <br />cyclopropene carbometallation opens unprecedented three-<br />component reactivity for stereoselective synthesis of poly-substituted cyclopropanes. A proof-of-principle demonstration of this novel carbometallation strategy is presented herein for a highly convergent access to poly-substituted aminocyclopropane framework via <br />carboamination. Preliminary results on asymmetric desymmetrization with commercial bisphosphine ligands attained high levels of enantioselection, offering a straightforward access to enantioenriched aminocyclopropanes bearing all-three chiral centers, including an all-carbon quaternary center. This strategy may underpin a host of novel synthetic protocols for poly-substituted cyclopropanes. <br />
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Zhanyu Li; Mengru Zhang; Yu Zhang; Shuang Liu; Jinbo Zhao; Qian Zhang
|
Organic Synthesis and Reactions; Ligands (Organomet.); Reaction (Organomet.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2018-08-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e96bdbb899b0ba37e60/original/enantioselective-multi-component-cyclopropane-synthesis-enabled-by-cu-catalyzed-cyclopropene-carbometallation-with-organoboron-reagent.pdf
|
66e8540851558a15ef284a57
|
10.26434/chemrxiv-2024-jzddb-v2
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Informing ion exchange membrane design targets for Donnan Dialysis-mediated lithium brine concentration
|
Combining experimental studies and computational modeling, we assess the potential of a Donnan dialysis (DD) process for lithium brine concentration and prioritize material design opportunities from a use-informed perspective. Bench-scale batch experiments show that DD achieves lithium concentration factors of 7.6-18.9× and recoveries of 22-74% for dilute lithium feed streams. The corresponding process model was adapted to assess DD performance for continuous pilot-scale operation on a representative direct lithium extraction product stream. Model outputs demonstrate that DD achieves comparable lithium concentration and recovery targets with similar or lower membrane area requirements than reverse osmosis and electrodialysis processes, respectively. A sensitivity analysis reveals the relative importance of key parameters in ion exchange membrane design (water content > charge content ≈ membrane thickness ≈ water permeability). The development of alkaline- and scaling-resistant cation exchange membranes is identified as a target material improvement to expand the solution compatibility limits of the DD process.
|
Kristen Abels; Victoria Yang; William Tarpeh
|
Polymer Science; Chemical Engineering and Industrial Chemistry; Natural Resource Recovery; Transport Phenomena (Chem. Eng.); Water Purification
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-09-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e8540851558a15ef284a57/original/informing-ion-exchange-membrane-design-targets-for-donnan-dialysis-mediated-lithium-brine-concentration.pdf
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655642666e0ec7777f14c3fc
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10.26434/chemrxiv-2023-vcmcl
|
SWERN Oxidation. Transition State Theory is OK
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We investigate the model originally used to compare deuterium kinetic isotope effects (KIE) computed for the intramolecular hydrogen transfer step in the mechanism of the Swern oxidation of alcohols to aldehydes with those measured. Whereas the replication of the original computed values reported in 2010 for the gas-phase proved entirely successful, several issues were discovered when a continuum solvent model was used. These included uncertainty regarding the parameters and methods used for the calculations and coordinates for the original reactant and transition states, via their provision as data in the electronic supporting information (ESI). The original conclusions, in which a numerical mis-match between the magnitude of the computed and experimentally measured KIE was attributed to significant deviations from transition state theory, are here instead rationalised as a manifestation of basis-set effects in the computation. Transition state theory appears to be operating successfully. We now recommend the use of basis sets of triple- or quadruple-ζ quality, rather than the split-valence level previously employed, that dispersion energy corrections be included and that a continuum solvent model using smoothed reaction cavities is essential for effective geometry optimisation and hence accurate normal coordinate analysis. An outlying experimental KIE obtained for chloroform as solvent is attributed to a small level of an explicit hydrogen bonded interaction with the substrate. A temperature outlier for the measured KIE at 195K is suggested for further experimental investigation, although it may also be an indication of an unusually abrupt incursion of hydrogen tunnelling, which would need non-Born-Oppenheimer methods in which nuclear quantum effects are included to be more accurately modelled. We predict KIE for new substituents, of which those for R=NMe2 are significantly larger than for R=H. This approach could be useful in designing variations of the Swern reagent that could lead to synthesis of aldehydes incorporating much higher levels of deuterium. The use of FAIR data rather than the traditional model of its inclusion in electronic supporting information (ESI) is discussed.
|
D. Christopher Braddock; Siwoo Lee; Henry S. Rzepa
|
Theoretical and Computational Chemistry
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CC BY 4.0
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CHEMRXIV
|
2023-11-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655642666e0ec7777f14c3fc/original/swern-oxidation-transition-state-theory-is-ok.pdf
|
60c75503bb8c1afd623dc336
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10.26434/chemrxiv.13710961.v2
|
Binding Profile Assessment of N501Y: a More Infectious Mutation on the Receptor Binding Domain of SARS-CoV-2 Spike Protein
|
<p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in December 2019 and has accumulated nearly a hundred million reported infections thereafter. This highly transmissible and pathogenic coronavirus has caused a pandemic of acute respiratory disease, coronavirus disease 2019 (COVID-19), which has caught extensive attention and greatly changed people’s lifestyles all over the world. As an RNA virus, SARS-CoV-2 mutates rapidly as the virus replicates. The world health organization is now closely monitoring the emergence of a new variant, N501Y, on the spike protein. This N501Y variant is found to have higher transmission ability and infectivity, and is believed to be related to the rapid increase of COVID-19 cases in December 2020 in the UK. It was recently reported that the N501Y variants reduce neutralization sensitivity to convalescent sera and monoclonal antibodies. The Tyr mutation at 501 is located at the receptor binding domain (RBD) of the spike protein, the area that directly contacts human ACE2 (hACE2). It’s urgent to figure out the driving force of the new mutant’s enhanced infectivity. Thus, a computational aided binding profile prediction is made to investigate the binding affinity alteration and potential structural change of the N501Y mutant. <a>The resulting structures of N501Y mutant from MD simulations could be used to develop drug inhibitors against hACE2/RBD binding. </a></p>
|
Yuzhao Zhang; Xibing He; Viet Hoang Man; Jingchen Zhai; Beihong Ji; Junmei Wang
|
Drug Discovery and Drug Delivery Systems
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CC BY NC ND 4.0
|
CHEMRXIV
|
2021-02-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75503bb8c1afd623dc336/original/binding-profile-assessment-of-n501y-a-more-infectious-mutation-on-the-receptor-binding-domain-of-sars-co-v-2-spike-protein.pdf
|
66919f93c9c6a5c07a1e42a7
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10.26434/chemrxiv-2024-hb9fx
|
Controlling the Transmembrane Transport of Chloride by Dynamic Covalent Chemistry with Azines
|
Stimuli-responsive transmembrane ion transport has become a prominent area of research due to its fundamental importance in cellular processes and potential therapeutic applications. Commonly used stimuli include pH, light, and reduction or oxidation agents. This paper presents the use of dynamic covalent chemistry based on azine bonds to activate and modulate the transmembrane transport of chloride in liposomes. An active chloride transporter was obtained in situ within the lipid bilayer by dynamic azine metathesis. The transport activity was further tuned by changing the structure of the added azines, while the dynamic covalent chemistry could be activated by lowering the pH. This dynamic combinatorial chemistry approach holds great promise for drug delivery systems.
|
Marcin Konopka; Lau Halgreen; Anca-Elena Dascalu; Matúš Chvojka; Hennie Valkenier
|
Organic Chemistry; Combinatorial Chemistry; Supramolecular Chemistry (Org.)
|
CC BY 4.0
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CHEMRXIV
|
2024-07-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66919f93c9c6a5c07a1e42a7/original/controlling-the-transmembrane-transport-of-chloride-by-dynamic-covalent-chemistry-with-azines.pdf
|
60c74d70337d6c85c6e27dc1
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10.26434/chemrxiv.12620072.v1
|
PySHS : A Python Open Source Software For Second Harmonic Scattering
|
PySHS package is a python open source software which simulates the Second Harmonic Scattering (SHS) of different kind of colloidal nano-object in various experimental configuration. This package is able to compute polarization resolved at a fixed scattered angle or angular distribution for different polarization configurations.
|
Lotfi Boudjema; Hanna Aarrass; Marwa assaf; marie morille; Gaelle Martin-Gassin; Pierre-marie Gassin
|
Computational Chemistry and Modeling; Theory - Computational; Biophysical Chemistry; Interfaces; Self-Assembly; Solution Chemistry; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d70337d6c85c6e27dc1/original/py-shs-a-python-open-source-software-for-second-harmonic-scattering.pdf
|
60c73e150f50db5ebd3955c1
|
10.26434/chemrxiv.6397115.v1
|
Local Deformation of Glasses Is Mediated by Rigidity Fluctuation and Granularity
|
Microscopic deformation processes lie at the origin of defect formation
on glass surfaces, thus determining the material’s resistance to
scratching and mechanical failure. While the macroscopic strength of
most glasses is not directly depending on material composition, local
deformation and flaw initiation are strongly affected by chemistry and
atomic arrangement. Aside empirical insight, however, the structural
origin of the fundamental deformation modes remains largely unknown.
Experimental methods which probe parameters on short or intermediate
length-scale such as atom-atom or super-structural correlations are
typically applied in the absence of alternatives. Drawing on recent
experimental advances, we now probe spatial variations in the
low-frequency vibrational density of states which result from sharp
contact deformation of vitreous silica. From direct observation of
deformation-induced variations on the characteristic length-scale of
molecular heterogeneity, we argue that rigidity fluctuation on the scale
of a few nanometers governs the deformation process of inorganic
glasses.
|
Omar Benzine; Sebastian Bruns; Zhiwen Pan; Karsten Durst; Lothar Wondraczek
|
Ceramics; Nanostructured Materials - Materials; Optical Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-06-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e150f50db5ebd3955c1/original/local-deformation-of-glasses-is-mediated-by-rigidity-fluctuation-and-granularity.pdf
|
6267868e103388b132fae2b1
|
10.26434/chemrxiv-2022-whnbj-v2
|
Optical manipulation in conjunction with photochemical/photothermal responses of materials
|
This article reviews optical manipulation coupled with photochemical/photothermal responses of nanometer sized materials including molecular systems, polymers, and inorganic nanoparticles. After the introduction, section 2 overviews the optical trapping of nanometer sized molecular systems including early-stage studies, such as trapping of polymer chains, micelles, and molecular aggregates in solution at room temperatures. Then, the conformation control of macromolecule assemblies and gels by optical force are introduced, followed by micro-fabrications achieved by combining optical trapping and photochemical reactions. Section 3 summarizes studies on the evaluation of optical force acting on nanometric molecular systems using fluorescence correlation techniques. Approaches to control optical force by using photochemical reactions are show in section 4, where the absorption band of target materials are modified through photochromic reactions, leading to micromechanical motion of small particles synchronizing with the photochemical reactions. Section 5 overviews photothermal effect in optical manipulation such as natural convection, Marangoni convection and thermophoresis, and applications of the thermal effects to develop new methods of micromanipulation achieved by combining optical force and photothermal responses.
|
Kenji Setoura; Syoji Ito
|
Physical Chemistry; Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-04-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6267868e103388b132fae2b1/original/optical-manipulation-in-conjunction-with-photochemical-photothermal-responses-of-materials.pdf
|
669778fa01103d79c53d2294
|
10.26434/chemrxiv-2024-21mv3-v2
|
Are Hazard Assessment Methods in the Assessment of Chemical Alternatives Suitable for REACH?
|
The assessment of chemical alternatives for hazardous substances is an important prerequisite for avoiding regrettable substitution, and several methods have been developed in the past to perform such an hazard assessment for chemical alternatives. We investigate here whether GreenScreen®, Cradle to Cradle®, Multi Criteria Decision Analysis (MCDA), the Pollution Prevention Options Analysis System, the U.S. EPA Safer Choice Standard and Criteria, and the GHS column model 2020 from IFA use similar criteria for the evaluation of substances as Article 57 of REACH and how suitable these methods are for assessing per- and polyfluoroalkyl substances. MCDA and GreenScreen® were analyzed in detail using two different datasets. The results of the assessments show that none of the investigated hazard assessment methods use the same criteria as described in Article 57 of REACH. It was also not possible to parameterize multi-attribute value theory (MAVT), a commonly used MCDA method, to align with Article 57 of REACH by using the relatively simple objective hierarchy that has been proposed in previous publications. There is therefore an urgent need for a modified/new method that can be used in the future to assess organic substances that are used within the European Economic Area.
|
Rachel L. London; Juliane Glüge; Martin Scheringer
|
Organic Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669778fa01103d79c53d2294/original/are-hazard-assessment-methods-in-the-assessment-of-chemical-alternatives-suitable-for-reach.pdf
|
60c758af9abda2f8bcf8e967
|
10.26434/chemrxiv.14576802.v1
|
Influence of Reduced Na Vacancy Concentrations in the Sodium Superionic Conductors Na11+xSn2P1−xMxS12 (M = Sn, Ge)
|
<p>Exploration of sulfidic sodium solid electrolytes and their design contributes to advances in solid state sodium batteries. Such design is guided by a better understanding of fast sodium transport, for instance in the herein studied Na<sub>11</sub>Sn<sub>2</sub>PS<sub>12</sub>-type materials. By using Rietveld refinements against synchrotron X-ray diffraction and electrochemical impedance spectroscopy, the influence of aliovalent substitution onto the structure and transport in Na<sub>11+<i>x</i></sub>Sn<sub>2</sub>P<sub>1−<i>x</i></sub><i>M<sub>x</sub></i>S<sub>12</sub> with <i>M</i> = Ge and Sn is investigated. Whereas Sn induces stronger structural changes than Ge, the found influence on the sodium sublattice and the ionic transport properties are comparable. Overall, a reduced in-grain activation energy of Na<sup>+</sup> transport can be found with the reducing Na<sup>+</sup> vacancy concentration. This work explores previously unreported phases in the Na<sub>11</sub>Sn<sub>2</sub>PS<sub>12</sub> structure type that, based on their determined properties reveal Na<sup>+</sup> vacancy concentrations to be an important factor guiding further understanding within Na<sub>11</sub>Sn<sub>2</sub>PS<sub>12</sub>-type materials.</p>
|
Marvin Kraft; Lara Gronych; Theodosios Famprikis; Wolfgang Zeier
|
Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758af9abda2f8bcf8e967/original/influence-of-reduced-na-vacancy-concentrations-in-the-sodium-superionic-conductors-na11-x-sn2p1-x-mx-s12-m-sn-ge.pdf
|
60c74dfcbb8c1a4c343db695
|
10.26434/chemrxiv.12652832.v2
|
Computational Drug Repurposing Studies on the ACE2-Spike (RBD) Interface of SARS-CoV-2
|
<p>The
novel coronavirus is known to enter the cell by binding to the human
transmembrane protein Angiotensin-Converting Enzyme 2 (ACE2). The S(Spike)-glycoprotein
of the SARS-CoV-2 forms a complex with the ACE2. Thus, the S-glycoprotein is
one of the hot targets, as it forms the first line of contact between the virus
and the human cell. Drug repurposing would help in identifying drugs that are
safe and have no or fewer side effects. Hence, in addition to the Food and Drug
Administration (FDA) approved molecules the compounds from natural sources were
also considered. The current study includes docking and simulations of the FDA
approved molecules and phytochemicals from Indian medicinal plants, targeting
the ACE2-Spike protein complex. Rutin DAB10 and swertiapuniside were obtained
as the top-ranked drugs from these two databases, respectively. The molecular
dynamics simulations of ligand-free, rutin DAB10-bound, and
swertiapuniside-bound ACE2-Spike complex revealed crucial ACE2-Spike interface residues
forming strong interactions with the two ligands molecules. This may infer,
that they may affect the ACE2 and spike binding. The conformational flexibility
in the drug-binding pocket was captured using the RMSD-based clustering of the
ligand-free simulations. An ensemble docking was performed wherein the two
databases were docked on each of the representatives of ACE2-Spike obtained
through clustering. The potential phytochemicals identified belonged to <i>Withania
somnifera, Swertia chirayita, Tinospora cordifolia, Andrographis paniculata,
Piper longum, and Azadirachta indica</i>. The FDA molecules identified were
rutin DAB10, fulvestrant, cefoperazone acid, escin, chlorhexidine diacetate,
echinacoside, capreomycin sulfate, and elbasvir.</p>
|
Vinod Jani; Shruti Koulgi; Mallikarjunachari Uppuladinne V N; Uddhavesh Sonavane; Rajendra Joshi
|
Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74dfcbb8c1a4c343db695/original/computational-drug-repurposing-studies-on-the-ace2-spike-rbd-interface-of-sars-co-v-2.pdf
|
67be62de6dde43c908825412
|
10.26434/chemrxiv-2025-dl116
|
Image Distinguishability Analysis Testing through Principal Components and its Application to Hot Spot Scale Invariance
|
Images are common means to represent spatial property variations in physical systems, but comparing images is nuanced due to stochastic variations and spatial correlations, which are neglected in routine analyses like the Kolmogorov-Smirnov test. To this end, we develop an image distinguishability analysis (IDA) test that makes pixel-by-pixel comparisons between image-like datasets through a generalized distance metric in the principal component (PC) space. Based on the supported hypothesis that inherent stochasticity is represented by independent Normal behavior of the PCs, we derive a statistical distribution and criticality criterion to determine whether images are distinguishable from established baselines. We apply the IDA test on images generated from molecular dynamics simulations to demonstrate scale invariance in the complex patterns of a nonequilibrium process. The IDA test is notably general with diverse potential applications, including microstructure classification and change detection, uncertainty quantification of property fields, and model validation against high-fidelity simulations and experiments.
|
Matthew Kroonblawd; Amitesh Maiti; Laurence Fried
|
Materials Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-02-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67be62de6dde43c908825412/original/image-distinguishability-analysis-testing-through-principal-components-and-its-application-to-hot-spot-scale-invariance.pdf
|
60c74ce4ee301c7ec7c7a181
|
10.26434/chemrxiv.12555230.v1
|
Low-Resistance Monovalent-Selective Cation Exchange Membranes for Energy-Efficient Ion Separations
|
<div>
<div>
<div>
<p>The desalination of brackish water provides water to tens of millions of people around the world, but
current technologies deplete much needed nutrients from the water, which is detrimental to both public
health and agriculture. A selective method for brackish water desalination, which retains the needed nutrients,
is electrodialysis (ED) using monovalent-selective cation exchange membranes (MVS-CEMs). However, due to
the trade-off between membrane selectivity and resistance, most MVS-CEMs demonstrate either high transport
resistance or low selectivity, which increase energy consumption and hinder the use of such membranes for
brackish water desalination by ED. Here, we used molecular layer deposition (MLD) to uniformly coat CEMs with
ultrathin layers of alucone. The positive surface charge of the alucone instills monovalent selectivity in the CEM.
Using MLD enabled us to precisely control and minimize the selective layer thickness, while the flexibility and
nanoporosity of the alucone prevent cracking and delamination. Under conditions simulating brackish water
desalination, this compound provides monovalent selectivity with negligible added resistance—the smallest
reported resistance for a monovalent-selective layer, to date—thereby alleviating the selectivity–resistance
trade-off. Addressing the water–energy nexus, we show that using these membranes in ED will cut at least half
of the energy required for selective brackish water desalination with current MVS-CEMs.
</p>
</div>
</div>
</div>
|
Eyal Wormser; Oded Nir; Eran Edri
|
Coating Materials; Composites; Hybrid Organic-Inorganic Materials; Multilayers; Nanostructured Materials - Materials; Polyelectrolytes - Materials; Water Purification
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ce4ee301c7ec7c7a181/original/low-resistance-monovalent-selective-cation-exchange-membranes-for-energy-efficient-ion-separations.pdf
|
60c74bbebdbb89c65ca39643
|
10.26434/chemrxiv.12376067.v1
|
Molecular Cu(I)-Cu(II) Photosensitizer-Catalyst Photoelectrode for Water Oxidation
|
Photochemical splitting of H<sub>2</sub>O to H<sub>2</sub> and O<sub>2</sub> is one approach to generate "solar fuels." Cu(II)-based electrocatalysts for water oxidation in aqueous solution have been studied previously, but photodriving these systems still remains a challenge. Light harvesting units can be employed for this purpose, that upon photoexcitation generate a high energy excited state and give rise to a charge separated state. In this work, a bis-diimine Cu(I)-based donor-chromophore-acceptor (D-C-A) system is synthesized, characterized, and applied as the light harvesting component of a photoanode. Here, this molecular assembly was integrated onto a zinc oxide (ZnO) nanowire surface on a fluorine-doped tin oxide (FTO) glass slide. Upon photoexcitation, chronoamperometric studies reveal that the integrated triad can inject electrons directly into the conduction band of zinc oxide generating oxidizing equivalents that are then transferred to a Cu(II) water oxidation catalyst in aqueous solution yielding O<sub>2</sub> from H<sub>2</sub>O with a Faradaic efficiency of 76%. <br />
|
Zujhar Singh; Pedro Donnarumma; Marek Majewski
|
Nanostructured Materials - Nanoscience; Coordination Chemistry (Inorg.); Transition Metal Complexes (Inorg.); Heterogeneous Catalysis; Photocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bbebdbb89c65ca39643/original/molecular-cu-i-cu-ii-photosensitizer-catalyst-photoelectrode-for-water-oxidation.pdf
|
60c7441d337d6c5b62e26d0c
|
10.26434/chemrxiv.9745334.v1
|
Mimicking Noncanonical Oxidations with Redox-Neutral Photocatalysis
|
Noncanonical oxygenases are a family of Fe-containing enzymes that catalyze oxidative radical cyclizations. Despite creating key structural features that often define a natural product’s complexity, the mechanisms of these oxidations remain poorly understood and difficult to mimic. In this work, we show that noncanonical cyclizations from lignan biosynthesis can be recreated when presumed biosynthetic radicals are generated using photocatalysis. These conditions afford the ensuing electron rich radicals sufficient time to undergo challenging 5- or 11-membered ring formation that create the defining structural features of the highly oxidized lignans taiwankadsurins A, B and kadsuphilin N. By showing that these cyclizations can occur without enzymatic assistance, we provide a more general strategy for mimicking noncanonical transformations that should broaden their use in organic synthesis.
|
Zheng Huang; Jean-Philip Lumb
|
Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-08-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7441d337d6c5b62e26d0c/original/mimicking-noncanonical-oxidations-with-redox-neutral-photocatalysis.pdf
|
652e21bebda59ceb9abdb8f8
|
10.26434/chemrxiv-2023-x7lvt
|
Calcium-Promoted [3+3] Annulation of Morita-Baylis-Hillman Ketones with 2-Aminobenzothiazoles to Construct Pyrimidobenzothiazoles
|
The reaction of Morita-Baylis-Hillman (MBH) ketones with 2-aminobenzothiazoles is used to construct new analogues of 4H-benzo [4,5] thiazolo [3,2-a] pyrimidine. MBH ketone provides a desirable reactivity with significant outcomes. The mechanism of the reaction involves aza-Michael addition followed by intramolecular cyclization with the removal of a water molecule. This approach tolerates a wide range of substrate scope adequacy, using minimal loading of inexpensive and more abundant Ca(II) catalyst.
|
Rajkiran Kumari; Srinivasan Easwar
|
Organic Chemistry; Chemical Education; Organic Compounds and Functional Groups; Organic Synthesis and Reactions
|
CC BY 4.0
|
CHEMRXIV
|
2023-10-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652e21bebda59ceb9abdb8f8/original/calcium-promoted-3-3-annulation-of-morita-baylis-hillman-ketones-with-2-aminobenzothiazoles-to-construct-pyrimidobenzothiazoles.pdf
|
6230eee474104fa944a62299
|
10.26434/chemrxiv-2022-x0jml
|
Chloro-silane vapor assisted in-plane delamination of liquid metal films for unconventional heterogeneous wettability
|
Numerous complex methods have been reported to generate heterogeneously wettable surfaces in the literature. These surfaces are well-sought in energy, water, health care, separation science, self-cleaning, biology, and other lab-on-chip applications. While most of the demonstrations of heterogeneous wettability rely on a series of complex fabrication protocols, we reveal an unconventional approach to achieving heterogeneous wettability through three simple steps (i.e., patterning, silanizing, and rinsing). Here, we show heterogeneous wettability on a planar substrate harnessing (a) the wetting and dewetting behavior of nano-textured conductive surface patterns of Gallium alloys and (b) interfacial chemical reactivity of the native surface oxides of these alloys in the presence of chloro-silane vapor. Alloys of Gallium (eGaIn and others) have emerged as one of the most promising soft metals for the fabrication of soft functional devices harnessing their surface oxides, mostly Gallium Oxide (Ga2O3). These alloys can be 2D patterned utilizing the wetting behavior of the Ga2O3, which seems impossible due to the high surface tension of the bare metal. We utilized such 2D metal patterns on the planar glass surface and exposed the patterns in chloro-silane vapors to begin our study. Chloro-silanes can alter the surface energy of different substrates (i.e., glass, silicon wafer) to offer hydrophobicity and releases Chlorine vapors which etch Ga2O3 that induces the delamination. A simple DI water rinsing operation reveals a thin hydrophilic layer on the pre-patterned area that we utilized for an open-ended microfluidic demonstration, as well. We confirmed hydrophilicity through contact angle measurements; elemental compositions, and Chlorine's presence through energy dispersive spectroscopic (EDS) analyses. We believe such an unconventional approach of achieving heterogeneous wettability has the potential for fundamental studies related to bioinspired and biomimetic applications.
|
Kazi Zihan Hossain ; Momena Monwar; M. Rashed Khan
|
Materials Science; Thin Films; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6230eee474104fa944a62299/original/chloro-silane-vapor-assisted-in-plane-delamination-of-liquid-metal-films-for-unconventional-heterogeneous-wettability.pdf
|
61d57b677f1d6713383bd917
|
10.26434/chemrxiv-2022-jwc57
|
Is [ReCl4(CN)2]2− a good Building Block for Single Molecule
Magnets? A Theoretical Investigation.
|
Building blocks containing $5d$ spin centres are promising for constructing single molecule magnets due to their large spin-orbit interaction, but experimental and computational results obtained so far indicate that this might not be the case for Re$^\textrm{IV}$ centres in an octahedral environment. Density functional results obtained in this work for [ReCl$_4$(CN)$_2$]$^{2-}$ and trinuclear complexes formed by attaching Mn$^\textrm{II}$ centres to the cyano ligands indicate that zero field splitting in such complexes exhibits large rhombicity (which leads to fast relaxation of the magnetisation) even if there are only small distortions from an ideal geometry with a four-fold symmetry axis. This is already apparent if second-order spin-orbit perturbation theory is applied but even more pronounced if higher-order spin-orbit effects are included as well, as demonstrated by wavefunction based calculations. Computational results are cast into a ligand field model and these simulations show that especially a distortion which is not along the $C_4/C_2$ axeshas a large effect on the rhombicity. Quantum simulations on these complexes are difficult because the zero field splitting strongly depends on the energetic position of the low-lying doublets from the $t_{2g}^3$ configuration.
|
Christoph van Wüllen; Eva M. V. Kessler
|
Theoretical and Computational Chemistry; Theory - Computational
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-01-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d57b677f1d6713383bd917/original/is-re-cl4-cn-2-2-a-good-building-block-for-single-molecule-magnets-a-theoretical-investigation.pdf
|
60c7449c702a9b76b818a87f
|
10.26434/chemrxiv.9782585.v2
|
Extraction, Isolation and Characterization of New Compound and Anti-Bacterial Potentials of the Chemical Constituents Compound from Leptadenia Hastata Leaf Extract
|
The research work is all about drug discovering in plants through isolation and characterization in the cause of looking an agent for infectious and disease control.
|
Isaac Umaru; Fasihuddin A. Badruddin; Hauwa A. Umaru
|
Biochemistry; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-09-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7449c702a9b76b818a87f/original/extraction-isolation-and-characterization-of-new-compound-and-anti-bacterial-potentials-of-the-chemical-constituents-compound-from-leptadenia-hastata-leaf-extract.pdf
|
65005974b338ec988a5991b0
|
10.26434/chemrxiv-2023-24zfl-v2
|
Using generative artificial intelligence in chemistry education research: prioritizing ethical use and accessibility
|
Generative artificial intelligence (GenAI) has the potential to drastically alter how we teach and conduct research in chemistry education. There have been many reports on the potential uses, limitations, and considerations for GenAI tools in teaching and learning, but there have been fewer discussions of how such tools could be leveraged in educational research, including in chemistry education research. GenAI tools can be used to facilitate and support researchers in every stage of traditional educational research projects (e.g. conducting literature reviews, designing research questions and methods, communicating results). However, these tools also have existing limitations that researchers must be aware of prior to and during use. In this research commentary, we share insights on how chemistry education researchers can use GenAI tools in their work ethically. We also share how GenAI tools can be leveraged to improve accessibility and equity in research.
|
Jacky M. Deng; Zahra Lalani; Lauren A. McDermaid; Alisha R. Szozda
|
Chemical Education; Chemical Education - General
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-09-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65005974b338ec988a5991b0/original/using-generative-artificial-intelligence-in-chemistry-education-research-prioritizing-ethical-use-and-accessibility.pdf
|
63864580c567531f659b11d2
|
10.26434/chemrxiv-2022-8fx09
|
On the existence of collective interactions
|
Recently, Sowlati-Hashjin et al.1 have used the exchange-correlation interaction collectivity index (ICIXC; ICIXC [0,1]) to conclude that the nature of the Li–C chemical bond in LiCF3 differs significantly from that in LiCPh3 (Ph = phenyl). Whereas the Li–C bond of LiCF3 is classified as a conventional two-center two-electron bond (ICIXC = 0.910, ICIXC > 0.9 and close to 1), that of LiCPh3 is categorized as a collective bond (ICIXC = 0.393). The authors claim that collective bonds take place in systems composed of MAR3 (M = metal; A = C, B or Al; R = substituent) when M forms a stronger bond with the substituents R than with the central atom A. They claim the M–A interaction is either destabilizing or weakly stabilizing, whilst the 1,3-M···R interactions are strongly stabilizing, but their method does not provide a causal mechanism that would demonstrate the correctness of this interpretation of the ICIXC index. Here, we prove the opposite, namely, that the Li–CPh3 bond is not reinforced or provided by collective interactions, but that it is weakened by 1,3-M•••R contacts, which reduce the bond overlap.
|
Jordi Poater; Pascal Vermeeren; Trevor A. Hamlin; F. Matthias Bickelhaupt; Miquel Solà
|
Theoretical and Computational Chemistry; Theory - Computational
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-12-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63864580c567531f659b11d2/original/on-the-existence-of-collective-interactions.pdf
|
65ba50039138d231611da968
|
10.26434/chemrxiv-2024-105l3
|
The Development and Application of SPSiBox Ligands: Cu-Catalyzed Enantioselective Carbene Insertion of Ge–H Bonds
|
A class of C2-symmetrical bisoxazoline ligands with a flexible chiral pocket has been developed, which could be readily prepared in three steps from enantiopure SPSiOLs. This type of ligands presented high level of enantioselectivity for the Cu-catalyzed asymmetric carbene insertion of Ge–H bonds with α-trifluoromethyl diazo compounds, thus providing an efficient method for the preparation of enantioenriched α-trifluoromethyl ogranogermanes. This reac-tion features a broad substrates scope, mild reaction conditions, excellent enantioselectivity, and low catalyst loading. Preliminary mechanistic studies un-veiled that this Cu-catalyzed Ge–H insertion might undergo a concerted mechanism, and computational studies unveiled the origin of chiral induction of this reaction with SPSiBox ligand.
|
Shi-Hao Chen; Shengye Zhang; Zi-Yang Chen; Yichen Wu; Peng Wang
|
Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Stereochemistry; Ligand Design
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-02-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ba50039138d231611da968/original/the-development-and-application-of-sp-si-box-ligands-cu-catalyzed-enantioselective-carbene-insertion-of-ge-h-bonds.pdf
|
67c7e496fa469535b9ff7f5d
|
10.26434/chemrxiv-2025-txdbz
|
Enzymatic Crosslinking of Polyelectrolyte Complexes Produces Strong, Reconstitutable Biomedical Adhesives
|
Tissue adhesives that offer rapid wound sealing, reduce blood loss, enhance aesthetic outcomes, and lower biomedical issues can significantly augment the wound treatment regimen. Taking inspiration from proteinaceous adhesives secreted by marine organisms, herein we designed anionic and cationic polyamide polyelectrolytes (PEs) containing Horseradish Peroxidase (HRP)-responsive phenolic pendants. These PEs underwent facile polyelectrolyte complex (PEC) formation in aqueous medium. The PEC-rich phase was employed to formulate water-based biomedical adhesives that demonstrated robust adhesion to diverse surfaces - from biological tissues like bone to materials such as wood, glass, and metal. The PEC adhesive worked on both dry and wet substrates and its adhesive strength increased with environmental humidity. The strongest adhesion was found for wood with adhesive strength up to 10 MPa. The adhesive could be kept in a lyophilized powder form and reconstituted prior to use without significant impact on the adhesive performance. Furthermore, the PEC adhesive exhibited strong hemostatic and wound-healing capabilities in vivo in mice, significantly surpassing the commercial cyanoacrylate-based tissue adhesives in performance. These findings, coupled with the adhesive's biocompatibility and hemocompatibility, position these enzyme-cured PEC adhesives as promising contender in wound healing applications.
|
Tanmay Dutta; Bhanwar Lal; Drishya Vats; Roop Singh Lodhi; Paramita Das; Debasis Nayak; Aasheesh Srivastava
|
Biological and Medicinal Chemistry; Polymer Science; Polyelectrolytes - Polymers
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c7e496fa469535b9ff7f5d/original/enzymatic-crosslinking-of-polyelectrolyte-complexes-produces-strong-reconstitutable-biomedical-adhesives.pdf
|
66ba1d485101a2ffa817eced
|
10.26434/chemrxiv-2024-jxd73
|
Metal Coordination and Enzymatic Reaction of the Glioma-Target R132H Isocitrate Dehydrogenase 1: Insights by Molecular Simulations
|
R132H IDH1 is an important therapeutic target for a variety of brain cancers, yet drug leads and radiotracers which selectively bind only to the mutant over the wild type are so far lacking. Here we have predicted the structural determinants of the Michaelis complex of this mutant using a QM/MM MD-based protocol. It shows some important differences with the X-ray structure, from the metal coordination to the positioning of key residues at the active site. In particular, one lysine residue at the active site emerges as a mostly likely proton donor in the R132H IDH1 catalytic reaction. Intriguingly, the same residue in its deprotonated state is likely to be involved in the reaction catalyzed by the wild-type enzyme. Our QM/MM protocol could also be used for other metal-based enzymes, which cannot be modeled easily by force field-based MD, like in this case.
|
Bharath Raghavan; Marco De Vivo; Paolo Carloni
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Biophysics; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ba1d485101a2ffa817eced/original/metal-coordination-and-enzymatic-reaction-of-the-glioma-target-r132h-isocitrate-dehydrogenase-1-insights-by-molecular-simulations.pdf
|
6356afd3ca86b861ecc15c89
|
10.26434/chemrxiv-2022-nqjmj
|
Thermal and (thermo-reversible) photochemical cycloisomerization of 1H-2-benzo[c]oxocins; From synthetic applications to the development of a new molecular photothermal switch
|
A novel photothermal molecular switch based on the reversible cyclization of 1H-2-benzo[c]oxocins to dihydro-4H-cyclobuta[c]isochromenes has been developed. The switching mechanism involves a light-triggered ring-contraction of 8 membered 1H-2-benzo[c]oxocins to 4,6-fused O heterocyclic dihydro-4H-cyclobuta[c]isochromene ring systems, with reversion back to the 1H-2-benzo[c]oxocin state accessible through heating. Both processes are unidirectional and proceed with good efficiency, with switching properties—including reversibility and half-life time—easily adjusted via structural functionalization. Our new molecular switching platform exhibits independence from solvent polarity, originating from it’s neutral-charge switching mechanism, a property highly sought after for biological applications. The photoinduced ring-contraction involves a [2+2] conjugated-diene cyclization that obeys the Woodward–Hoffmann rules. In contrast, the reverse process initiates via a thermal ring-opening (T > 60oC) to produce the anti-Woodward–Hoffmann product, proposed to proceed via an ortho-quinodimethane (o-QDM) intermediate. The proposed switching mechanisms are supported by experimental observations and density functional theory (DFT) calculations. Other transformations of 1H-2-benzo[c]oxocins were found upon altering reaction conditions: prolonged heating the 1H-2-benzo[c]oxocins at significantly elevated temperature (72 h at 120°C), with the resulting dihydronaphthalenes formed via the o QDM intermediate. These reactions also proceed with good chemoselectivities, providing new synthetic protocols for motifs found in several bioactive molecules, but are otherwise difficult to access.
|
Minghui Zhou; Simon Mathew; Bas de Bruin
|
Physical Chemistry; Organic Chemistry; Materials Science; Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2022-10-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6356afd3ca86b861ecc15c89/original/thermal-and-thermo-reversible-photochemical-cycloisomerization-of-1h-2-benzo-c-oxocins-from-synthetic-applications-to-the-development-of-a-new-molecular-photothermal-switch.pdf
|
6791388d81d2151a026a7976
|
10.26434/chemrxiv-2024-f58l0-v4
|
Phosphorylated Sporopollenin as a Sustainable Catalyst for Selective 5-Hydroxymethylfurfural Formation in Water: Insights into Phosphate Functionalization, and Mechanism
|
Metal-free Brønsted acid catalysts in water often lead to undesirable side reactions, complicating the synthesis of 5-hydroxymethylfurfural (5-HMF). As a result, organic heterogeneous catalysts with high selectivity for 5-HMF are highly sought after. Hence, this study uses sporopollenin (exine) as a heterogeneous support. 31P CP/MAS NMR showed that conventional H3PO4 cleaning of spores not only produces empty sporopollenin (ESP) but also functionalizes it with mono- and di-phosphoesters (41:59). This functionalized ESP, termed ESP-Phos, serves as a selective catalyst for the formation of 5-HMF from glucose. By activating ESP-Phos at 200 °C, the di-phosphoester ratio increases to 29:71, improving 5-HMF yield (92%) and selectivity (96%) in H2O. DFT calculations reveal strong glucose interactions with di-phosphoester, explaining enhanced catalysis. Mechanistic studies involving isotopic labelling, 13C NMR, and DFT calculations suggest direct glucose dehydration to form 5-HMF. Despite humin deposition causing deactivation, calcining at 200 °C restores catalytic activity. This method is environmentally friendly and suitable for large-scale 5-HMF production.
|
Raina Sharma; Tamilmani Selvaraj; Gowri Vijayendran; Jithin John Varghese; Govindasamy Jayamurugan
|
Catalysis; Polymer Science; Nanoscience; Nanostructured Materials - Nanoscience; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6791388d81d2151a026a7976/original/phosphorylated-sporopollenin-as-a-sustainable-catalyst-for-selective-5-hydroxymethylfurfural-formation-in-water-insights-into-phosphate-functionalization-and-mechanism.pdf
|
6771c6f56dde43c908b94e78
|
10.26434/chemrxiv-2025-qhvvj
|
Regioselective Hydrocyanation of Internal Alkynes Enabled by a Transition-Metal-Free Dual-Catalytic System
|
Since its discovery in 1954, the hydrocyanation of multiple carbon-carbon bonds has emerged as a powerful strategy for the synthesis of nitriles. However, the elusive control of selectivity and typical reliance on expensive and toxic transition metal (TM) based catalysts significantly hinder the utility of this process. Here, we report an exclusively regioselective hydrocyanation of unbiased alkynes, driven by base-catalyzed reversible alkyne-allene isomerization and phosphine-catalyzed HCN transfer to the allene. This TM-free, dual-catalytic approach introduces a novel mode of selectivity control via regioselective hydrocyanation of the allene intermediate. The methodology secures a cost-effective access to a broad range of vinyl nitriles (37 examples) with yields up to 97% and Z/E stereoselectivity up to >20:1, including complex natural product derivatives. A comparison with TM-based systems highlighted a 2500-fold cost reduction, as well as the elimination of the troublesome separation of the regioisomers. Mechanistic studies elucidated the reaction pathway, shedding light on the achieved regioselectivity. By altering one catalyst in a dual-catalytic system, we demonstrated the regioselectivity switch, thereby facilitating regiodivergent hydrocyanation. In a broader context, the disclosed approach offers a foundation for developing the next generation of TM-free strategies for the regioselective hydrofunctionalizations of unbiased alkynes.
|
Aleksandra Zasada; Dawid Lichosyt
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Organocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2025-01-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6771c6f56dde43c908b94e78/original/regioselective-hydrocyanation-of-internal-alkynes-enabled-by-a-transition-metal-free-dual-catalytic-system.pdf
|
67bb17346dde43c9081836e4
|
10.26434/chemrxiv-2025-0s8n8
|
2,8-Dihalogenated diazocines: versatile reactants for functionalised photoswitches
|
Diazocine photoswitches possess distinctive structural characteristics and remarkable photochemical properties, leading to their growing application in photopharmacology and smart materials. We report the synthesis of 2,8-pseudo-para substituted diazocines with two bromo, two iodo, or a combination of both substituents, achieving effective scalability. Besides demonstrating good reactivity in Suzuki cross-coupling reactions, the substituted diazocines predominantly retain their good photochemical properties, rendering them valuable components for said applications.
|
Maximilian J. Notheis; Vigan Sahiti; Vivienne Prangenberg; Johannes S. Kruse; Larissa K. S. von Krbek
|
Organic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-02-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bb17346dde43c9081836e4/original/2-8-dihalogenated-diazocines-versatile-reactants-for-functionalised-photoswitches.pdf
|
60c758979abda2628cf8e93b
|
10.26434/chemrxiv.14564301.v1
|
Occurrence and Distribution of Pharmaceuticals and their Transformation Products in Luxembourgish Surface Waters
|
<p>This pre-print describes the analysis of
pharmaceuticals and their transformation products in surface water samples
collected in Luxembourg from 2019 to 2020. Details of the experimental and
computational tools and workflows used are fully described in the manuscript.
Links to the suspect lists, codes used, and data files are also provided.</p>
|
Randolph Singh; Adelene Lai; Jessy Krier; Todor Kondić; Philippe Diderich; Emma Schymanski
|
Chemoinformatics; Environmental Analysis; Mass Spectrometry; High-throughput Screening
|
CC BY 4.0
|
CHEMRXIV
|
2021-05-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758979abda2628cf8e93b/original/occurrence-and-distribution-of-pharmaceuticals-and-their-transformation-products-in-luxembourgish-surface-waters.pdf
|
66acc251c9c6a5c07ad421db
|
10.26434/chemrxiv-2024-slhhv
|
Batch and continuous synthesis of well-defined Pt/Al2O3 catalysts for the dehydrogenation of homocyclic LOHCs
|
In this work, the controlled synthesis of supported Pt nanoparticles with well-defined nanoparticle sizes from 1.9 to 6.0 nm and their application in the dehydrogenation of cyclic liquid organic hydrogen carrier (LOHC) molecules are demonstrated. For this purpose, a colloidal approach is used in which a stabilized Pt precursor solution is chemically reduced with aqueous solutions of sodium borohydride (NaBH4). In this batch process, an increased pH increases the stability of the reduction solution and thus enhances the control of the size of the resulting Pt nanoparticles. Various synthesis parameters are varied and their effects on the properties of the Pt nanoparticles are studied. Additionally, the nanoparticles were supported on powder Al2O3 support and the general suitability of the catalysts for the dehydrogenation of the LOHC perhydro benzyltoluene (H12-BT) is demonstrated. The transferability of the catalyst synthesis route from powder to shaped supports, as commonly used in LOHC dehydrogenation reactors, is successfully demonstrated. Moreover, a successful upscaling of the synthesis procedure is realized, where larger amounts of catalysts are synthesized without significant deviations in nanoparticle size and catalytic activity. Finally, a continuous synthesis of Pt/Al2O3 catalysts is implemented using a microfluidic reactor. The prepared catalysts from small-scale, large-scale, and continuous syntheses display a comparable Pt-based productivity in the dehydrogenation of H12 BT.
|
Yazan Mahayni; Lukas Maurer; Ina Baumeister; Franziska Auer; Peter Wasserscheid; Moritz Wolf
|
Catalysis; Energy; Heterogeneous Catalysis; Energy Storage; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-08-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66acc251c9c6a5c07ad421db/original/batch-and-continuous-synthesis-of-well-defined-pt-al2o3-catalysts-for-the-dehydrogenation-of-homocyclic-loh-cs.pdf
|
674551f4f9980725cff1d167
|
10.26434/chemrxiv-2024-wj7s8
|
Step edge defects have nanoscale impact on electronic structure in semiconducting transition metal dichalcogenide electrocatalysts
|
This work uses MoTe2 single crystals to address the challenge in heterogeneous catalysis of identifying active sites and determining the electronic factors responsible for catalytic activity. We find that for semiconducting MoTe2, spots that fall along step edges show more catalytic activity than spots that fall solely on the basal plane. In contrast, for a semimetallic phase of MoTe2, there is no measurable difference between H2 evolution activity at the step edges and at the basal plane, indicating that the active sites for H2 evolution catalysis on transition metal dichalcogenides are phase dependent. We additionally find that the local H2 evolution activity correlates with local potential differences, higher conductance, and faster rates of outer-sphere electron transfer to a redox-active probe in solution. Interestingly, in the semiconducting phase of MoTe2, these local electronic structure differences were measured both at the edge sites and at basal plane sites next to the edge, extending > 50 nm away from the edge. These results indicate that for MoTe2, basal plane sites near the edge may have stronger free energies of H adsorption, ΔGHads, than basal plane sites farther from the edge. Thus, we propose that edge sites in semiconducting transition metal dichalcogenides are better thought of as defect sites that substantially modulate the electronic structure in the surrounding region, rather than solely as undercoordinated active sites. These results provide exciting opportunities to use defects to alter the electronic structure at existing active sites in semiconductor electrocatalysts.
|
Kenneth Ortiz Chua; Megan Jackson
|
Catalysis; Energy; Electrocatalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674551f4f9980725cff1d167/original/step-edge-defects-have-nanoscale-impact-on-electronic-structure-in-semiconducting-transition-metal-dichalcogenide-electrocatalysts.pdf
|
635ba64a55a0818ec0c8e43b
|
10.26434/chemrxiv-2022-vmm6q
|
A field-induced exchange flip in a spin linear trimer in a coordination polymer of cobalt and melamine
|
A coordination polymer of linear trimeric cobalt and melamine has been synthesized.
The magnetic isotherms of violet coloured crystals as long as 400 μm show a field-induced transition in an external field of about 2 T at temperatures below 2 K. It is addressed that by assuming the coexistent positive and negative exchange between the nearest-neighbour spins in the linear trimer, this metamagnetic transition can be understood as a transition from antiferromagnetic to ferromagnetic exchange within each trimeric spin cluster without considering long-range magnetic ordering.
Although weak inter-cluster or inter-chain exchange to yield a long-range magnetic order is not excluded as another possible and often attributed origin of metamagnetism in low-dimensional spin systems, the present study demonstrates the significance of the exchange flip within each cluster in clustered spin networks.
This paves the way towards the realization of stable, yet switchable states of a spin trimer in the realm of coordination chemistry.
|
Ignacio Bernabe Virseda; Alexander Prado-Roller; Michael Eisterer; Hidetsugu Shiozawa
|
Materials Science; Hybrid Organic-Inorganic Materials; Magnetic Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635ba64a55a0818ec0c8e43b/original/a-field-induced-exchange-flip-in-a-spin-linear-trimer-in-a-coordination-polymer-of-cobalt-and-melamine.pdf
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66b06d3c01103d79c5c5f2e1
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10.26434/chemrxiv-2024-m51gh
|
Automatic Molecular Fragmentation by Evolutionary Optimisation
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Molecular fragmentation is an effective suite of approaches to reduce the formal computational complexity of quantum chemistry calculations while enhancing their algorithmic parallelisability. However, the practical applicability of fragmentation techniques remains hindered by a dearth of automation and effective metrics to assess the quality of a fragmentation scheme. In this article, we present the Quick Fragmentation via Automated Genetic Search (QFRAGS), a novel automated fragmentation algorithm that uses a genetic optimisation procedure to generate molecular fragments that yield low energy errors when adopted in Many Body Expansions (MBEs). Benchmark testing of QFRAGS on protein systems with less than 500 atoms, using two-body (MBE2) and three-body (MBE3) MBE calculations at the HF/6-31G* level, reveals mean absolute energy errors (MAEE) of 20.6 and 2.2~kJ~mol$^{-1}$, respectively. For larger protein systems exceeding 500 atoms, MAEEs are 181.5~kJ~mol$^{-1}$ for MBE2 and 24.3~kJ~mol$^{-1}$ for MBE3. Furthermore, when compared to three manual fragmentation schemes on a 40-protein dataset, using both MBE and Fragment Molecular Orbital techniques, QFRAGS achieves comparable or often lower MAEEs. When applied to a 10-lipoglycan/glycolipid dataset, MAEs of 7.9 and 0.3~kJ~mol$^{-1}$ were observed at the MBE2 and MBE3 levels, respectively.
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Fiona Yu; Jorge Galvez-Vallejo; Giuseppe Maria Junior Barca
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Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-06
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b06d3c01103d79c5c5f2e1/original/automatic-molecular-fragmentation-by-evolutionary-optimisation.pdf
|
6665831212188379d8b298e5
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10.26434/chemrxiv-2024-99blk
|
Structure and Excitation Spectra of Third-Row Transition Metal Hexafluorides Based on Multi-Reference Exact Two-Component Theory
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The structures and some vertical excitation energies of third-row transition metal hexafluorides (MF6, M = Re, Os, Ir, Pt, Au, Hg) were calculated using the multi-reference configuration interaction (MRCI) theory based on exact two-component (X2C) Hamiltonian. The spin-orbit coupling (SOC) was variationally included at the Hartree-Fock level, enabling us to analyze the SOC at the orbital level. The excitation spectra were assigned based on the double group, a relativistic group theory applicable to states with the SOC. This study provides a fundamental understanding of the ligand field splitting, including the SOC, that is useful for the photochemistry and spin chemistry involving heavy elements.
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Ayaki Sunaga
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Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Spectroscopy (Inorg.); Theory - Inorganic; Transition Metal Complexes (Inorg.)
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CC BY 4.0
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CHEMRXIV
|
2024-06-10
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6665831212188379d8b298e5/original/structure-and-excitation-spectra-of-third-row-transition-metal-hexafluorides-based-on-multi-reference-exact-two-component-theory.pdf
|
60c75815337d6c4b8de29170
|
10.26434/chemrxiv.14456259.v1
|
Desymmetrization of Pibrentasvir for Efficient Prodrug Synthesis
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A novel and practical desymmetrization tactic is
described to access a new class of pibrentasvir prodrugs. The homotopic
benzimidazoles of pibrentasvir (PIB) are differentiated via a one-pot di-Boc/mono-de-Boc
selective <i>N</i>-Boc protection and formaldehyde adduct formation sequence,
both enabled by crystallization-induced selectivity. The first step represents
the only known application of the Horeau principle of statistical amplification
for <i>C</i><sub>2</sub>-symmetric polyheterocycle
regioselective functionalization. The resulting versatile intermediate is employed
in the high-yielding preparation of several pibrentasvir prodrug candidates.
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Eric Voight; Stephen Greszler; John Hartung; Jianguo Ji; Russell C. Klix; John T. Randolph; Bhadra Shelat; Jan E. Waters; David A. DeGoey
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Organic Synthesis and Reactions
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CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75815337d6c4b8de29170/original/desymmetrization-of-pibrentasvir-for-efficient-prodrug-synthesis.pdf
|
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