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60c73cc90f50db86ba3953bc
|
10.26434/chemrxiv.14753523.v1
|
Electro-mediated PhotoRedox Catalysis for Selective C(sp3)-O Cleavages of Phosphinates to Carbanions
|
We report a novel example of electro-mediated photoredox catalysis
(e-PRC) in the reductive cleavage of C(sp<sup>3</sup>)-O bonds of phosphinates
to alkyl carbanions. As well as deoxygenations, olefinations are reported which
are <i>E</i>-selective and can be made <i>Z</i>-selective in a tandem
reduction/photosensitization process where both steps are
photoelectrochemically promoted. Spectroscopy, computation and catalyst structural
variations reveal that our new naphthalene monoimide-type catalyst allows for a
more intimate dispersive precomplexation of its radical anion form with the
phosphinate substrate, facilitating a reactivity-determining C(sp<sup>3</sup>)-O
cleavage. Surprisingly and in contrast to previously
reported photoexcited radical anion chemistries, our conditions i) tolerate
aryl chlorides/bromides and ii) do not give rise to Birch-type reductions.
|
Xianhai Tian; Tobias Karl; Sebastian Reiter; Shahboz Yakubov; Regina de Vivie-Riedle; Burkhard Koenig; Joshua Barham
|
Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry; Computational Chemistry and Modeling; Electrocatalysis; Homogeneous Catalysis; Organocatalysis; Photocatalysis; Redox Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-06-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc90f50db86ba3953bc/original/electro-mediated-photo-redox-catalysis-for-selective-c-sp3-o-cleavages-of-phosphinates-to-carbanions.pdf
|
6442989083fa35f8f603c057
|
10.26434/chemrxiv-2023-l84np-v2
|
Magnesium(I) Reduction of Aluminum(III) Hydride Complexes: Generation of Mixed Valence Aluminum (AlI/Al0) Hydride Cluster Compounds, [Al6H8(NR3)2{Mg(-diketiminate)}4]
|
Reduction of a range of amido- and aryloxy-aluminum dihydride complexes, e.g. [AlH2(NR3){N(SiMe3)2}] (NR3 = NMe3 or N-methylpiperidine (NMP)), with -diketiminato dimagnesium(I) reagents, [{(ArNacnac)Mg}2] (ArNacnac = [HC(MeCNAr)2]-, Ar = mesityl (Mes) or 2,6-xylyl (Xyl)), have afforded deep red mixed valence aluminum hydride cluster compounds, [Al6H8(NR3)2{Mg(ArNacnac)}4], which have an average Al oxidation state of +0.66, the lowest for any well-defined aluminum hydride compound. In the solid-state, the clusters are shown to have distorted octahedral Al6 cores, having zero-valent Al axial sites and mono-valent AlH2- equatorial units. Several novel by-products were isolated from the reactions that gave the clusters, including the Mg‒Al bonded magnesio-aluminate complexes, [(ArNacnac)(Me3N)Mg‒Al(-H)3[{Mg(ArNacnac)}2(-H)]]. Computational analyses of one aluminum hydride cluster revealed its Al6 core to be electronically delocalized, and to possess one unoccupied, and six occupied, skeletal molecular orbitals.
|
Sneha Mullassery; K. Yuvaraj; Deepak Dange; Dafydd Jones; Iker del Rosal; Ross Piltz; Alison Edwards; Laurent Maron; Cameron Jones
|
Inorganic Chemistry; Organometallic Chemistry; Main Group Chemistry (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6442989083fa35f8f603c057/original/magnesium-i-reduction-of-aluminum-iii-hydride-complexes-generation-of-mixed-valence-aluminum-al-i-al0-hydride-cluster-compounds-al6h8-nr3-2-mg-diketiminate-4.pdf
|
60c7433c0f50db8351395eae
|
10.26434/chemrxiv.7994309.v2
|
Where Do the Ions Reside in a Highly Charged Droplet?
|
Droplets in atmospheric and electrosprayed aerosols carry more often than less, a multitude of ions. We address the question of the location of a collection of ions in charged aqueous droplets with linear dimensions in the nanometer<br />range using atomistic molecular dynamics and analytical theory. All the details of the computations have been described in the manuscript.<br />
|
Victor Kwan; Anatoly Malevanets; Styliani Consta
|
Clusters; Interfaces; Solution Chemistry; Structure
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-07-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7433c0f50db8351395eae/original/where-do-the-ions-reside-in-a-highly-charged-droplet.pdf
|
66b2b155c9c6a5c07a37d2b9
|
10.26434/chemrxiv-2024-f2vxg
|
A Broadly Applicable Strategy to Aminate Azines Enabled by Electronically Tuned Phosphine Reagents.
|
We describe a strategy for aminating pyridines and other azines via phosphonium salt intermediates. Precisely tuning the electronic properties of the phosphonium ion was key for C–N bond formation via an SNAr-halogenation, SNAr-amination sequence. The process accommodates a wide range of amine classes and pyridine coupling partners and is viable for applications such as late-stage amination of complex pharmaceuticals and fragment-fragment coupling reactions. The capacity to rapidly modify the structure of the phosphine reagent was decisive and is a valuable feature in pseudohalide design.
|
Jeffrey N. Levy; Ren-Rong Liu; Andrew McNally
|
Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b2b155c9c6a5c07a37d2b9/original/a-broadly-applicable-strategy-to-aminate-azines-enabled-by-electronically-tuned-phosphine-reagents.pdf
|
661f7e7091aefa6ce1bb8522
|
10.26434/chemrxiv-2024-nsv59
|
Albumin Nanoparticles in Cancer Therapeutics: Clinical Status, Challenges, and Future Directions
|
Cancer, a global health burden, is characterized by uncontrolled cell growth and metastasis, often resulting in debilitating treatments and mortality. While conventional therapeutic strategies have improved survival rates, they are limited by challenges such as off-target toxicity and drug resistance. With their design to enable targeted drug delivery, nanoparticles have presented a promising avenue to overcome these limitations. Protein-based nanoparticles, particularly those based on albumin, are notable for their biocompatibility, stability, and ease of modification. The approval of Abraxane, an albumin-based nanoparticle formulation of paclitaxel, for metastatic breast cancer marked a significant milestone. However, further approvals have been slow to materialize until the recent approval of Fyarro® in 2021. This mini-review highlights the potential of albumin-based nanoparticles, focusing on their advantages, their current state, and progress in clinical use as anticancer therapeutics. We also discuss challenges impeding new approvals and future directions for unlocking the full potential of this technology.
|
HACHEMI KADRI; Mesk Alshatfa; Feras Z Alsalloum; Abdelbary Elhissi; Anis Daou; Mouhamad Khoder
|
Nanoscience
|
CC BY 4.0
|
CHEMRXIV
|
2024-04-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661f7e7091aefa6ce1bb8522/original/albumin-nanoparticles-in-cancer-therapeutics-clinical-status-challenges-and-future-directions.pdf
|
61ba0a1af52bc40c6fc1e54f
|
10.26434/chemrxiv-2021-4zs27-v3
|
Breaking the aristotype: featurisation of polyhedral distortions in perovskite crystals
|
While traditional crystallographic representations of structure play an important role in materials science, they are unsuitable for efficient machine learning. A range of effective numerical descriptors have been developed for molecular and crystal structures. We are interested in a special case, where distortions emerge relative to an ideal high-symmetry parent structure. We demonstrate that irreducible representations form an efficient basis for the featurisation of polyhedral deformations with respect to such an aristotype. Applied to dataset of 552 octahedra in ABO3 perovskite-type materials, we use unsupervised machine learning with irreducible representation descriptors to identify four distinct classes of behaviour, associated with predominately corner, edge, face, and mixed connectivity between neighbouring octahedral units. Through this analysis, we identify SrCrO3 as a material with tuneable multiferroic behaviour. We further show, through supervised machine learning, that thermally activated structural distortions of CsPbI3 are well described by this approach.
|
Kazuki Morita; Daniel Davies; Keith Butler; Aron Walsh
|
Theoretical and Computational Chemistry; Materials Science; Inorganic Chemistry; Solid State Chemistry; Computational Chemistry and Modeling; Machine Learning
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-12-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ba0a1af52bc40c6fc1e54f/original/breaking-the-aristotype-featurisation-of-polyhedral-distortions-in-perovskite-crystals.pdf
|
66ed683d51558a15ef90d6d5
|
10.26434/chemrxiv-2024-cnw9h
|
Direct coordination of phenol reductants to copper enables the Cu(II) reduction in Lytic polysaccharide monooxygenases
|
Copper-dependent lytic polysaccharide monooxygenases (LPMOs) are key enzymes involved in the breakdown of recalcitrant polysaccharides such as cellulose and chitin. LPMOs require external electrons for the activations of either O2 or H2O2, which can be supplied by enzymatic electron donors or small molecule reductants. As quite abundant reductants in nature, phenolic compounds can serve as efficient reducing agents for reactions of LPMOs. Despite extensive studies, how phenolic compounds fuel the reactions of LPMOs is enigmatic. In this study, we report a novel mechanism for the reduction of LPMO-Cu(II) by the phenol reductants. Among various mechanisms investigated, we found the most favorable one involves the coordination re-placement of water by the phenol reductant. The coordination of pyrogallol (Pyr) to LPMO-Cu(II) can remarkably facilitate both the electron transfer from Pyr to Cu(II) and the proton transfer from the ligated OH group to the adjacent Glu148, thereby enhancing proton-coupled electron transfer process for the reduction of LPMO-Cu(II). Detailed comparisons and analysis have shown that the different ligand effects between LPMOs and the copper-dependent pMMO can result in the divergent mecha-nisms for Cu(II) reduction in two enzymes. These insights have greatly expanded our understanding on the interaction machin-ery of copper-dependent enzymes with phenol compounds in nature.
|
Langxing Liao; Jian Kuang; Wei Peng; Peng Wu; Xianhang Sang; Heng Yin; Changlin Tian; Lu Yu; Binju Wang
|
Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Biocatalysis; Quantum Mechanics
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-09-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ed683d51558a15ef90d6d5/original/direct-coordination-of-phenol-reductants-to-copper-enables-the-cu-ii-reduction-in-lytic-polysaccharide-monooxygenases.pdf
|
644f87bb80f4b75b536c03c9
|
10.26434/chemrxiv-2023-sh0bx
|
Linking the Pre-steady-state, Steady-state, and Zero-order kinetic parameters together for Industrial and allied applications
|
Background: There is an increasing application of enzymes to achieving the industrial goal of the production of biomolecules of different kinds relevant to food, textiles, pharmaceuticals, automobiles, environmental remediation, etc.; there appears not to have been a way of linking pre-zero-order kinetics to zero-order kinetics so as to garner key kinetic parameters at very high industrial concentrations of the substrate. This ought to be a prerequisite for industrial (batch or reactor) design. Objectives: The study is carried out with the objectives of deriving equations that can be explored in relating pre-zero-order (otherwise known as pre-steady-state (prss)) to zero-order kinetic parameters, such as the Michaelis-Menten constant (KM), maximum velocity of catalysis (Vmax), and specificity constant (SC), and ultimately evaluating the equations with experimental data. Methods: The study was theoretical and experimental, backed by the Bernfeld method of generating initial rates. Results and discussion: The Vmax for the higher industrial-type concentration of the enzyme (alpha-amylase) is 7812.5 micromoles/L/min, while the KM is 115.1 g/L. The SC obtained by calculation, either by the new equation (Eq. (25b)) or the ratio Vmax:KM, is 67.88 micromoles L/g min, and surprisingly, as against the literature, the SC obtained by a new graphical method is 275.4 micromoles L/g min using sub-KM values of substrate concentrations. The prss Vmax and KM are 2348.62 ± 479.94 micromoles L/g min and 7.41 ± 1.77 g/L. Conclusion: The need to derive an equation linking prss and the zero-order kinetic parameter is justified by the result obtained. In order to establish consistency, future studies may focus on assays at high concentrations of the enzyme and sub-KM concentrations of the substrate so as to observe a repeat of higher SC.
|
Ikechukwu Udema
|
Catalysis; Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644f87bb80f4b75b536c03c9/original/linking-the-pre-steady-state-steady-state-and-zero-order-kinetic-parameters-together-for-industrial-and-allied-applications.pdf
|
60c75446bb8c1ab5af3dc1cc
|
10.26434/chemrxiv.13636586.v1
|
[CrIII8NiII6]n+ Heterometallic Coordination Cubes
|
Three new heterometallic [CrIII8NiII6] coordination cubes of formulae
[CrIII8NiII6L24(H2O)12](NO3)12 (1), [CrIII8NiII6L24(MeCN)7(H2O)5](ClO4)12 (2) and [CrIII8NiII6L24Cl12] (3) (where
HL = 1-(4-pyridyl)butane-1,3-dione), were synthesised using the paramagnetic metalloligand [CrIIIL3] and
the corresponding NiII salt. The magnetic skeleton of each capsule describes a face-centred cube in which
the eight CrIII and six NiII ions occupy the eight vertices and six faces of the structure, respectively. Direct
current magnetic susceptibility measurements on (1) reveal weak ferromagnetic interactions between the
CrIII and NiII ions, with JCr-Ni = +0.045 cm-1
. EPR spectra are consistent with weak exchange, being dominated
by the zero-field splitting of the CrIII ions. Excluding wheel-like structures, examples of large
heterometallic clusters containing both CrIII and NiII ions are rather rare, and we demonstrate that the use
of metalloligands with predictable bonding modes allows for a modular approach to building families of
related polymetallic complexes. Compounds (1)-(3) join the previously published, structurally related
family of [MIII8MII6] cubes, where MIII = Cr, Fe and MII = Cu, Co, Mn, Pd. <br />
|
Helen O'Connor; Sergio Sanz; Aaron Scott; Mateusz Pitak; Wim Klooster; Simon Coles; Nicholas Chilton; Eric J. L. McInnes; Paul J. Lusby; Hogni Weihe; Stergios Piligkos; Euan Brechin
|
Coordination Chemistry (Inorg.); Ligands (Inorg.); Magnetism; Supramolecular Chemistry (Inorg.); Transition Metal Complexes (Inorg.); Crystallography – Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-01-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75446bb8c1ab5af3dc1cc/original/cr-iii8ni-ii6-n-heterometallic-coordination-cubes.pdf
|
66e9528b12ff75c3a1966623
|
10.26434/chemrxiv-2024-1ns4k
|
Automated database generation and electron density analysis for NOS bond identification
|
Nitrogen-oxygen-sulfur (NOS) linkages between lysine and cysteine residues represent novel chemical patterns crucial for cellular redox regulation and signalling. Despite their significance, automated identification of these linkages in protein structures remains challenging. Here, we present an algorithm that integrates geometric and electron density screening to detect likely NOS bonds in protein structures. We use a combination of two approaches: a Mid-point approach and a quantum mechanics-informed (QM-point) approach, each applied with varying search radii. We evaluated the algorithm using two datasets: one containing structures which upon manual inspection are confirmed as likely NOS candidates, and a control set where although the N-S distances are within established thresholds, there are is no evidence of NOS formation. The Mid-point method demonstrated strong performance across different search radii, with success rates ranging from 48% to 55% for likely NOS structures. The QM-point approach showed high specificity (99% success rate) for unlikely-NOS structures at a 2.0 Å radius. We propose a two-step screening process that uses the strengths of both methods to optimize NOS bond detection. This approach is an initial step towards automated identification of chemical patterns in protein structures, potentially uncovering previously overlooked linkages and contributing to a deeper understanding of chemical bonds in protein structures.
|
Sophia Bazzi; Maike Mücke; Jin Ye; Ricardo A. Mata
|
Biological and Medicinal Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-09-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e9528b12ff75c3a1966623/original/automated-database-generation-and-electron-density-analysis-for-nos-bond-identification.pdf
|
652e370a8bab5d205583d90d
|
10.26434/chemrxiv-2023-pn3bw
|
Data-driven discovery of intrinsic direct-gap 2D photocatalysts for overall water splitting
|
Intrinsic direct-gap two-dimensional (2D) materials hold great promise as photocatalysts advancing the application of photocatalytic water splitting for hydrogen production. However, the time- and resource-efficient exploration and identification of such 2D materials from a vast compositional and structural chemical space present a significant challenge within the realm of materials science research. To this end, we perform a data-driven study to find new 2D materials with intrinsic direct-gap and desirable photocatalytic properties for overall water splitting. By implementing a three-staged large-scale screening, which incorporates machine learning, high-throughput density functional theory (DFT) and hybrid-DFT calculations, we identify 16 new direct-gap 2D materials as promising photocatalysts. Subsequently, we conduct a comprehensive assessment of material properties that are related with the solar water splitting performance, which includes electronic and optical properties, solar-to-hydrogen conversion efficiencies, and carrier mobilities. Therefore, this study not only presents 16 new 2D photocatalysts but also introduces a rigorous data-driven approach for the future discovery of functional 2D materials from currently unexplored chemical spaces.
|
Yatong Wang; Geert Brocks; Süleyman Er
|
Materials Science; Catalysis; Energy; Photocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652e370a8bab5d205583d90d/original/data-driven-discovery-of-intrinsic-direct-gap-2d-photocatalysts-for-overall-water-splitting.pdf
|
60ec6351338e92f5950a55bd
|
10.26434/chemrxiv-2021-mdjwx
|
BH9, a New Comprehensive Benchmark Dataset for Barrier Heights and Reaction Energies: Assessment of Density Functional Approximations and Basis Set Incompleteness Potentials
|
The calculation of accurate reaction energies and barrier heights is essential in computational studies of reaction mechanisms and thermochemistry. In order to assess methods regarding their ability to predict these two properties, high-quality benchmark sets are required that comprise a reasonably large and diverse set of organic reactions. Due to the time-consuming nature of both
locating transition states and computing accurate reference energies for reactions involving large molecules, previous benchmark sets have been limited in scope, the number of reactions considered, and the size of the reactant and product molecules. Recent advances in coupled-cluster theory, in particular local correlation methods like DLPNO-CCSD(T), now allow the calculation of reaction energies and barrier heights for relatively large systems. In this work, we present a comprehensive, and diverse benchmark set of barrier heights and reaction energies based on DLPNO-CCSD(T)/CBS, called BH9. BH9 comprises 449 chemical reactions belonging to nine types common in organic
chemistry and biochemistry. We examine the accuracy of DLPNO-CCSD(T) vis-a-vis canonical CCSD(T) for a subset of BH9 and conclude that, although there is a penalty in using the DLPNO approximation, the reference data are accurate enough to serve as benchmark for density-functional
theory (DFT) methods. We then present two applications of the BH9 set. First, we examine the performance of several density functional approximations commonly used in thermochemical and mechanistic studies. Second, we assess our basis set incompleteness potentials regarding their ability to mitigate basis set incompleteness error. The number of data points, the diversity of the reactions
considered, and the relatively large size of the reactant molecules make BH9 the most comprehensive
thermochemical benchmark set to date, and a useful tool for the development and assessment of
computational methods.
|
Viki Kumar Prasad; Zhipeng Pei; Simon Edelmann; Alberto Otero-de-la-Roza; Gino DiLabio
|
Theoretical and Computational Chemistry; Organic Chemistry; Physical Organic Chemistry; Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-07-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60ec6351338e92f5950a55bd/original/bh9-a-new-comprehensive-benchmark-dataset-for-barrier-heights-and-reaction-energies-assessment-of-density-functional-approximations-and-basis-set-incompleteness-potentials.pdf
|
63dfc362068fd7597923218c
|
10.26434/chemrxiv-2022-d990c-v2
|
Switching of photocurrent polarity in electrochemical cells with light via an excited state proton transfer mechanism
|
Light is the most targeted source of energy for sustainable energy technologies such as in photocurrent generation. While practically all light-harvesting types of applications utilize the electrons in their excited state (ES), here, we introduce a new conceptual approach that is based on ES proton transfer (ESPT). We use Brønsted photoacids and photobases that can donate or accept a proton, respectively, but only in their ES. Here, we use these molecules solvated in a photoelectrochemical single cell and explore the role of ESPT in photocurrent generation. We show at different bias regimes that the formed ions following the ESPT process can serve as electron donors or acceptors to the electrodes, which is dependent on the system and the presence of a photoacid or a photobase, resulting in modulating the photocurrent generation toward positive or negative currents. We further use an H-cell configuration that allows us to control the current polarity by switching the illumination between the cell containing the photoacid to the one containing the photobase. Our study represents a new approach in photoelectrochemistry by introducing ESPT processes, which can be further utilized in future devices targeting light-responsive energy production, energy storage, and hydrogen formation applications.
|
Anna Yuchnovsky; Yaniv Shlosberg; Noam Adir; Nadav Amdursky
|
Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study; Photochemistry (Physical Chem.); Physical and Chemical Processes
|
CC BY 4.0
|
CHEMRXIV
|
2023-02-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63dfc362068fd7597923218c/original/switching-of-photocurrent-polarity-in-electrochemical-cells-with-light-via-an-excited-state-proton-transfer-mechanism.pdf
|
66b278c701103d79c5ef14df
|
10.26434/chemrxiv-2024-7h2hp
|
MOFs with the Stability for Practical Gas Adsorption Applications Require New Design Rules
|
Metal-organic frameworks (MOFs) have been widely studied for their ability to capture and store greenhouse gases. However, most chemical discovery efforts use computational study of hypothetical MOFs without consideration of their stability, limiting the practical application of novel materials. We overcome this limitation by screening hypothetical ultrastable MOFs that have predicted high thermal and activation stability, as judged by machine learning (ML) models trained on experimental measures of stability. We enhance this set by computing the bulk modulus as a measure of mechanical stability and filter 1,102 mechanically robust hypothetical MOFs from a database of ultrastable MOFs (USMOF DB). Grand Canonical Monte Carlo simulations are then employed to examine the gas adsorption properties of these hypothetical MOFs, alongside a database of experimental MOFs. We identify privileged building blocks that allow MOFs in USMOF DB to show exceptional working capacities compared to the experimental MOFs. We interpret these differences by training ML models on CO2 and CH4 adsorption in these databases, showing how poor model transferability between datasets indicates that novel design rules can be derived from USMOF DB that would not have been gathered through assessment of structurally characterized MOFs. We identify geometric features and node chemistry that will enable the rational design of MOFs with enhanced gas adsorption properties in synthetically realizable MOFs.
|
Changhwan Oh; Aditya Nandy; Shuwen Yue; Heather Kulik
|
Theoretical and Computational Chemistry; Materials Science; Nanostructured Materials - Materials; Machine Learning
|
CC BY 4.0
|
CHEMRXIV
|
2024-08-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b278c701103d79c5ef14df/original/mo-fs-with-the-stability-for-practical-gas-adsorption-applications-require-new-design-rules.pdf
|
60c757799abda21a89f8e73c
|
10.26434/chemrxiv.14411003.v1
|
Gd Matrix Effects on Eu Isotope Fractionation in Geological Rocks Using MC-ICP-MS: Optimizing Europium Isotope Ratio Measurements in Geological Samples
|
<p></p><p>Eu has only two isotopes (151Eu and 153 Eu). Eu and Gd are one of the rare earth elements that are very difficult to completely separate from each other. Eu isotope ratio can be determined by MC-ICP-MS using internal Sm or Gd spikes to correct for mass discrimination. NIST3117a ultrapure chemical reagent shows almost no Eu isotope fractionation regardless of the kind of normalization isotope pair. However, Eu isotope ratio in the silicate rocks was effected by Gd matrix during MC-ICP-MS measurement if a trace amount of Gd impurity remains in the purified Eu fraction. In this report, we tried to determine optimizing conditions for precise and accurate Europium isotope ratio measurements in geological samples using MC-ICP-MS. The pure Eu fraction with almost no Gd matrix separated from geological samples and NIST3117a ultrapure chemical reagent show almost same degree of Eu isotope fractionation regardless of the kind of normalization isotope pair. However, Eu isotope ratio in the silicate rocks was
effected by Gd matrix during MC-ICP-MS measurement using if 154 Gd interference relative to
154 Sm as internal standard is more than ca. 0.1%. Particularly, highly fractionated granite and high silica volcanic rock with extremely low Eu concentration compared to Gd require high – purity Eu separation with a high recovery rate to obtain the true value of the Eu isotope fractionation in the geological rocks. <br /></p><br /><p></p>
|
Seung-Gu Lee; Tsuyoshi Tanaka
|
Geochemistry; Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757799abda21a89f8e73c/original/gd-matrix-effects-on-eu-isotope-fractionation-in-geological-rocks-using-mc-icp-ms-optimizing-europium-isotope-ratio-measurements-in-geological-samples.pdf
|
60c7583dbb8c1aad3a3dc9d2
|
10.26434/chemrxiv.14527299.v1
|
Topology Automated Force-Field Interactions (TAFFI): A Framework for Developing Transferable Force-Fields
|
<div>
<div>
<div>
<p>Force-field development has undergone a revolution in the past decade with the
proliferation of quantum chemistry based parameterizations and the introduction of
machine learning approximations of the atomistic potential energy surface. Nevertheless, transferable force-fields with broad coverage of organic chemical space remain
necessary for applications in materials and chemical discovery where throughput, consistency, and computational cost are paramount. Here we introduce a force-field development framework called Topology Automated Force-Field Interactions (TAFFI) for
developing transferable force-fields of varying complexity against an extensible database of quantum chemistry calculations. TAFFI formalizes the concept of atom typing and
makes it the basis for generating systematic training data that maintains a one-to-one
correspondence with force-field terms. This feature makes TAFFI arbitrarily extensible to new chemistries while maintaining internal consistency and transferability. As
a demonstration of TAFFI, we have developed a fixed-charge force-field, TAFFI-gen,
from scratch that includes coverage for common organic functional groups that is comparable to established transferable force-fields. The performance of TAFFI-gen was
benchmarked against OPLS and GAFF for reproducing several experimental proper-
ties of 87 organic liquids. The consistent performance of these force-fields, despite their
distinct origins, validates the TAFFI framework while also providing evidence of the
representability limitations of fixed-charge force-fields.</p>
</div>
</div>
</div>
|
bumjoon seo; Zih-Yu Lin; Qiyuan Zhao; Michael Webb; Brett Savoie
|
Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7583dbb8c1aad3a3dc9d2/original/topology-automated-force-field-interactions-taffi-a-framework-for-developing-transferable-force-fields.pdf
|
615e13a40ad1ff72528cad81
|
10.26434/chemrxiv-2021-kwrtm-v2
|
A Small Organic molecule Based on Benzothiadiazole for Electrocatalytic Hydrogen Production
|
A small organic molecule 2,1,3-benzothiadiazole-4, 7-dicarbonitrile (BTDN) is assessed for electrocatalytic hydrogen, showing a hydrogen production faradaic efficiency of 82% in presence of salicylic acid. The key catalytic intermediates of reduced species BTDN−• and protonated intermediates are identified and characterized by using various spectroscopic methods and density functional theory (DFT) based calculations. With the experimental and theoretical results, a catalytic mechanism of BTDN for electrocatalytic H2 evolution is proposed.
|
Martin Axelsson; Cleber
F. N. Marchiori; Ping Huang; C. Moyses Araujo; Haining Tian
|
Catalysis; Electrocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-10-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615e13a40ad1ff72528cad81/original/a-small-organic-molecule-based-on-benzothiadiazole-for-electrocatalytic-hydrogen-production.pdf
|
60c74e10bdbb897f7ea39af2
|
10.26434/chemrxiv.12652997.v2
|
Multitarget Virtual Screening for Drug Repurposing in COVID19
|
Therapeutic or preventive research for coronavirus SARS-CoV2 is an extremely active topic of research since its outbreak in January 2020. In this paper we report the results from a virtual drug screening analysis that, to the best of our knowledge, is the widest work in terms of target proteins and compound library. Our study was focused on the repurposing of currently commercialized drugs, and especially those that can interact with multiple viral proteins and several binding sites within each protein. Additionally, we performed a second virtual screening analysis in which we compared our results to the predicted binding affinities for the drugs currently in clinical trials. We show that the best molecules in our screening compares favorably to those in clinical trials, suggesting their suitability for therapeutic or preventive applications.
|
carlos oscar Sorzano; Enrique Crisman; Jose Maria Carazo; rafael leon
|
Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Microbiology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e10bdbb897f7ea39af2/original/multitarget-virtual-screening-for-drug-repurposing-in-covid19.pdf
|
64349da60784a63aeee78660
|
10.26434/chemrxiv-2023-tdfnq
|
Basic principle from electrospray ionization to soft ionization mass spectrometry and development of ion source:part Ⅰ
|
Since the electrospray phenomenon was discovered, there is still an unsolved mystery about the prinple of generating charged analyte in the soft ionization phenomenon which represented by ESI. Scientists have described this process from different perspectives, but current theories still can not explain many experimental phenomena. At the same time, the slow development of the theory restricts the design and development of ion source, making it encounter many bottlenecks from the laboratory to commercialization. In this paper, the principle of electrospray ionization and soft ionization mass spectrometry is briefly introduced, and the application of ion migrate and transport mechanism is discussed, all are expected to be used in the development of ion sources.
|
jiehong luo
|
Analytical Chemistry; Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64349da60784a63aeee78660/original/basic-principle-from-electrospray-ionization-to-soft-ionization-mass-spectrometry-and-development-of-ion-source-part-i.pdf
|
61886c2cd828a485016fa6b2
|
10.26434/chemrxiv-2021-9kq0r
|
Bipolar doping and thermoelectric properties of Zintl arsenide Eu5In2As6
|
Zintl compounds exhibit promising thermoelectric properties because of the feasibility of the chemical tuning of their electrical and thermal transport. While most Zintl pnictides are known to show p-type polarity, recent developments in high-performance n-type Mg3Sb2-based thermoelectric materials have encouraged further identification of n-type Zintl pnictides. In this study, we demonstrate the bipolar dopability of the Zintl arsenide Eu5In2As6. The electrical resistivity at 300 K with n-type polarity was decreased to 7.6 x 10^-1 ohmcm using La as an electron dopant. In contrast to the relatively high resistivity of n-type Eu5In2As6, the p-type resistivity at 300 K was decreased to 5.9 x 10^-3 ohmcm with a carrier concentration of 2.8 x 10^20 /cm3 using Zn as a hole dopant. This doping asymmetry is discussed in terms of the weighted mobility of electrons and holes. Furthermore, a very low lattice thermal conductivity of 0.7 W/mK was observed at 773 K, which is comparable to that of the Sb-containing analogue Eu5In2Sb6. The dimensionless figure of merit ZT = 0.29 at 773 K for Zn-doped p-type Eu5In2As6. This study shows that bipolar dopable Eu5In2As6 can be a platform to facilitate a better understanding of the doping asymmetry in Zintl pnictides.
|
Naoki Tomitaka; Yosuke Goto; Kota Morino; Kazuhisa Hoshi; Yuki Nakahira; Hiroaki Ito; Akira Miura; Hidetomo Usui; Yoshikazu Mizuguchi
|
Materials Science; Inorganic Chemistry; Energy; Piezoelectricity and Thermoelectricity
|
CC BY NC 4.0
|
CHEMRXIV
|
2021-11-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61886c2cd828a485016fa6b2/original/bipolar-doping-and-thermoelectric-properties-of-zintl-arsenide-eu5in2as6.pdf
|
64e44020694bf1540cc27c08
|
10.26434/chemrxiv-2023-6qpsl
|
A complex approach to study the electrode-solution region. Surface layer, electrical double layer, medium properties and chemical reactivity
|
A complex approach to the study of the electrode-solution region is proposed that consists in the coupled study of molecular reactivity x and collective properties X. The general conclusion on the presence and value of the electrode effects for x is established by comparing the products of xdir, xhom of the direct electrolysis and the homogeneous catalytic ET- process HOMEC. The change in x with distance L from the electrode surface x = f(L) (1) is found by electrolysis using a near-electrode tomography NELTO by gradually varying the HOMEC´s contribution, the dependence (1) is established by solving the corresponding diffusion-kinetic equations. The collective characteristics X are related to the material and surface structure of the electrode, as well as the properties of the near-electrode medium - viscosity, dielectric constant, etc., which are measured by spectro-electrochemical and electrochemical-atomic force microscopy techniques; hence the dependence X=F(L) (2) is found. Some results, using previously published and also unpublished data, are given. The combined x, X - measurements and comparison of dependencies (1) and (2) open up new possibilities for establishing the nature of electrode phenomena
|
Victor Mairanovsky
|
Physical Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-08-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e44020694bf1540cc27c08/original/a-complex-approach-to-study-the-electrode-solution-region-surface-layer-electrical-double-layer-medium-properties-and-chemical-reactivity.pdf
|
65e105659138d231615bfdec
|
10.26434/chemrxiv-2024-2z7kt
|
Bioinspired Synthesis of (–)-Hunterine A: Deciphering a Unique Deconstructive Route
|
A short, bioinspired, and enantioselective synthesis of (–)- hunterine A, an odd 6/7/6/6/5 pentacyclic natural product, is described. The key step in the synthesis of this daunting structure is the 6-exo selective epoxide ring-opening reaction, which is interwoven with a deconstructive step of the indolenine part to create the unusual 7-membered azepine bridge motif. Our work also reveals the possible mechanism and stereochemical prerequisite of this unique skeletal rearrangement, which provides a vantage point for understanding how (–)-hunterine A is likely to be generated in nature.
|
Bálint Zsigulics; Péter Angyal; Bence Balázs Mészáros; János Daru; Szilárd Varga; Tibor Soós
|
Organic Chemistry; Natural Products; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e105659138d231615bfdec/original/bioinspired-synthesis-of-hunterine-a-deciphering-a-unique-deconstructive-route.pdf
|
658782119138d2316160350e
|
10.26434/chemrxiv-2023-9vrz0
|
Selective Adsorption of the Super Greenhouse Gas Tetrafluoromethane within a Metal–Organic Framework with Dynamic Corrugated Ultramicropores
|
Perfluorocompound (PFC) gases play vital roles in microelectronics processing. Requirements for ulta-high purities traditionally necessitate use of virgin sources and thereby hinder the capture, purification, and reuse of these costly gases. Most importantly, gaseous PFCs are incredibly potent greenhouse gases with atmospheric lifetimes on the order of 103-104 years, and thus any environmental emissions have an outsized and prolonged impact on our climate. The development of sorbents that can capture PFC gases from industrial waste streams has lagged substantially behind the progress made over the last decade in capturing CO2 from both point emission sources and directly from air. Herein, we show that the metal–organic framework Zn(fba) (fba2– = 4,4’-(hexafluoroisopropylidene)bis-benzoate) displays an equilibrium selectivity for CF4 adsorption over N2 that surpasses those of all water-stable sorbents that have been reported for this separation. This selectivity is enabled by adsorption within narrow corrugated channels lined with ligand-based aryl rings, a site within this material that has not previously been realized as being accessible to guests. Analyses of adsorption kinetics and X-ray diffraction data are used to characterize sorption and diffusion of small adsorbates within these channels and strongly implicate rotation of the linker aryl rings as a gate that modulates transport of CF4 through a crystallite. Multi-component breakthrough measurements demonstrate that Zn(fba) is able to resolve CF4 and N2 under flowing mixed-gas conditions. Taken together, this work illuminates a more complete picture of the dynamic structure of Zn(fba), and also points toward general design principles that can enable large CF4 selectivities in sorbents with more favorable kinetic profiles.
|
Bevan Whitehead; William Brennessel; Shane Michtavy; Hope Silva; Jaehwan Kim; Phillip Milner; Marc Porosoff; Brandon Barnett
|
Materials Science; Inorganic Chemistry; Hybrid Organic-Inorganic Materials; Solid State Chemistry; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658782119138d2316160350e/original/selective-adsorption-of-the-super-greenhouse-gas-tetrafluoromethane-within-a-metal-organic-framework-with-dynamic-corrugated-ultramicropores.pdf
|
60c74cb4702a9b304018b6fd
|
10.26434/chemrxiv.12522233.v1
|
Predicting Excitation Energies of Twisted Intramolecular Charge-Transfer States with Time-Dependent Density Functional Theory: Comparison with Experimental Measurements in the Gas-Phase and Solvents Ranging from Hexanes to Acetonitrile
|
Electronically-excited states characterized by intramolecular charge-transfer play
an essential role in many biological processes and optical devices. The ability to make
quantitative ab initio predictions of the relative energetics involved is a challenging
yet desirable goal, especially for large molecules in solution. In this work we present a
data set of 61 experimental measurements of absorption and emission processes, both
in the gas phase and solvents representing a broad range of polarities, which involve intramolecular charge-transfer mediated by a non-zero, “twisted” dihedral angle between one or more donor and acceptor subunits. Among a variety of density functionals investigated within the framework of linear-response theory, the “optimally tuned”
LRC-ωPBE functional, which utilizes a system-specific yet non-empirical procedure
to specify the range-separation parameter, emerges as the preferred choice. For the
entire set of excitation energies, involving changes in dipole moment ranging from 4
to >20 Debye, the mean signed and absolute errors are 0.02 and 0.18 eV, respectively
(compared, e.g., to -0.30 and 0.30 for PBE0, 0.44 and 0.47 for LRC-ωPBEh, 0.83 and
0.83 for ωB97X-V). The performance of polarizable continuum solvation models for
these charge-transfer excited states is closely examined, and clear trends emerge when
measurements corresponding to the four small DMABN-like molecules and a charged
species are excluded. We make the case that the large errors found only for small
molecules in the gas phase and weak solvents cannot be expected to improve via the
optimal tuning procedure, which enforces a condition that is exact only in the wellseparated donor-acceptor limit, and present empirical evidence implicating the outsized
importance for small donor-acceptor systems of relaxation effects that cannot be accounted for by linear-response TDDFT within the adiabatic approximation. Finally, we
demonstrate the utility of the optimally tuned density functional approach by targeting the charge-transfer states of a large biomimetic model system for light-harvesting
structures in Photosystem II.
|
James Shee; Martin Head-Gordon
|
Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cb4702a9b304018b6fd/original/predicting-excitation-energies-of-twisted-intramolecular-charge-transfer-states-with-time-dependent-density-functional-theory-comparison-with-experimental-measurements-in-the-gas-phase-and-solvents-ranging-from-hexanes-to-acetonitrile.pdf
|
62b043eb1fdc3461a040883f
|
10.26434/chemrxiv-2022-v78s5
|
Encapsulation of Size-Selected Ru3 Clusters into RF-Deposited TiO2
|
In this study Ru3 clusters are deposited onto radio frequency-sputter deposited TiO2 (RF-TiO2) substrates by both solution submersion and chemical vapor deposition (CVD) of Ru3(CO)12, as well as cluster source depositions of bare Ru3. TiO2(100) and SiO2 are used as comparison surfaces with differing cluster-surface interactions. Temperature-dependent X-ray photoelectron spectroscopy (XPS), angle-resolved XPS, and temperature-dependent low energy ion scattering (TD-LEIS) are used to probe how the cluster-surface interaction changes due to heat treatment. Results show that bare Ru3 supported on SiO2 remain on the surface layer but agglomerates upon heating. Conversely, when supported on sputter-treated RF-TiO2, bare Ru3 is encapsulated by a layer of titania substrate material as-deposited. Ligated Ru3(CO)12 is also covered by a layer of titania when deposited onto sputter-treated RF-TiO2 but heat treatment is required to remove most of the ligands. TD-LEIS is used to directly measure the encapsulation of CVD Ru3(CO)12 clusters on sputter-treated RF-TiO2 and determine the substrate overlayer thickness. The overlayer was found to be 1-2 monolayers, which is thin enough for catalytic or photocatalytic reactions to occur without Ru being present in the outermost layer.
|
Liam Howard-Fabretto; Timothy J. Gorey; Guangjing Li; Siriluck Tesana; Gregory F. Metha; Scott L. Anderson; Gunther G. Andersson
|
Physical Chemistry; Materials Science; Nanoscience; Nanostructured Materials - Materials; Clusters; Surface
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-06-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b043eb1fdc3461a040883f/original/encapsulation-of-size-selected-ru3-clusters-into-rf-deposited-ti-o2.pdf
|
653df95848dad231209ff497
|
10.26434/chemrxiv-2023-54w5m
|
Deep Neural Network Assisted Quantum Chemistry Calculations on Quantum Computers
|
The variational quantum eigensolver (VQE) is a widely employed method to solve electronic structure problems on the current noisy intermediate-scale quantum (NISQ) devices. However, due to inherent noise in the NISQ devices, VQE results on NISQ devices often deviate significantly from the results obtained on noiseless statevector simulators or traditional classical computers. The iterative nature of the VQE further amplifies the errors in each loop. Recent works have explored ways to integrate deep neural networks (DNN) with VQE to mitigate the iterative errors, albeit, primarily limited to the noiseless statevector simulators. In this work, we trained DNN models across various quantum circuits and examined the potential of two DNN-VQE approaches, DNN1 and DNNF, for predicting the ground state energies of small molecules in the presence of device noise. We carefully examined the accuracy of the DNN1, DNNF, and VQE methods on both noisy simulators and real quantum devices by considering different ansatzes of varying qubit counts and circuit depths. Our results illustrate the advantages and limitations of both VQE and DNN-VQE approaches. Notably, both DNN1 and DNNF methods consistently outperform the standard VQE method in providing more accurate ground-state energies in noisy environments. However, despite being more accurate than VQE, the energies predicted using these methods on real quantum hardware remain meaningful only at reasonable circuit depths (depth = 15, gates = 21). At higher depths (depth = 83, gates = 112), they deviate significantly from the exact results. Additionally, we find that DNNF does not offer any notable advantage over VQE in terms of speed. Consequently, our study recommends DNN1 as the preferred method for obtaining quick and accurate ground state energies of molecules on the current quantum hardware, particularly for quantum circuits with lower depth and fewer qubits.
|
Kalpak Ghosh; Sumit Kumar; Nirmal M. R.; Sharma S. R. K. C. Yamijala
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Quantum Computing
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653df95848dad231209ff497/original/deep-neural-network-assisted-quantum-chemistry-calculations-on-quantum-computers.pdf
|
60c75906bb8c1ac4b33dcb45
|
10.26434/chemrxiv.14635569.v1
|
Theoretical Determination of Rate Constants from Excited-States: Application to Benzophenone
|
A cost-effective
method of theoretically predicting electronic transition rate constants from the
excited-states of molecules is reported.
This method is based on density functional theory calculations
of electronic states and quantitative rate constant determination with the
Fermi golden rule.
|
Katsuyuki Shizu; Hironori Kaji
|
Photochemistry (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75906bb8c1ac4b33dcb45/original/theoretical-determination-of-rate-constants-from-excited-states-application-to-benzophenone.pdf
|
640c1076e53eff1af3f0ddce
|
10.26434/chemrxiv-2023-jw4p3
|
Hydrogen Adsorption in Ultramicroporous Metal-organic Frameworks Possessing Silent Open Metal Sites
|
Herein, we report the use of an ultramicroporous (pore size <0.7 nm) metal-organic framework (MOF), [Ni3(pzdc)2(ade)2(H2O)4]2.18H2O (H3pzdc: pyrazole-3,5-dicarboxylic acid, ade: adenine), for hydrogen (H2) adsorption. Upon activation, [Ni3(pzdc)2(ade)2] was generated, and in situ carbon monoxide loading transmission infrared spectroscopy revealed that open Ni(II) sites could be generated. The MOF displayed a Brunauer-Emmett-Teller (BET) surface area of 160 m2/g. Hydrogen adsorption collected on this MOF at 77 K revealed a steep uptake at low pressure, and H2 uptake saturation was achieved at 0.15 bar. The affinity of this MOF for H2 is 9.7 1.0 kJ/mol. An interplay of in situ H2 loading experiments and computations confirmed that H2 does not bind to the open Ni(II) sites of the MOF, and the observed high affinity of the MOF for H2 is mainly attributed to its narrow pore size. To shed light on the impact of ultramicropores on H2 uptake, we experimentally compared the H2 uptake per surface area unit as a function of the pore size of other ultramicroporous, microporous, and mesoporous MOFs. Our results showcase that ultramicropores contribute the most to H2 uptake, and the size, shape, and functionality of our MOF are ideal and can be used as guiding principles for the design and synthesis of novel adsorbents for efficient H2 storage and delivery.
|
Nan Chieh Chiu; Dalton Compton; Andrzej Gladysiak; Scott Simrod; Konstantin Khivantsev; Tom Woo; Nicholas Stadie; Kyriakos Stylianou
|
Materials Science; Hydrogen Storage Materials; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640c1076e53eff1af3f0ddce/original/hydrogen-adsorption-in-ultramicroporous-metal-organic-frameworks-possessing-silent-open-metal-sites.pdf
|
6784ff2d6dde43c908525e43
|
10.26434/chemrxiv-2024-fk6qk-v2
|
Nanodiamond synthesis from adamantane by electron-beam driven C–H activation at 100 K
|
Diamond and adamantane (Ad) share a Td-symmetric carbon skeleton, but converting Ad to diamond has been challenging due to selective C–H bond cleavage and monomer assembly into a diamond lattice. Electron irradiation (80–200 keV) of Ad sub-microcrystals in vacuum at 100 K for tens of seconds yielded defect-free nanodiamonds (NDs) of cubic crystal structure 2–4 nm in diameter, accompanied by hydrogen gas evolution. Time-resolved transmission electron microscopy revealed the initial formation of Ad oligomers transforming into spherical NDs. A sizable kinetic isotope effect confirmed C–H cleavage as rate-determining. Other hydrocarbons failed to form NDs, underscoring the unique suitability of Ad. This approach distinctively differs from the conventional high-temperature, high-pressure approach, exemplifying the value of controlled C–H activation for diamond synthesis.
|
Jiarui Fu; Takayuki Nakamuro; Eiichi Nakamura
|
Nanoscience; Nanostructured Materials - Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6784ff2d6dde43c908525e43/original/nanodiamond-synthesis-from-adamantane-by-electron-beam-driven-c-h-activation-at-100-k.pdf
|
60f9143b0321144351b6ff31
|
10.26434/chemrxiv-2021-5714s-v2
|
Catalytic Enantioselective Nucleophilic Desymmetrisation of Phosphonate
Esters
|
Compounds containing one or more stereogenic phosphorous atoms in the P(V) oxidation
state are important to chemistry, biology and medicine. These include marketed
antiviral drugs such as Tenofovir alafenamide and Remdesivir, an effective treatment
for Ebola which has also recently been approved for use against SARS-CoV-2 in the US.
Existing approaches for the stereoselective synthesis of P-stereogenic centers, while
elegant, remain mostly diastereoselective, with catalytic enantioselective approaches
being limited in application. Accordingly, conceptually novel, broad-scope, catalytic
strategies for the efficient stereoselective synthesis of diverse stereogenic P(V) containing
compounds remain essential.
To this end, we describe a novel enantioselective two-stage strategy, exploiting a catalytic and highly enantioselective desymmetrisation of phosphonate esters. Pivoting on the first stereocontrolled, sequential nucleophilic substitution of enantiotopic leaving groups from readily accessible pro-chiral P(V) precursors, a bifunctional iminophosphorane (BIMP) superbase catalyst was found to be essential in delivering reactive desymmetrised intermediates capable of downstream enantiospecific substitution. This uniquely modular, catalytic platform allows broad-scope, stereoselective access to a diverse library of chiral P(V) compounds including those with O, N and S-linkages.
|
Michele Formica; Tatiana Rogova; Heyao Shi; Naoto Sahara; Alistair J. M. Farley; Kirsten E. Christensen; Fernanda Duarte; Darren J. Dixon
|
Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Stereochemistry; Base Catalysis; Organocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-07-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f9143b0321144351b6ff31/original/catalytic-enantioselective-nucleophilic-desymmetrisation-of-phosphonate-esters.pdf
|
60c74cecbdbb892669a398ce
|
10.26434/chemrxiv.12562355.v1
|
Photoinduced Aerobic Iodoarene-Catalyzed Spirocyclization of N-Oxy-Amides to N-Fused Spirolactams
|
Using the spiro-cyclization of amides as a model reaction we have demonstrated that aerobic iodoarene catalysis can be enabled by relying on a pyrylium photocatalyst under blue light irradiation. This unprecedented dual organocatalytic system allows the use of low catalytic loading of both catalysts under very mild operating conditions.<br />
|
Loïc Habert; Kevin Cariou
|
Organic Synthesis and Reactions; Photochemistry (Org.); Organocatalysis; Photocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cecbdbb892669a398ce/original/photoinduced-aerobic-iodoarene-catalyzed-spirocyclization-of-n-oxy-amides-to-n-fused-spirolactams.pdf
|
6787d7be81d2151a0245fc72
|
10.26434/chemrxiv-2025-9qsq1
|
Photocatalyst-Dependent Enantioselectivity in the Light-Driven Deracemization of Cyclic α-Aryl Ketones
|
We report a photoredox-enabled deracemization of cyclic α-aryl ketones that occurs with high stereoselectivity and yield and proceeds by mechanistically distinct proton transfer reactions. This reaction is jointly mediated by a visible-light photocatalyst and a chiral phosphate base co-catalyst under blue light irradiation. Notably, the extent of deracemization for this reaction exhibits an unexpected dependence on the identity of the photocatalyst and the concentration of a chiral base co-catalyst, wherein the extent of deracemization can be increased by employing photocatalysts with more positive ground-state reduction potentials, raising the concentration of the chiral base co-catalyst, or by a combination of these factors. This effect is attributed to two competing processes, back electron transfer and deprotonation, that consume the same reaction intermediate, and we propose a kinetic model that rationalizes this behavior. We also demonstrate that the redox properties of the photocatalyst also impact the stereoselectivity of the product-forming step, which is the dominant stereoselective step in this transformation. Together, these mechanistic insights facilitate a deeper understanding of the complexity of light-driven deracemization reactions involving reversible electron transfer and suggest approaches by which the stereoselectivity of these processes may be increased.
|
Justin Wang; Eris Villalona; Robert Knowles
|
Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6787d7be81d2151a0245fc72/original/photocatalyst-dependent-enantioselectivity-in-the-light-driven-deracemization-of-cyclic-aryl-ketones.pdf
|
60c74ead9abda22d05f8d6d1
|
10.26434/chemrxiv.12732689.v2
|
Bifunctional Small Molecules That Mediate the Degradation of Extracellular Proteins
|
<p>Targeted protein degradation (TPD) has emerged as a promising and exciting therapeutic strategy. The majority of existing TPD technologies rely on the ubiquitin-proteasome system, and are therefore limited to targeting intracellular proteins. To address this limitation, we developed a class of modularly designed, bifunctional synthetic molecules called <b>MoDE-A</b>s (<b>Mo</b>lecular <b>D</b>egraders of <b>E</b>xtracellular proteins through the <b>A</b>sialoglycoprotein receptor (ASGPR)), which are capable of mediating the degradation of extracellular proteins. MoDE-A molecules mediate the formation of a ternary complex between a target protein and the ASGPR, which is expressed primarily on hepatocytes. The target protein is then endocytosed and degraded by lysosomal proteases. We demonstrated the modularity of the MoDE-A technology by synthesizing bifunctional molecules that induce the degradation of both antibody and pro-inflammatory cytokine proteins. To our knowledge, these data represent the first experimental evidence that non-proteinogenic, synthetic molecules can be employed for the TPD of extracellular proteins both <i>in vitro</i> and <i>in vivo</i>. We believe that TPD mediated by the MoDE-A technology will have widespread applications for disease treatment.</p>
|
David Caianiello; Mengwen Zhang; Jason Ray; Jake Swartzel; Emily Branham; Egor Chirkin; Venkata Sabbasani; Angela Gong; David Mcdonald; Viswanathan Muthusamy; David Spiegel
|
Bioorganic Chemistry; Organic Synthesis and Reactions; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ead9abda22d05f8d6d1/original/bifunctional-small-molecules-that-mediate-the-degradation-of-extracellular-proteins.pdf
|
62065b470aec1a45ea19de19
|
10.26434/chemrxiv-2022-s5jq3
|
Prussian blue nanozymes with enhanced catalytic activity: size tuning and application in ELISA-like immunoassay
|
Prussian blue nanozymes possessing peroxidase-like activity gather significant attention as alternatives to natural enzymes in therapy, biosensing, and environmental remediation. Recently, prussian blue nanoparticles with enhanced catalytic activity prepared by reduction of FeCl3/K3[Fe(CN)6] mixture have been reported. These nanoparticles were denoted as ‘artificial peroxidase’ nanozymes. Our study provides insights into the process of synthesis of ‘artificial peroxidase’ nanozymes. We studied how the size of nanozymes and synthesis yield can be controlled via adjustment of the synthesis conditions. Based on these results, we developed a reproducible and scalable method for the preparation of ‘artificial peroxidase’ with tunable sizes allowing the obtaining of nanozymes with enhanced catalytic activity. ‘Artificial peroxidase’ nanozymes modified with gelatin shell and functionalized with affine molecules were applied as labels in colorimetric immunoassays of prostate-specific antigen and tetanus antibodies, enabling detection of these analytes in the range of clinically relevant concentrations. Protein coating provides excellent colloidal stability of nanozymes in physiological conditions and stability upon long-term storage.
|
Pavel Khramtsov; Maria Kropaneva; Artem Minin; Maria Bochkova; Valeria Timganova; Andrey Maximov; Alexey Puzik; Svetlana Zamorina; Mikhail Rayev
|
Catalysis; Analytical Chemistry; Nanoscience; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-02-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62065b470aec1a45ea19de19/original/prussian-blue-nanozymes-with-enhanced-catalytic-activity-size-tuning-and-application-in-elisa-like-immunoassay.pdf
|
634676df692d8d5786e37e87
|
10.26434/chemrxiv-2022-dlndt
|
Variety of steady and excited state interactions in BODIPY aggregates: photophysics in antisolvent systems and floating layers
|
Associative behavior of geometrically anisotropic meso-(4-octadecyloxy-phenyl)-boron-dipyrrin (BODIPY) studied spectroscopically in binary solvent mixtures and upon compression in Langmuir floating layers.
Different steady and excited state species were found upon monolayer compression and facilitated aggregation in water / acetonitrile systems. This discrepancy points to a big concern in possibility of commonly applied generalizations across different aggregating systems.
Broad range of decay fitting models were examined to reveal their benefits and pitfalls specific to examination of dye aggregates. Radiative constant gamma-distribution approach and free form fluorescence lifetime distribution with maximum entropy method (MEM) outperformed multiple common techniques for analysis of complex fluorescence decays. MEM could be recommended for analysis of systems where complicated lifetime distributions appear over time or upon external stimuli.
Findings and protocols could be utilized as tools in studies of steady and excited-state photophysics of BODIPY aggregates.
|
Sergey Usoltsev; Oleg Raitman; Alexander Shokurov; Yuriy Marfin
|
Physical Chemistry; Analytical Chemistry; Self-Assembly; Solution Chemistry; Spectroscopy (Physical Chem.)
|
CC BY 4.0
|
CHEMRXIV
|
2022-10-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634676df692d8d5786e37e87/original/variety-of-steady-and-excited-state-interactions-in-bodipy-aggregates-photophysics-in-antisolvent-systems-and-floating-layers.pdf
|
66421dda91aefa6ce1dd801e
|
10.26434/chemrxiv-2024-tx6bb
|
Non-Conventional Bulk Heterojunction Nanoparticle Photocatalysts for Sacrificial Hydrogen Evolution from Water
|
Photocatalyst systems combining donor polymers with acceptor molecules have shown the highest evolution rates for sacrificial hydrogen production from water for organic systems to date. Here, new donor molecules have been designed and synthesised taking inspiration from the structure-performance relationships which have been established in the development of non-fullerene acceptors. While a conventional bulk heterojunction (BHJ) pairing consists of a donor polymer and acceptor small molecules, here we have successfully reversed this approach by using our new molecules in combination with a n-type conjugated polymer to produce non-conventional BHJ nanoparticles and applied these blends to the sacrificial hydrogen evolution from water. The best performing heterojunction displayed high activity for sacrificial hydrogen production from water with a hydrogen evolution rate of 22,321 µmol h−1 g−1 which compares well with the state-of-the-art for conventional BHJ photocatalyst systems.
|
Jai-Ram Mistry; Ewan McQueen; Fabio Nudelman; Reiner Sebastian Sprick; Iain A. Wright
|
Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Heterogeneous Catalysis; Photocatalysis; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66421dda91aefa6ce1dd801e/original/non-conventional-bulk-heterojunction-nanoparticle-photocatalysts-for-sacrificial-hydrogen-evolution-from-water.pdf
|
67aac6c0fa469535b9ce4790
|
10.26434/chemrxiv-2025-v2650
|
Stereoselective 1,3-Cyclotelomerization of Butadiene with Dienophiles under Nickel Catalysis
|
The discovery of new chemoselectivity with readily accessible chemicals is important to expand the reaction space for modern chemistry. For dienes and dienophiles, most people will naturally use them to carry out the classic Diels-Alder reaction to construct six-membered cyclic compounds. Here, we demonstrated a chemoselective coupling of butadiene with dienophiles through a stereoselective 1,3-cyclotelomerization. By utilizing robust Ni/IPr catalysis, valuable bicyclic products were created with high regio- and chemoselectivities under mild conditions. Asymmetric cyclotelomerization enabled by chiral NHC ligand was also performed, generating enantioenriched bicyclic compounds. Mechanistic studies reveal that the reaction might start with oxidative cyclometallation between two molecules of 1,3-diene and Ni(0) species, which then undergoes [3+2]-cycloaddition via an electron transfer process. The products can undergo a variety of intricate transformations, which emphasizes the potential applications of this strategy. It is hoped that the discovery of this protocol will further inspire people to rethink the classic organic reactions.
|
Ying Li; Li-Ming Zhang; Xue-Ting Li; Heng Liu; Ting-Ting Song; Ding-Wei Ji; Qing-An Chen
|
Organic Chemistry; Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-02-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67aac6c0fa469535b9ce4790/original/stereoselective-1-3-cyclotelomerization-of-butadiene-with-dienophiles-under-nickel-catalysis.pdf
|
674228f55a82cea2fa90b238
|
10.26434/chemrxiv-2024-zghgx
|
The Asymmetric Olefinative Conjugate Addition
|
The asymmetric olefinative conjugate addition (AOCA) is presented, which involves an enantioselective conjugate addition to an olefin activated by a traceless electron-withdrawing group, which then allows for an olefinative quench with a carbonyl com-pound. This approach is demonstrated by the Cu-catalyzed enantioselective conjugate addition of organoboron and organozinc reagents to an alkenyl phosphonate, followed by quenching with a carbonyl compound to yield the corresponding alkene via Horner-Wadsworth-Emmons olefination. This one-pot sequence efficiently produces chiral internal olefins, addressing a common limitation of Cu-catalyzed enantioselective allylic substitutions, which typically only generate terminal alkenes. The versatility of this strategy is showcased through the synthesis of various structurally diverse products with high yields, complete diastereocon-trol, and enantiomeric ratios of up to 98:2.
|
Francesco Vaghi; Piero Soppelsa; Klaus Wurst; Licini Giulia; Manuel Orlandi
|
Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674228f55a82cea2fa90b238/original/the-asymmetric-olefinative-conjugate-addition.pdf
|
60c74271702a9b077818a48e
|
10.26434/chemrxiv.8298641.v1
|
MicroED Structure of Hexagonal Ice Ih
|
The structure of ice Ih is solved from a single nanocrystal to a resolution of 0.53Å using the cryoEM method microcrystal electron diffraction (MicroED). Data were collected at just above liquid nitrogen temperatures (~80K) in ultra-high vacuum (~8 x 10-7 Pa) using a total exposure of less than 1e- Å-2. <br />
|
Michael
W. Martynowycz; Tamir Gonen
|
Nanostructured Materials - Nanoscience; Structure
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-06-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74271702a9b077818a48e/original/micro-ed-structure-of-hexagonal-ice-ih.pdf
|
60c73e58842e6529f2db18ff
|
10.26434/chemrxiv.6946058.v1
|
Cyclic Hypervalent Iodine Reagents for Azidation: Safer Reagents and Photoredox Catalyzed Ring Expansion
|
Azides are building blocks of increasing importance in
synthetic chemistry, chemical biology and materials science. Azidobenziodoxolone
(ABX, Zhdankin reagent) is a valuable azide source, but its safety profile has
not been thoroughly established. Herein, we report a safety study of ABX, which
shows its highly hazardous nature. We further introduce and study two
derivatives, <i>t</i>Bu-ABX and ABZ
(azidobenziodazolone). ABZ displayed a similar reactivity but a better safety
profile than ABX, and could be used in established photoredox- and
metal-mediated azidation processes, as well as in a new ring-expansion of
silylated cyclobutanols to give azidated cyclopentanones.
|
Sebastien Alazet; Johannes preindl; raphael simonet davin; Stefano Nicolai; Annik Nanchen; Thierry Meyer; Jerome Waser
|
Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.); Photocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e58842e6529f2db18ff/original/cyclic-hypervalent-iodine-reagents-for-azidation-safer-reagents-and-photoredox-catalyzed-ring-expansion.pdf
|
60c73fa2567dfe004bec3a87
|
10.26434/chemrxiv.7466633.v1
|
Kinetic Control of Interpenetration in Fe-Biphenyl-4,4′-dicarboxylate MOFs by Coordination and Oxidation Modulation
|
Phase control in the self-assembly of metal-organic frameworks (MOFs) – materials wherein organic ligands connect metal ions or clusters into network solids with potential porosity – is often a case of trial and error. Judicious control over a number of synthetic variables is required to select for the desired topology and control features such as interpenetration and defectivity, which have significant impact on physical properties and application. Herein, we present a comprehensive investigation of self-assembly in the Fe-biphenyl-4,4'-dicarboxylate system, demonstrating that coordination modulation, the addition of competing ligands into solvothermal syntheses, can reliably tune between the kinetic product, non-interpenetrated MIL-88D(Fe), and the thermodynamic product, two-fold interpenetrated MIL-126(Fe). DFT simulations reveal that correlated disorder of the terminal anions on the metal clusters in the interpentrated phase results in H-bonding between adjacent nets and is the thermodynamic driving force for its formation. Coordination modulation slows self-assembly and therefore selects the thermodynamic product MIL-126(Fe), while offering fine control over defectivity, inducing mesoporosity, but electron microscopy shows the MIL-88D(Fe) phase persists in many samples despite not being evident in diffraction experiments, suggesting its presence accounts for the lower than predicted surface areas reported for samples to date. Interpenetration control is also demonstrated by utilizing the 2,2'-bipyridine-5,5'-dicarboxylate linker; DFT simulations show that it is energetically prohibitive for it to adopt the twisted conformation required to form the interpenetrated phase, and are confirmed by experimental data, although multiple alternative phases are identified due to additional coordination of the Fe cations to the N-donors of the ligand. Finally, we introduce oxidation modulation – the concept of using metal precursors in a different oxidation state to that found in the final MOF – as a further protocol to kinetically control self-assembly. Combining coordination and oxidation modulation allows the synthesis of pristine MIL-126(Fe) with BET surface areas close to the predicted maximum capacity for the first time, suggesting that combining the two may be a powerful methodology for the controlled self-assembly of high-valent MOFs.<br /><br />
|
Dominic Bara; Claire Wilson; Max Mörtel; Marat M. Khusniyarov; ben slater; Stephen Sproules; Ross Forgan
|
Hybrid Organic-Inorganic Materials; Coordination Chemistry (Inorg.); Kinetics and Mechanism - Inorganic Reactions; Solid State Chemistry; Supramolecular Chemistry (Inorg.); Self-Assembly
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-12-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fa2567dfe004bec3a87/original/kinetic-control-of-interpenetration-in-fe-biphenyl-4-4-dicarboxylate-mo-fs-by-coordination-and-oxidation-modulation.pdf
|
65a4e660e9ebbb4db930fa47
|
10.26434/chemrxiv-2024-r7hxq
|
Direct Observation of Enamine-Derived Radicals with Time-Resolved Electron Paramagnetic Resonance
|
This study presents the direct observation of α-imino radical intermediates involved in the photoredox catalytic activation of enamines using the ultrawide single sideband phase-sensitive detection time-resolved electron paramagnetic reso-nance (U-PSD TREPR) technique. Enamines have been exten-sively used in singly occupied molecular orbital (SOMO) catal-ysis. The redox properties of enamines allow for facile oxida-tion, forming α-imino radical species that participate in vari-ous coupling reactions. Despite the synthetic value of these transformations, direct observation of the key radical inter-mediates has been limited. The U-PSD TREPR technique ena-bled direct in-situ observation of transient enamine radical cation and α-imino radical intermediates for the first time. Spectroscopic characterization and kinetic analysis provided insights into the structure and reactivity of these intermedi-ates. The results demonstrated the involvement of enamine radical cations as the key intermediates in the photoredox transformations by primary aminocatalysis.
|
Shixue Zhang; Liang Cheng; Jian-Qing Qi; Zongbin Jia; Long Zhang; Lei Jiao; Xingwei Guo; Sanzhong Luo
|
Organic Chemistry; Catalysis; Physical Organic Chemistry; Organocatalysis; Photocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a4e660e9ebbb4db930fa47/original/direct-observation-of-enamine-derived-radicals-with-time-resolved-electron-paramagnetic-resonance.pdf
|
67c71bc1fa469535b9eb27f1
|
10.26434/chemrxiv-2025-7b7rl
|
Stable, bioactive hydrogel coating on silicone surfaces for non-invasive decontamination via photochemical treatment
|
Polydimethylsiloxane (PDMS) is widely used in biomedical applications due to its biocompatibility, chemical stability, flexibility, and resistance to degradation in physiological environments. However, its intrinsic inertness limits further (bio)functionalization, and its hydrophobic recovery compromises the longevity of conventional surface modifications. To address these challenges, we developed a nanoprecipitation method for the straightforward colloidal deposition, covalent thermal crosslinking, and surface anchoring of a chemically tunable, biocompatible polyacrylamide with reactive hydroxyl groups, enabling further surface modifications. This polymer incorporates ~6% bioinspired catechol units, introduced via an elegant one-pot Kabachnik-Fields reaction, to facilitate thermally induced network formation and enhance adhesion to plasma-activated PDMS. The resulting uniform coatings exhibited tunable dry layer thicknesses up to 44 ± 7 nm and effectively suppressed PDMS chain rearrangement even after steam autoclaving, ensuring long-term stability in aqueous and ambient environments for at least 60 days. The bioactive post-modification potential was demonstrated in a proof-of-concept study by immobilizing the photosensitizer rose bengal at surface concentrations of 20 or 40 µg cm⁻². The coating exhibited antimicrobial activity against S. aureus, achieving a 4-log reduction (99.99%) in colony-forming units after 30 minutes of irradiation at 554 nm (342 J cm⁻²), even when bacteria were suspended in liquid, without direct surface contact. In contrast, antimicrobial activity against E. coli was only observed when the liquid volume was minimized, bringing the motile bacteria into close contact with the surface. This work established a straightforward and versatile strategy for the stable and bioactive functionalization of PDMS surfaces for application in non-invasive surface decontamination.
|
Romina Berger; Alina Rahtz; Alexander Schweigerdt; Andrea Cosimi; Daniel Stöbener; Wibke Dempwolf; Henning Menzel; Sonja Johannsmeier; Marie Weinhart
|
Biological and Medicinal Chemistry; Materials Science; Polymer Science; Coating Materials; Photosensitizers; Hydrogels
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c71bc1fa469535b9eb27f1/original/stable-bioactive-hydrogel-coating-on-silicone-surfaces-for-non-invasive-decontamination-via-photochemical-treatment.pdf
|
630d11a5521cb784ceab1436
|
10.26434/chemrxiv-2022-8r90r-v3
|
Boronated Cyanometallates
|
Thirteen boronated cyanometallates [M(CN-BR3)6]3/4/5– (M = Cr, Mn, Fe, Ru, Os; BR3 = BPh3, B(2,4,6,-F3C6H2)3, B(C6F5)3) and one boratonitrile [Cr(NC-BPh3)6]3– have been characterized by X-ray crystallography and spectroscopy [UV-vis-NIR, NMR, IR, spectroelectrochemistry, and magnetic circular dichroism (MCD)]; CASSCF+NEVPT2 methods were employed in calculations of electronic structures. For (t2g)5 electronic configurations, the lowest energy ligand-to-metal charge transfer (LMCT) absorptions and MCD C-terms in the spectra of boronated species have been assigned to transitions from cyanide σ+π + B-C borane σ orbitals. CASSCF+NEVPT2 cal-culations including t1u and t2u orbitals reproduced t1u/t2u → t2g excitation energies. All [M(CN-BR3)6]3/4− complexes exhibited highly electrochemically reversible redox couples. Notably, the formal potentials of all five [M(CN-B(C6F5)3)6]3− anions scale with LMCT energies, and Mn(I) and Cr(II) compounds, (K(18-crown-6))5[Mn(CN-B(C6F5)3)6] and (TBA)4[Cr(CN-B(C6F5)3)6], are surprisingly stable. Continuous wave and pulsed electron paramagnetic resonance (hyperfine sublevel correlation) spectra were collected for all Cr(III) complexes; as expected, 14N hyperfine splittings are greater for (Ph4As)3[Cr(NC-BPh3)6] than for (Ph4As)3[Cr(CN-BPh3)6].
|
Brendon McNicholas; Cherish Nie; Anex Jose; Paul Oyala; Michael Takase; Larry Henling; Alexandra Barth; Alessio Amaolo; Ryan Hadt; Edward Solomon; Jay Winkler; Harry Gray; Emmanuelle Despagnet-Ayoub
|
Inorganic Chemistry; Electrochemistry; Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-08-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630d11a5521cb784ceab1436/original/boronated-cyanometallates.pdf
|
61dc144df51b22a71c105f09
|
10.26434/chemrxiv-2021-875wn-v4
|
A method for determining stoichiometric coefficients using minors of a matrix
|
Spinel materials often have complex structures and as a result, balancing of reactions with these compounds by traditional methods become very time consuming. A method to calculate the stoichiometric coefficients for chemical reactions using first a modified matrix-inverse method and then an optimised method is proposed. Both methods are explored using linear algebra and the result demonstrated using a typical chromite reduction reaction.
|
Rainier Lombaard
|
Inorganic Chemistry; Chemical Education; Chemical Education - General; Reaction (Inorg.)
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-01-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61dc144df51b22a71c105f09/original/a-method-for-determining-stoichiometric-coefficients-using-minors-of-a-matrix.pdf
|
60c73f4d0f50db672b395758
|
10.26434/chemrxiv.7291205.v1
|
Evolving and Nano Data Enabled Machine Intelligence for Chemical Reaction Optimization
|
<p>Optimizing reaction conditions is an essential routine in synthetic chemistry. However, selecting appropriate experiments remains tightly connected to expert chemistry knowledge. Here, to streamline the reaction yield optimization process and disconnect it from chemical intuition, we developed an adaptive machine intelligence to navigate multidimensional reaction conditions’ spaces. Our approach (LabMate.AI) employs an interpretable algorithm and requires only <0.05% of all search space as input data. LabMate.AI optimizes many reaction parameters simultaneously, and uses minimal computational resources and time. We demonstrate how LabMate.AI can identify optimal conditions for a Ugi and a C–N cross-coupling reaction in a more efficient and faster manner than human experts, while affording reactivity insights. Our approach formalizes chemical intuition, and acquires expert chemistry knowledge autonomously, thereby providing an innovative framework towards informed and automated experiment selection. The results support machine learning for hastening experimental design, democratizing synthetic chemistry, and freeing chemists for non-routine tasks.</p>
|
Daniel Reker; Gonçalo Bernardes; Tiago Rodrigues
|
Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-11-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f4d0f50db672b395758/original/evolving-and-nano-data-enabled-machine-intelligence-for-chemical-reaction-optimization.pdf
|
60c74716bdbb8953c3a38d21
|
10.26434/chemrxiv.11320130.v2
|
A Thorough Theoretical Exploration of Intriguing Characteristics of Cyclo[18]carbon: Geometry, Bonding Nature, Aromaticity, Weak Interaction, Reactivity, Excited States, Vibrations, Molecular Dynamics and Various Molecular Properties
|
Although cyclo[18]carbon has been theoretically and experimentally investigated since long time ago, only very recently it was prepared and directly observed by means of STM/AFM in condensed phase (Kaiser et al., <i>Science</i>, <b>365</b>, 1299 (2019)). The unique ring structure and dual 18-center π delocalization feature bring a variety of unusual characteristics and properties to the cyclo[18]carbon, which are quite worth to be explored. In this work, we present an extremely comprehensive and detailed investigation on almost all aspects of the cyclo[18]carbon, including (1) Geometric characteristics (2) Bonding nature (3) Electron delocalization and aromaticity (4) Intermolecular interaction (5) Reactivity (6) Electronic excitation and UV/Vis spectrum (7) Molecular vibration and IR/Raman spectrum (8) Molecular dynamics (9) Response to external field (10) Electron ionization, affinity and accompanied process (11) Various molecular properties. We believe that our full characterization of the cyclo[18]carbon will greatly deepen researchers' understanding of this system, and thereby help them to utilize it in practice and design its various valuable derivatives.
|
Tian Lu; Qinxue Chen; Zeyu Liu
|
Optical Materials; Bonding; Computational Chemistry and Modeling; Theory - Computational; Clusters; Optics; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Structure
|
CC BY NC ND 4.0
|
CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74716bdbb8953c3a38d21/original/a-thorough-theoretical-exploration-of-intriguing-characteristics-of-cyclo-18-carbon-geometry-bonding-nature-aromaticity-weak-interaction-reactivity-excited-states-vibrations-molecular-dynamics-and-various-molecular-properties.pdf
|
622b2f0b0350ddd672d43051
|
10.26434/chemrxiv-2022-mhz5t
|
Photochemical approach for multiplexed biofunctionalisation of GaAs
|
The optoelectronic properties of gallium arsenide
(GaAs) hold great promise in biosensing applications,
currently being held back by the lack of methodologies
reporting the functionalisation of this material
with multiple biomolecules. Here, we exploit the use
of a photoreactive crosslinker - a diazirine derivative -
for spatially selective covalent immobilisation of multiple
bioreceptors on the GaAs surface. As a proof of
principle we show the immobilisation of two proteins:
neutravidin and endosulfi ne alpha protein. X-ray photoelectron spectroscopy results showed the presence of the biomolecules on the GaAs regions selectively exposed to UV light. The approach presented here is applicable to
the covalent attachment of other biomolecules, paving
the way for using GaAs as a platform for multiplexed
biosensing.
|
Bárbara Santos Gomes; Francesco Masia
|
Biological and Medicinal Chemistry; Materials Science; Nanoscience; Thin Films; Nanostructured Materials - Nanoscience; Bioengineering and Biotechnology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622b2f0b0350ddd672d43051/original/photochemical-approach-for-multiplexed-biofunctionalisation-of-ga-as.pdf
|
6798d3f46dde43c908b5df77
|
10.26434/chemrxiv-2025-7h5k4
|
Multiple Atropo Selectivity by κ2-N,O-Oxazoline Urea Ligands in Cobaltaelectro-Catalyzed C–H Activations: Decoding Selectivity with Data Science Integration
|
Enantioselective catalysis is one of the most prominent strategies in organic synthesis to access chiral bioactive compounds and advanced organic materials. Particularly the development of chiral ligands has significantly advanced the efficiency and selectivity of transition metal-catalyzed enantioselective transformations. Over recent decades, numerous chiral ligand classes with distinct geometrical and electronic properties were established. Despite these advances, the demand for novel, tunable, and highly effective chiral ligands persist, driven by the need for structurally diverse chiral molecules and the pursuit of greener, more sustainable catalytic processes. Herein, we introduce a novel class of chiral oxazoline ureas and demonstrate their potential as k2-N,O-preligands in enantioselective transition metal catalysis. The chiral oxazoline urea ligands were featurized and compared with amide and enol derivatives using the physical organic descriptors. A multivariate linear regression model was constructed to quantitatively describe the effect of the quinoline fragment from the substrate and the ligand on enantioselectivity. Moreover, the model was effectively applied to atropo-enantioselective cobaltaelectro-catalyzed C–H annulations of 1-alkynyl indoles.
|
Philipp Boos; Neeraj Kumar Pandit; Suman Dana; Tristan von Münchow; Airu Hashidoko; Laura Haberstock; Regine Herbst-Irmer; Dietmar Stalke; Lutz Ackermann
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Theoretical and Computational Chemistry; Organic Chemistry; Catalysis
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CC BY 4.0
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CHEMRXIV
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2025-01-30
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6798d3f46dde43c908b5df77/original/multiple-atropo-selectivity-by-2-n-o-oxazoline-urea-ligands-in-cobaltaelectro-catalyzed-c-h-activations-decoding-selectivity-with-data-science-integration.pdf
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67922fef6dde43c908fb01e8
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10.26434/chemrxiv-2025-4fg1t
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Evidence of a Three-State Mechanism in DNA Hairpins Folding
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DNA hairpins are a model system for biomolecule folding as well as key structures in biology and nanotechnology. However, limitations in traditional solution-phase spectroscopy shorten the window of observable kinetics and cannot account for stat-ic heterogeneity. Here, we show that the application of 2-Dimenstional Fluorescence Lifetime Correlation Spectroscopy (2DFLCS) to a solution-phase molecule trapped in an anti-Brownian Electrokinetic (ABEL) trap bypasses those limitations, enabling kinetic analysis of the dynamics of single solution-phase molecules on a broad range of timescales down to micro-seconds. The analysis unambiguously shows that DNA hairpin folding proceeds via a three-state system, where hairpins fold initially on the scale of 10s-100s of microseconds from a random coil to a partially closed intermediate, and then form a sta-ble fully closed state.
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Brendan Cullinane; Kunihiko Ishii; Simi Kaur; Tahei Tahara; Randall Goldsmith
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Physical Chemistry; Biological and Medicinal Chemistry; Nanoscience; Nanofluidics; Biophysics; Chemical Kinetics
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CC BY NC ND 4.0
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CHEMRXIV
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2025-01-24
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67922fef6dde43c908fb01e8/original/evidence-of-a-three-state-mechanism-in-dna-hairpins-folding.pdf
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6659ae7321291e5d1dbc8a48
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10.26434/chemrxiv-2024-1tpfx
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Chemical Exposomics in Human Plasma by Lipid Removal and Large Volume Injection Gas Chromatography High-Resolution Mass Spectrometry
|
For comprehensive chemical exposomics in blood, analytical workflows are evolving through advances in sample preparation and instrumental methods. We hypothesized that gas chromatography high-resolution mass spectrometry (GC-HRMS) workflows could be enhanced by minimizing lipid co-extractives, thereby enabling larger injection volumes and lower matrix interference for improved sensitivity and molecular discovery. A simple protocol was developed for small plasma volumes (100-200 µL) by using isohexane (H) to extract supernatants of acetonitrile-plasma (A-P). The HA-P method was quantitative for a wide range of hydrophobic multiclass target analytes (i.e. log Kow >3.0), and the extracts were free of major lipids, thereby enabling robust large-volume injections (LVI; 25 µL) in long sequences to a GC-Orbitrap HRMS. Without lipid removal, LVI was counter-productive because method sensitivity suffered from the abundant matrix signal, resulting in low ion injection times to the Orbitrap. The median method quantification limit was 0.08 ng/mL (range 0.005–4.83 ng/mL), and good accuracy was shown for a certified reference serum. Applying the method to plasma from a Swedish cohort (n=32; 100 µL), 51 of 103 target analytes were detected. Simultaneous nontarget analysis resulted in 112 structural annotations (12.8% annotation rate), and Level 1 identification was achieved for 7 of 8 substances in follow-up confirmations. The HA-P method is potentially scalable for application in cohort studies and is also compatible with many liquid-chromatography-based exposomics workflows.
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Hongyu Xie; Kalliroi Sdougkou; Stefano Papazian; Bénilde Bonnefille; Ingvar Bergdahl; Panu Rantakokko; Jonathan Martin
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Earth, Space, and Environmental Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2024-06-03
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6659ae7321291e5d1dbc8a48/original/chemical-exposomics-in-human-plasma-by-lipid-removal-and-large-volume-injection-gas-chromatography-high-resolution-mass-spectrometry.pdf
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64d8931169bfb8925adae946
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10.26434/chemrxiv-2023-g5w6g
|
Alternative Concept of One-Dimensional Superconductivity – Key Role of Defects Revealed by Quantum Chemical Calculations of Lead Apatite
|
Doped lead apatite has been recently reported to feature superconductivity at room temperature and ambient pressure, which may have huge impact on the progress of the humanity in general. The first principle calculations, aiming at understanding the reasons for such behavior, suggest that reduced form of undoped and copper-doped lead apatite contain one dimensional channels, which are free of ions, but with electrostatic potential inside providing conditions for unimpeded electron mobility, potentially leading to superconductivity. Key aspect is that channels are surrounded by lead cations, which generate the necessary electrostatic field but due to their high atomic mass have reduced mobility and do not block the channels even at ambient temperature. Our observations on the modeled structures allowed us to present an alternative concept for features, giving rise of the superconductivity based on chemical understanding of the structure and frontier orbital of the material.
|
Georgi Vayssilov; Petko Petkov; Hristiyan Aleksandrov
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Theoretical and Computational Chemistry; Materials Chemistry
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CC BY NC 4.0
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CHEMRXIV
|
2023-08-14
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d8931169bfb8925adae946/original/alternative-concept-of-one-dimensional-superconductivity-key-role-of-defects-revealed-by-quantum-chemical-calculations-of-lead-apatite.pdf
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663ccede21291e5d1dd986a7
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10.26434/chemrxiv-2024-vdzzq
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Iron-Catalyzed Late-Stage Radical C–H Alkylamination of Phenol-Containing Drugs and Biomolecules
|
A modular site-selective iron-catalyzed radical amination of a number of phenol-containing biomolecules such as tyrosine-containing peptides, estrogens and other phenol-based pharmaceuticals has been developed. The method features the use of the cost-efficient combination of FeBr3 as catalyst along with triflic acid as Brønsted acid, thereby enabling the predictable appendance of morpholine and related heterocycles at the ortho C–H bond of phenols in a late-stage fashion. This alkylamination technique leverages the electron-rich nature of phenols to undergo oxidation to the corresponding phenoxyl radicals and further coupling with in situ formed electrophilic aminium radical cation species.
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Paula Andrade-Sampedro; Arkaitz Correa
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Organic Chemistry; Organic Synthesis and Reactions
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-05-10
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663ccede21291e5d1dd986a7/original/iron-catalyzed-late-stage-radical-c-h-alkylamination-of-phenol-containing-drugs-and-biomolecules.pdf
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62d6c8b2a7d17e7a5a62c38b
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10.26434/chemrxiv-2022-5bcq2
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Functional Group Pair Distance based Descriptor for Isomerization in Porous Molecular Framework Materials
|
Molecular Framework Materials (MFMs), including Metal Organic Frameworks (MOFs), Covalent Organic Frameworks (COFs) and their discrete equivalents, Metal Organic Polyhedra (MOPs) and Porous Organic Cages (POCs) are porous materials, composed of molecular fragments, bound in one of many topologies. MFMs have a wide variety of potential and realised adsorption applications. In order to design an ideal framework material for a particular application, the composition of molecular fragments is not the only factor, but the arrangement of the those fragments is also important, especially when the fragments (molecular building blocks) are chemically functionalised and lack symmetry. As has been observed in Metal Organic Frameworks, the flexibility and absorption properties may differ greatly when altering the orientation of the building units or changing the position of functional groups. However, although the position of functional group has a great influence on a targeted property, studies on functional group arrangements have only been performed on a small set of MOF structures.
In this contribution, we develop a fingerprint/descriptor for optimising functionalised molecular framework structures using machine learning. We begin from the perspective of a molecular framework structure described as a collection of discrete pore shapes. To describe the chemical environment of the pore, we derive a fingerprint based on the occurrence of pairwise distances between functional groups in each pore. We present the possibilities of functional group arrangements in the 14 most common pore shapes, created by ditopic (2-connected) linkers are presented. The method to enumerate and identify possible isomers is explained. Finally the fingerprints of the 14 pore shapes are presented.
|
Maryam Nurhuda; Yusuf Hafidh; Carole C. Perry; Matthew A. Addicoat
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Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry; Materials Chemistry
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CC BY 4.0
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CHEMRXIV
|
2022-07-20
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d6c8b2a7d17e7a5a62c38b/original/functional-group-pair-distance-based-descriptor-for-isomerization-in-porous-molecular-framework-materials.pdf
|
622bd10f10d1437e00cc9803
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10.26434/chemrxiv-2022-0m66l
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Temperature Extrapolation of Molecular Dynamics Simulations of Complex Chemistry to Microsecond Timescales using Kinetic Models: Applications to Hydrocarbon Pyrolysis
|
Molecular Dynamics (MD) simulations are a key tool to understand the mechanism of complex chemical system and observe their outcomes in different conditions. However, such simulations are computationally expensive, which limits their timescales to the nanoseconds. This limitation is inconsequential at high temperatures, where equilibrium is reached quickly, but it is limiting at low temperatures as the complex system cannot be equilibrated within the timescale of MD simulations. In this article we develop a method to construct kinetic models of hydrocarbon pyrolysis using the information from the high-temperature high-reactivity regime. We then extrapolate this model to low temperatures, which allows for microsecond-long simulations to be performed. It is demonstrated that this approach lead to the accurate prediction of the evolution of small molecules, as well as the size and composition of long carbon chains for a wide range of temperatures and compositions. The temperature range for which the extrapolation is robust can easily be improved by adding more simulations to the training data. When compared to experimental results our kinetic model leads to similar compositional trends while allowing for more detailed kinetic and mechanistic insights.
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Vincent Dufour-Decieux; Brandi Ransom; Rodrigo Freitas; Jose Blanchet; Evan Reed
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Theoretical and Computational Chemistry
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CC BY 4.0
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CHEMRXIV
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2022-03-15
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622bd10f10d1437e00cc9803/original/temperature-extrapolation-of-molecular-dynamics-simulations-of-complex-chemistry-to-microsecond-timescales-using-kinetic-models-applications-to-hydrocarbon-pyrolysis.pdf
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6643ecc191aefa6ce1059033
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10.26434/chemrxiv-2023-kjgxz-v4
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Exogenous Photocatalyst-Free Aryl Radical Generation from Diaryliodonium Salts and use in Metal-Catalyzed C–H Arylation
|
We demonstrate 1) that halogen bonding is not critical for enabling light-driven radical generation from diaryliodonium salts and 2) radi-cals generated by this route can be captured by transition-metals for C–H arylation reactions. These results are the first step toward devel-oping new metal-catalyzed aryl radical couplings without exogenous photocatalysts.
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Jonathan Galicia; Nicholas McDonald; Christopher Bennett; Jiajun He; Mark Glossbrenner; Erik Romero
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Organic Chemistry; Photochemistry (Org.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-05-15
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6643ecc191aefa6ce1059033/original/exogenous-photocatalyst-free-aryl-radical-generation-from-diaryliodonium-salts-and-use-in-metal-catalyzed-c-h-arylation.pdf
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60ee1aabaf9cdb0074dba2f8
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10.26434/chemrxiv-2021-mkt6v
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Electronic structure of NdO via slow photoelectron velocity-map imaging spectroscopy of NdO¯
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Electronically excited NdO is a possible product of the chemistry associated with the release of Nd into the ionosphere, and emission from these states may contribute to the observations following such experiments. To better characterize the energetics and spectroscopy of NdO, we report a combined experimental and theoretical study using slow photoelectron velocity-map imaging spectroscopy of cryogenically cooled NdO¯ anions (cryo-SEVI) supplemented by wavefunction-based quantum-chemical calculations. Using cryo-SEVI, we measure the electron affinity of NdO to be 1.0091(7) eV and resolve numerous transitions to low-lying electronic and vibrational states of NdO that are assigned with the aid of the electronic structure calculations. Additionally, temperature-dependent data suggests contributions from the (2)4.5 state of NdO¯ residing 2350 cm-1 above the ground anion state. Photodetachment to higher-lying excited states of NdO is also reported, which may help clarify observations from prior release experiments.
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Mark Babin; Martin DeWitt; Jessalyn DeVine; David McDonald II; Shuan Ard; Nicholas Shuman; Albert Viggiano; Lan Cheng; Daniel Neumark
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Physical Chemistry; Spectroscopy (Physical Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-07-14
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60ee1aabaf9cdb0074dba2f8/original/electronic-structure-of-nd-o-via-slow-photoelectron-velocity-map-imaging-spectroscopy-of-nd-o.pdf
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60c7462fbb8c1a7cd63da829
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10.26434/chemrxiv.11119883.v1
|
Models for Understanding Divergent Reactivity in Lewis Acid-Catalyzed Transformations of Carbonyls and Olefins
|
<div>Carbonyl-ene, Prins and carbonyl-olefin metathesis reactions represent powerful strategies for carbon-carbon bond formation relying on Lewis acid catalysts. Although common Lewis acids are able to provide efficient activation, the reactions often proceed with low regio-, or chemoselectivity while high selectivity frequently requires the use of well-designed metal-ligand complexes. Here we demonstrate that simple Lewis acids including Me<sub>2</sub>AlCl, FeCl<sub>3</sub>, and SnCl<sub>4</sub> can show remarkable selectivity in dif-ferentiating between distinct transformations of carbonyl and olefin functional groups resulting in either carbonyl-ene or carbonyl-olefin metathesis products. Specifically, we report the development of predictive multivariate linear regression models that rely on kinetic and thermodynamic information obtained in DFT calculations to gain important insights into the complex potential energy surfaces (PES) of these competing reaction paths. The presented results further our understanding of Lewis acid reactivity and suggest that even simple Lewis acids have the potential to function as highly selective catalysts.</div>
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Marc R. Becker; Jolene P. Reid; Katie Rykaczewski; Corinna Schindler
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Acid Catalysis; Homogeneous Catalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2019-11-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7462fbb8c1a7cd63da829/original/models-for-understanding-divergent-reactivity-in-lewis-acid-catalyzed-transformations-of-carbonyls-and-olefins.pdf
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6555311e2c3c11ed71781055
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10.26434/chemrxiv-2023-mp1r9-v2
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71Ga NMR Signatures of Lewis and Brønsted Acid Sites in Gallium Silicates Evidenced and Deciphered upon Interaction with Probe Molecules
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Determining the structure of Ga surface sites in Ga-based materials, used in catalysis, is critical for understanding their reactivity. However, obtaining molecular-level insights into their structure remains challenging. Here, using solid state Nuclear Magnetic Resonance (NMR) spectroscopy (71Ga, 31P and 15N), two different families of acid sites are identified in a gallosilicate material (Ga@SiO2), prepared via Surface Organometallic Chemistry and used as an efficient heterogeneous propane dehydrogenation catalysts or catalyst support. Through probe molecule studies using pyridine (Py) and triphenylphosphine oxide (TPPO), coupled with the synthesis of well-defined molecular analogs of surface sites and computational modelling on related cluster models using density functional theory, the Ga NMR signatures and the molecular structure of two types of sites, namely Brønsted acid sites and Lewis acid sites, are identified. These tetra-coordinate sites can be described as Ga sites bound to three anionic siloxide surface ligands along with a silanol or a siloxane bridge, respectively, each associated with specific NMR parameters, which change markedly upon interaction with Py or TPPO, thereby enabling their structural characterization.
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Scott Docherty; Laura Völker; Alexander Yakimov; René Verel; Christophe Copéret
|
Physical Chemistry; Inorganic Chemistry; Catalysis; Spectroscopy (Inorg.); Surface
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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/6555311e2c3c11ed71781055/original/71ga-nmr-signatures-of-lewis-and-br-nsted-acid-sites-in-gallium-silicates-evidenced-and-deciphered-upon-interaction-with-probe-molecules.pdf
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675b8a56085116a1333a1e53
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10.26434/chemrxiv-2024-w75kq
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KatG protein analysis: Misfolding and drug resistance
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Tuberculosis is caused by Mycobacterium tuberculosis and is commonly treated with antibiotics. Recently, drug resistance to isoniazid, the most common drug utilized to treat tuberculosis, has been becoming more prevalent. Hence, this study aimed to analyze factors affecting isoniazid resistance using a bioinformatics pipeline. The KatG gene sequence was obtained from NCBI and variants from UniProt, which then underwent domain analysis, 2D and 3D structure analysis, molecular docking, and molecular dynamics. The Ramachandran plot was used to highlight the domain analysis. Molecular docking results show that the resistant variant with KatG mutation had a higher binding affinity, which was odd since a decrease in medication efficiency should result in a lower binding affinity. The visualization of the docking was discussed in detail, along with the molecular dynamic simulation.
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Daniel Ryan Fugaha; Juan Lorell; Dhannyo Putta; Dennis Lunnoto; Arli Aditya Parikesit
|
Biological and Medicinal Chemistry; Bioinformatics and Computational Biology
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CC BY NC 4.0
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CHEMRXIV
|
2024-12-16
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675b8a56085116a1333a1e53/original/kat-g-protein-analysis-misfolding-and-drug-resistance.pdf
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67d5f28f6dde43c908f24f44
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10.26434/chemrxiv-2024-bznm6-v2
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Data Scaling and Generalization Insights for Medicinal Chemistry Deep Learning Models
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Predictive models hold considerable promise in enabling the faster discovery of safe, efficacious therapeutics. To better understand and improve the performance of small molecule predictive models for drug discovery, we conduct multiple experiments with deep learning and traditional machine learning approaches, leveraging our large internal datasets as well as publicly available datasets. The experiments include assessing performance on random, temporal, and reverse-temporal data ablation tasks, as well as tasks testing model extrapolation to different property spaces. We identify factors that contribute to higher performance of predictive models built using graph neural networks compared to traditional methods such as XGboost and random forest. These insights were successfully used to develop a scaling relationship that explains 81% of the variance in model performance across various assays and data regimes. This relationship can be used to estimate the performance of models for ADMET (absorption, distribution, metabolism, excretion, and toxicity) endpoints, as well as for drug discovery assay data more broadly. The findings offer guidance for further improving model performance in drug discovery.
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Jacky Chen; Yunsie Chung; Jonathan Tynan; Chen Cheng; Song Yang; Alan Cheng
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Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning
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CC BY NC ND 4.0
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CHEMRXIV
|
2025-03-18
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d5f28f6dde43c908f24f44/original/data-scaling-and-generalization-insights-for-medicinal-chemistry-deep-learning-models.pdf
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60c7584bbb8c1aeb9b3dc9dc
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10.26434/chemrxiv.14531847.v1
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A Single-Step Asymmetric Phosphodiester Synthesis from Alcohols with Phosphoenolpyruvate Phosphodiester
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Phosphodiester are important structural motifs observed in a diverse field of molecular science. It is, thus, important to develop a simple and robust way to synthesize them from corresponding alcohols. Here we report a single-step asymmetric phosphodiester synthesis from alcohols with phosphoenolpyruvate phosphodiesters as phosphoryl donors. This transformation allows for the use of various functionalized alcohols as substrates, and would be useful for diverse fields including biology and medicine.<br />
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Kohei Fujiyoshi; Shigehiro Kawashima; Kenzo Yamatsugu; Motomu Kanai
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Organic Synthesis and Reactions
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-05-05
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7584bbb8c1aeb9b3dc9dc/original/a-single-step-asymmetric-phosphodiester-synthesis-from-alcohols-with-phosphoenolpyruvate-phosphodiester.pdf
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61fabf6ae0f52955c3a4d50c
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10.26434/chemrxiv-2022-thdpk
|
Dynamic Amino Acid Side-Chains Grafting on Folded Peptide Backbone
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An efficient strategy for the synthesis of large libraries of conformationnally defined peptides is reported,
using dynamic combinatorial chemistry as a tool to graft amino acid side chains on a well-ordered 3D
peptide backbone. Combining rationnally designed scaffolds with combinatorial side chains selection
represents an alternative method to access peptide libraries for structures that are not genetically
encodable. This method would allow a breakthrough for the discovery of protein mimetic for unconventional
targets for which little is known.
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Benjamin Zagiel; Taleen Peker; Rodrigue Marquant; Guillaume Cazals; Gabrielle Webb; Emeric Miclet; Bich Claudia; Emmanuelle Sachon; Roba Moumné
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Biological and Medicinal Chemistry; Chemical Biology
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-02-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61fabf6ae0f52955c3a4d50c/original/dynamic-amino-acid-side-chains-grafting-on-folded-peptide-backbone.pdf
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64d2708869bfb8925a977631
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10.26434/chemrxiv-2023-pq5g2
|
A Crossover between Conventional Cross-Coupling and Carbene Insertion Reaction Pathways in a Pd Catalyzed C(sp2)-H Insertion
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Computational methods (Density Functional Theory) along with experimental tools are used to probe the mechanism and stereocontrol in a Pd(II)-catalyzed enantioselective C–H insertion reaction. The mechanistic aspects reveal a crossover between general transition metal-catalyzed carbene insertion reactions and typical Pd-catalyzed cross-coupling reactions. We demonstrate the intermediacy of a metal hydride species which contrasts the previously studied mechanistic routes taken in the case of all other transition metals (Rh, Fe, Au, Cu, etc.). Detailed investigation into the origin of stereoselectivity again throws up a new paradigm wherein stereocontrol arises during the formation of the metallocarbene itself. Novel mechanistic routes illustrated in this report provide crucial insights into the differential reactivity exhibited by Pd in carbene insertion reactions.
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Arushi Tyagi; Anubhav Goswami; Garima Jindal
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Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry; Computational Chemistry and Modeling; Theory - Computational; Kinetics and Mechanism - Organometallic Reactions
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-08-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d2708869bfb8925a977631/original/a-crossover-between-conventional-cross-coupling-and-carbene-insertion-reaction-pathways-in-a-pd-catalyzed-c-sp2-h-insertion.pdf
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60c7465bbb8c1a126c3da87d
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10.26434/chemrxiv.11309390.v1
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Site-Selective [2+2+n] Cycloadditions for Rapid, Scalable Access to Alkynylated Polycyclic Aromatic Hydrocarbons
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Polycyclic aromatic hydrocarbons (PAHs) are attractive synthetic building blocks for more complex conjugated nanocarbons, but their use for this purpose requires appreciable quantities of a PAH with reactive functional groups. Despite tremendous recent advances, most synthetic methods cannot satisfy these demands. Here we present a general and scalable [2+2+n] (n = 1 or 2) cycloaddition strategy to access PAHs that are decorated with synthetically versatile alkynyl groups and its application to seven structurally diverse PAH ring systems (thirteen new alkynylated PAHs in total). The critical discovery is the site-selectivity of an Ir-catalyzed [2+2+2] cycloaddition, which preferentially cyclizes tethered diyne units with preservation of other (peripheral) alkynyl groups. The potential for generalization of the site-selectivity to other [2+2+n] reactions is demonstrated by identification of a Cp<sub>2</sub>Zr-mediated [2+2+1] / metallacycle transfer sequence for synthesis of an alkynylated, selenophene-annulated PAH. The new PAHs are excellent synthons for macrocyclic conjugated nanocarbons. As a proof of concept, four were subjected to Mo catalysis to afford large, PAH-containing arylene ethylene macrocycles, which possess a range of cavity sizes reaching well into the nanometer regime. More generally, this work is a demonstration of how site-selective reactions can be harnessed to rapidly build up structural complexity in a practical, scalable fashion.
|
Gavin R. Kiel; Harrison Bergman; T. Don Tilley
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Organic Synthesis and Reactions
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CC BY NC ND 4.0
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CHEMRXIV
|
2019-12-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7465bbb8c1a126c3da87d/original/site-selective-2-2-n-cycloadditions-for-rapid-scalable-access-to-alkynylated-polycyclic-aromatic-hydrocarbons.pdf
|
6679e1c65101a2ffa86b4b52
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10.26434/chemrxiv-2024-frq7j
|
Boosting Cathodic Performance of Ni-rich NCM811 via Uric Acid Derived Nitrogen-doped Carbon-Coating in Lithium-Ion Batteries
|
The nickel-rich layered Li[Ni0.8Co0.1Mn0.1]O2, popularly known as NCM811, is considered a high-performance cathode material in lithium-ion batteries (LIBs) due to its high specific capacity and energy density. However, because of its poor structural stability, it suffers from long-run performance in LIBs. The surface coating technique can enhance the performance of the NCM811 cathode by preventing its surface degradation during prolonged contact with electrolytes. Herein, we report a uric acid-derived nitrogen-doped carbon-coated NCM811 cathode to enhance the cathodic performance. The materials were prepared by a facile one-step calcination in which different weights of uric acid are mixed well with NCM811 through ball milling followed by sintering. The XRD peaks confirm the formation of a pure phase in both the bare and modified NCM811 materials. The morphological characteristics and coating thickness are observed by FE-SEM and FE-TEM analysis, respectively. Electrochemical characterizations such as galvanostatic charge-discharge (GCD), cyclic performance, and rate capability studies show that the 0.1-NCM811 material can effectively tailor the electrochemical performance of the cathode in LIBs. The capacity retention of 0.1-NCM811 material is 92.7% and 85.8% at 100 cycles in 0.1C and 300 cycles in 1C, respectively. The improved electrochemical performance of coated NCM811 cathode is associated with the effective coating of nitrogen-doped carbon which can hinder the electrode dissolution process while amplifying the ionic conductivity.
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Kirankumar Venkatesan Savunthari; Pulia Venkatachalapathy Keerthivasan; Saravanan Ashok Vallal; Aswin kumar Anbalagan; Asad A. Salem
|
Materials Science; Inorganic Chemistry; Energy; Electrochemistry; Energy Storage
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CC BY 4.0
|
CHEMRXIV
|
2024-06-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6679e1c65101a2ffa86b4b52/original/boosting-cathodic-performance-of-ni-rich-ncm811-via-uric-acid-derived-nitrogen-doped-carbon-coating-in-lithium-ion-batteries.pdf
|
60c756e64c89191bf3ad48da
|
10.26434/chemrxiv.14333411.v1
|
Practical Synthesis of Iboxamycin, a Potent Antibiotic Candidate, in Amounts Suitable for Studies in Animal Infection Models
|
A gram-scale
synthesis of iboxamycin, an antibiotic candidate bearing a fused bicyclic amino
acid residue, is presented. A pivotal transformation in the route involves an
intramolecular hydrosilylation–oxidation sequence to set the ring-fusion
stereocenters of the bicyclic scaffold. Other notable features of the synthesis
include a high-yielding, highly diastereoselective alkylation of a
pseudoephenamine amide, a convergent sp<sup>3</sup>–sp<sup>2</sup> Negishi
coupling, and a one-pot transacetalization–reduction reaction to form the
target compound’s oxepane ring. Implementation of this synthetic strategy has
provided ample quantities of iboxamycin to allow for its <i>in vivo</i> profiling in murine models of infection.
|
Jeremy Mason; Daniel W. Terwilliger; Aditya R. Pote; Andrew G. Myers
|
Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756e64c89191bf3ad48da/original/practical-synthesis-of-iboxamycin-a-potent-antibiotic-candidate-in-amounts-suitable-for-studies-in-animal-infection-models.pdf
|
60c74127702a9b359418a1f8
|
10.26434/chemrxiv.7977566.v1
|
Formation and Trapping of the Thermodynamically Unfavoured Inverted-Hemicucurbit[6]uril
|
Amplification
of a thermodynamically unfavoured macrocyclic product through the directed
shift of the equilibrium between dynamic covalent chemistry library members is
difficult to achieve. We show for the first time that during condensation of
formaldehyde and <i>cis</i>-<i>N,N'</i>-cyclohexa-1,2-diylurea formation of <i>inverted-cis</i>-cyclohexanohemicucurbit[6]uril
(<i>i-cis</i>-cycHC[6]) can be induced at
the expense of thermodynamically favoured <i>cis</i>-cyclohexanohemicucurbit[6]uril
(<i>cis</i>-cycHC[6]). The formation of <i>i-cis-</i>cycHC[6] is enhanced in low
concentration of the templating chloride anion and suppressed in excess of this
template. We found that reaction selectivity is governed by the solution-based template-aided
dynamic combinatorial chemistry and continuous removal of the formed cycHC[6] macrocycles
from the equilibrating solution by precipitation. Notably, the <i>i-cis</i>-cycHC[6] was isolated with 33%
yield. Different binding affinities of three diastereomeric <i>i-cis</i>-, <i>cis</i>-cycHC[6] and their chiral isomer (<i>R,R</i>)-cycHC[6] for trifluoroacetic acid demonstrate the influence of
macrocycle geometry on complex formation.
|
Elena Prigorchenko; Sandra Kaabel; Triin Narva; Anastassia Baškir; Maria Fomitšenko; Jasper Adamson; Ivar Järving; Kari Rissanen; Toomas Tamm; Riina Aav
|
Organic Synthesis and Reactions; Stereochemistry; Supramolecular Chemistry (Org.); Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-04-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74127702a9b359418a1f8/original/formation-and-trapping-of-the-thermodynamically-unfavoured-inverted-hemicucurbit-6-uril.pdf
|
60c742dd469df4d19df43069
|
10.26434/chemrxiv.8796650.v1
|
Interactions of Na+ Cations with a Highly Charged Fatty Acid Langmuir Monolayer: Molecular Description of the Phase Transition
|
Vibrational sum frequency spectroscopy has been
used to study the molecular properties upon compression of a highly charged
arachidic acid Langmuir monolayer, which displays a first order phase
transition plateau in the surface pressure - molecular area (p-A) isotherm. By targeting vibrational modes
from the carboxylic acid headgroup, alkyl chain, and interfacial water
molecules, information regarding the surface charge, surface potential, type of
ion pair formed, and conformational order of the monolayer could be extracted. The
monolayer in the liquid expanded phase is found to be fully charged until
reaching the 2D-phase transition plateau, where partial reprotonation, as well
as the formation of COO⎺ Na<sup>+ </sup>contact-ion
pairs, start to take place. In the condensed phase after the transition, three
headgroup species, mainly hydrated COO⎺, COOH, and COO⎺ Na<sup>+ </sup>contact-ion pairs could be
identified and their proportions quantified. Comparison with theoretical models
shows that despite the low ionic strengths used (i.e. 10 mM), the predictions
from the Gouy Chapman model are only adequate for the lowest surface densities,
when the surface charge does not exceed -0.1 C/m<sup>2</sup>. In contrast, a
modified Poisson-Boltzmann (MPB) model that accounts for the steric effects
associated with the finite ion-size, captures many of the experimental
observables, including the partial reprotonation, and surface potential changes
upon compression. The agreement highlights the importance of hydronium ion –
carboxylate interactions, as well as the layer of sodium ions packed at the
steric limit, for explaining the phase transition behavior. The MPB model,
however, does not explicitly consider the formation of contact ion pairs with
the sodium counterion. The experimental results provide a quantitative molecular
insight that could be used to test potential extensions to the theory.
|
Adrien Sthoer; Eric Tyrode
|
Interfaces; Solution Chemistry; Spectroscopy (Physical Chem.); Surface; Thermodynamics (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-07-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742dd469df4d19df43069/original/interactions-of-na-cations-with-a-highly-charged-fatty-acid-langmuir-monolayer-molecular-description-of-the-phase-transition.pdf
|
61116eb1e540bbad0e74a1b9
|
10.26434/chemrxiv-2021-pjq7f
|
LT-LiMn0.5Ni0.5O2: A Unique Co-Free Cathode for High Energy Li-Ion Cells
|
A new Li-ion battery cathode, ‘LT-LiMn0.5Ni0.5O2’, where LT refers to its relatively low synthesis temperature (400 oC), has been identified. Electrochemical data indicate that Li/LT-LiMn0.5Ni0.5O2 cells operate between 5.0 and 2.5 V with good cycling stability, yielding a cathode capacity of 225 mAh/g. The electrochemical reactions occur in two distinct steps centered at ~3.75 V and ~4.7 V during charge, and at ~4.6 V and ~3.5 V during discharge. High-angle, annular-dark-field (HAADF) scanning-transmission electron microscopy (STEM) provide evidence that LT-LiMn0.5Ni0.5O2 consists of a unique, partially-disordered LiMn0.5Ni0.5O2 structure with predominant lithiated-spinel- and layered-like character. Structural analysis of LT-LiMn0.5Ni0.5O2 with synchrotron X-ray diffraction data shows, surprisingly, that lithiated-spinel and layered models with approximately 16% (~1/6) disorder between the lithium and manganese/nickel ions, yield an identical fit to the data, complicating the determination of the exact nature and level of disorder in each structural model. We believe that this is the first report of a Mn-stabilized, lithium-nickel-oxide spinel-related structure in which the redox reactions occur almost entirely on the nickel ions, with the likelihood that oxygen redox also contributes to some capacity above 4.7 V.
|
Boyu Shi; Jihyeon Gim; Linze Li; Chongmin Wang; Anh Vu; Jason Croy; Michael Thackeray; Eungje Lee
|
Materials Science; Energy; Energy Storage; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-08-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61116eb1e540bbad0e74a1b9/original/lt-li-mn0-5ni0-5o2-a-unique-co-free-cathode-for-high-energy-li-ion-cells.pdf
|
658484129138d2316135297e
|
10.26434/chemrxiv-2023-tnfnl
|
Spin-Forbidden Formation of Amide Molecules in the Interstellar Medium
|
In this study, two-state spin-forbidden mechanisms are proposed for the barrierless formation of amide isomers in the C2H5NO family of molecules. This family belongs to the first level of complexity among the molecules with peptide bond that are precursors to proteins, which are building blocks of life, and therefore are highly relevant to astrochemistry and astrobiology. Our density functional theory study demonstrates the significance of spin-forbidden pathways in the formation of acetamide (CH3CONH2), N-methyl-formamide (CH3NHCHO), and acetimidic acid (CH3COHNH) from the acetaldehyde, imidogen, formamide, and methylene reactants. Considering the rate constants of analogous reactions in the interstellar medium (ISM), we anticipate that the detected abundances of acetamide and N-methyl-formamide in the Sagittarius B2 North region can be rationalized by the suggested formation pathways. The proposed mechanism also predicts the synthesis of acetimidic acid, motivating future observational efforts to identify this molecule in the ISM.
|
Amir Mirzanejad; Sergey Varganov
|
Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658484129138d2316135297e/original/spin-forbidden-formation-of-amide-molecules-in-the-interstellar-medium.pdf
|
60ea947a9ab06e2e274d6cd7
|
10.26434/chemrxiv-2021-11r61
|
3D Computer Vision Models Predict DFT-Level HOMO-LUMO Gap Energies from Force-Field-Optimized Geometries
|
We investigate 3D deep learning methods for predicting quantum mechanical energies at high-theory-level accuracy from inexpensive, rapidly computed molecular geometries. Using space-filled volumetric representations (voxels), we explore the effects of radial decay from atom centers and rotational data augmentation on learnability. We test several published computer vision models for 3D shape learning, and construct our own architecture based on 3D inception networks with physically meaningful kernels. We provide a framework for further studies and propose a modeling challenge for the computer vision and molecular machine learning communities.
|
Michael R. Maser; Sarah E. Reisman
|
Theoretical and Computational Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-07-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60ea947a9ab06e2e274d6cd7/original/3d-computer-vision-models-predict-dft-level-homo-lumo-gap-energies-from-force-field-optimized-geometries.pdf
|
664da2c191aefa6ce1a657c6
|
10.26434/chemrxiv-2024-1sx0b
|
Synthesis of Cs3Cu2I5 Nanocrystals in a Continuous Flow System
|
Achieving the goal of generating all of the world’s energy via renewable sources and significantly reducing
our energy usage will require the development of novel abundant, nontoxic energy conversion materials. Here,
we develop a cost-efficient and scalable continuous flow synthesis of Cs3Cu2I5 nanocrystals as a basis for the
rapid advancement of novel nanomaterials. Ideal precursor solutions were obtained through a novel batch
synthesis, whose product served as a benchmark for the subsequent flow synthesis. Realizing this setup enabled
a reproducible fabrication of Cs3Cu2I5 nanocrystals. We determined the effect of volumetric flow rate and
temperature on the final product’s morphology and optical properties, obtaining 21% quantum yield with the
optimal configuration. Consequently, we can tune the size and morphology of the nanocrystals with far more
precision and in a much wider range than previously achievable. The flow setup is easily applicable to other
relevant nanomaterials. It should enable a rapid determination of a material’s potential and subsequently
optimize its desired properties for renewable energy generation or efficient optoelectronics.
|
Ksenija Arslanova; Patrick Ganswindt; Tizian Lorenzen; Ekaterina Kostyurina; Konstantin Karghiosoff; Bert Nickel; Knut Müller-Caspary; Alexander S. Urban
|
Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Physical and Chemical Properties; Spectroscopy (Physical Chem.)
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-05-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664da2c191aefa6ce1a657c6/original/synthesis-of-cs3cu2i5-nanocrystals-in-a-continuous-flow-system.pdf
|
6246b0c78048820ce600b607
|
10.26434/chemrxiv-2022-rjcvc
|
Facile collisional dissociation of N2 on a Si(111)-7x7 surface at room temperature
|
We demonstrate that the strong N2 bond can be efficiently dissociated at low pressure and ambient temperature on a
Si(111)-7x7 surface. The reaction was experimentally investigated by scanning tunnelling microscopy and X-ray
photoemission spectroscopy. Experimental and density functional theory results suggest that relatively low thermal energy collision of N2 with the surface can facilitate electron transfer from the Si(111)-7x7 surface to the p*-antibonding orbitals of N2 that significantly weaken the N2 bond. This facile N2 triple bond dissociation on the surface leads to the formation of a Si3N interface.
|
Elie GEAGEA; Judicael JEANNOUTOT; Frank PALMINO; Nicolas BREAULT; Alain ROCHEFORT; Samar HAJJAR; Carmelo PIRRI; Christophe THOMAS; Frederic CHERIOUX
|
Nanoscience; Nanostructured Materials - Nanoscience
|
CC BY 4.0
|
CHEMRXIV
|
2022-04-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6246b0c78048820ce600b607/original/facile-collisional-dissociation-of-n2-on-a-si-111-7x7-surface-at-room-temperature.pdf
|
671f543d83f22e42146c9c9b
|
10.26434/chemrxiv-2024-shsjs-v3
|
New fluorogenic triacylglycerols as sensors for dynamic measurement of lipid oxidation
|
Lipids are major constituents of food but are also highly relevant substructures of drugs and are increasingly applied for the development of lipid-based drug delivery systems. Lipids are prone to oxidative degradation, thus affecting the quality of food or medicines. Therefore, analytical methods or tools that enable to assess the degree of lipid oxidation are of utmost importance to guarantee food and drug safety. Herein, we report the design, synthesis, and application of the first-in-class fluorogenic triacylglycerols that enable a dynamic monitoring of lipid oxidation via straightforward fluorescence readout. Our fluorogenic triacylglycerols can be used both in an aqueous and lipid-based environment. Further, we showed that the sensitivity of our fluorescent tracers towards oxidation can be tuned by incorporating either saturated or unsaturated acyl chains in their triacylglycerol core structure. With this, we provide a first proof-of-principle for the applicability of fluorescently labelled triacylglycerols as tracers to monitor the dynamics of lipid oxidation, thus paving the way for novel discoveries in the area of lipid analytics.
|
Maria Handke; Frank Beierlein; Petra Imhof; Matthias Schiedel; Simon Hammann
|
Biological and Medicinal Chemistry; Analytical Chemistry; Agriculture and Food Chemistry; Analytical Chemistry - General; Food
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671f543d83f22e42146c9c9b/original/new-fluorogenic-triacylglycerols-as-sensors-for-dynamic-measurement-of-lipid-oxidation.pdf
|
67b710f3fa469535b9245c97
|
10.26434/chemrxiv-2025-dndx6-v2
|
What can be learned from the electrostatic environments within nitrogenase enzymes?
|
Nitrogen fixation is a fundamental, and yet challenging, chemical transformation due to the intrinsic inertness of dinitrogen (N₂). Whereas industrial ammonia synthesis relies on the energy-intensive Haber–Bosch process, nitrogenase enzymes achieve this transformation under ambient conditions—yet at the expense of a remarkably high ATP demand. Understanding their mode of operation could inspire the development of more efficient synthetic catalysts. In this study, we scrutinize the role of electrostatics in nitrogenase’s active site, surrounding the so-called M-cluster. Strikingly, all M-clusters reveal similar trends, exhibiting distinct electrostatic environments at the metal sites that have been proposed as potential N2-coordination sites. Specifically, a strong local electric field pointing away from the Fe2 site favors the cleavage of the Fe6–S–Fe2 sulfido bridge, exposing the Fe6 center for N₂ binding. Moreover, an oriented long-range electric field along the Fe2–Fe6 axis is identified, which may assist in N₂ activation towards hydrogenation, once the nitrogen takes on a bridging configuration between both metal sites. Our findings suggest that nitrogenases likely exploit electrostatic effects in an unconventional manner; rather than directly favoring the coordination of N2 to the M-cluster, they primarily modulate the kinetics (and thermodynamics) of key mechanistic steps preceding, and following, the absorption step. Overall, this study highlights the importance of local electric fields in enzymatic catalysis, even for substrates that have only limited susceptibility to electric fields, and provides insights that could inform the design of improved nitrogen fixation catalysts.
|
Thijs Stuyver; Olena Protsenko; Davide Avagliano; Thomas Ward
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Biology; Computational Chemistry and Modeling
|
CC BY 4.0
|
CHEMRXIV
|
2025-02-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b710f3fa469535b9245c97/original/what-can-be-learned-from-the-electrostatic-environments-within-nitrogenase-enzymes.pdf
|
60c7490bbb8c1a49653dad76
|
10.26434/chemrxiv.12016974.v1
|
Optimal Duration of the Preincubation Phase in Enzyme Inhibition Experiments
|
This report describes an algebraic formula to
calculate the optimal duration of the pre-incubation phase in enzyme-inhibition
experiments, based on the assumed range of expected values for the dissociation
equilibrium constant of the enzyme–inhibitor complex and for the bimolecular
association rate constant. Three typical experimental scenarios are treated, namely,
(1) single-point primary screening at relatively high inhibitor concentrations;
(2) dose-response secondary screening of relatively weakly bound inhibitors; (3)
dose-response screening of tightly-bound inhibitors.
|
Petr Kuzmic
|
Biochemistry; Biophysics; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7490bbb8c1a49653dad76/original/optimal-duration-of-the-preincubation-phase-in-enzyme-inhibition-experiments.pdf
|
60c73e55bdbb89b6d2a37de4
|
10.26434/chemrxiv.6831065.v1
|
Resonance Energy Transfer Mediated by Metal-Dielectric Composite Nanostructures
|
<p>Nanostructure-mediated energy transfer has attracted considerable attention</p>
<p>as a template for photocatalysis and solar energy conversion, and the use</p>
<p>of noble metal nanoparticles that support localized surface plasmon</p>
<p>resonances (LSPRs) has been widely explored as a medium for realizing</p>
<p>this paradigm. On the other hand, composite nanoparticles (CNPs)</p>
<p>comprised of a large dielectric bead and smaller metal nanostructures have</p>
<p>been shown to achieve efficient energy transfer to small-molecule</p>
<p>adsorbates through the interplay between dielectric scattering resonances</p>
<p>and the broad-band absorption associated with the metal nanostructure.</p>
<p>This scattering mediated absorption can enable selective photochemistry</p>
<p>without relying on the plasmonic properties of noble metal nanoparticles.</p>
<p>While the precise photochemical mechanisms themselves remain unknown,</p>
<p>resonance energy transfer (RET) is one feasible route for initiating the</p>
<p>photochemistry. We demonstrate computationally that CNPs indeed</p>
<p>facilitate RET to small-molecule adsorbates and that CNPs offer a</p>
<p>framework in which one can design RET donors that outperform typical</p>
<p>plasmonic nanoparticles employed within LSPR-driven RET under comparable</p>
<p>illumination conditions. We also exploit the tunability of the resonances</p>
<p>on the CNPs to realize strong coupling between the CNP and LSPR modes.</p>
|
Noor Eldabagh; Matthew Micek; A. Eugene DePrince, III; Jonathan J. Foley
|
Plasmonic and Photonic Structures and Devices; Optics; Photochemistry (Physical Chem.); Physical and Chemical Properties; Quantum Mechanics
|
CC BY 4.0
|
CHEMRXIV
|
2018-07-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e55bdbb89b6d2a37de4/original/resonance-energy-transfer-mediated-by-metal-dielectric-composite-nanostructures.pdf
|
60c73e164c8919ba23ad1d17
|
10.26434/chemrxiv.6483830.v1
|
Simple Preparation of Cellulosic Lightweight Materials from Eucalyptus Pulp
|
Cellulosic foams and aerogels are tridimensional
materials prepared from cellulose fibers and nanostructures that display
interesting properties, such as extremely low density, high fluid permeability,
sound and heat insulation. Currently, the most common techniques to obtain such
porous matrices are gel or foam forming, followed by freeze-drying or critical
point drying, which are energy and time-consuming processes for solvent
removal. In this work, we present a new methodology to produce cellulosic lightweight
materials from eucalyptus pulp, using cellulose fibers partially hydrolyzed
with sulfuric acid. This method is based on a drying step easily performed at
mild temperatures around 60°C in a convection oven and eliminates the need of
more sophisticated drying techniques. In addition, the procedure does not
require the use of surfactants or special foam forming equipment. Micro-CT and
FESEM analysis showed the formation of a porous and lightweight material
(density as low as 0.15 g/cm³), where the fibers are randomly assembled in a
3D-network with a few contact points. Mechanical testing reveled that foams of
hydrolyzed fibers have great performance under compressive strain, with high
mechanical energy absorption (<i>ca.</i> 360
kJ/m³). This purely cellulosic material is suitable for the incorporation of
particles or functional groups aiming a wide range of final applications.
|
Elisa S. Ferreira; Camila Alves Rezende
|
Biological Materials; Cellulosic materials; Nanostructured Materials - Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-06-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e164c8919ba23ad1d17/original/simple-preparation-of-cellulosic-lightweight-materials-from-eucalyptus-pulp.pdf
|
60e77eb2551cb06ecbadb7a4
|
10.26434/chemrxiv-2021-kn5xp
|
Low-Valent Tungsten Catalysis Enables Site-Selective Isomerization–Hydroboration of Unactivated Alkenes
|
A tungsten-catalyzed hydroboration of unactivated alkenes at distal C(sp3)–H bonds aided by native directing groups is described herein. The method is characterized by its simplicity, exquisite regio- and chemoselectivity and wide substrate scope, offering a complementary site-selectivity pattern to other metal-catalyzed borylation reactions and chain-walking protocols.
|
Tanner Jankins; Raul Martin-Montero; Phillippa Cooper; Ruben Martin; Keary Engle
|
Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Compounds and Functional Groups; Homogeneous Catalysis; Redox Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-07-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e77eb2551cb06ecbadb7a4/original/low-valent-tungsten-catalysis-enables-site-selective-isomerization-hydroboration-of-unactivated-alkenes.pdf
|
656a2b645bc9fcb5c9d80a48
|
10.26434/chemrxiv-2023-dw3w5
|
Redox-Neutral Multicatalytic Cerium Photoredox-Enabled Cleavage of O–H Bearing Substrates
|
The need for synthetic methodologies capable of rapidly altering molecular structure are in high demand. Most existing methods to modify scaffolds rely on net exothermicity to drive the desired transformation. We sought to develop a general strategy for the cleavage of C–C bonds beta to hydroxyl groups independent of inherent substrate strain. To this end we have applied a multicatalytic cerium photoredox-based system capable of activating O–H bonds in lactols to deliver formate esters. The same system is also capable of effecting hydrodecarboxylation and hydrodecarbonylation reactions. Initial mechanistic probes demonstrate atomic chlorine (Cl•) is generated under the reaction conditions, but substrate activation through cerium-alkoxides or -carboxylates cannot be ruled out.
|
Louis Barriault; Avery Morris
|
Organic Chemistry; Catalysis; Photocatalysis; Redox Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656a2b645bc9fcb5c9d80a48/original/redox-neutral-multicatalytic-cerium-photoredox-enabled-cleavage-of-o-h-bearing-substrates.pdf
|
60c7464a337d6c7e66e27134
|
10.26434/chemrxiv.11302613.v1
|
Shedding Light on the Effect of Fish Oil Supplementation on Dark Adaptation Capabilities
|
<p>This is the first study to directly relate the uptake of
fatty acids from fish oil supplements (as measured by blood analysis) to
changes in dark adaptation capabilities. During the dosing and abstention phases of the regimen, the
rise and fall in blood levels of the acids is mirrored by a reversible increase
in perception capabilities.</p>
|
Beth McMurchie; Roberto King; Martin Lindley; Jim Reynolds; George Torrens; Paul Kelly
|
Biochemistry; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-12-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7464a337d6c7e66e27134/original/shedding-light-on-the-effect-of-fish-oil-supplementation-on-dark-adaptation-capabilities.pdf
|
60c7578c9abda28fe0f8e767
|
10.26434/chemrxiv.12860981.v2
|
Foldamer-Based Ultrapermeable and Highly Selective Artificial Water Channels that Exclude Protons
|
The outstanding capacity of aquaporins (AQPs) for mediating highly selective superfast water transport1-7 has inspired recent development of supramolecular monovalent ion-excluding artificial water channels (AWCs). AWC-based bioinspired membranes are proposed for desalination, water purification, and other separations applications8-18. While some recent progress has been made in synthesizing AWCs that approach the water permeability and ion selectivity of AQPs, a hallmark feature of AQPs – high water transport while excluding protons has not been reproduced. We report on a class of biomimetic, helically folded pore-forming polymeric foldamers, that can serve as long sought-after highly selective ultrafast water-conducting channels exceeding those of AQPs (1.1 × 1010 H2O molecules/s for AQP17), with high water over monovalent ion transport selectivity (~108 water molecules over Cl- ion) conferred by the modularly tunable hydrophobicity of the interior pore surface. The best-performing AWC reported here delivers water transport at an exceptionally high rate, 2.5 times that of AQP1, while concurrently rejecting salts (NaCl and KCl) and even protons.
|
Arundhati Roy; Jie Shen; Himanshu Joshi; Woochul Song; Yu-Ming Tu; Ratul Chowdhury; Ye Ruijuan; Ning Li; Changliang Ren; Manish Kumar; Aleksei Aksimentiev; Huaqiang Zeng
|
Supramolecular Chemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7578c9abda28fe0f8e767/original/foldamer-based-ultrapermeable-and-highly-selective-artificial-water-channels-that-exclude-protons.pdf
|
67ade3d781d2151a02476ad9
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10.26434/chemrxiv-2025-v69sh
|
Hydrogen Bonds under Electric Fields with Quantum Accuracy
|
Hydrogen bonds (H-bonds) are pivotal in various chemical and biological systems and exhibit complex behavior under
external perturbations. This study investigates the structural, vibrational, and energetic properties of prototypical H-bonded dimers – water (H2O)2, hydrogen fluoride (HF)2, hydrogen sulfide (H2S)2, and ammonia (NH3)2 – and the respective monomers under static and homogeneous electric fields (EFs) using accurate explicitly correlated singles and doubles coupled cluster method (CCSD) for equilibrium geometries and harmonic vibrational frequencies, and the perturbative triples CCSD(T) method for energies. As for the vibrational response of the H2O, HF, H2S, and NH3 monomers, it turns out that dipole derivatives primarily govern geometry relaxation. Perturbation theory including cubic anharmonicity can reproduce CCSD results on the vibrational Stark effect, except for NH3, where deviations arise due to its floppiness. The field-induced modifications in H-bond lengths, vibrational Stark effects, binding energies, and charge-transfer mechanisms in monomers and dimers are elucidated. Symmetry-adapted perturbation theory (SAPT) analysis on dimers reveals that electrostatics dominate the stabilization of H-bonds across all field strengths, while induction contributions increase significantly with stronger fields, particularly in systems with more polarizable atoms. Our results reveal a universal strengthening of intermolecular interactions at moderate to strong field intensities, with significant variability among dimers due to inherent differences in molecular polarizability and charge distribution. Notably, a direct correlation is observed between the binding energies and the vibrational Stark effect of the stretching mode of the H-bond donor molecule, both in relation to the charge-transfer energy term, across all the investigated dimers. All these findings provide insights into the EF-driven modulation of H-bonds, highlighting implications for catalysis, hydrogen-based technologies, and biological processes.
|
Alessandro Amadeo; Marco Francesco Torre; Klaudia Mràzikovà; Franz Saija; Sebastiano Trusso; Jing Xie; Matteo Tommasini; Giuseppe Cassone
|
Theoretical and Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-02-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ade3d781d2151a02476ad9/original/hydrogen-bonds-under-electric-fields-with-quantum-accuracy.pdf
|
63a17ea204902a069009b4b9
|
10.26434/chemrxiv-2022-w1086
|
Bifunctional Iminophosphorane-Catalyzed Enantioselective Nitroalkane Addition to Unactivated α,β-Unsaturated Esters
|
Herein we describe the enantioselective conjugate addition of nitroalkanes to unactivated α,β-un-saturated esters, catalyzed by a bifunctional iminophosphorane (BIMP) superbase. The transformation provides the most direct access to pharmaceutically relevant enantioenriched γ-nitroesters, utilizing feedstock chemicals, via unprecedented, yet fundamental reactivity. The methodology exhibits a broad substrate scope, including alkyl, aryl and heteroaryl electrophiles substituted in the β-position, and represents the most general entry to enantioenriched γ-nitroesters. The methodology was successfully applied on a gram scale with reduced catalyst loading, and additionally catalyst recovery was carried out, furthermore, the formal synthesis of a range of drugs, and the enantioselective synthesis of (S)-rolipram were achieved.
|
Daniel Rozsar; Alistair J. M. Farley; Iain McLauchlan; Darren J. Dixon
|
Organic Chemistry; Catalysis; Base Catalysis; Organocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-12-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a17ea204902a069009b4b9/original/bifunctional-iminophosphorane-catalyzed-enantioselective-nitroalkane-addition-to-unactivated-unsaturated-esters.pdf
|
624050bcd6d3edb1a1a0e9ad
|
10.26434/chemrxiv-2022-740ds
|
Photomediated Tandem Sulfonyl Addition-Chemoselective N-Cyclization of o- Alkenyl Aryl Ureas: Direct Assembly of Functionalized Dihydroquinazolinones
|
Photoredox mediated tandem addition-chemoselective cyclization of o-alkenyl aryl ureas are reported for the synthesis of sulfonyl and other electrophilic radical decorated dihydroquinazolinones. By a careful choice of o-alkenyl aryl urea starting materials, we have achieved chemoselective N-cyclization in the presence of a more reactive amidic oxygen. We have demonstrated the scope of the methodology with a variety of o-alkenyl aryl ureas and sulfonyl chlorides including simple aliphatic sulfonyl chlorides, which are less commonly explored. Finally, we also demonstrated the application of our methodology with other electrophilic radicals, which afforded the resultant products in good yields under slightly modified conditions. Quenching studies with TEMPO, revealed a radical mechanism and finally, large-scale synthesis of sulfonyl substituted dihydroquinazolinone showcases the synthetic utility of the methodology.
|
Sakamuri Sarath Babu; Gopinath Purushothaman
|
Organic Chemistry; Catalysis; Photocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624050bcd6d3edb1a1a0e9ad/original/photomediated-tandem-sulfonyl-addition-chemoselective-n-cyclization-of-o-alkenyl-aryl-ureas-direct-assembly-of-functionalized-dihydroquinazolinones.pdf
|
6792a79b6dde43c9081a13df
|
10.26434/chemrxiv-2025-19k8q
|
High-Throughput Microdroplet-Based Synthesis using Automated Array-to-Array Transfer
|
Automation of chemical synthesis and high-throughput (HT) screening are important for speeding up drug discovery. Here, we describe an automated HT picomole scale synthesis system which uses desorption electrospray ionization (DESI) to create microdroplets of reaction mixtures at individual positions from a two-dimensional reactant array and transfer them to a corresponding position in an array of collected reaction products. On-the-fly chemical transformations are facilitated by the reaction acceleration phenomenon in microdroplets and high reaction conversions are achieved during the milliseconds droplet flight time from the reactant to the product array. Successful functionalization of bioactive molecules is demonstrated through the generation of 172 analogs (64% success rate) using multiple reaction types. Synthesis throughput is ~45 seconds/reaction including droplet formation, reaction, and collection steps, all of which occur in an integrated fashion, generating product amounts sufficient for subsequent bioactivity screening (low ng to low µg). Quantitative performance was validated using LC/MS. This system bridges the demonstrated capabilities of HT-DESI for reaction screening and label-free bioassays, allowing consolidation of the key early drug discovery steps around a single synthetic-analytical technology.
|
Kai-Hung Huang; Kitmin Chen; Nicolás M. Morato; Thomas C. Sams; Eric T. Dziekonski; R. Graham Cooks
|
Organic Chemistry; Analytical Chemistry; Organic Synthesis and Reactions; Mass Spectrometry; High-throughput Screening
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6792a79b6dde43c9081a13df/original/high-throughput-microdroplet-based-synthesis-using-automated-array-to-array-transfer.pdf
|
60c7504dbdbb896e90a39eed
|
10.26434/chemrxiv.12980774.v2
|
BonDNet: A Graph Neural Network for the Prediction of Bond Dissociation Energies for Charged Molecules
|
<div><div><div><p>A broad collection of technologies, including e.g. drug metabolism, biofuel combustion, photochemical decontamination of water, and interfacial passivation in energy production/storage systems rely on chemical processes that involve bond-breaking molecular reactions. In this context, a fundamental thermodynamic property of interest is the bond dissociation energy (BDE) which measures the strength of a chemical bond. Fast and accurate prediction of BDEs for arbitrary molecules would lay the groundwork for data-driven projections of complex reaction cascades and hence a deeper understanding of these critical chemical processes and, ultimately, how to reverse design them. In this paper, we propose a chemically inspired graph neural network machine learning model, BonDNet, for the rapid and accurate prediction of BDEs. BonDNet maps the difference between the molecular representations of the reactants and products to the reaction BDE. Because of the use of this difference representation and the introduction of global features, including molecular charge, it is the first machine learning model capable of predicting both homolytic and heterolytic BDEs for molecules of any charge. To test the model, we have constructed a dataset of both homolytic and heterolytic BDEs for neutral and charged (1 and +1) molecules. BonDNet achieves a mean absolute error (MAE) of 0.022 eV for unseen test data, significantly below chemical accuracy (0.043 eV). Besides the ability to handle complex bond dissociation reactions that no previous model could con- sider, BonDNet distinguishes itself even in only predicting homolytic BDEs for neutral molecules; it achieves an MAE of 0.020 eV on the PubChem BDE dataset, a 20% improvement over the previous best performing model. We gain additional insight into the model’s predictions by analyzing the patterns in the features representing the molecules and the bond dissociation reactions, which are qualitatively consistent with chemical rules and intuition. BonDNet is just one application of our general approach to representing and learning chemical reactivity, and it could be easily extended to the prediction of other reaction properties in the future.</p></div></div></div>
|
Mingjian Wen; Samuel Blau; Evan Spotte-Smith; Shyam Dwaraknath; Kristin Persson
|
Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry; Physical and Chemical Properties; Thermodynamics (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-09-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7504dbdbb896e90a39eed/original/bon-d-net-a-graph-neural-network-for-the-prediction-of-bond-dissociation-energies-for-charged-molecules.pdf
|
6793501d81d2151a02be7e20
|
10.26434/chemrxiv-2025-8mt3k
|
Body center tetragonal Pseudo-diamond C20: Crystal Chemistry and first principles Investigations
|
Extending the investigation of the graphite to diamond G2Dlike changes of carbon crystal systems implying 2D planar trigonal C(sp2)like paving to 3D tetrahedral sp3 to 3D trigonal to tetrahedral transformation, original body centered tetragonal BCT C20 allotrope with dia (diamond) topology was devised from crystal chemistry rationale and demonstrated to behave like diamond for all the physical properties. The investigations were based on crystal chemistry and first principles investigations within the Density Functional theory with comparisons to available experimental observations. Holistic assessment of the results let assign BCT C20 a pseudo-diamond label.
|
Samir MATAR
|
Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2025-01-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6793501d81d2151a02be7e20/original/body-center-tetragonal-pseudo-diamond-c20-crystal-chemistry-and-first-principles-investigations.pdf
|
60c74767ee301c03e5c796c0
|
10.26434/chemrxiv.11653260.v1
|
Robust Synthesis of NIR-Emissive P-Rhodamine Fluorophores
|
P-rhodamines were
accessed by implementing a robust three step sequence consisting of (i) addition of m-metallated anilines
to dichlorophosphine oxides, (ii)
selective dibromination, and (iii)
cyclization of the diaryllithium reagents derived from the dibromides to form
the dihydroacridophosphine core of P-rhodamines. A modified route to produce
non-symmetric P-rhodamines was additionally developed. A library of the prepared
P-rhodamines provides first insight into dependence of fluorophore properties
on the structure of P-rhodamines. A P-rhodamine with highest batochromic shifts
and quantum yields in the class was identified.
|
Maria Sauer; Veselin Nasufovic; Hans-Dieter Arndt; Ivan Vilotijevic
|
Organic Compounds and Functional Groups; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-01-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74767ee301c03e5c796c0/original/robust-synthesis-of-nir-emissive-p-rhodamine-fluorophores.pdf
|
67d172596dde43c90887e77f
|
10.26434/chemrxiv-2025-hl2k7
|
Foam-to-Adhesive Recycling of Self-Blown Non-Isocyanate Polyurethane Foams Facilitated by Integration of Disulfide Exchangeable Bonds and Moisture
|
Non-isocyanate polyurethane foams (NIPUFs) are promising, safer, and more sustainable alternatives to conventional isocyanate-based counterparts dominating the foam market. Despite bearing covalent adaptable bonds, NIPUFs of the polyhydroxyurethane-type demand intensive reprocessing procedures for their recycling/repurposing. Herein, NIPUFs incorporating dynamic disulfide bonds, prepared by a water-induced process, show mechanical and thermal properties comparable to disulfide-free analogs while presenting strongly enhanced recyclability features under mild hot-pressing conditions (120 °C, 0.5–2 Tons, 30 min). Stress relaxation analysis shows a direct correlation between disulfide bonds content and relaxation time (τ) in reprocessed films. Importantly, foam hydroplasticization, typically referred to as a drawback in NIPUFs, is exploited here to accelerate bond exchange dynamics, facilitating the foam-to-film recycling at unprecedented, reduced temperature (i.e., 90 °C). Leveraging this reprocessing capacity, the films are transformed into easy-to-apply adhesives with lap-shear strengths comparable to commercial adhesives on stainless steel, glass-stainless steel, and nylon fabrics. Importantly, the NIPU adhesives showcase superior creep resistance, ductility, on-demand reversible adhesion and recyclability. This work presents a facile approach to constructing recyclable NIPUFs that can be repurposed into adhesives under mild conditions, enhancing their versatility and lifespan while addressing other key polyurethane applications.
|
Victor Lechuga-Islas; Emeline Gillissen; Maxime Bourguignon; Bruno Grignard; Christophe Detrembleur
|
Materials Science; Polymer Science; Organic Polymers; Polymerization (Polymers); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d172596dde43c90887e77f/original/foam-to-adhesive-recycling-of-self-blown-non-isocyanate-polyurethane-foams-facilitated-by-integration-of-disulfide-exchangeable-bonds-and-moisture.pdf
|
61a6bcc9a9c8d5d06b63b8bd
|
10.26434/chemrxiv-2021-mf70j
|
A Nonaqueous Redox-Matched Flow Battery with Charge Storage in Insoluble Polymer Beads
|
We describe the nonaqueous redox-matched flow battery (RMFB), where charge is stored on redox-active moieties covalently tethered to non-circulating, insoluble polymer beads and charge is transferred between the electrodes and the beads via soluble mediators with redox potentials matched to the active moieties on the beads. The RMFB reported herein uses ferrocene and viologen derivatives bound to crosslinked polystyrene beads. Charge storage in the beads leads to a high (approximately 1.0-1.7 M) effective concentration of active material in the reservoirs while preventing crossover of that material. The relatively low concentration of soluble mediators (15 mM) eliminates the need for high-solubility molecules to create high energy density batteries. Nernstian redox exchange between the beads and redox-matched mediators was fast relative to the cycle time of the RMFB. This approach is generalizable to many different redox-active moieties via attachment to the versatile Merrifield resin.
|
Dukhan Kim; Melanie Sanford; Thomas Vaid; Anne McNeil
|
Polymer Science; Energy; Organic Polymers; Energy Storage; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-12-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a6bcc9a9c8d5d06b63b8bd/original/a-nonaqueous-redox-matched-flow-battery-with-charge-storage-in-insoluble-polymer-beads.pdf
|
67dbdb976dde43c9088dcce1
|
10.26434/chemrxiv-2025-xjswq
|
Hydrogen evolution via hydride transfer by a small organic benzothiadiazole-caffeine electrocata-lyst
|
The synthesis of fuels using small organic electrocatalysts has gained significant attention in recent years. Understanding the mechanisms governing the reactivity of these molecules is important in order to design better catalysts. In this work, we have developed a catalyst based on two caffeine units cova-lently linked to a benzothiadiazole core. This catalyst is able to electrochemically store up to three elec-trons in a fully reversible manner. Under reductive conditions and in the presence of strong acids such as trifluoroacetic acid and phytic acid, this molecule can form an organic hydride donor that is electroac-tive towards H2 evolution at a mild potential (Ecat/2 = 1.45 V vs Fc+/Fc) in DMSO. Faradaic efficiency up to 92 ± 5 % and turnover number up to 23 ± 4 were achieved after 4-hour controlled potential elec-trolysis with no apparent decomposition of the electrocatalyst. A reaction mechanism involving a hy-dride transfer step is proposed based on the chemical species found under electrocatalytic conditions and DFT calculations. The development of this small organic molecule is a step forward in the quest to find low-cost, active and long-term stable electrocatalysts for H2 evolution.
|
Carlos Enrique Torres-Méndez ; Haining Tian
|
Catalysis; Electrocatalysis; Homogeneous Catalysis; Organocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2025-03-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dbdb976dde43c9088dcce1/original/hydrogen-evolution-via-hydride-transfer-by-a-small-organic-benzothiadiazole-caffeine-electrocata-lyst.pdf
|
64bfc06dae3d1a7b0d4ff555
|
10.26434/chemrxiv-2023-rlxjk
|
Sampling and Mapping Chemical Space with Extended Similarity Indices
|
Visualization of the chemical space is useful in many aspects of chemistry including compound library design, diversity analysis, and exploring structure-property relationships, to name a few. Examples of notable research areas where visualization of chemical space has strong applications are drug discovery and natural product research. However, the sheer volume of even comparatively small sub-sections of chemical space implies that we need to use approximations at the time of navigating through chemical space. ChemMaps is a visualization methodology that approximates the distribution of compounds in large datasets based on the selection of satellite compounds that yield a similar mapping of the whole dataset when principal component analysis on similarity matrix was performed. Here, we show how the recently proposed extended similarity indices can help to find regions that are relevant to sample satellites and reduce the amount of high dimensional data needed to describe a library’s chemical space.
|
Kenneth Lopez Perez; Edgar Lopez Lopez; Jose Luis Medina Franco; Ramon Miranda-Quintana
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Machine Learning; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-07-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64bfc06dae3d1a7b0d4ff555/original/sampling-and-mapping-chemical-space-with-extended-similarity-indices.pdf
|
60c74611567dfe9b22ec4578
|
10.26434/chemrxiv.9698861.v2
|
Visualization of Very Large High-Dimensional Data Sets as Minimum Spanning Trees
|
<p>The chemical
sciences are producing an unprecedented amount of large, high-dimensional data
sets containing chemical structures and associated properties. However, there
are currently no algorithms to visualize such data while preserving both global
and local features with a sufficient level of detail to allow for human
inspection and interpretation. Here, we propose a solution to this problem with
a new data visualization method, TMAP, capable of representing data sets of up
to millions of data points and arbitrary high dimensionality as a
two-dimensional tree (http://tmap.gdb.tools). Visualizations based on TMAP are
better suited than t-SNE or UMAP for the exploration and interpretation of large
data sets due to their tree-like nature, increased local and global
neighborhood and structure preservation, and the transparency of the methods
the algorithm is based on. We apply TMAP to the most used chemistry data sets
including databases of molecules such as ChEMBL, FDB17, the Natural Products
Atlas, DSSTox, DrugBank, as well as to the MoleculeNet benchmark collection of
data sets. We also show its broad applicability with further examples from
biology, particle physics, and literature.</p>
|
Daniel Probst; Jean-Louis Reymond
|
Theory - Computational; Machine Learning; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-11-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74611567dfe9b22ec4578/original/visualization-of-very-large-high-dimensional-data-sets-as-minimum-spanning-trees.pdf
|
656dea0acf8b3c3cd7c3ebff
|
10.26434/chemrxiv-2023-8c1mt
|
Molecular mechanisms of phosphoester bond formation in abiotic conditions with reactive neural network potentials
|
RNA is likely to be the first biomolecule to have appeared during evolution, but the abiotic synthesis of long oligonucleotides through phosphoester bond formation is an unsolved problem. Because the uncatalyzed reaction is extremely slow, experimental studies bring limited and indirect information on the molecular mechanism, the nature of which remains debated. We solve this issue by using neural network potentials systematically trained to explore, with enhanced sampling strategies, the chemical phase space for such complex reaction involving several proton transfers and exchanges of heavy atoms in explicit solvent, with quantum accuracy but moderate computational cost. A dissociative mechanism is thermodynamically favored over an associative one, with the formation of a metaphosphate transition state and direct participation of water solvent molecules. These observations rationalize unexplained experimental results and the temperature-dependence of the reaction rate, and they pave the way for the design of more efficient abiotic catalysts and activating groups.
|
Zakarya Benayad; Rolf David; Guillaume Stirnemann
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-12-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656dea0acf8b3c3cd7c3ebff/original/molecular-mechanisms-of-phosphoester-bond-formation-in-abiotic-conditions-with-reactive-neural-network-potentials.pdf
|
60c74957567dfe4bb4ec4bbe
|
10.26434/chemrxiv.12052884.v1
|
Ligand Field-Actuated Non-Innocence of Acetylacetonate
|
<p>The quest for simple ligands to participate in concerted base metal-ligand multiple-electron redox events is driven by perspectives of replacing noble metals in catalysis and for discovering novel chemical reactivity. Yet the vast majority of simple ligand systems displays electrochemical potentials impractical for catalytic cycles substantiating the importance of new strategies towards aligned metal–ligand orbital energy levels. We herein demonstrate the possibility to establish and tame the elusive <i>non-innocence</i> of the ubiquitous acetylacetonate (acac), that is the most commonly employed anionic, chelating ligand towards elements across the entire Periodic Table. By employing the ligand field in the high-spin Cr(II) as a thermodynamic switch, we were able to chemically tailor the occurrence of metal–ligand redox events. The very mechanism can be understood as a destabilization of the d<i><sub>z</sub></i>2 orbital relative to the <i>pi</i>* LUMO of acac, which proffers a generalizable strategy to synthetically engineer non-innocence with seemingly redox-inactive ligands. </p>
|
Morten Gotthold Vinum; Laura Voigt; Steen Hansen; Colby Bell; Kensha Marie Clark; René Wugt Larsen; Kasper Pedersen
|
Coordination Chemistry (Inorg.); Ligands (Inorg.); Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.); Crystallography – Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74957567dfe4bb4ec4bbe/original/ligand-field-actuated-non-innocence-of-acetylacetonate.pdf
|
60c75a3a469df46189f45979
|
10.26434/chemrxiv.14465424.v4
|
A theoretical analysis of the burn-out times of an isothermal particle of coal char under air-firing, gasification and oxyfuel combustion in fluidised beds
|
<p></p><p>The
combustion of coal in air, its gasification with carbon dioxide, and oxyfuel
combustion in oxygen/carbon dioxide mixtures was studied at high process temperatures
in a bubbling fluidised bed reactor where burning is controlled by external
mass transfer conditions. Theoretical
analysis of the burn-out times of an isothermal particle of coal char in air is
provided for the case where a fraction of carbon monoxide is oxidized close to
the char particle. Burn-out time equations are provided for the gasification of
char in carbon dioxide. Both burn-out time equations are compared to analytical
equations derived for the oxy-fuel combustion of char particles in
oxygen/carbon dioxide mixtures. The results are particularly relevant for
retrofitting existing bubbling fluidised bed reactors for sustainable energy
generation to meet global warming targets. </p><p></p>
|
Toyin Omojola
|
Reaction Engineering; Transport Phenomena (Chem. Eng.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75a3a469df46189f45979/original/a-theoretical-analysis-of-the-burn-out-times-of-an-isothermal-particle-of-coal-char-under-air-firing-gasification-and-oxyfuel-combustion-in-fluidised-beds.pdf
|
60c75a09469df44363f4595d
|
10.26434/chemrxiv.14369618.v2
|
Ab-Initio Computational Study on Fe2NiP schreibersite: Bulk and Surface Characterization
|
<p>Phosphorous is ubiquitous in planet Earth and
plays a fundamental role in all living systems. Finding a reasonable prebiotic
source of phosphorous is not trivial, as common sources where it is present
nowadays are in the form of phosphate minerals, which are rather insoluble and non-reactive
materials, and, accordingly, unavailable for being readily incorporated in
living organisms. A possible source of phosphorous is from the exogenous
meteoritic bombardment and, in particular, in iron/nickel phosphites. These materials,
by simple interaction with water, produce oxygenated phosphorous compounds,
which can easily react with organic molecules, thus forming C-O-P bonds. In the
present work, periodic ab-initio simulations at PBE level (inclusive of
dispersive interactions) have been carried out on metallic Fe<sub>2</sub>NiP-schreibersite,
as a relative abundant component of metallic meteorites, in order to
characterize structural, energetics and vibrational properties of both bulk and
surfaces of this material. The aim is to study the relative stability among
different surfaces, to characterize both the nanocrystal morphology and the
reactivity towards water molecules. </p>
|
Stefano Pantaleone; Marta Corno; Albert Rimola; Nadia Balucani; Piero Ugliengo
|
Space Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-06-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75a09469df44363f4595d/original/ab-initio-computational-study-on-fe2ni-p-schreibersite-bulk-and-surface-characterization.pdf
|
67621d996dde43c908780be8
|
10.26434/chemrxiv-2024-qs0pc-v2
|
Moltiverse: Molecular Conformer Generation Using Enhanced Sampling Methods
|
Accurately predicting the diverse bound-state conformations of small molecules is crucial for successful drug discovery and design, particularly when detailed protein-ligand interactions are unknown. Established tools exist, but efficiently exploring the vast conformational space remains challenging. This work introduces Moltiverse, a novel protocol using enhanced sampling molecular dynamics (MD) simulations for conformer generation. The extended adaptive biasing force (eABF) algorithm combined with metadynamics, guided by a single collective variable (radius of gyration, RDGYR), efficiently samples the conformational landscape of a small molecule. Moltiverse demonstrates comparable accuracy and, in some cases, superior quality when benchmarked against established software like RDKit, CONFORGE, ConfGenX, Torsional diffusion, and Conformator. We present an exhaustive ranking based on eight quantitative metrics and statistical analysis for robust conformer generation algorithms comparison and provide recommendations for their improvement based on our findings. We introduce the Cofactorv1 dataset, a complementary resource for conformer generator evaluation. Unlike traditional datasets with thousands of single-conformer molecules, the Cofactorv1 dataset features only seven small molecule cofactors but with hundreds to thousands of experimental conformers per molecule (sourced from the PDB). This diversity, encompassing 15-29 rotatable bonds, poses a significant challenge for conformer generation benchmarks. Cofactorv1 is a complementary dataset that serves as a valuable resource for developing and evaluating conformer generation methods like Moltiverse, pushing the boundaries of accuracy and diversity in this relevant field.
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Mauricio Bedoya; Francisco Adasme-Carreño; Paula Andrea Peña-Martínez; Camila Muñoz-Gutiérrez; Luciano Peña-Tejo; José C.E. Márquez Montesinos; Erix W. Hernández-Rodríguez; Wendy González; Leandro Martínez; Jans Alzate-Morales
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Theoretical and Computational Chemistry; Computational Chemistry and Modeling
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CC BY 4.0
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CHEMRXIV
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2024-12-18
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67621d996dde43c908780be8/original/moltiverse-molecular-conformer-generation-using-enhanced-sampling-methods.pdf
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