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673ba8f87be152b1d088bcc7
|
10.26434/chemrxiv-2024-9zp2l
|
Protein-Based Enzyme Bionanoreactor for Efficient CO2 Mineralization under Benign Conditions
|
Mineralization is an emerging approach for carbon capture and sequestration (CCS), but current methods rely on high pH conditions to overcome the kinetic and thermodynamic barriers of CO2 reacting with metal cations to form carbonate minerals. This is often achieved through adding alkaline chemicals or using electrochemical catalysis, which are resource-intensive, environmentally disruptive, and require extensive pH adjustments. Inspired by natural biomineralization, this study presents a novel enzyme bionanoreactor approach based on self-assembling lumazine synthase AaLS-13 protein nanocages to facilitate efficient CO2 mineralization under mild conditions. The AaLS-13 nanocage actively encapsulates and concentrates metal cations within its cavity, with its assembled structure playing a critical role in enhancing the cation availability for subsequent reactions. By encapsulating carbonic anhydrase into the nanocages, the resultant bionanoreactors integrate CA catalysis with metal cation concentration, showing significantly improved catalytic performance. They efficiently convert dissolved CO2 into carbonate minerals as well as capture and mineralize atmospheric CO2 under benign, ambient conditions. This research lays the groundwork for developing AaLS-13 nanocage-based bionanoreactors for sustainable carbon mineralization, offering an eco-friendly CCS alternative. It also provides new insights into leveraging AaLS-13 nanocage-substrate interactions to modulate local microenvironments and optimize enzyme catalysis for diverse nanotechnological, biomedical, and environmental applications.
|
Yifei Ma; Meng Wang
|
Biological and Medicinal Chemistry; Nanoscience; Earth, Space, and Environmental Chemistry; Bioengineering and Biotechnology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673ba8f87be152b1d088bcc7/original/protein-based-enzyme-bionanoreactor-for-efficient-co2-mineralization-under-benign-conditions.pdf
|
6167ee80fb861912d0f7eb5b
|
10.26434/chemrxiv-2021-pcw03-v3
|
Bioorthogonal Photo-Catalytic Activation of an Anti-Cancer Prodrug by Riboflavin
|
Chemotherapies for cancer treatment usually suffer from poor targeting ability and serious side-effects. To improve the treatment efficiency and reduce side effects, photoactivatable chemotherapy has been recently proposed for precise cancer treatment with high spatiotemporal resolution. However, most photoactivatable prodrugs require decoration by stoichiometric photo-cleavable groups, which are only responsive to ultraviolet irradiation and suffer from low reaction efficiency. To tackle these challenges, we herein propose a bioorthogonal photo-catalytic activation strategy with riboflavin as the catalyst for in situ transformation of prodrug dihydrochelerythrine (DHCHE) prodrug into anti-cancer drug chelerythrine (CHE), which can efficiently kill cancer cells and inhibit in vivo tumor growth under light irradiation. Meanwhile, the photo-catalytic transformation from DHCHE into CHE was in situ monitored by green-to-red fluorescence conversion, which can be used for precise control of the therapeutic dose. The photocatalytic mechanism was also fully explored by means of density functional theory (DFT) calculations. We believe this imaging-guided bioorthogonal photo-catalytic activation strategy is promising for cancer chemotherapy in clinical applications.
|
Xin Yang; Limin Ma; Hongwei Shao; Xia Ling; Mengyu Yao; Guowen Luo; Stefano Scoditti; Emilia Sicilia; Gloria Mazzone; Meng Gao; Ben Zhong Tang
|
Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-10-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6167ee80fb861912d0f7eb5b/original/bioorthogonal-photo-catalytic-activation-of-an-anti-cancer-prodrug-by-riboflavin.pdf
|
60c7588d567dfe66ffec6890
|
10.26434/chemrxiv.14525619.v1
|
Breaking C–C Bonds via Electrochemically Mediated Hydrogen Atom Transfer Reactions
|
Cleaving
inert sp<sup>3</sup>-sp<sup>3</sup> carbon-carbon (C-C) bonds selectively remains
a major challenge in organic chemistry and a main bottleneck in the chemical upcycling
of recalcitrant polyolefin waste. Here, we present an electrochemical strategy
using redox mediators to activate and break C-C bonds at room temperature and
ambient pressure. Specifically, we use <i>N</i>-hydroxyphthalimide
(NHPI) as a redox mediator that undergoes electrochemical oxidation to form the
<a>phthalimide-<i>N</i>-oxyl
(PINO) radical </a>to initiate hydrogen atom transfer (HAT) reactions with benzylic
C-H bonds. The resulting benzylic carbon radical is readily captured by molecular
oxygen to form a peroxy radical that decomposes into oxygenated C-C bond-scission
fragments. This indirect, mediated approach for C<sub>sp3</sub>-C<sub>sp3</sub>
bond cleavage reduces the oxidation potential by > 1.2 V compared
to the direct oxidation of the substrate, thereby eliminating deleterious side
reactions, such as solvent oxidation, that may occur at high potentials. Studies
with a bibenzyl model compound revealed a bifurcated reaction pathway following
the initial HAT step. At a bibenzyl conversion of 61.0%, the C-C bond cleavage
pathway generates benzaldehyde and benzoic acid products at 38.4% selectivity, and
the C-H bond oxygenation pathway leads to 1,2-diphenylethanone and benzil products
at 39.2% selectivity. Changes in reaction selectivity were investigated with various
model compounds, including bibenzyl, 1,3-diphenylpropane, 1,4-diphenylbutane,
and their derivatives. Product selectivity is correlated with the C-C bond
strength of the reactant, with weaker C-C bonds favoring the C-C bond cleavage pathway.
We also evaluated the mediated oxidation of oligomeric styrene (<i>M</i><sub>n</sub> = 510 Da,
OS<sub>510</sub>) which were converted into oxygenated products. Lastly, proof-of-concept
depolymerization of polystyrene (PS, ~10,000 Da) into oxygenated monomers,
dimers, and oligomers was demonstrated using NHPI-mediated oxidation.
|
Bing Yan; Changxia Shi; Gregg T. Beckham; Eugene Y.-X. Chen; Yuriy Román-Leshkov
|
Electrocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7588d567dfe66ffec6890/original/breaking-c-c-bonds-via-electrochemically-mediated-hydrogen-atom-transfer-reactions.pdf
|
60c74bca842e654441db31f8
|
10.26434/chemrxiv.12377861.v1
|
Population Distributions from Native Mass Spectrometry Titrations Reveal Nearest-Neighbor Cooperativity in the Ring-Shaped Oligomeric Protein TRAP
|
Allostery pervades macromolecular function and drives cooperative binding of ligands to macromolecules. To decipher the mechanisms of cooperative ligand binding it is necessary to define, at a microscopic level, the thermodynamic consequences of binding of each ligand to its energetically coupled site(s). However, extracting these microscopic constants is difficult for macromolecules with more than two binding constants. This goal is complicated because the observable (e.g., NMR chemical shift changes, fluorescence, enthalpy) can be altered by allostery, thereby distorting its proportionality to populations of states. Because it measures mass, native mass spectrometry (MS) can directly quantify the populations of homo-oligomeric protein species with different numbers of bound ligands, provided the populations are proportional to ion counts and that MS-compatible electrolytes do not alter the overall thermodynamics. These measurements can help decipher allosteric mechanisms by providing unparalleled access to the statistical thermodynamic partition function. We used native MS (nMS) to study the cooperative binding of tryptophan (Trp) to Bacillus stearothermophilus trp RNA-binding attenuation protein (TRAP), a ring-shaped homo-oligomeric protein complex with 11 identical binding sites. Mass spectrometrycompatible solutions did not significantly perturb protein structure and thermodynamics as assessed by ITC and NMR spectroscopy. Populations of Trpn-TRAP11 states were quantified as a function of Trp concentration by native mass spectrometry. Population distributions cannot be explained by a non-cooperative binding model but are well described by a nearest neighbor cooperative model. Non-linear least-squares fitting of the populations to a mechanistic model yielded microscopic thermodynamic constants that define the interactions between neighboring binding sites that result in homotropic cooperativity in Trp binding to TRAP.
|
Melody Holmquist; Elihu Ihms; Paul Gollnick; Vicki Wysocki; Mark Foster
|
Biochemical Analysis; Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bca842e654441db31f8/original/population-distributions-from-native-mass-spectrometry-titrations-reveal-nearest-neighbor-cooperativity-in-the-ring-shaped-oligomeric-protein-trap.pdf
|
60c74713469df46630f43787
|
10.26434/chemrxiv.11536053.v1
|
Concise Total Synthesis of N¹⁴-Desacetoxytubulysin H
|
Access to analogues within the highly cytotoxic natural product family of tubulysins has previously required lengthy routes involving multiple functional group manipulations that is costly and time intensive on scale. A concise and modular total synthesis of the highly potent N¹⁴-desacetoxytubulysin H has been accomplished in a short sequence from commercially available building blocks. Our work highlights the complexity augmenting and route shortening power of multicomponent reaction (MCR) as well as the role of catalysts in controlling diastereoselectivity. Our operationally simple and s tep economical total synthesis can be easily performed on gram scale without compromising the yield.
|
Thimmalapura M. Vishwanatha; Ben Giepmans; Alexander Domling
|
Natural Products; Organic Synthesis and Reactions; Stereochemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-01-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74713469df46630f43787/original/concise-total-synthesis-of-n14-desacetoxytubulysin-h.pdf
|
60c7583af96a001a40288dba
|
10.26434/chemrxiv.14519733.v1
|
Downstream Paradigm in Enamine Catalysis: Comment on “On Stereocontrol in Organocatalytic α-Chlorinations of Aldehydes”
|
<p>We present kinetic modeling results in order to evaluate different mechanistic proposals that have been presented concerning the role of “downstream intermediates” in enamine catalysis. The focus of the debate is the identity and role of aminal intermediates. Are the aminals <i>syn</i> or are they <i>anti</i>, or are both observed? Do they lie on the catalytic cycle, as we suggest, or are they off-cycle species?</p>
|
Jordi Bures; Alan Armstrong; Donna Blackmond
|
Homogeneous Catalysis; Organocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7583af96a001a40288dba/original/downstream-paradigm-in-enamine-catalysis-comment-on-on-stereocontrol-in-organocatalytic-chlorinations-of-aldehydes.pdf
|
679a6107fa469535b954b490
|
10.26434/chemrxiv-2025-hp665
|
Physical Parameters Optimization for Cost Minimization of Perovskite Solar Cell with Inexpensive HTM, ETM and Back Contact Material
|
In this study, an all-perovskite solar cell is proposed consists of MASnI3, CsSnI3 and MAGeI3 proposed to
replace conventional expensive HTM, ETM. Several physical parameters of each layer (HTM, ETM and
Absorber) of the proposed cell including thickness, doping density, defect density, electron affinity,
temperature, series resistance and metal work function have been analyzed. After analyzing the physical
parameters of each layer of the proposed cell it is found that MASnI3, CsSnI3 and MAGeI3 can be costeffective and non-toxic alternatives of expensive and toxic HTM, absorber and ETM to provide optimal
efficiency. Although several back contact materials can provide maximum efficiency for the proposed cell,
Ni has the lowest cost among them. Hence, we have considered Ni as the back contact for the proposed
cell. The proposed cell with Ni as back contact can provide an open circuit voltage (Voc) of 0.97V, a short
circuit current (Jsc) of 35.16mA/cm2, a fill factor (FF) of 82.92% and a power conversion efficiency (PCE)
of 28.28%.
|
Rukon Uddin; Subarata Bhowmik
|
Energy; Photovoltaics
|
CC BY 4.0
|
CHEMRXIV
|
2025-01-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679a6107fa469535b954b490/original/physical-parameters-optimization-for-cost-minimization-of-perovskite-solar-cell-with-inexpensive-htm-etm-and-back-contact-material.pdf
|
65b5783266c1381729685660
|
10.26434/chemrxiv-2024-1tst6
|
Hydrogen-Bonded Supramolecular Network Triggers High-Efficiency Blue Room-Temperature Phosphorescence
|
Hydrogen bonding has been employed to suppress non-radiative decay in organic compounds that show room temperature phosphorescence (RTP); however, the small number of structurally diverse examples makes it unclear how general is this a strategy to turn on RTP. In this study, we report highly efficient blue RTP from 4,4',4''-nitrilotribenzoic acid (TPA-CO2H) in five structurally and chemically distinct hydrogen-bonded supramolecular networks. In doped films in polyvinyl alcohol (PVA) the phosphorescence quantum yield and lifetime (Ph and Ph) reach a PLQY 52% and lifetime of 275 ms. Boric acid also can be used to turn on RTP, and the performance changes significantly with the sample is heated beyond the dehydration temperature of this host where there is a 14-fold enhancement in the Ph after heat treatment. Blue RTP similar to that observed in PVA was also observed using granulated sugar, gelatine and paper has host matrices. We demonstrated how the emission color could be tuned by co-doping the films with Rhodamine 6G. This work elucidates for the first time the role and the generality of hydrogen bonding in activating efficient blue RTP in an organic guest containing no heavy atoms.
|
Sen Wu; Tao Wang; Eli Zysman-Colman
|
Physical Chemistry; Organic Chemistry; Supramolecular Chemistry (Org.); Spectroscopy (Physical Chem.); Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-01-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b5783266c1381729685660/original/hydrogen-bonded-supramolecular-network-triggers-high-efficiency-blue-room-temperature-phosphorescence.pdf
|
60c73f22842e652b49db1a2e
|
10.26434/chemrxiv.7264175.v1
|
PythoMS: A Python Framework to Simplify and Assist in the Processing and Interpretation of Mass Spectrometric Data
|
Mass spectrometric data are copious and generate
a processing burden that is best dealt with programmatically. PythoMS is a
collection of tools based on the Python programming language that assist
researchers in creating figures and video output that is informative, clear and
visually compelling. The PythoMS framework introduces a library of classes and
a variety of scripts that quickly perform time-consuming tasks: making
proprietary output readable; binning intensity vs time data to simulate longer
scan times (and hence reduce noise); calculate theoretical isotope patterns and
overlay them in histogram form on experimental data (an approach that works
even for overlapping signals); render videos that enable zooming into the baseline
of intensity vs. time plots (useful to make sense of data collected over a
large dynamic range) or that depict the evolution of different species in a
time-lapse format; calculate aggregates; and provide a quick first-pass at
identifying fragments in MS/MS spectra. PythoMS is a living project that will
continue to evolve as additional scripts are developed and deployed.
|
Lars Yunker; Darien Yeung; J Scott McIndoe
|
Chemoinformatics; Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-10-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f22842e652b49db1a2e/original/pytho-ms-a-python-framework-to-simplify-and-assist-in-the-processing-and-interpretation-of-mass-spectrometric-data.pdf
|
60c7561b4c89198f27ad47a9
|
10.26434/chemrxiv.14213711.v1
|
Ruthenium Complex Hydride Catalysts as a Platform for Ammonia Synthesis
|
Mild-condition ammonia synthesis from N2 and H2 is a long-sought-after scientific goal and a practical need, especially for the intensively pursued “Green Ammonia” production using renewable H2. Under this context, there have been growing interests in the development of new catalysts for effectively catalyzing N2+H2 to NH3. Particular attention has been given to Ru-based catalysts because they are well known to be more active at lower temperatures and pressures than non-noble-metal based catalysts. Here, we demonstrate that a series of Ru complex hydrides An[RuHm], where A is alkali or alkaline earth metal, n= 2, 3 or 4 and m = 6 or 7, exhibit universal and high catalytic activities that far exceed the benchmark Ru metal catalysts under mild conditions. Detailed investigations on the ternary Ru complex hydride catalytic system disclose that the kinetic behaviors depend strongly on the identity of alkali or alkaline earth metal cations. In clear contrast to the closed packed Ru metal catalyst, the unique configuration and synergized scenario of the Ru complex hydride center prefer a non-dissociative mechanism for N2 activation and hydrogenation, which provides a new platform for the design and development of efficient NH3 synthesis catalysts.
|
Qianru Wang; Jianping Guo; Ping Chen
|
Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7561b4c89198f27ad47a9/original/ruthenium-complex-hydride-catalysts-as-a-platform-for-ammonia-synthesis.pdf
|
61e51f5b6afbef9dd5676bfb
|
10.26434/chemrxiv-2022-0nq0v
|
PbI2 nanocrystal growth by atomic layer deposition of Pb(tmhd)2 and HI
|
Atomic layer deposition (ALD) allows for a great level of control over the thickness and stoichiometry of materials. ALD provides a suitable route to deposit lead halides, which can further be converted to perovskite for photovoltaics, photoemission, and photodetection, among other applications. Deposition of lead halides by ALD has already begun to be explored; however, the precursors used in published processes are highly hazardous, require expensive fabrication processes, or contain impurities that can jeopardize the optoelectronic properties of metal halide perovskites after conversion. We sought to deposit lead iodide (PbI2) by a facile ALD process involving only two readily accessible, low-cost precursors and without involving any unwanted impurities that could act as recombination centers once the PbI2 is later converted to perovskite. Crystalline PbI2 nanocrystals were grown on soda-lime glass (SLG), silicon dioxide support grids, and silicon wafer substrates and provide the groundwork for further investigation into developing lead halide perovskite processes by ALD. The ALD-grown PbI2 was characterized by annular dark field scanning transmission electron microscopy (ADF-STEM), atomic force microscopy (AFM), and x-ray photoemission spectroscopy (XPS), among other methods. This work presents the first step to synthesize lead halide perovskites with atomic control for applications such as interfacial layers in photovoltaics and for deposition in microcavities for lasing.
|
Juan-Pablo Correa-Baena; Jacob Vagott; Kathryn Bairley; Carlo Andrea Riccardo Perini; Andres Felipe Castro Mendez; Juanita Hidalgo; Sarah Lombardo; Josh Kacher; Barry Lai
|
Materials Science; Energy; Materials Processing; Photovoltaics; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-01-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e51f5b6afbef9dd5676bfb/original/pb-i2-nanocrystal-growth-by-atomic-layer-deposition-of-pb-tmhd-2-and-hi.pdf
|
6229f5b450b62150c0f0b0be
|
10.26434/chemrxiv-2021-qhvq1-v2
|
Ni/Photoredox Dual Catalysis Sulfone Compounds Synthesised with Carbon Nitride as the Semiheterogeneous Photocatalyst
|
An easily available heterogeneous semiconductor material, g-CN, proved to be feasible when combined with homogeneous nickel catalysts for light-mediated C(sp2)-SO2Ar bond formation of aryl bromides with aryl sulfinates under mild conditions and base-free, unlocking a variety of cross-couplings. The metal-free heterogeneous semiconductor is totally recyclable from reaction system, and experimental results demonstrated a series of differently substituted substrates including electron donating groups and electron withdrawing groups can be tolerated with a satisfactory result. The method could even pro-duce the classic drug Dapsone in large scale, showing strong practical application potential.
|
Yang Liu; Joost Berkhong
|
Organic Chemistry; Catalysis; Heterogeneous Catalysis; Photocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2022-03-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6229f5b450b62150c0f0b0be/original/ni-photoredox-dual-catalysis-sulfone-compounds-synthesised-with-carbon-nitride-as-the-semiheterogeneous-photocatalyst.pdf
|
60c741260f50db24b7395a73
|
10.26434/chemrxiv.7967291.v1
|
Design of a Small Molecule That Stimulates VEGFA Informed from an Expanded Encyclopedia of RNA Fold-Small Molecule Interactions
|
<p>Vascular Endothelial Growth Factor A<i></i>(VEGFA) stimulates angiogenesis in human endothelial cells and increasing its expression is a potential treatment for heart failure, currently accomplished via gene or mRNA therapy. Herein, we describe a designed small molecule (TGP-377) that specifically and potently enhances VEGFA expression by targeting of a non-coding microRNA that regulates its expression. This investigation was initiated by studying the RNA motifs that bound small molecules from a subset of the AstraZeneca compound collection. A two-dimensional combinatorial screen (2DCS) revealed preferences in small molecule chemotypes that bind RNA and preferences in the RNA motifs that bind small molecules, increasing the known information by 20-fold. Analysis of this dataset against the RNA-mediated pathways that regulate VEGFA defined that the microRNA-377 precursor (pre-miR-377), which represses <i>VEGFA</i>mRNA translation, is druggable in a selective manner. The compound potently and specifically upregulated VEGFA in Human Umbilical Vein Endothelial Cells (HUVEC). Analysis of the proteome and angiogenic phenotype affected by TGP-377 demonstrated that the compound is highly potent and selective. These studies illustrate the power of 2DCS to define molecular recognition events between “undruggable” biomolecules and small molecules and the ability of sequence-based design to deliver efficacious compounds that target RNA and precisely and potently modulate disease-associated pathways.</p>
|
Hafeez Haniff; Laurent Knerr; Xiaohui Liu; Gogce Crynen; Jonas Boström; Daniel Abegg; Alexander Adibekian; Malin Lemurell; Matthew Disney
|
Chemical Biology; Drug Discovery and Drug Delivery Systems
|
CC BY 4.0
|
CHEMRXIV
|
2019-04-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741260f50db24b7395a73/original/design-of-a-small-molecule-that-stimulates-vegfa-informed-from-an-expanded-encyclopedia-of-rna-fold-small-molecule-interactions.pdf
|
67a2ccb6fa469535b915b8fb
|
10.26434/chemrxiv-2024-hbbfj-v2
|
Atomic-Scale Observation of Moiré potential in Twisted Hexagonal Boron Nitride Layers by Electron Microscopy
|
Moiré superlattices (MSLs) are an emerging class of two-dimensional functional materials whose electronic states can be tuned by the twist angle between two van der Waals layers and/or the relative placement of the layers. The intriguing prop-erties of MSLs are closely correlated to the moiré potential, which is the electrostatic potential induced by interlayer cou-pling. Intensive efforts have been made to understand the nature and distribution of the moiré potential by using various experimental and theoretical techniques. However, the experimental observation of the moiré potential is still challenging because of the possible presence of the surface and/or interlayer contaminants. In this work, we develop a method to obtain hexagonal boron nitride (hBN) nanolayers (with or without twist) using a specially designed chemical exfoliation tech-nique. The resulting hBN nanolayers are atomically clean and strain free, hence providing ideal MSLs for the investigation of their moiré potential. Aberration-corrected high resolution transmission electron microscopy measurements on the twisted hBN nanolayers allow us to observe moiré diffraction spots in Fourier space. Then, the moiré potential is recon-structed by the inverse fast Fourier transform of the moiré diffraction spots. It has been revealed that the local interlayer atomic overlap plays a decisive role in determining the periodicity and distribution of the moiré potential, as supported by density functional theory calculations. This work not only provides a general strategy to observe the moiré potential in MSLs, but it also expands the application of electron microscopy to the further study of MSLs with atomic resolution.
|
Rina Mishima; Takuro Nagai; Hiroyo Segawa; Masahiro Ehara; Takashi Uchino
|
Theoretical and Computational Chemistry; Nanoscience; Nanofabrication; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2025-02-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a2ccb6fa469535b915b8fb/original/atomic-scale-observation-of-moire-potential-in-twisted-hexagonal-boron-nitride-layers-by-electron-microscopy.pdf
|
6789410681d2151a026ca475
|
10.26434/chemrxiv-2025-njv4t
|
Knotting a tetrahedral cage mechanically locks guests inside
|
Interwoven molecular structures underpin the functions of many biomolecules,1–3 yet synthesizing artificial topologically-complex structures in high yield remains challenging.4,5 Here we describe a streamlined, high yield one-pot synthesis of knotted cage frameworks through the use of a subcomponent designed to bridge over the faces of a predesigned cage framework. A ZnII4L3 open-faced cage framework was employed as the basis for a topologically chiral ‘perplexane’,6 and a ZnII4L4 tetrahedron was built into a topologically chiral ‘trefoil tetrahedron’. Both interwoven architectures can be prepared through one-pot subcomponent self-assembly from a trialdehyde, the bridging triamine, and a zinc(II) salt. The ‘trefoil tetrahedron’ was observed to mechanically lock guests inside the cavity, resulting in a guest exchange half-life 17000 times longer than that of the original tetrahedral cage. Both cage frameworks were reduced and demetallated to yield metal-free interwoven structures, with the ‘perplexane’ producing an achiral product, and the ‘trefoil tetrahedron’ maintaining its topological chirality. Our strategy may enable the many existing cage frameworks produced using subcomponent self-assembly to be knotted, enhancing their robustness and locking guests inside.
|
Yuchong Yang; Tanya K. Ronson; Paula C.P. Teeuwen; Simone Zucchelli; Andrew W. Heard; Paola Posocco; David J. Wales; Jonathan R. Nitschke
|
Organic Chemistry; Inorganic Chemistry; Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6789410681d2151a026ca475/original/knotting-a-tetrahedral-cage-mechanically-locks-guests-inside.pdf
|
67c38e7ffa469535b985d52a
|
10.26434/chemrxiv-2024-f5ngq-v2
|
A Simple Solution for Triple Tube Heat Exchanger with Non-Adiabatic Outer Wall Condition by Analogy with Moving Bed Heat Exchanger
|
Triple Tube Heat Exchangers (TTHEs) are suitable equipment for thick viscosity products, with or without particulates, with various applications in the food and pharmaceutical industries. Although less commonly used than Double Tube Heat Exchangers (DTHEs), TTHEs often perform better than DTHEs. However, in the case of thermal models of TTHEs with Heat Loss (TTHEs-HL) to the surroundings, there is no analytical solution in which the character of the roots has been analyzed – except for the analogous problem of a Tubular Moving Bed Heat Exchanger with Heat Loss to the surroundings and indirectly heated (MBHE-HL), for specific flow configurations –. Thus, it is not certain that the known solutions are of general application. Furthermore, regarding the critical design parameter for co-current flow TTHEs – the crossover point – limited information is available about TTHEs-HL. Also, recently published analogies provide an opportunity to synergistically increase the knowledge of TTHEs and MBHEs, for the case of non-adiabatic outer wall. Aware of these needs and opportunities, the present work starts from a known analytical solution for a MBHE-HL thermal model and, by analogy, develops a compact form of an analytical solution for TTHE-HL, suitable for co-current and counter-current flow arrangements. The character of the roots is determined from literature results for the MBHE-HL, by analogy with the TTHE-HL. These results are based on parallel flow and counter-current flow of the fluid in the intermediate tube, for a wide range of parameters. From the solution obtained, it was possible to determine approximate expressions for crossover points. For the case studies analyzed, the values calculated by the analytical solution and the numerical solution using the compound method Trapezoidal Rule/Regressive Differentiation Formula (TR-BDF2) are almost identical. By comparison with other analytical solutions in the literature for thermal models of TTHE-HL, we have shown that the present solution is the first – to the best of our knowledge – that correctly represents the temperatures of the three fluids in co-current flow, and for a wide range of parameters in the counter-current flow of the fluid in the inner annular section. To better understand the underlying physics, a scale analysis is carried out.
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Sávio Bertoli; Jesús Apolinar-Hernández; Natan Padoin; Cíntia Soares
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Chemical Engineering and Industrial Chemistry; Transport Phenomena (Chem. Eng.)
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CC BY 4.0
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CHEMRXIV
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2025-03-04
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c38e7ffa469535b985d52a/original/a-simple-solution-for-triple-tube-heat-exchanger-with-non-adiabatic-outer-wall-condition-by-analogy-with-moving-bed-heat-exchanger.pdf
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60c74e7a4c8919706aad3a39
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10.26434/chemrxiv.12762266.v1
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Hydrodechlorination of Dichloromethane by a Metal-Free Triazole-Porphyrin Electrocatalyst: Demonstration of Main-Group Element Electrocatalysis
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<p>In this work, the electrocatalytic reduction of dichloromethane (CH<sub>2</sub>Cl<sub>2</sub>) into hydrocarbons involving a main group element-based molecular triazole-porphyrin electrocatalyst H2PorT8 is reported. This catalyst converted CH<sub>2</sub>Cl<sub>2</sub> in acetonitrile to various hydrocarbons (methane, ethane, and ethylene) with a Faradaic efficiency of 70% and current density of –13 mA/cm<sup>2</sup> at a potential of –2.2 V vs. Fc/Fc<sup>+</sup> using water as a proton source. The findings of this study and its mechanistic interpretations demonstrated that H2PorT8 was an efficient and stable catalyst for the hydrodechlorination of CH<sub>2</sub>Cl<sub>2</sub> and that main group catalysts could be potentially used for exploring new catalytic reaction mechanisms.</p>
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Caroline Williams; Amir Lashgari; Marcus Ang; Pranita Dhungana; Jianbing Jiang
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Electrocatalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-08-05
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e7a4c8919706aad3a39/original/hydrodechlorination-of-dichloromethane-by-a-metal-free-triazole-porphyrin-electrocatalyst-demonstration-of-main-group-element-electrocatalysis.pdf
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668e470001103d79c595b23c
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10.26434/chemrxiv-2024-hs1fg
|
Choline Oxidase and Choline Ionic Liquids in Biocatalytic Heme Peroxidase Cascades
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Choline oxidase from Alcaligenes sp. (ChOx) is used to generate hydrogen peroxide in situ from choline-based ionic liquids (ILs) to fuel peroxidase-mediated biocatalysis, while mitigating oxidative degradation of the heme-dependent enzymes. Horseradish peroxidase (HRP) and chloroperoxidase from Caldariomyces fumago (CPO), in combination with the ChOx, are evaluated in enzymatic cascades for the ability of the biocatalytic systems to withstand elevated concentrations of different choline additives in oxidative and halogenative enzymatic assays. The findings are applied in various synthetic scenarios to produce important oxygen- and nitrogen-containing heterocycles, using choline ILs in a dual-purpose fashion, as a substrate-solubilizing component in the reaction medium as well as the source for hydrogen peroxide. The ChOx/HRP couple is used to induce intramolecular cyclizations of hydroxamic acids and hydroxycarbamates in a nitroso-ene-type pathway with choline dihydrogen phosphate as IL additive. The ChOx/CPO cascade successfully mediates brominative cyclizations of α-allenic alcohols, while amphiphilic surfactants are employed to turn the aqueous choline propionate IL media into a colloidal suspension. ChOx/CPO partnering is also evaluated in an oxygenative rearrangement of 1-furylethanol with choline acetate IL. The results show the wide potential of choline oxidase for hydrogen peroxide-driven biocatalysis with both aqueous and micellar choline ionic liquid solutions.
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Marleen Hallamaa; Janne M. Naapuri; Rafaela A. L. Silva; Andreia A. Rosatella; Jan Deska
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Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Bioorganic Chemistry; Organic Synthesis and Reactions; Biocatalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-07-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668e470001103d79c595b23c/original/choline-oxidase-and-choline-ionic-liquids-in-biocatalytic-heme-peroxidase-cascades.pdf
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665f75e421291e5d1d14050e
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10.26434/chemrxiv-2024-3xd1k
|
Catalyst Deactivation Modes in Nickel-Catalyzed Suzuki–Miyaura Cross-Coupling Reactions Using an NHC-Pyridonate Ligand
|
The catalytic activity of an NHC-pyridonate-supported nickel(0) complex for Suzuki–Miyaura coupling of aryl halides was evaluated. Product formation was observed in the absence of a basic additive. However, low turnover numbers resulted from competitive catalyst deactivation. The nature of catalyst deactivation—dimerization of the nickel(II) aryl intermediate—was elucidated through a combination of NMR monitoring, direct synthesis, and X-ray diffraction. This discovery was leveraged to identify additives that enable improved catalyst stability and turnover, thereby highlighting both the promise and pitfalls associated with incorporating secondary-sphere modifications for cooperative catalysis.
|
C. Rose Kennedy; Abhishek Kadam; Medina Afandiyeva; William Brennessel
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Catalysis; Organometallic Chemistry; Catalysis; Ligand Design
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-06-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665f75e421291e5d1d14050e/original/catalyst-deactivation-modes-in-nickel-catalyzed-suzuki-miyaura-cross-coupling-reactions-using-an-nhc-pyridonate-ligand.pdf
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6515d5bcade1178b244ca4bc
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10.26434/chemrxiv-2023-bl1xc
|
Photoswitchable Inhibitors of the Sarco(endo)plasmic Calcium Pump
|
Targeting the sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) offers a promising strategy for treating drug-resistant cancers. However, as SERCA activity is essential for all cells types, specific inhibitors such as thapsigargin (TG) possess general toxicity. We explored the potential for developing SERCA inhibitors controllable with light by synthesizing TG derivatives containing an azobenzene photoswitch. These compounds (AzTG derivatives) were assessed by their ability to inhibit SERCA ATPase activity. We have identified cis-active and trans-active derivatives and our results reveal a ~2-fold difference in IC50 in response to photoisomerization, demonstrating an effect of the incorporated photoswitch. Furthermore, X-ray structures of SERCA in complex with two AzTG derivatives were obtained, revealing two different binding modes for the photoswitch group of these compounds. Taken together, we have developed photo-activatable SERCA inhibitors that can serve as tools to study the function of their target protein, and our results build the foundation for the design of improved, next-generation photoswitchable inhibitors.
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Samuel Hjorth-Jensen; David Konrad; Esben Quistgaard; Line Hansen; Alexander Novak; Hang Chu; Michal Jurášek ; Tomáš Zimmermann; Jacob Andersen; Phil Baran; Poul Nissen; Dirk Trauner
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Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Biochemistry; Chemical Biology
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CC BY 4.0
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CHEMRXIV
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2023-09-29
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6515d5bcade1178b244ca4bc/original/photoswitchable-inhibitors-of-the-sarco-endo-plasmic-calcium-pump.pdf
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666f5bbe5101a2ffa8bc6826
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10.26434/chemrxiv-2024-wv36k
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Applying Metallo-Organic Ligand Design Principles to the Stereoselective Synthesis of a Peptide-Based Pd2L4X4 Cage
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The rational and controlled synthesis of metallo-organic cages using polyaromatic ligands is well established in the literature. There is a strong interest to advance this field towards the use of chiral ligands capable of yielding cages in a stereoselective manner. Herein, we demonstrate that the classical approach for designing metallo-organic cages can be translated to polyproline peptides, a biocompatible class of chiral ligands. We have successfully designed a series of polyprolines, which mimic the topology of ditopic polyaromatic ligands, to yield the stereoselective synthesis of a novel Pd lantern cage. This work will pave the way towards the stereospecific synthesis of more complex, functionalized peptide cages.
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Dominic F. Brightwell; Kushal Samanta; Jimmy Muldoon; Patricia C. Fleming; Yannick Ortin; Lina Mardiana ; Paul G. Waddell; Michael J. Hall; Ewan R. Clark; Felipe Fantuzzi; Aniello Palma
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Organic Chemistry; Inorganic Chemistry; Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.); Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-06-18
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666f5bbe5101a2ffa8bc6826/original/applying-metallo-organic-ligand-design-principles-to-the-stereoselective-synthesis-of-a-peptide-based-pd2l4x4-cage.pdf
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64ca1564dfabaf06ff925ee2
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10.26434/chemrxiv-2023-f7qnk
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Local Oxidation States in {FeNO}6–8 Porphyrins: Insights from DMRG/CASSCF-CASPT2 Calculations
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A first DMRG/CASSCF-CASPT2 study of a series of paradigmatic {FeNO}6, {FeNO}7, and {FeNO}8 heme-nitrosyl complexes has led to substantial new insight, as well as uncovered key shortcomings of the DFT approach. By virtue of its balanced treatment of static and dynamic correlation, the calculations have provided some of the most authoritative information available to date on low- versus high-spin states of different classes of heme-nitrosyl complexes. Thus, the calculations indicate low doublet-quartet gaps of 1–4 kcal/mol for {FeNO}7 complexes, and high singlet-triplet gaps of ≳20 kcal/mol for both {FeNO}6 and {FeNO}8 complexes. In contrast, DFT calculations yield widely divergent spin state gaps as a function of the exchange-correlation functional. DMRG-CASSCF calculations also help calibrate DFT spin densities for {FeNO}7 complexes, pointing to those obtained from classic pure functionals as the most accurate. The general picture appears to be that nearly all the spin density of Fe[P](NO) is localized on the Fe, while the axial ligand imidazole (ImH) in Fe[P](NO)(ImH) pushes a part of the spin density onto the NO moiety. An analysis of the DMRG-CASSCF wave function in terms of localized orbitals and of the resulting CSFs into resonance forms with varying NO(*) occupancies has allowed us to address the long-standing question of local oxidation states in heme-nitrosyl complexes. The analysis indicates NO(neutral) resonance forms [i.e., Fe(II)-NO0 and Fe(III)-NO0] as the major contributors to both {FeNO}6 and {FeNO}7 complexes. This finding is at variance with the common formulation of {FeNO}6 hemes as Fe(II)-NO+ species, but is consonant with an Fe L-edge XAS analysis by Solomon and coworkers. For the {FeNO}8 complex {Fe[P](NO)}–, our analysis suggests a resonance hybrid description: Fe(I)-NO0 Fe(II)-NO–, in agreement with earlier DFT studies. Vibrational analyses of the compounds studied indicate an imperfect but fair correlation between the NO stretching frequency and NO(*) occupancy, highlighting the usefulness of vibrational data as a preliminary indicator of NO oxidation state.
|
Quan Phung; Ho Ngoc Nam; Abhik Ghosh
|
Theoretical and Computational Chemistry; Inorganic Chemistry; Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Theory - Inorganic
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CC BY 4.0
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CHEMRXIV
|
2023-08-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ca1564dfabaf06ff925ee2/original/local-oxidation-states-in-fe-no-6-8-porphyrins-insights-from-dmrg-casscf-caspt2-calculations.pdf
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61403be3b817b414b31c706c
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10.26434/chemrxiv-2021-56ds7
|
Relative Binding Free Energy Predictions for Inhibitors of Tetrameric Influenza Virus Neuraminidase
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Accurate methods to predict the free energies of protein-ligand interactions have great potential to assist rational drug design. In this work, we used molecular dynamics simulations with alchemical perturbation to predict the binding of carbohydrate-based ligands to influenza virus neuraminidase (N2). This specific drug target is a challenging test system for alchemical free energy methods because it has flexible binding site motifs. We use a molecular dynamics protocol that works for longer time scales than are often reported in previous molecular dynamics studies of N2. We demonstrated that N2-ligand complex stability and that accurate N2 150-loop dynamics, on a 350 ns time scale, are both force field-dependent (AMBER99SB-ILDN, GAFF and TIP4P water are required). Further, we showed that crystallographic waters must be retained to maintain stability of N2-ligand complexes over 350 ns. Using our modelling protocol, we were able to determine relative binding free energy values between neuraminidase ligands which correlated strongly with experimental differences in pIC50 values (R = -0.96, ρ = 0.86, N = 13, sig < 0.0001). It is anticipated that the molecular dynamics protocol and the relative binding free energy methods reported here, will both be useful in expediting the discovery of novel therapeutics for N2 and other homologous glycohydrolases.
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Billy J Williams-Noonan; Elizabeth Yuriev; David K Chalmers
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Theoretical and Computational Chemistry; Computational Chemistry and Modeling
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-09-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61403be3b817b414b31c706c/original/relative-binding-free-energy-predictions-for-inhibitors-of-tetrameric-influenza-virus-neuraminidase.pdf
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654d0a802c3c11ed71166f64
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10.26434/chemrxiv-2023-0l7fm
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2-Aminophenanthrolines Enable the Mild, Undirected Borylation of Alkyl C–H Bonds
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The catalytic, undirected borylation of alkyl C–H bonds typically occurs at high reaction temperatures or with excess substrate, or both, because of the low reactivity of alkyl C–H bonds. Here we report a new iridium system comprising 2-anilino-1,10-phenanthroline as ligand that catalyzes the borylation of alkyl C–H bonds with little to no induction period and with high reaction rates. This superior activation and reactivity profile of 2-aminophenanthroline catalysts leads to broader scope of the reaction, including those with sensitive reactants, such as epoxides and glycosidic acetals, enhanced diastereoselectivity, and higher yields of borylated products. These catalysts also enable the borylation of alkanes, amines, and ethers at room temperature for the first time. Mechanistic studies imply that facile N-borylation occurs under the reaction conditions, and that iridium complexes containing N-boryl aminophenanthrolines are competent precatalysts for the reaction.
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Isaac Yu; Kyan D'Angelo; Ángel Hernandez-Mejías; Nanrun Cheng; John Hartwig
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Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Bond Activation; Ligand Design
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-11-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654d0a802c3c11ed71166f64/original/2-aminophenanthrolines-enable-the-mild-undirected-borylation-of-alkyl-c-h-bonds.pdf
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61c0695e203b40d5ef939aa3
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10.26434/chemrxiv-2021-qsbtd
|
Monitoring the chemical changes in fingermark residue over time using synchrotron infrared spectroscopy
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Degradation of fingermark residue has a major impact on the successful forensic detection of latent fingermarks. The time course of degradation has been previously explored with bulk chemical analyses, but little is known about chemical alterations at the micron-scale. Here we report the use of synchrotron-sourced attenuated total reflection-Fourier transform infrared (ATR-FTIR) microscopy to provide spatio-temporal resolution of chemical changes within fingermark droplets, as a function of time since deposition. Eccrine and sebaceous material within natural fingermark droplets were imaged on the micron scales at hourly intervals for the first 6 – 12 hours after deposition, revealing that substantial dehydration occurred within the first 8 hours. Changes to lipid material was more varied, with samples exhibiting an increase or decrease in lipid concentration due to the degradation and redistribution of this material. Across 12 donors, it was noticeable that the initial chemical composition and morphology of the droplet varied greatly, which appeared to influence on the rate of change of the droplet over time. Further, this study attempted to quantify the total water content within fingermark samples. The wide-spread nature and strength of the absorption of Terahertz/Far-infrared (THz/Far-IR) radiation by water vapour molecules were exploited for this purpose, using THz/Far-IR spectroscopy. Upon heating, water confined in natural fingermarks was evaporated and expanded in a vacuum chamber equipped with multipass optics. The amount of water vapour was then quantified by high-spectral resolution analysis, and fingermarks were observed to lose approximately 14 – 20 µg of water. The combination of both ATR-FTIR and Far-IR highlight important implications for experimental design in fingermark research, and operational practices used by law enforcement agencies.
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Rhiannon Boseley; Jitraporn Vongsvivut; Dominique Appadoo; Mark Hackett; Simon Lewis
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Analytical Chemistry; Microscopy; Spectroscopy (Anal. Chem.)
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CC BY NC ND 4.0
|
CHEMRXIV
|
2021-12-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c0695e203b40d5ef939aa3/original/monitoring-the-chemical-changes-in-fingermark-residue-over-time-using-synchrotron-infrared-spectroscopy.pdf
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60c74a5bbb8c1a69933dafd1
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10.26434/chemrxiv.12115251.v2
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Drug Repurposing of Approved Drugs Elbasvir, Ledipasvir, Paritaprevir, Velpatasvir, Antrafenine and Ergotamine for Combating COVID19
|
<p>Pneumonia of unknown
cause detected in Wuhan, China was first reported to the WHO Country Office in
China on 31 December 2019. The outbreak was declared a Public Health Emergency
of International Concern on 30 January 2020. Currently, there is no Vaccine
against COVID-19 pandemic and infection is spreading worldwide vary rapidly
there is an exigent requirement of practicable drug treatment. Drug repurposing
is one of the most promising approaches for that. Many reports are available
with <i>in silico</i> drug repurposing but the majority of them engrossed on a
single target. The present study aimed at screening the approved against
Covid19 protein and extract the combination of operational comprehensively. A total
of 1735 drug molecules against all COVID19 protein structures and sequential
screening recognize the better potential of anti-HCV drugs over anti-HIV drugs.
The study designated Elbasvir, Ledipasvir, Paritaprevir, Velpatasvir,
Antrafenine Ergotamin as promising drug candidates for covid19 treatment. The
computational analysis also reveled the better potential of proposed drugs over
the currently used drug combination for COVID19 drugs. </p>
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Vishal Mevada; Pravin Dudhagara; Himani Gandhi; Nilam Vaghamshi; Urvisha Beladiya; Rajesh Patel
|
Bioinformatics and Computational Biology
|
CC BY 4.0
|
CHEMRXIV
|
2020-04-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a5bbb8c1a69933dafd1/original/drug-repurposing-of-approved-drugs-elbasvir-ledipasvir-paritaprevir-velpatasvir-antrafenine-and-ergotamine-for-combating-covid19.pdf
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60c741d09abda2b8ccf8bf05
|
10.26434/chemrxiv.8141993.v1
|
Desulfonylative Arylation of Redox-Active Alkyl Sulfones with Aryl Bromides
|
Herein we describe the development of the first
reductive cross-electrophile coupling between alkyl sulfones and aryl bromides.
The use of alkyl sulfones as coupling partners offers strategic advantages over
other alkyl electrophiles used in reductive coupling reactions, as the sulfone moiety
can be incorporated into molecules in unique ways and permits α-functionalization
prior to coupling. The conditions developed here can be applied to incorporate
a wide array of aromatic rings onto (fluoro)alkyl scaffolds with broad
functional group tolerance and generality, making this a practical method for
late-stage diversification.
|
Jonathan Hughes; Patrick Fier
|
Organic Compounds and Functional Groups; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-05-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741d09abda2b8ccf8bf05/original/desulfonylative-arylation-of-redox-active-alkyl-sulfones-with-aryl-bromides.pdf
|
66711ff3c9c6a5c07ab6dc9c
|
10.26434/chemrxiv-2024-cl4pc
|
A Facile Supramolecular Strategy to Switch Photodynamic Pathway and Augment ROS Production of Sensitizers for Enhanced Tumor Therapy
|
The photosensitizers (PSs) capable of generating radical reactive oxygen species (ROS) via the type-I electron transfer pathway under photoirradiation offer a promising solution to the challenge of unsatisfactory photodynamic therapy (PDT) in hypoxic environments. Classical PSs (type-II), however, primarily transfer excited energy to ground state O2 rather than undergoing photoinduced electron transfer, posing a tough challenge in promoting the type-I pathway through existing strategies. Herein, we demonstrate a novel and straightforward approach using bioinspired supramolecular assembly to convert classical type-II PSs into type-I supramolecular PSs with augmented ROS production. The phosphate-templated assembly facilitated the formation of nanoscale aggregates with orderly and efficient packing of PSs, effectively suppressing the energy transfer pathway by promoting photoinduced charge- separation between PSs (resulting in PS+· and PS−·), thereby enhancing the generation of superoxide radicals (O2−·) through electron transfer from PS−· to O2 (Scheme 1). Additionally, this shift of photosensitization pathway also enhances overall ROS production, overcoming the typical inhibition usually associated with PS aggregation and indicating the highly efficient ROS generation via the type-I pathway. Consequently, the type-I supramolecular PSs demonstrated excellent ROS generation capability in the treatment of hypoxic tumors, thus achieving outstanding therapeutic outcomes. This study not only addresses a critical challenge in PDT under hypoxic conditions but also opens a new avenue for modifying the sensitization behavior of clinically approved type-II PSs to achieve superior therapeutic outcomes.
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Ruihua Guo; Han Sun; habtom gobeze; Kanyashree Jana; yingnan wu; Kirk Schanze; zhiliang li; fengling song
|
Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66711ff3c9c6a5c07ab6dc9c/original/a-facile-supramolecular-strategy-to-switch-photodynamic-pathway-and-augment-ros-production-of-sensitizers-for-enhanced-tumor-therapy.pdf
|
614a5c914853d24f15ade160
|
10.26434/chemrxiv-2021-509z6
|
A Theory-guided X-ray Absorption Spectroscopy Approach for Identifying Active Sites in Atomically Dispersed Transition Metal Catalysts
|
Atomically dispersed supported metal catalysts offer new properties and the benefits of maximized metal accessibility and utilization. The characterization of these materials, however, remains challenging. Using atomically-dispersed Pt supported on crystalline MgO (chosen for its well-defined bonding sites for Pt) as a prototypical example, in this work, we demonstrate how systematic density functional theory calculations (for assessing all the potentially stable Pt sites) combined with automated EXAFS analysis can lead to unbiased identification of isolated, surface-enveloped platinum cations as the catalytic species for CO oxidation. The catalyst has been characterized by atomic-resolution imaging, EXAFS, and HERFD-XANES spectroscopies; the proposed Pt site are in full agreement with experiment. This theory-guided workflow leads to rigorously determined structural models and provides a more detailed picture of the structure of the catalytically active sites than what is currently possible with conventional EXAFS analysis. As this approach is efficient and agnostic to the metal, support, and catalytic reaction, we posit that it will be of broad interest to the materials characterization and catalysis communities.
|
Yizhen Chen; Rachita Rana; Tyler Sours; FERNANDO D. VILA; Shaohong Cao; Thomas Blum; Jiyun Hong; Adam Hoffman; Chia-Yu Fang; Zhennan Huang; Chunyan Shang; Chuanhao Wang; Jie Zeng; Miaofang Chi; Coleman Kronawitter; Simon Bare; Bruce Gates; Ambarish Kulkarni
|
Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Heterogeneous Catalysis; Spectroscopy (Physical Chem.); Surface
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-09-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614a5c914853d24f15ade160/original/a-theory-guided-x-ray-absorption-spectroscopy-approach-for-identifying-active-sites-in-atomically-dispersed-transition-metal-catalysts.pdf
|
60c74479337d6c1a44e26de7
|
10.26434/chemrxiv.9827336.v1
|
Real Time Nuclear Magnetic Resonance Detection of Fumarase Activity using Parahydrogen-Hyperpolarized [1-13C]fumarate
|
Hyperpolarized fumarate can be used as a probe of real-time metabolism
in vivo, using carbon-13 magnetic resonance imaging. Dissolution dynamic
nuclear polarization is commonly used to produce hyperpolarized fumarate, but a
cheaper and faster alternative is to produce hyperpolarized fumarate via PHIP (parahydrogen
induced polarization). In this work we <i>trans</i>-hydrogenate [1-<sup>13</sup>C]acetylene
dicarboxylate with <i>para</i>-enriched hydrogen using a commercially available
Ru catalyst in water to produce hyperpolarized [1-<sup>13</sup>C]fumarate. We
show that fumarate is produced in 89% yield, with succinate as a side product
in 11% yield. The proton polarization is converted into <sup>13</sup>C
magnetization using a constant adiabaticity field cycle, and a polarization
level of 25% is achieved using 86% <i>para</i>-enriched hydrogen gas. We inject
the hyperpolarized [1-<sup>13</sup>C]fumarate into cell suspensions and track
the metabolism. This work opens the path to greatly accelerated preclinical
studies using fumarate as a biomarker.
|
James Eills; Eleonora Cavallari; Carla Carrera; Dmitry Budker; Silvio Aime; Francesca Reineri
|
Cell and Molecular Biology; Spectroscopy (Physical Chem.)
|
CC BY 4.0
|
CHEMRXIV
|
2019-09-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74479337d6c1a44e26de7/original/real-time-nuclear-magnetic-resonance-detection-of-fumarase-activity-using-parahydrogen-hyperpolarized-1-13c-fumarate.pdf
|
652056a845aaa5fdbb71582b
|
10.26434/chemrxiv-2023-n31xc
|
Exploring Bismuth coordination complexes as visible light absorbers: Synthesis, characterization and photophysical properties
|
Bismuth based coordination complexes are advantageous over other metal complexes, as Bismuth is the heaviest non-toxic element with high spin orbit coupling and potential optoelectronics applications. Herein, four Bismuth halide-based coordination complexes [Bi2Cl6(phen-thio)2] (1), [Bi2Br6(phen-thio)2] (2), [Bi2I6(phen-thio)2] (3), and [Bi2I6(phen-Me)2] (4) were synthesized, characterized and subjected to detailed photophysical studies. The complexes were characterized by single crystal X-ray diffraction, powder X-ray diffraction and NMR studies. Spectroscopic analysis of 1-4 in solutions of different polarities were performed to understand the role of organic and inorganic components in determining the ground and excited state properties of the complexes. The photophysical properties of the complexes were characterized by ground state absorption, steady state photoluminescence, microsecond time-resolved photoluminescence and absorption spectroscopy. Periodic Density Functional Theory (DFT) calculations were performed on the solid state structures to understand the role of organic and inorganic part of the complexes. The studies showed that changing the ancillary ligand from chlorine (Cl), bromine (Br) to iodine (I) bathochromically shifts the absorption band along with enhancing the absorption coefficient. Also, changing the halides (Cl, Br to I) affect the photoluminescent quantum yields of the ligand centered (LC) emissive state without markedly affecting the lifetimes. The combined results confirmed that ground state properties are strongly influenced by the inorganic part and the lower energy excited state is LC. This study paves the way to design novel bismuth coordination complexes for optoelectronic applications by rigorously choosing the ligands and bismuth salt.
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Harsh Bhatia; Junjun Guo; Christopher N. Savory; Martyn Rush; David Iain James; Avishek Dey; Charles Chen; Dejan-Krešimir Bučar; Tracey M. Clarke; David O. Scanlon; Robert G. Palgrave; Bob C. Schroeder
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Organometallic Chemistry; Coordination Chemistry (Organomet.); Ligands (Organomet.); Spectroscopy (Organomet.)
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CC BY 4.0
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CHEMRXIV
|
2023-10-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652056a845aaa5fdbb71582b/original/exploring-bismuth-coordination-complexes-as-visible-light-absorbers-synthesis-characterization-and-photophysical-properties.pdf
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63479ce463f35a909654857d
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10.26434/chemrxiv-2022-0l7qf
|
Synthesis and characterization of new N-Heterocyclic-BF3 adducts and their reactivity vs water
|
Species derived from N-Heterocycles with BF3 Lewis acids generate adducts that are redox active. Here we report the synthesis and characterization of 5 N-Heterocycle-BF3 adducts: Py-(BF3)2, Q-(BF3)2, Ph-(BF3)2, TMQ-(BF3), and Dipy-(BF3)2. The new adducts were structurally characterized by 1H, 11B, and 19F NMR. As an example, the Q-BF3 adduct is stable in an inert environment but in the presence of oxygen or water, its voltammetric profile decays, suggesting chemical decomposition of the adduct. Furthermore, this decomposition is accompanied by the generation of BF4-. The crystalline structure of the reaction product of TMQ-(BF3) with traces of water was obtained, showing that the BF3 generates BF4- counterion. Based on our observations, we proposed a plausible reaction mechanism for the generation of BF4-.
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Adolfo I. B. Romo; Md Sazzad Hossain; Toby J. Woods; Joaquin Rodriguez-Lopez
|
Inorganic Chemistry; Analytical Chemistry; Energy; Analytical Chemistry - General; Coordination Chemistry (Inorg.); Inorganic Acid/Base Chemistry
|
CC BY NC 4.0
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CHEMRXIV
|
2022-10-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63479ce463f35a909654857d/original/synthesis-and-characterization-of-new-n-heterocyclic-bf3-adducts-and-their-reactivity-vs-water.pdf
|
6426fa9adb1a20696e4e546c
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10.26434/chemrxiv-2023-h1498
|
How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques
|
Enzymatic catalysis is a complex process that can involve multiple conformations of the enzyme:substrate complex and several competitive reaction pathways, resulting in a multi-dimensional free energy landscape. The study of enzymatic activity often requires deep knowledge of the system to establish the catalytic mechanism and identify the possible reactive conformations of the complex. Here, we present an enhanced sampling and machine learning-based approach to explore the catalytic reaction space and characterize the transformation from reactive to non-reactive conformations with minimal a priori knowledge of the system. We applied this approach to study the rate-determining step of the glycolysis reaction of maltopentose catalyzed by human pancreatic α-amylase, an important enzyme in glucose production as well as a major drug target for the treatment of type-II diabetes. We unravel the complexity of the enzymatic reaction, reveal three binding modes of the substrate in the catalytic pocket, and highlight the role of water in the catalytic process and in the stepwise conversion of reaction-ready to non-reactive conformations. Overall, these insights offer atomistic details on the catalytic mechanism and dynamics of the active site, allowing to shed light on two fundamental questions in enzymatic catalysis, that is how and when does an enzyme react?
|
Sudip Das; Umberto Raucci; Rui Neves ; Maria Ramos ; Michele Parrinello
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Computational Chemistry and Modeling; Machine Learning; Biocatalysis
|
CC BY NC ND 4.0
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CHEMRXIV
|
2023-04-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6426fa9adb1a20696e4e546c/original/how-and-when-does-an-enzyme-react-unraveling-amylase-catalytic-activity-with-enhanced-sampling-techniques.pdf
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60c740200f50dbc9f83958e8
|
10.26434/chemrxiv.7635746.v1
|
Discovery of Superbroad Mid-Infrared Luminescent Metal-Organic Framework Glass
|
<p>Metal-organic framework
(MOF) glasses are a newly discovered family of melt-quenched glasses.
However, so far it is not known whether these glasses exhibit photonic
functionalities. Here, we show the discovery of the luminescent behavior of a
MOF glass, i.e., the cobalt doped zeolitic imidazolate frameworks-62 (ZIF-62)
glass (Zn<sub>1-<i>x</i></sub> Co<i><sub>x</sub></i> (Im)<sub>1.9</sub> (bIm)<sub>0.1</sub>,
<i>x</i> = 0, 0.1 and 0.5), which was obtained by melt-quenching its
corresponding ZIF-62 crystal. The synthesized crystal was precipitated in the
form of spherical nano/micro-crystalline structure, which collapses structurally to form laminated
glass with ultrahigh glass forming ability and the same short
range molecular structure of the parent crystalline MOF. We observed the super-broadband mid-infrared (Mid-IR) luminescence (in the
wavelength range of 1.5 µm – 4.8 µm) both in the crystalline and amorphous
phases. The observed Mid-IR emission originates from d-d transition of Co<sup>2+</sup>
ions that is protected by the strong Co-N coordination. The discovery of the luminescent glasses may
pave the way towards new photonic applications of bulk MOF glasses,
such as Mid-IR lasers.
</p>
|
Mohamed. A. Ali; Jinjun Ren; Xiaofeng Liu; Youjie Hua; Yuanzheng Yue; Qiu Jianrong
|
Hybrid Organic-Inorganic Materials; Optics; Structure
|
CC BY NC ND 4.0
|
CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740200f50dbc9f83958e8/original/discovery-of-superbroad-mid-infrared-luminescent-metal-organic-framework-glass.pdf
|
676476bafa469535b91fa223
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10.26434/chemrxiv-2024-h09tl
|
Programmable Metal Arrangements in Metal-Organic Polyhedra and Frameworks
|
The preparation of regioisomers of small molecules is routine, but an analogous concept of positional isomerism is absent for extended materials. Crystalline frameworks such as zeolites and metal-organic frameworks (MOFs) can furnish well-defined active sites for heterogeneous catalysis, but their arrangement cannot be tuned in isolation. Here we show that a mobility-tuned synthesis approach permits selective synthesis of multiple different “structomers”, which are isostructural and compositionally identical but which feature different metal arrangements. High-fidelity access to each targeted metal arrangement was confirmed by operationally facile electron paramagnetic resonance analysis and validated by mass spectrometry. The performance of Rh centers in propene hydrogenation catalysis differs substantially for different metal arrangements within the framework, even though all Rh centers have identical primary coordination environments. For properties that depend on metal distances, structomer-selective synthesis thus presents a new paradigm for fundamental study and performance optimization.
|
Qiming Jin; Paolo Cleto Bruzzese; Alessandro Vetere; Claudia Weidenthaler; Eko Budiyanto; Mir Henglin; Nils Nöthling; Alexander Schnegg; Constanze Neumann
|
Materials Science; Catalysis; Nanostructured Materials - Materials; Heterogeneous Catalysis; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-12-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676476bafa469535b91fa223/original/programmable-metal-arrangements-in-metal-organic-polyhedra-and-frameworks.pdf
|
60c740e3f96a003419286366
|
10.26434/chemrxiv.7701044.v2
|
First-Principles Study of AlPO4-H3, a Hydrated Aluminophosphate Zeotype Containing Two Different Types of Adsorbed Water Molecules
|
<div>Porous aluminophosphate zeotypes (AlPOs) are promising materials for heat transformation applications using water as a working fluid. Two "types" of adsorbed water molecules can be distinguished in hydrated AlPOs: Water molecules adsorbed in the direct proximity of framework aluminium atoms form bonds to these Al atoms, with the coordination number of Al increasing from four to five or six. The remaining water molecules that are adsorbed in other parts of the accessible pore space are not strongly bonded to any framework atom, they interact with their environment exclusively through hydrogen bonds. The APC-type small-pore aluminophosphate AlPO<sub>4</sub>-H3 contains both types of H<sub>2</sub>O molecules. In the present work, this prototypical hydrated AlPO is studied using dispersion-corrected density functional theory (DFT) calculations. After validating the computations against experimental crystal structure and Raman spectroscopy data, three interrelated aspects are addressed: First, calculations for various partially hydrated models are used to establish that such partially hydrated phases are not thermodynamically stable, as the interaction with the adsorbed water molecules is distinctly weaker than in fully hydrated AlPO<sub>4</sub>-H3. Second, IR and Raman spectra are computed and compared to those of the dehydrated analogue AlPO<sub>4</sub>-C, leading to the identification of a few "fingerprint" modes that could be used as indicators for the presence of Al-coordinated water molecules. Finally, DFT-based molecular dynamics calculations are employed to study the dynamics of the adsorbed water molecules. All in all, this in-depth computational study of AlPO<sub>4</sub>-H3 contributes to the fundamental understanding of hydrated AlPOs, and should therefore provide valuable information for future computational and experimental studies of these systems.</div>
|
Michael Fischer
|
Solid State Chemistry; Theory - Inorganic; Computational Chemistry and Modeling
|
CC BY 4.0
|
CHEMRXIV
|
2019-02-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e3f96a003419286366/original/first-principles-study-of-al-po4-h3-a-hydrated-aluminophosphate-zeotype-containing-two-different-types-of-adsorbed-water-molecules.pdf
|
60c74dffbb8c1aa58e3db6a3
|
10.26434/chemrxiv.12689444.v1
|
Synthesis and Characterization of Phosphate Doped BaPr1-y(Y/Yb/Tm)yO3-δ
|
<p>In this paper we examine the effects of doping phosphate into yttrium,
ytterbium, and thulium doped BaPrO<sub>3</sub>. Through phosphate doping it is
possible to achieve high levels of Y/Yb/Tm, and we show that it is possible to
completely replace all the Pr with this co-doping strategy, albeit such phases
contained small impurities. The
samples were analysed through a combination of X-ray diffraction, TGA, Raman
spectroscopy and conductivity measurements. Conductivity data indicated that
these heavily Y/Yb/Tm doped samples, however, showed lower conductivities than
reported for previously for low levels (10-20%) of Y/Yb doping. </p>
|
Phil Keenan; Alaric smith; Peter Slater
|
Ceramics; Solid State Chemistry; Fuel Cells
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74dffbb8c1aa58e3db6a3/original/synthesis-and-characterization-of-phosphate-doped-ba-pr1-y-y-yb-tm-y-o3.pdf
|
60c7453a4c891937aead2952
|
10.26434/chemrxiv.9980825.v1
|
Synthesis of Phospho-Amino Acid Analogues as Tissue Adhesive Cement Additives
|
We report the synthesis of a library of phospho-amino acid analogues using a novel allyl-phosphoester deprotection strategy. By reacting phenols and alcohols with a combination of POCl3 and allyl alcohol we generate protected phosphoesters that can be subsequently deprotected via treatment with Pd(OAc)2. We go on to show that the generated phosphoserine and phosphotyrosine analogues can be used to generate adhesive calcium phosphate cements with potential applications in the treatment of bone defects. In particular, we use mechanical testing to demonstrate the importance of multiple calcium binding motifs and steric arrangement in promoting adhgesive strength.
|
Christopher Spicer; Michael Pujari-Palmer; Hélène Autefage; Gerard Insley; Philip Procter; Håkan Engqvist; Molly Stevens
|
Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Biocompatible Materials; Ceramics
|
CC BY NC 4.0
|
CHEMRXIV
|
2019-10-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7453a4c891937aead2952/original/synthesis-of-phospho-amino-acid-analogues-as-tissue-adhesive-cement-additives.pdf
|
64709dac4f8b1884b751f232
|
10.26434/chemrxiv-2022-kckfp-v3
|
Investigating the role of compression rates in pressure induced polymerization of crystalline acrylamide using ab initio molecular dynamics
|
Varying the rate at which pressure is applied on a crystal is experimentally known to yield different pressure induced polymorphic structures. Herein, we explore the effect of pressure increase rate on pressure induced polymerization in crystalline acrylamide, using a density functional theory based approach. While quasi-static compression at 0 K stabilizes a 3-dimensional topochemical polymer, Pol-I, at 23 GPa, rapid compression optimizations suggest the presence of multiple polymeric intermediates in the system. Room temperature ab initio molecular dynamics performed with two different compression rates - 0.4 GPa/ps and 2 GPa/ps - revealed very different structural evolution of the system. While both rates ultimately yielded a metastable 1-dimensional polymer at pressures beyond 64 GPa, rapid compression resulted in many disordered polymers at lower pressures with unanticipated linkages. The mechanisms leading to polymerization as well as the structure and electronic properties of the various polymer polymorphs obtained in the two compression routes are described. While large kinetic barriers delay the formation of the thermodynamically favored polymer Pol- I, our simulations suggest a hierarchical route for the pressure induced polymerization of solid acrylamide towards the thermodynamically favorable Pol-I.
|
Rashid Rafeek V. Valappil; Sayan Maity; Ashwini Anshu; Lavanya M. Ramaniah; Varadharajan Srinivasan
|
Theoretical and Computational Chemistry; Physical Chemistry; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64709dac4f8b1884b751f232/original/investigating-the-role-of-compression-rates-in-pressure-induced-polymerization-of-crystalline-acrylamide-using-ab-initio-molecular-dynamics.pdf
|
65323467c3693ca993b43b11
|
10.26434/chemrxiv-2023-h7b6m
|
Metabolic pathways of acylcarnitine synthesis
|
Acylcarnitines are important markers in metabolic studies of many diseases, including metabolic, cardiovascular, and neurological disorders. We reviewed analytical methods for analyzing acylcarnitines with respect to the available structural information, the technical limitations of older methods, and the potential of new mass spectrometry-based techniques to provide new information on metabolite structure. We summarized the nomenclature of acylcarnitines based on historical common names and common abbreviations, and we propose the use of systematic abbreviations derived from the shorthand notation for lipid structures. The transition to systematic nomenclature will facilitate acylcarnitine annotation, reporting, and standardization in metabolomics. We have reviewed the metabolic origins of acylcarnitines important for the biological interpretation of human metabolomic profiles. We identified neglected isomers of acylcarnitines and summarized the metabolic pathways involved in the synthesis and degradation of acylcarnitines, including branched-chain lipids and amino acids. We reviewed the primary literature, mapped the metabolic transformations of acyl-CoAs to acylcarnitines, and created a freely available WikiPathway WP5423 to help researchers navigate the acylcarnitine field. The WikiPathway was curated, metabolites and metabolic reactions were annotated, and references were included. We also provide a table for conversion between common names and abbreviations and systematic abbreviations linked to the LIPID MAPS or Human Metabolome Database.
|
Jana Brejchova; Kristyna Brejchova; Ondrej Kuda
|
Analytical Chemistry; Biochemical Analysis; Chemoinformatics; Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65323467c3693ca993b43b11/original/metabolic-pathways-of-acylcarnitine-synthesis.pdf
|
60c7490e0f50dbb813396858
|
10.26434/chemrxiv.12018963.v1
|
Parallel Implementation of Density Functional Theory Methods in the Quantum Interaction Computational Kernel Program
|
<div>
<div>
<div>
<p>We present the details of a GPU capable exchange correlation (XC) scheme integrated into the open source QUantum
Interaction Computational Kernel (QUICK) program. Our implementation features an octree based numerical grid point partitioning scheme, GPU enabled grid pruning and basis/primitive function prescreening and fully GPU capable XC energy and gradient
algorithms. Benchmarking against the CPU version demonstrated that the GPU implementation is capable of delivering an impres-
sive performance while retaining excellent accuracy. For small to medium size protein/organic molecular systems, the realized
speedups in double precision XC energy and gradient computation on a NVIDIA V100 GPU were 60 to 80-fold and 140 to 780-
fold respectively as compared to the serial CPU implementation. The acceleration gained in density functional theory calculations
from a single V100 GPU significantly exceeds that of a modern CPU with 40 cores running in parallel.
</p>
</div>
</div>
</div>
|
Madushanka Manathunga; Yipu Miao; Dawei Mu; Andreas Goetz; Kenneth M. Merz Jr.
|
Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-03-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7490e0f50dbb813396858/original/parallel-implementation-of-density-functional-theory-methods-in-the-quantum-interaction-computational-kernel-program.pdf
|
6156992fef08e6bc961ef5a4
|
10.26434/chemrxiv-2021-43zr3
|
pH-responsive polymer-based biomacromolecule nanosponges as biodegradable carriers for DOX delivery
|
Cellulose is the most abundant renewable biomaterial on earth and beta-cyclodextrin (BCD) is among the most commonly used biocompatible drug encapsulation agents. Combining these bio-organic materials is a very powerful approach to greatly enhance the bioavailability of many drugs. These systems also allow for optimal selective drug release profiles, high biocompatibility, as well as “green nanomedicine” approaches that are eco-friendly in their synthesis and have minimal ecological toxicity. herein, we designed a new type of green and biopolymer-based nanosponge drug carriers which is polymerized by crosslinking beta-cyclodextrin ethylene diamine (βCD-EDA) with bifunctional hairy nanocellulose (BHNC). BHNC contains, besides aldehyde groups, carboxyl groups which can react with amino groups in βCD-EDA. Firstly, the crosslinker βCD-EDA was obtained through a simple nucleophilic substitution reaction between beta-cyclodextrin carbonyl imidazole (βCD-CI) and ethylene diamine (EDA). Secondly, BHNC was functionalized with the crosslinker βCD-EDA through a facile nucleophilic substitution crosslinking reaction of the BHNC activated carboxyl groups by the amines of βCD-EDA. We refer to the polymerized highly crosslinked BHNC-βCD-EDA network as BBE. Various ratios of βCD-EDA and BHNC were polymerized with the help of DMTMM as an activator, which resulted in different morphological shapes of BBE, and thus in different release profiles and pH-responsiveness. Unlike other polymer-based βCDs and nanosponges, these new types of crosslinked polymer were prepared in a green and safe solvent (water) and with very short reaction times and at low temperatures. Finally, the BBE polymers were tested as biocompatible nanocarriers for controllable doxorubicin (DOX) delivery. These hyper crosslinked polymers show a high capacity for loading DOX with extended drug release. Furthermore, breast cancer cell cultures show lower cell viability when DOX was loaded in various BBEs than control samples or DOX alone, indicating that our DOX-BBE drug delivery systems are better anticancer agents than DOX alone.
|
Marzieh Heidari Nia; Said Ashkar; Jose G. Munguia-Lopez; Joseph M. Kinsella; Theo G.M. van de Ven
|
Biological and Medicinal Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Bioengineering and Biotechnology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-10-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6156992fef08e6bc961ef5a4/original/p-h-responsive-polymer-based-biomacromolecule-nanosponges-as-biodegradable-carriers-for-dox-delivery.pdf
|
634771c80322f3783849130a
|
10.26434/chemrxiv-2022-98nn4
|
High-voltage supercapacitive swing adsorption of carbon dioxide
|
We report Supercapacitive Swing Adsorption (SSA) with garlic roots-derived activated carbon achieving a record adsorption capacity of 312 mmol/kg at a low energy consumption of 72 kJ/mol and high mass loadings (>30 mg/cm2) at 1 V. The activated carbons are inexpensively prepared in a one-step process using potassium carbonate, and air as activators. The adsorption capacity further increases with increasing voltage. Up to a voltage of 1.4 V there is only minor increase in energy consumption, and a sorption capacity of 524 mmol/kg at an energy consumption of 130 kJ/mol can be achieved. The volumetric sorption capacity is also enhanced, and reaches values of 85.7 mol.m-3 at 1.0 V, and 126 mol.m-3 at 1.4 V. Cycle stability for at least 130 h is demonstrated.
|
Muhammad Bilal; Jiajie Li; Hao Guo; Kai Landskron
|
Energy; Chemical Engineering and Industrial Chemistry; Energy Storage; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2022-10-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634771c80322f3783849130a/original/high-voltage-supercapacitive-swing-adsorption-of-carbon-dioxide.pdf
|
60c7428cf96a0030e728661e
|
10.26434/chemrxiv.8307629.v1
|
Asymmetric Redox-Neutral Radical Cyclization Catalyzed by Flavin-Dependent ‘Ene’-Reductases
|
<p>Flavin-dependent ‘ene’-reductases (EREDs) are exquisite catalysts for effecting stereoselective reductions. While these reactions typically proceed through a hydride transfer mechanism, we recently found that EREDs can also catalyze reductive dehalogenations and cyclizations via single electron transfer mechanisms. Here we demonstrate that these enzymes can catalyze redox-neutral radical cyclizations to produce enantioenriched oxindoles from a-haloamides. This transformation is a C–C bond forming reaction currently unknown in nature and one for which there are no catalytic asymmetric examples. Mechanistic studies indicate the reaction proceeds via the flavin semiquinone/quinone redox couple, where ground state flavin semiquinone provides the electron for substrate reduction and flavin quinone oxidizes the vinylogous a-amido radical formed after cyclization. This mechanistic manifold was previously unknown for this enzyme family, highlighting the versatility of EREDs in asymmetric synthesis.</p>
|
Michael Black; Kyle F. Biegasiewicz; Andrew J. Meichan; Daniel G. Oblinsky; bryan kudish; Gregory Scholes; Todd Hyster
|
Organic Synthesis and Reactions; Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-06-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7428cf96a0030e728661e/original/asymmetric-redox-neutral-radical-cyclization-catalyzed-by-flavin-dependent-ene-reductases.pdf
|
64ae6459ba3e99daeff4d3c6
|
10.26434/chemrxiv-2023-kx7wh-v3
|
Electrostatic tuning of transmission in NbS2/WSe2 2D Lateral Hetero-Structures: A computational study
|
We present a first-principles computational study of the NbS2/WSe2 junction between two transition metal dichalcogenide monolayers as a prototypical metal/semiconductor 2-dimensional (2D) lateral hetero-structure (LH) to investigate the effects of electrostatic perturbations on electron transport in 2D LH systems. In order to simulate electrostatic (charged or dipolar) defects in the substrate, we introduce ionic systems (LiF lines) properly positioned in two different configurations and study cases, corresponding to modeling two different phenomena: (i) an electrostatic defect in the middle of the semiconducting part of the hetero-structure (qualitatively analogous to a gate voltage opposing transmission), and (ii) an electrostatic perturbation re-aligning and flattening the electrostatic potential along the asymmetric LH junction. In the former case, we determine a substantial decrease of transmission even for small values of the perturbation (providing information that can be used to achieve a quantitative correlation between substrate-induced defectivity and device performance degradation in experiment), whereas in the latter we predict that electron transport can be significantly enhanced by properly tuning external electrostatic perturbations at the interface.
|
Poonam Kumari; Zahra Golsanamlou; Alexander Smogunov; Luca Sementa; Alessandro Fortunelli
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-07-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ae6459ba3e99daeff4d3c6/original/electrostatic-tuning-of-transmission-in-nb-s2-w-se2-2d-lateral-hetero-structures-a-computational-study.pdf
|
6216933d91a2e60d14d94b41
|
10.26434/chemrxiv-2022-bsnlw
|
Hyperthermia-induced in situ drug amorphization by superparamagnetic nanoparticles in oral dosage forms
|
Superparamagnetic iron oxide nanoparticles (SPIONs) generate heat upon exposure to an alternating magnetic field (AMF) which has been studied for hyperthermia treatment and triggered drug release. This study introduces a novel application of magnetic hyperthermia to induce amorphization of a poorly aqueous soluble drug, celecoxib, in situ in tablets for oral administration. In situ amorphization can overcome the drug development hurdle of poor aqueous solubility by molecularly dispersing the drug in a polymeric network inside a tablet. However, current shortcomings of this approach include low drug loading in the tablets, toxicity of enabling excipients, and drug degradation. Here, SPIONs produced by flame spray pyrolysis are compacted with polyvinylpyrolidone and celecoxib, and exposed to an AMF. The degree of amorphization is strongly linked to the maximum tablet temperature achieved during AMF exposure, which depends on SPION composition and content in the tablets. Manganese ferrites exhibit no toxicity in human intestinal Caco-2 cell lines and are more effective than zinc ferrites in inducing complete amorphization of celecoxib. The resulting rapid dissolution and high solubility of in situ amorphized celecoxib in biorelevant intestinal fluid demonstrates the promising capability of SPIONs as enabling excipients to magnetically induce amorphization in situ in oral dosage forms.
|
Shaquib Rahman Ansari; Nele-Johanna Hempel; Shno Asad; Peter Svedlindh; Christel A. S. Bergström; Korbinian Löbmann; Alexandra Teleki
|
Materials Science; Nanoscience; Magnetic Materials
|
CC BY 4.0
|
CHEMRXIV
|
2022-02-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6216933d91a2e60d14d94b41/original/hyperthermia-induced-in-situ-drug-amorphization-by-superparamagnetic-nanoparticles-in-oral-dosage-forms.pdf
|
60c740dd9abda23c57f8bd70
|
10.26434/chemrxiv.7844720.v1
|
Anomalous Cracking in a Metal-Organic Framework Glass
|
<p>Metal-organic
framework (MOF) glasses is a newly discovered family of melt-quenched glasses. Recently, several intriguing features (e.g.,
ultrahigh glass forming ability and low liquid fragility) have been discovered in
the glasses obtained from zeolitic imidazolate frameworks (ZIFs) that are a subset of MOFs. However, the fracture behavior of ZIF glasses remains elusive.
Here, we report on the first important finding, namely, the anomalous crack behavior
in a representative ZIF glass, i.e., ZIF-62 glass with the chemical composition of<a> ZnIm<sub>2-<i>x</i></sub>bIm<i><sub>x</sub></i></a>, where the
central node – zinc - is coordinated to imidazolate (Im) and benzimidazole
(bIm) ligands. By performing micro- and nano-indentation and atomic
force microscopy (AFM) analysis, we
observe a unique sub-surface cracking phenomenon with induced shear bands on the
indent faces, in contrast to the cracking behavior of other types of network
glasses. The occurrence of shear bands could be attributed to the breakage of
coordinative bonds that are much weaker than ionic and covalent The observed
anomalous cracking behavior accords with the high Poisson’s ratio (=0.34) of the
ZIF-62 glass. </p>
|
Malwina Stepniewska; Kacper Januchta; Chao Zhou; Ang Qiao; Morten M. Smedskjaer; Yuanzheng Yue
|
Hybrid Organic-Inorganic Materials; Ligands (Organomet.); Physical and Chemical Properties; Surface
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-03-15
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740dd9abda23c57f8bd70/original/anomalous-cracking-in-a-metal-organic-framework-glass.pdf
|
660aabb5e9ebbb4db91e9bc3
|
10.26434/chemrxiv-2024-mlsds-v2
|
Unveiling the unusual i-motif-derived architecture of a DNA aptamer exhibiting high affinity for influenza A virus
|
Non-canonical nucleic acid structures have been shown the capacity to selectively interact with proteins, thereby exerting influence over various intracellular processes. Among these structures, both natural and artificial G-quadruplexes have been extensively studied in relation to their structure-activity relationships. In contrast, the role of i-motifs remains incompletely evaluated. In this study the artificial aptamer BV42 possessing a high affinity for hemagglutinin of influenza A virus was proven to contain the i-motif structure even at neutral pH. However, conformational heterogeneity of BV42 poses challenges for in-depth structural investigations. Using molecular dynamics simulations and introducing chemical modifications for molecular probing, a putative binding site in the aptamer was suggested. These findings have enabled us to redesign the aptamer, eliminating the conformational diversity associated with the i-motif while preserving its binding affinity. Subsequent validation through NMR spectroscopy confirms the presence of the i-motif/duplex junction with the 3-cytosine loop located near the junction. This study elucidates a distinctive instance of an unusual nucleic acid architecture involved in molecular recognition, thereby shedding light on the structural peculiarities of functional i-motifs.
|
Vladimir Tsvetkov; Bartomeu Mir; Rugiya Alieva; Alexander Arutyunyan; Ilya Oleynikov; Roman Novikov; Elizaveta Boravleva; Polina Kamzeeva; Timofei Zatsepin; Andrey Aralov; Carlos González; Elena Zavyalova
|
Biological and Medicinal Chemistry; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-04-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660aabb5e9ebbb4db91e9bc3/original/unveiling-the-unusual-i-motif-derived-architecture-of-a-dna-aptamer-exhibiting-high-affinity-for-influenza-a-virus.pdf
|
60c7567a567dfe36daec64b3
|
10.26434/chemrxiv.14248889.v1
|
Thermodynamic Cyclic Voltammograms: Peak Positions and Shapes
|
Based on a mean-field description of thermodynamic cyclic voltammograms (CVs), we analyse here in full generality, how CV peak positions and shapes are related to the underlying interface energetics, in particular when also including electrostatic double layer (DL) effects. We show in particular, how non-Nernstian behaviour is related to capacitive DL charging, and how this relates to common adsorbate-centered interpretations such as a changed adsorption energetics due to dipole-field interactions and the electrosorption valency -- the number of exchanged electrons upon electrosorption per adsorbate. Using Ag(111) in halide-containing solutions as test case, we demonstrate that DL effects can introduce peak shifts that are already explained by rationalizing the interaction of isolated adsorbates with the interfacial fields, while alterations of the peak shape are mainly driven by the coverage-dependence of the adsorbate dipoles. In addition, we analyse in detail how changing the experimental conditions such as the ion concentrations in the solvent but also of the background electrolyte can affect the CV peaks via their impact on the potential drop in the DL and the DL capacitance, respectively. These results suggest new routes to analyse experimental CVs and use of those for a detailed assessment of the accuracy of atomistic models of electrified interfaces e.g. with and without explicitly treated interfacial solvent and/or approximate implicit solvent models.
|
Nicolas G Hörmann; Karsten Reuter
|
Electrochemistry; Electrochemistry - Mechanisms, Theory & Study
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7567a567dfe36daec64b3/original/thermodynamic-cyclic-voltammograms-peak-positions-and-shapes.pdf
|
6731c55b5a82cea2fabf27d4
|
10.26434/chemrxiv-2024-l0z77
|
Could HIV-Vif complex docking ligands protect human-A3G?
|
This work computationally explored the possible protection of human A3G hypermutation, one of the most potent human natural inhibitors of human immunodeficiency viral (HIV) infections. This work focused on the possible inhibition of HIV Viral infectivity factor (Vif) which destroys A3G in natural infections. Due to the different assemblies of Vif with several human proteins, development of antiVif inhibitors as drugs have been limited. To propose new antiVif molecules for experimental testing, docking to recently described Vif-sA3G interfaces, were explored here by evolutionary docking. Tens of thousands of new molecular children were generated from previous antiVif and star-like parent molecules. Hundreds of children fitting Vif-cavity sA3G interfaces were then selected by consensus docking. Results predicted low-toxicity top-children displaying ~ 10-100 fold higher consensus docking-affinities including targeting similar amino acids than those previously described for antiVif drugs inhibiting HIV. Consensus top-children are proposed to test for possible experimental restoration of A3G hypermutation in the presence of HIV-Vif infections
|
julio coll
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems
|
CC BY 4.0
|
CHEMRXIV
|
2024-11-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6731c55b5a82cea2fabf27d4/original/could-hiv-vif-complex-docking-ligands-protect-human-a3g.pdf
|
66af54c001103d79c5b7219a
|
10.26434/chemrxiv-2024-j1mj2
|
Lithium and Sodium Benzimidazolate Coordination Networks: Syntheses, Structures and Thermal Properties
|
Alkali metal imidazolates are important compounds, serving as intermediates in organic synthesis and additives in alkali ion electrolytes. However, their solid-state structures and thermal behaviors remain largely unexplored. In this study, we present the synthesis, structural analysis and thermal characterization of lithium and sodium benzimidazolate (bim–). The crystal structures of these microcrystalline materials, determined by 3D-electron diffraction, reveal closely related layered coordination networks. In these structures, fourfold N-coordinated alkali ions are bridged in two dimensions by bim– linkers, with the networks’ surfaces decorated by the phenyl rings of the bim– linkers, stacking atop one another in the solid state. Differential scanning calorimetry combined with variable temperature X-ray powder diffraction indicate that both materials melt above 450 °C. Additionally, Na(bim) undergoes a displacive phase transition from an ordered alpha-phase to a highly disordered beta-phase before melting. Structural variations, primarily attributable to the differing ionic radii of Li+ and Na+, result in distinct coordination environments of the alkali metal ions and varying orientations of the bim– linkers. These differences lead to markedly distinct thermal behaviors: Li(bim) exhibits positive thermal expansion along all crystal axes, whereas Na(bim) switches from area negative thermal expansion (NTE) to linear NTE during the alpha→beta phase transition.
|
Pascal Kolodzeiski; Erik Svensson Grape; Roman Pallach; Lennard Richter; A. Ken Inge; Sebastian Henke
|
Inorganic Chemistry; Coordination Chemistry (Inorg.); Solid State Chemistry; Materials Chemistry; Crystallography – Inorganic
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-08-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66af54c001103d79c5b7219a/original/lithium-and-sodium-benzimidazolate-coordination-networks-syntheses-structures-and-thermal-properties.pdf
|
62210fc297f210d747fc1c11
|
10.26434/chemrxiv-2022-3ptwx
|
A flexible and scalable scheme for mixing computed formation energies from different levels of theory
|
Phase stability predictions are central to computational materials discovery efforts and have been made possible by large databases of computed properties from high-throughput density functional theory (DFT) calculations. Such databases now contain millions of calculations at the generalized gradient approximation (GGA) level of theory, representing an enormous investment of computational resources. Although it is now feasible to carry out large numbers of calculations using more accurate methods, such as meta-GGA functionals, recomputing the entirety of a database with a higher-fidelity method is impractical and would not effectively leverage the value embodied in existing calculations. Instead, we propose in this work a general procedure by which higher-fidelity, low-coverage calculations (e.g., meta-GGA calculations for selected chemical systems) can be combined with lower-fidelity, high-coverage calculations (e.g., an existing database of GGA calculations) in a robust and scalable manner to yield improved phase stability predictions. We demonstrate our scheme using legacy GGA(+\textit{U}) calculations and new r$^2$SCAN meta-GGA calculations from the Materials Project and illustrate its application to solid and aqueous phase stability. We discuss practical considerations for constructing mixed phase diagrams and present guidelines for prioritizing high-fidelity calculations for maximum benefit.
|
Ryan Kingsbury; Andrew S. Rosen; Ayush S. Gupta; Jason Munro; Shyue Ping Ong; Anubhav Jain; Shyam Dwaraknath; Matthew K. Horton; Kristin A. Persson
|
Theoretical and Computational Chemistry; Materials Science; Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62210fc297f210d747fc1c11/original/a-flexible-and-scalable-scheme-for-mixing-computed-formation-energies-from-different-levels-of-theory.pdf
|
63c6c7b230e3e51ae09398c6
|
10.26434/chemrxiv-2023-wrsqc-v2
|
Electrochemical logic to synthesize disilanes and oligosilanes from chlorosilanes
|
Oligosilanes are important compounds in industrial and synthetic chemistry. Here, we develop a general approach for the synthesis of linear and cyclic oligosilanes via the reductive activation of readily available chlorosilanes. The efficient and selective generation of silyl anion intermediates, which are arduous to achieve by other means, allows for the synthesis of various novel oligosilanes. In particular, this work presents a modular synthesis for a variety of functionalized cyclosilanes, which may give rise to materials with distinct properties from linear silanes but remain challenging synthetic targets. In comparison to the traditional Wurtz coupling, our method features milder conditions and improved chemoselectivity, broadening the functional groups that are compatible in oligosilane preparation. Computational studies support a mechanism whereby differential activation of two sterically and electronically distinct chlorosilanes are achieved in an electrochemically driven radical-polar crossover mechanism.
|
weiyang guan; Lingxiang Lu; Qifeng Jiang; Alexandra Gittens; Yi Wang; Luiz Novaes; Rebekka Klausen; Song Lin
|
Organic Chemistry; Inorganic Chemistry; Organic Synthesis and Reactions; Electrochemistry; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-01-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c6c7b230e3e51ae09398c6/original/electrochemical-logic-to-synthesize-disilanes-and-oligosilanes-from-chlorosilanes.pdf
|
60c75424bdbb89bd2fa3a5d2
|
10.26434/chemrxiv.13618982.v1
|
Atomic-Scale Structure and its Impact on Chemical Properties of Aluminum Oxide Layers Prepared by Atomic Layer Deposition on Silica
|
We report the atomic-scale structure of alumina layers obtained by atomic layer deposition (ALD) of trimethylaluminium onto partially dehydroxylated silica. Such a detailed insight into the atomic structure of the species formed with increasing Al content was gained using a variety of one- and two-dimensional solid-state nuclear magnetic resonance (NMR) experiments involving <sup>27</sup>Al, <sup>1</sup>H and <sup>29</sup>Si nuclei. <sup>15</sup>N dynamic nuclear polarization surface-enhanced NMR spectroscopy (<sup>15</sup>N DNP SENS) and infrared spectroscopy using <sup>15</sup>N-labelled pyridine as a probe molecule reveal that aluminium oxide layers on amorphous silica contain both strong Bronsted and strong Lewis acid sites, whereby the relative abundance and nature of these sites, and therefore the acidity of the surface, evolve with increasing thickness of the alumina film. <br />
|
Monu Kaushik; César Leroy; Zixuan Chen; David Gajan; Elena Willinger; Christoph Müller; Franck Fayon; Dominique Massiot; Alexey Fedorov; Christophe Copéret; Anne Lesage; Pierre Florian
|
Spectroscopy (Inorg.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-01-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75424bdbb89bd2fa3a5d2/original/atomic-scale-structure-and-its-impact-on-chemical-properties-of-aluminum-oxide-layers-prepared-by-atomic-layer-deposition-on-silica.pdf
|
650b8bfc60c37f4f7627f824
|
10.26434/chemrxiv-2022-dclvh-v2
|
Selective Photocatalytic Reduction of Acetylene to Ethylene Powered by a Cobalt-Porphyrin Metal–Organic Framework
|
The production of polymer-grade ethylene requires the purification of the ethylene feed from acetylene contaminant. Accomplishing this task by state-of-the-art thermal hydrogenation requires high temperature, an external feed of H2 gas, and noble metal catalysts, and is not only expensive and energy-intensive but also prone to over-hydrogenation to ethane. This paper reports the photocatalytic semihydrogenation of acetylene to ethylene using the metal-organic framework (MOF) Co-PCN-222. Under pure acetylene atmosphere the system achieves an overall conversion of 1.6 mol g-1 Co, and remains catalytically active for one week. Under a mixed acetylene/ethylene atmosphere (1 vol.% acetylene, 30 vol.% ethylene, the industrially relevant conditions), the system achieves nearly 100% conversion of acetylene after 87 hours with >99.9% ethylene selectivity over ethane. The cobalt active species is contained within the Zr-based Co-PCN-222 framework and the heterogeneous nature of the MOF lends advantages over the homogeneous catalyst, namely facile recyclability and increased longevity. These features also offer substantial advantages over current thermocatalytic hydrogenation technologies with respect to selectivity and sustainability. While MOFs have been pursued academically for the physical separation of acetylene and ethylene, this is the first demonstration of the potential MOFs have as catalysts for the selective, photocatalytic conversion of acetylene to ethylene.
|
Aaron Stone; Luka Dordevic; Samuel Stupp; Emily Weiss; Francesca Arcudi; Joseph Hupp
|
Catalysis; Nanoscience; Heterogeneous Catalysis; Photocatalysis; Redox Catalysis; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-09-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650b8bfc60c37f4f7627f824/original/selective-photocatalytic-reduction-of-acetylene-to-ethylene-powered-by-a-cobalt-porphyrin-metal-organic-framework.pdf
|
60c74cc5842e6578fcdb335d
|
10.26434/chemrxiv.12529631.v1
|
Molecular Growth upon Ionization of Van Der Waals Clusters Containing HCCH and HCN is a Pathway to Prebiotic Molecules
|
The growth mechanisms of organic molecules in an ionizing environment such as the interstellar medium are not completely understood. Here we examine by means of ab initio molecular dynamics (AIMD) simulations and density functional theory (DFT) computations the possibility of bond formation and molecular growth upon ionization of Van der Waals clusters of pure HCN clusters, and mixed clusters of HCN and HCCH, both of which are widespread in the interstellar medium. Ionization of van der Waals clusters can potentially lead to growth in low temperature and low-density environments. Our results show, that upon ionization of the pure HCN clusters, strongly bound stable structures are formed that contain NH bonds, and growth beyond pairwise HCN molecules is seen only in a small percentage of cases. In contrast, mixed clusters, where HCCH is preferentially ionized over HCN, can grow up to 3 or 4 units long with new carbon-carbon and carbon-nitrogen covalent bonds. Moreover, cyclic molecules formed, such as the radical cation of pyridine, which is a prebiotic molecule. The results presented here are significant as they provide a feasible pathway for molecular growth of small organic molecules containing both carbon and nitrogen in cold and relatively denser environments such as in dense molecular clouds but closer to the photo-dissociation regions, and protoplanetary disks. In the mechanism we propose, first, a neutral van der Waals cluster is formed. Once the cluster is formed it can undergo photoionization which leads to chemical reactivity without any reaction barrier.
|
Tamar Stein; Partha P. Bera; Timothy
J. Lee; Martin Head-Gordon
|
Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cc5842e6578fcdb335d/original/molecular-growth-upon-ionization-of-van-der-waals-clusters-containing-hcch-and-hcn-is-a-pathway-to-prebiotic-molecules.pdf
|
6617961b418a5379b09b9db7
|
10.26434/chemrxiv-2024-lzv43
|
Counterion Effects in [Ru(bpy)3](X)2-Photocatalyzed Energy Transfer Reactions
|
In this report, we show that modification of the X counterions constitutive of [Ru(bpy)3](X)2 photocatalysts modulates their catalytic activities in intermolecular [2+2] cycloaddition reactions operating through triplet-triplet energy transfer (TTEnT). Particularly noteworthy is the dramatic impact observed in low-dielectric constant solvent over the excited state quenching coefficient, which varies by two orders of magnitude depending on whether X is a large weakly bound (BArF-) or a tightly bound anion (TsO-). In addition, the counterion identity also greatly affects the photophysical properties of the cationic ruthenium complex, with [Ru(bpy)3](BArF4)2 exhibiting the shortest 3MLCT excited state lifetime, highest excited state energy and photostability, enabling remarkably enhanced performance (up to >1000 TON at low 500 ppm catalyst loading) in TTEnT photocatalysis.
|
Juliette Zanzi; Zachary Pastorel; Carine Duhayon; Elise Lognon; Christophe Coudret; Antonio Monari; Isabelle Dixon; Yves Canac; Michael Smietana; Olivier BASLE
|
Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Photocatalysis; Theory - Organometallic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-04-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6617961b418a5379b09b9db7/original/counterion-effects-in-ru-bpy-3-x-2-photocatalyzed-energy-transfer-reactions.pdf
|
60c758724c891959abad4bc3
|
10.26434/chemrxiv.14551329.v1
|
Optimizing Nannochloropsis Growing Conditions for Biodiesel Production Through Analysis of Lipid Content
|
Fossil fuels have propelled society to our current technology, but the future of energy lies in renewable resources, starting with vehicles. Despite constituting only 5% of the total vehicles in the United States, medium to heavy-duty trucks, which consume diesel fuel, are responsible for an astounding 23% of annual CO2 emissions in the transportation sector. The full implementation of greener biodiesel is often deemed an infeasible method for mitigating pollution because the production of such biodiesel directly competes with the agricultural industry for the available arable land. Energy-dense algae are more suitable feedstocks for biodiesel and circumvent many of the problems posed by current biodiesel feedstocks, and their potential can be used to propel the biodiesel industry into the future of sustainable energy. Nannochloropsis is a promising genus of algae due to its high productivity and lipid content. Here I show how to optimize the growing medium composition for increased biodiesel quality while maintaining high productivity by quantifying the constituent fatty acid type and composition using gas chromatography (GC). The algae are grown in two groups of three 2.5 L glass jugs spanning three concentration levels of nitrates and phosphates. A growing “f/2” medium is kept constant across trials. The algae are harvested using a flocculating solution of aluminum sulfate and vacuum filtration. In situ transesterification is used to achieve maximum conversion of fatty acids into fatty acid methyl esters, which are then analyzed using GC. The algae grown in low, medium, and high nutrient concentrations produced average absorbance values (a measure of biomass concentration) at 750 nm of 0.91, 0.99, and 1.18, respectively, after 32 days of growth. The maximum monounsaturated fatty acid (MUFA) concentration of 62.68% of total fatty acids was reached in a low nutrient concentration, which corresponds to high-quality biodiesel. Through this study, a scientific breakthrough was achieved by maximizing both the quality of biodiesel produced, which is beyond any currently available biodiesel, and also the quantity with a productivity of greater than 100 times the current biodiesel feedstocks.
|
Steven Liu; Devon Renock
|
Fuels - Energy Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758724c891959abad4bc3/original/optimizing-nannochloropsis-growing-conditions-for-biodiesel-production-through-analysis-of-lipid-content.pdf
|
60c747510f50db81cb3965b0
|
10.26434/chemrxiv.11628267.v1
|
Universal Scaling and Real-Time Monitoring of the Production of Liquid Exfoliated Graphene
|
<div>Shear-assisted liquid exfoliation is a primary candidate for producing defect-free two-dimensional materials from labs to industry. Diverse hydrodynamic conditions exist across production methods, and combined with low-throughput, high-cost characterization techniques, strongly contribute to the wide variability in performance and material quality. Through investigations on strikingly different flow regimes, and using graphene as the prototypical two-dimensional material, we find that scaling of production depends on local stress fi eld distributions and precursor residence time. We report a novel indirect diffuse reflectance method to measure graphene concentration in real-time, using low-cost optoelectronics and without the need to remove the precursor material from the heterogeneous dispersions. We show that this high-throughput, <i>in situ</i> approach has broad applicability by controlling the number of atomic layers on the fly, rapidly optimising green solvent design for maximum yield, and viewing live production rates. Combining insights on the hydrodynamics of exfoliation with this scalable monitoring technique, targeted process intensi fication, quality control, batch traceability and individually customisable materials on-demand are possible.</div>
|
Jason Stafford; Nwachukwu Uzo; Usmaan Farooq; Silvia Favero; Si Wang; Hseuh-Hung Chen; Anouk L'Hermitte; Camille Petit; Omar Matar
|
Carbon-based Materials; Materials Processing; Multilayers; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Fluid Mechanics; Process Control; Transport Phenomena (Chem. Eng.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-01-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747510f50db81cb3965b0/original/universal-scaling-and-real-time-monitoring-of-the-production-of-liquid-exfoliated-graphene.pdf
|
60c74e3e4c8919a35fad39a8
|
10.26434/chemrxiv.12729044.v1
|
In Silico Identification of the Potential Natural Inhibitors of SARS-CoV-2 Guanine-N7 Methyltransferase.
|
The outbreak of the COVID-19 pandemic caused by the SARS-CoV-2 has triggered intense
scientific research into the possible therapeutic strategies that can combat the ravaging disease.
One of such strategies is the inhibition of an important enzyme that affects an important
physiological process of the virus. The enzyme, Guanine 7 Methyltransferase is responsible for
the capping of the SARS-CoV-2 mRNA to conceal it from the host’s cellular defense. The study
aims at computationally identifying the potential natural inhibitors of the SARS-CoV-2 GuanineN7 methyltransferase binding at the active site (Pocket 41). A library of small molecules was
obtained from edible African plants and were molecularly docked against the SARS-CoV-2
Guanine-N7 methyltransferase (QHD43415_13. pdb) using the Pyrx software. Sinefungin, an
approved antiviral drug which had a binding score of -7.6 kcal/ mol with the target was chosen as
a standard. Using the molecular descriptors of the compounds, a virtual screening for oral
availability was performed using the Pubchem and SWISSADME web tools. The online servers
PKCSM and Molinspiration were used for further screening for pharmacokinetic properties and
bioactivity respectively. The molecular dynamic simulation and analyses of the Apo and Holo
proteins was performed using the GROMACS software on the Galaxy webserver. The lead
compounds are Crinamidine, Marmesin and Sinensetin which are obtained from waterleaf,
mango, and orange plants respectively. All the lead compounds performed better than the
standard. Crinamidine is predicted to show the greatest inhibitory activity. Further tests are
required to further investigate the inhibitory activities of the lead compounds.
|
adekunle rowaiye; Olukemi Onuh; Joy Awulika Oladimeji-Salami; Doofan Bur; Moses Njoku; Nma Helen Ifedilichukwu,; Comfort Ojochenemi John; Olanike Binuyo; Faith Udo Pius
|
Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e3e4c8919a35fad39a8/original/in-silico-identification-of-the-potential-natural-inhibitors-of-sars-co-v-2-guanine-n7-methyltransferase.pdf
|
63fd255932cd591f1291c7a5
|
10.26434/chemrxiv-2023-n28nb
|
Capture and Stabilization of the Hydroxyl Radical in a Uranyl Peroxide Cluster
|
Radiolysis of water in spent nuclear fuel is known to contribute to the degradation of extractants used in reprocessing schemes; however, much less is known about how free radical species (•OH, HO2-•, e-(aq), •H) formed during water radiolysis interact with actinide cations in aqueous solution. Here we describe the synthesis and characterization of a new uranyl peroxide cluster (UPC), U60Ox30*, that is analogous to the previous characterized U60Ox30, which captures and stabilizes oxygen-based free radicals for more than one week. These radical species were first detected with a nitroblue tetrazolium colorimetric assay and U60Ox30* was characterized by single crystal X-ray diffraction as well as infrared (IR), Raman, UV-Vis-NIR, and electron paramagnetic resonance (EPR) spectroscopies. Identification and further characterization of the free radicals present in U60Ox30* was done via room temperature solid and solution state X-band EPR studies using spin trapping methods. The spin trapping agent 5,5-dimethyl-1-pyrroline N-oxide (DMPO) was definitive for identifying the free radicals in U60Ox30*, which are hydroxyl radicals (•OH) that are stable for up to ten days that also persist upon addition of the metalloenzymes catalase and superoxide dismutase. Addition of the spin trapping agent α-(4-pyridyl N-oxide)-N-tert-butylnitrone (POBN) further confirmed the radicals were oxygen based and not part of the oxalate ligands in the cluster, and deuteration experiments confirmed that the origin of the free radicals was from water radiolysis. The results here demonstrate that highly oxidizing species such as the •OH radical can be stabilized in UPC systems, which alters our understanding of the role of radiolysis products and their potential to interact with actinyl species in spent nuclear fuel.
|
Brett Lottes; Korey Carter
|
Inorganic Chemistry; Lanthanides and Actinides; Spectroscopy (Inorg.); Crystallography – Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-02-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63fd255932cd591f1291c7a5/original/capture-and-stabilization-of-the-hydroxyl-radical-in-a-uranyl-peroxide-cluster.pdf
|
60c73ed3f96a00313a285fa6
|
10.26434/chemrxiv.7094003.v1
|
On the Conrotatory Ring Opening of 3-Carbomethoxycyclobutene Vis-À-Vis 3-Carbomethoxy-1,2-Benzocyclobutene and the Predominant Inward Opening of 3-Dimethylaminocarbonyl-1,2-Benzocyclobutene
|
<p>The torquoselectivity of conrotatory ring opening of 3-carbomethoxycyclobutene is controlled by p<sub>C1C2</sub>→s*<sub>C3C4</sub> and s<sub>C3C4</sub>→p*<sub>CO</sub> interactions in the transition state in a 4-electron process as opposed to only s<sub>C3C4</sub>→p*<sub>CO</sub> interaction in an apparently 8-electron event in 3-carbomethoxy-1,2-benzocyclobutene. The ring opening of 3-carbomethoxy-1,2-benzocyclobutene is sufficiently endothermic. We therefore argue that the reverse ring closing reaction is faster than the forward ring opening reaction and, thus, it establishes an equilibrium between the two and subsequently allows formation of the more stable species <i>via</i> outward ring opening reaction. Application of this argument to 3-dimethylaminocarbonyl-1,2-benzocyclobutene explains the predominantly observed inward opening.</p>
|
Veejendra Yadav; Dasari L V K Prasad; Arpita Yadav; Maddali L N Rao
|
Stereochemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-09-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ed3f96a00313a285fa6/original/on-the-conrotatory-ring-opening-of-3-carbomethoxycyclobutene-vis-a-vis-3-carbomethoxy-1-2-benzocyclobutene-and-the-predominant-inward-opening-of-3-dimethylaminocarbonyl-1-2-benzocyclobutene.pdf
|
65b7d4779138d23161fca41b
|
10.26434/chemrxiv-2024-pfbjf
|
Molecular dynamics simulation of hydrocalumite as adsorbent for anionic radionuclides
|
Hydrocalumite, is a hydration product of aluminum-rich cements, and is known in cement chemistry as an AFm phase. Structurally, it belongs to the family of layered double hydroxides, or “anionic clays”, where positively charged crystal layers require the presence of negatively charged ions in the interlayer space. Therefore, AFm phases can serve as a potential adsorbents for anionic radionuclides (e.g., 35Cl−, 125I−, 129I−, 131I−) from aqueous solutions. Here we use classical molecular dynamic simulations to analyze the structure and properties of AFm phases containing Cl− and I−. The classical ClayFF force field is used to quantitatively study the structure, energetics and mobility of anions and H2O molecules in the interlayers of these phases and at their interfaces with CsCl and CsI aqueous solutions. The basal (001) surfaces of AFm phases can strongly adsorb hydrated Cl− and I− anions due to the donated hydrogen bonds from the interfacial hydroxyls. However, the adsorption of I− is weaker than that of Cl−, leading to the higher surface mobility of I− due to its stronger chaotropic effect. The interlayer diffusional mobility of the Cl− and I− anions in the AFm phases is investigated by using the Eyring-Vineyard approach and is shown to be significantly lower than in larger nanopores. Hence, the most likely transport of radionuclides takes places through the nano- and micro-pores of hardened cement.
|
Artem A. Glushak; Evgeny V. Tararushkin; Grigory S. Smirnov; Andrey G. Kalinichev
|
Theoretical and Computational Chemistry; Materials Science; Computational Chemistry and Modeling; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b7d4779138d23161fca41b/original/molecular-dynamics-simulation-of-hydrocalumite-as-adsorbent-for-anionic-radionuclides.pdf
|
60e43b08a4e06b232a700558
|
10.26434/chemrxiv-2021-16msm-v2
|
Time-Dependent Long-Range-Corrected Double-Hybrid Density Functionals with Spin-Component and Spin-Opposite Scaling: A Comprehensive Analysis of Singlet-Singlet and Singlet-Triplet Excitation Energies
|
Following the work on spin-component and spin-opposite scaled (SCS/SOS) global double hybrids for singlet-singlet excitations by Schwabe and Goerigk [J. Chem. Theory Comput. 2017, 13, 4307-4323] and our own works on new long-range corrected (LC) double hybrids for singlet-singlet and singlet-triplet excitations [J. Chem. Theory Comput. 2019, 15, 4735- 4744; J. Chem. Phys. 2020, 153, 064106], we present new LC double hybrids with SCS/SOS that demonstrate further improvement over previously published results and methods. We introduce new unscaled and scaled versions of different global and LC double hybrids based on Becke88 or PBE exchange combined with LYP, PBE or P86 correlation. For singlet-singlet excitations, we cross-validate them on six benchmark sets that cover small to medium-sized chromophores with different excitation types (local valence, Rydberg, and charge transfer). For singlet-triplet excitations, we perform the cross-validation on three different benchmark sets following the same analysis as in our previous work in 2020. In total, 203 unique excitations are analyzed. Our results confirm and extend those of Schwabe and Goerigk regarding the superior performance of SCS and SOS variants compared to their unscaled parents by decreasing mean absolute deviations, root-mean-square deviations or error spans by more than half and bringing absolute mean deviations closer to zero. Our SCS/SOS variants show to be highly efficient and robust for the computation of vertical excitation energies, which even outperform specialized double hybrids that also contain an LC in their perturbative part. In particular, our new SCS/SOS-ωPBEPP86 and SCS/SOS-ωB88PP86 functionals are four of the most accurate and robust methods tested in this work and we fully recommend them for future applications. However, if the relevant SCS and SOS algorithms are not available to the user, we suggest ωPBEPP86 as the best unscaled method in this work.
|
Marcos Casanova Paez; Lars Goerigk
|
Theoretical and Computational Chemistry; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-07-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e43b08a4e06b232a700558/original/time-dependent-long-range-corrected-double-hybrid-density-functionals-with-spin-component-and-spin-opposite-scaling-a-comprehensive-analysis-of-singlet-singlet-and-singlet-triplet-excitation-energies.pdf
|
6388991244ccbc1731090a96
|
10.26434/chemrxiv-2022-gnq3w-v2
|
Do machines dream of atoms? Crippen's logP as a quantitative molecular benchmark for explainable AI heatmaps
|
While there is a great deal of interest in methods aimed at explaining machine learning predictions of chemical properties, it is difficult to quantitatively benchmark such methods, especially for regression tasks. We show that the Crippen logP model (J. Chem. Inf. Comput. Sci. 1999, 39, 868) provides an excellent benchmark for atomic attribution/heatmap approaches, especially if the ground truth heatmaps can be adjusted to reflect the molecular representation. The “atom attribution from finger prints”-method developed by Riniker and Landrum (J. Chem. Inf. Comput. Sci. 2013, 5, 43) gives atomic attribution heatmaps that are in reasonable agreement with the atomic contribution heatmaps of the Crippen logP model for most molecules, with average heatmap overlaps of up to 0.54. The agreement is increased significantly (to 0.75) when the atomic contributions are adjusted to match the fact that the molecular representation is fragment-based rather than atom-based (the finger print-adapted (FPA) ground truth vector). Most heatmaps and the corresponding FPA overlaps are relatively insensitive to the training set size and the results are close to converged for a training set size of 1000 molecules, although for molecules with low overlap some heatmaps change significantly. Using the “remove an atom” approach for graph convolutional neural networks (GCNNs) suggested by Matveieva and Polishchuk (J. Cheminform. 2021, 13, 41) we find an average heatmap overlap of 0.47 for the atomic contribution heatmaps of the Crippen logP model. Like the simpler attribution benchmarks for classification tasks that have come before it, this work sets the bar for regression tasks.
|
Maria H. Rasmussen; Diana S. Christensen; Jan H. Jensen
|
Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence
|
CC BY 4.0
|
CHEMRXIV
|
2022-12-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6388991244ccbc1731090a96/original/do-machines-dream-of-atoms-crippen-s-log-p-as-a-quantitative-molecular-benchmark-for-explainable-ai-heatmaps.pdf
|
670a6c3851558a15efdb0257
|
10.26434/chemrxiv-2024-hnmdn
|
New capabilities of the gmx2qmmm software
|
We present an update to the hybrid quantum mechanics/molecular mechanics (QM/MM) interface “gmx2qmmm”. Version 2.0 of the software is now capable of interfacing between the more recent versions of the MM package Gromacs and various other QM packages, in addition to the previously supported Gaussian16. The additional QM packages are ORCA, Turbomole and Serenity; especially the latter drastically increases the potential for QM/MM with extensively large QM regions. While the implementation of the QM packages was for most cases analogous to Gaussian, updating the compatibility to recent Gromacs versions required omission of large parts of the system, which was previously done via the now deprecated energy group exclusion scheme. The new version, gmx2qmmm 2.0, explicitly removes any surplus atoms or point charges that are not affecting the potential of any unrestrained atom (active region). It is thus more consis- tent with previous QM/MM publications, which often reduce the computational workload by deleting all but the necessary parts of the solvent shell. We fur- ther introduced numerical normal mode analyses and a linear coordinate scan function to facilitate basic potential energy surface studies, both for electronic ground and excited states.
|
Florian Anders; Alina Jansen; Nicola Alnicola; Yuan-Wei Pi; Simon Petry; Jan-Oliver Kapp-Joswig; Denis G. Artiukhin; Jan Philipp Götze
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-10-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670a6c3851558a15efdb0257/original/new-capabilities-of-the-gmx2qmmm-software.pdf
|
67d5f519fa469535b95ccbad
|
10.26434/chemrxiv-2025-f6hbv
|
Catalytic Resonance Theory:
Parametric Uncertainty in Microkinetic Predictions of Dynamic Rate Enhancement
|
Microkinetic models are useful tools for screening catalytic materials, however, error in their input parameters can lead to significant uncertainty in model predictions of catalyst performance. Herein, we investigate the impact of linear scaling and Brønsted-Evans-Polanyi relation parametric uncertainty on microkinetic predictions of programmable catalyst performance. Two case studies are considered, a generic A-to-B prototype reaction and the oxygen evolution reaction (OER). Results show that error-unaware models can accurately predict trends and, for the prototype reaction, values of optimal waveform parameters. The specific model parameters driving output uncertainty are identified using a variance-based global sensitivity analysis. However, predictions of dynamic rate enhancement may decrease when uncertainty is propagated into the models. In both cases, operating conditions are identified where the programmable catalyst achieves one-or-more orders of magnitude rate enhancement despite parametric uncertainty in the model, supporting programmable catalysis as a viable strategy for exceeding the Sabatier limit.
|
Sallye Gathmann; Seongjoo Jung; Paul Dauenhauer
|
Physical Chemistry; Catalysis; Heterogeneous Catalysis; Chemical Kinetics; Interfaces
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d5f519fa469535b95ccbad/original/catalytic-resonance-theory-parametric-uncertainty-in-microkinetic-predictions-of-dynamic-rate-enhancement.pdf
|
660e839491aefa6ce1c336ae
|
10.26434/chemrxiv-2024-ln735
|
A Thermodynamic Landscape of Hydrogen Cyanide-Derived Molecules and Polymers
|
Hydrogen cyanide (HCN)-derived molecules and polymers feature in several hypotheses on the origin of life. Over half-a-century of investigations into HCN self-reactions have led to many suggestions regarding the structural nature of the products, and an even greater number of proposed polymerization pathways. A comprehensive overview of possible reactions and structures is missing. In this work, we use quantum chemical calculations to map the relative free energy of most HCN-derived molecules and polymers that have been discussed in the literature. Our computed free energies indicate that several previously considered polymerization pathways are not spontaneous and should be discarded from future consideration. Among the most thermodynamically favored products are polyaminoimidazole and adenine.
|
Hilda Sandström; Fernando Izquierdo-Ruiz; Marco Cappelletti; Rana Dogan; Siddhant Sharma; Clara Bailey; Martin Rahm
|
Theoretical and Computational Chemistry; Earth, Space, and Environmental Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-04-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660e839491aefa6ce1c336ae/original/a-thermodynamic-landscape-of-hydrogen-cyanide-derived-molecules-and-polymers.pdf
|
65caa6e166c13817297f81c9
|
10.26434/chemrxiv-2024-l7d1c
|
Lumina-Chip - a tubular lumen-based microfluidic approach
for enhanced physiological relevance in modeling
cancer metastasis
|
Organ-on-Chip (OoC) systems are advanced in vitro models containing compartments and microchannels
in which the in vivo characteristics of the microenvironment of human organs are emulated
to enhance physiological relevance. OoC models often include microchannel-based vessels and
ducts with rectangular cross-sections, and therefore these lack the geometry and morphology found
in tubular structures in vivo. Channels with round cross sections can better mimic the physiology
and cellular behavior of tubular structures, such as (micro)vessels and breast ducts, via providing
a more in vivo-like geometry and a uniform wall shear stress under physiological flow conditions.
Here, we utilize femtosecond laser machining to integrate tubular lumens in an Organ-on-Chip device;
our "Lumina-Chip" contains two tubular lumens, both connected to a central channel along
their entire length. This versatile fabrication technique enables us to obtain a medium-throughput
version of the device including nine Lumina-Chips. Compared with rectangular channels, culture of
endothelial cells in our tubular channels results in better cell coverage along the entire channel cross
section and therefore better integrity of the endothelium, as well as in different cell morphology and
alignment due to the channel curvature. Permeability analysis shows that the vessel wall in the
Lumina-Chip has good barrier functionality. We demonstrate the we can use the Lumina-Chip to
mimic and observe breast cancer invasion from a breast duct (formed in the first lumen, lined with
normal epithelial cells), into extracellular matrix (formed by collagen I in the central channel), and
subsequent intravasation into a vessel (formed in the second lumen, lined with endothelial cells).
Two types of cancer cells (invasive and non-invasive) show distinctly different behavior throughout
this process. We demonstrate our model with cancer metastasis, but it also can be useful for other
biological applications in which epithelial ducts and vessels are essential components.
|
Mohammad Jouybar; Sophie van der Kallen; Hamed Moradi; Pan Zuo; Oscar Stassen; Jaap M.J. den Toonder
|
Biological and Medicinal Chemistry; Chemical Engineering and Industrial Chemistry; Bioengineering and Biotechnology; Cell and Molecular Biology; Fluid Mechanics
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-02-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65caa6e166c13817297f81c9/original/lumina-chip-a-tubular-lumen-based-microfluidic-approach-for-enhanced-physiological-relevance-in-modeling-cancer-metastasis.pdf
|
60c74101842e65c47cdb1dbf
|
10.26434/chemrxiv.7056767.v2
|
Standardization of PGC-LC-MS-based glycomics for sample specific glycotyping
|
<p></p><p>Porous graphitized carbon (PGC) based chromatography
achieves high-resolution separation of glycan structures released from
glycoproteins. This approach is especially valuable when resolving structurally
similar isomers and for discovery of novel and/or sample-specific glycan
structures. However, the implementation of PGC-based separations in glycomics
studies has been limited because system-independent retention values have not
been established to normalize technical variation. To address this limitation,
this study combined the use of hydrolyzed dextran as an internal standard and
Skyline software for post-acquisition normalization to reduce retention time and
peak area technical variation in PGC-based glycan analyses. This approach
allowed assignment of system-independent retention values that are applicable
to typical PGC-based glycan separations and supported the construction of a library
containing >300 PGC-separated glycan structures with normalized glucose unit
(GU) retention values. To enable the automation of this normalization method, a
spectral MS/MS library was developed of the dextran ladder, achieving
confident discrimination against isomeric glycans. The utility of this approach is demonstrated in two
ways. First, to inform the search space for bioinformatically predicted but unobserved
glycan structures, predictive models for two structural modifications,
core-fucosylation and bisecting GlcNAc, were developed based on the GU library.
Second, the applicability of this method for the analysis of complex biological
samples is evidenced by the ability to discriminate between cell culture and
tissue sample types by the normalized intensity of <i>N-</i>glycan structures alone. Overall, the methods and data described
here are expected to support the future development of more automated approaches
to glycan identification and quantitation.</p><br /><p></p>
|
Christopher Ashwood; Brian Pratt; Brendan MacLean; Rebekah L. Gundry; Nicolle H. Packer
|
Mass Spectrometry; Separation Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-03-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74101842e65c47cdb1dbf/original/standardization-of-pgc-lc-ms-based-glycomics-for-sample-specific-glycotyping.pdf
|
62f35f10e78f70da7d3642c9
|
10.26434/chemrxiv-2022-7d47x
|
Copper-Catalyzed Regioselective [4+2] Annulations between Diaryliodonium Salts and Alkynes: Design, Development, and Applications
|
Herein, a new reaction pattern of diaryliodonium salts was reported as novelty oxa-1,4-dipoles to undergo [4+2] cycloaddition reactions with alkynes. Broad spectrum of the two reaction partners could be utilized in this protocol, enabling an operationally simple, high yielding, and regioselective synthetic approach to isocoumarins. Particularly, good to excellent regioselectivities were achieved for the sterically unbiased unsymmetrical diaryl acetylenes, which was challenging for other transition metal-catalyzed processes. The reaction could be scaled up with the ideal 1:1 stoichiometry and the isocoumarin type natural products Oospolactone and Thunberginol A could be obtained in one or three steps through this methodology.
|
Weilin Wang; Junrui Zhou; Chao Wang; Congdi Zhang; Xiao-Qian Zhang; Youliang Wang
|
Organic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-08-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f35f10e78f70da7d3642c9/original/copper-catalyzed-regioselective-4-2-annulations-between-diaryliodonium-salts-and-alkynes-design-development-and-applications.pdf
|
677f3df581d2151a0263121c
|
10.26434/chemrxiv-2025-lkl4q
|
Phase-migrating Z-scheme charge transportation enables photoredox catalysis harnessing water as an electron source
|
Z-schematic photocatalytic reactions are of considerable interest because of their potential for application to reductive molecular conversions into value-added chemicals using water as an electron source. However, most demonstrations of Z-scheme photocatalysis have far been limited to overall water splitting. In particular, it has been basically impossible to couple the reduction of “water-insoluble compounds” with water oxidation by conventional Z-scheme systems in aqueous solution. In this work, an unconventional Z-scheme electron transportation system with a “phase-migrating” redox mediator is constructed that enables photocatalytic conversion of water-insoluble compounds by using water as an electron/proton source.
|
Ren Itagaki; Akinobu Nakada; Hajime Suzuki; Osamu Tomita; Ho-Chol Chang; Ryu Abe
|
Catalysis; Energy; Photocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677f3df581d2151a0263121c/original/phase-migrating-z-scheme-charge-transportation-enables-photoredox-catalysis-harnessing-water-as-an-electron-source.pdf
|
644a9e566ee8e6b5ed2feacd
|
10.26434/chemrxiv-2023-qd0kj
|
Adenosine Monophosphate as Shape-inducing Agent: The Case of Gold Nanostars
|
The seed-mediated growth of gold nanostructures is known to be intensely dependent on the gold seed nanocrystal structure but also in the presence of different additives that may influence the morphology and, therefore, the crystalline structure of the final nanoparticle. Among the different additives or capping ligands, biomolecules are an exciting family due to their potential biomedical applications, such as drug delivery, bioimaging, biosensing, phototherapy, and antimicrobial activities. Here, we develop a seed-mediated strategy for synthesizing uniform Au nanostars with tuneable optical properties that involve adenosine monophosphate (AMP) as a capping ligand. The experimental data reveal the key role of AMP, not just providing colloidal stability and directing the reduction of the gold precursor via complexation but also mediating the anisotropic growth of the Au seeds via its selective adsorption on the different crystalline facets of Au nanoparticles. These observations agree with theoretical simulations carried out using molecular dynamics and density functional theory (DFT) calculations. Interestingly, the obtained Au nanostars showed high thermal and colloidal stability in polar organic solvents, which allowed their direct silica coating via the Stöber method. Importantly, we also explored the mimic enzymatic activity of the resulting gold nanostars and observed a superior catalytic activity compared with the other gold nanoparticles reported in the literature.
|
Carlos Fernández-Lodeiro; Javier Fernández-Lodeiro; Adrián Fernández-Lodeiro; Silvia Nuti; Carlos Lodeiro; Alec P. LaGrow; Ignacio Pérez-Juste; Jorge Pérez-Juste; Isabel Isabel Pastoriza-Santos
|
Inorganic Chemistry; Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644a9e566ee8e6b5ed2feacd/original/adenosine-monophosphate-as-shape-inducing-agent-the-case-of-gold-nanostars.pdf
|
67861bb1fa469535b9e9b20a
|
10.26434/chemrxiv-2024-z0f6s-v2
|
Photo-induced Vicinal Difunctionalization of Diaryliodonium Salts to Access Bis(tetraphenylphosphonium) Salts
|
Vicinal bis(tetraarylphosphonium) salts have scarcely been reported in the literatures. In this study, we demonstrate that visible-light-induced difunctionalization of ortho-trifluoromethylsulfonylated diaryliodonium salts conveniently furnishes symmetric bis(phosphonium) salts without additional catalysts or photo-initiators. The methodology establishes a practical platform for the prep-aration of bis(phosphonium) salts using readily available tertiary phosphines. The bis(tetraarylphosphonium) salts are anticipated to garner wide interest in catalytic and medicinal chemistry.
|
Yu Wang; Limin Wang; Jianwei Han
|
Organic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67861bb1fa469535b9e9b20a/original/photo-induced-vicinal-difunctionalization-of-diaryliodonium-salts-to-access-bis-tetraphenylphosphonium-salts.pdf
|
671bcb9298c8527d9e605e5b
|
10.26434/chemrxiv-2024-5fdkt
|
Ni-Catalyzed Sulfur Excision Reactions
|
The construction of C–C bonds by contractive “deletion” of the sulfur atom from a C–S–C motif is a useful transformation for synthesis of complex heterocycles. The transformation allows a user to take advantage of the nucleophilic reactivity of sulfur (e.g. for SNAr reactions) and remove that temporary atom at a late stage. A few homogeneous metal systems have been reported to mediate such desulfurizations, but under harsh conditions and, due to the formation of stable oligomeric sulfido complexes, without catalytic turnover. Here, we report a catalytic solution, using an accessible Ni precatalyst, inexpensive additives, and mild conditions. The method provides rapid access to a broad scope of fused heterocycles. Preliminary mechanistic studies provide insight into key aspects of the transformation including the order of C–S bond activations, synergistic effects of the unusual combination of additives, and the fate of the excised sulfur atom.
|
Jianhan Zhou; Richard Liu
|
Organic Chemistry; Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671bcb9298c8527d9e605e5b/original/ni-catalyzed-sulfur-excision-reactions.pdf
|
65647c71cf8b3c3cd73acc02
|
10.26434/chemrxiv-2023-6c07v
|
Synchronous electrochromism and electrofluorochromism in a zirconium pyrenetetrabenzoate metal-organic framework
|
Redox-active materials which exhibit both electrochromism and electrofluorochromism have great potential as multifunctional elements in optoelectronics. Here we present in situ spectroelectrochemistry on NU-1000, a zirconium pyrenetetrabenzoate metal-organic framework. A thin film of NU-1000 exhibits reversible color changes between light yellow and dark blue when subjected to an alternating electrochemical potential. In situ fluorescence excitation-emission spectral mapping elucidates a dominant blue emission of highly fluorescent electrochromic NU-1000 that is being quenched via an oxidation reaction. Density-functional theory calculations reveal the the forbidden optical transition between the singly-occupied molecular orbital (SOMO) and the lowest unoccupied molecular orbital (LUMO) in the oxidized linker as the cause of the quenching. Double potential step chronoamperometry meaures response times as fast as a dozen seconds and excellent switching stability over 500 cycles without noticeable attenuation of the color contrast. These findings provide valuable insight into the electrochromism and electrofluorochromism in metal-organic frameworks, offering exciting opportunities for developing advanced multifunctional porous materials with potential applications in optoelectronics and sensing.
|
Abdelqader El Guerraf; Wenyi Zeng; Arthur Mantel; El Hassan Benhsina; Jia Min Chin; Hidetsugu Shiozawa
|
Physical Chemistry; Materials Science; Nanoscience; Hybrid Organic-Inorganic Materials; Optical Materials; Electrochemistry - Mechanisms, Theory & Study
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-11-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65647c71cf8b3c3cd73acc02/original/synchronous-electrochromism-and-electrofluorochromism-in-a-zirconium-pyrenetetrabenzoate-metal-organic-framework.pdf
|
60c74abe567dfe0a23ec4e11
|
10.26434/chemrxiv.12241166.v1
|
Molecular Docking and Dynamics Simulation Study of Telomerase Inhibitors as Potential Anti-Cancer Agents
|
<p>Normal cells’ genomic identity is protected by
telomeres and sometimes chromosomal instability was observed due to shortening
of telomerase because of successive cell divisions. Reports indicate that
telomerase length is crucial in determining telomerase activity which in turn
leads to cancer initiation. It is reported
that telomere
length regulation has been identified as a plausible strategy for cancer
diagnostics and treatment. In the present MS, we explored the telomerase
inhibitory activity of catechin analogues and it’s oligomers using
computational methods. The structural properties of different ligands discussed
in the MS were computed using density functional theory. Conformational effect of different chromene
subunit such as 2R, 3R conformations were explored using computational methods.
The stereochemical contributions
to receptor binding such as intra ligand π-interactions of these ligands were also
investigated. We herein propose that these stereochemical aspects
of catechins and their oligomers as the most vital factor deciding the
effective binding with the N-terminal domain of telomerase which is an
efficient strategy in cancer therapy. </p>
|
Sherin D R; Thanathu Krishnan Manojkumar; R. Prakash Chandran; Sobha V Nair
|
Biochemistry; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74abe567dfe0a23ec4e11/original/molecular-docking-and-dynamics-simulation-study-of-telomerase-inhibitors-as-potential-anti-cancer-agents.pdf
|
65d87f0266c138172953cef3
|
10.26434/chemrxiv-2024-75npw
|
Bio produced nanoparticles load into extracellular vesicles and support horizontal transfer of therapeutic antimiR
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The extracellular vesicles (EVs) serve for cell-to-cell communication and delivery of signaling molecules and they represent interesting approach in targeted therapy. This study focuses on an EV-mediated transfer of functionalized nanoparticles into recipient tumor cells.
We used biologically produced gold nanoparticles (AuNPs) with known physical-chemical properties and decorated them with an inhibitory RNA targeting oncogenic microRNA-135b (AuNPs-antimiR 135 b) and transferrin (AuNPs-antimiR 135 b-Tf). The AuNPs were added to the breast cancer 4T1 cell line at a non-toxic dose 0.03 µg/µL. The 4T1-autologous EVs (with or without the AuNPs) were extracted and analyzed. The amount of endocytosed and excreted AuNPs was determined by graphite furnace atomic absorption spectrometry. The protein content was analyzed using sodium dodecyl-sulfate polyacrylamide gel electrophoresis and liquid chromatography with mass spectrometry (LC–MS). The fate of EVs and/or AuNPs was characterized using a Transmission Electron Microscopy and Zetasizer. The target-specific silencing effect of the antimir-135b was analyzed with a quantitative real-time PCR (qPCR).
The AuNPs produced by Fusarium oxysporum possessed round shape, size of 5 nm and a zeta potential of -33 mV. We observed two types of EV populations: 60 nm and 250 nm. Out of the initial 58.7 µg of AuNPs added to the cells, 52.68 ± 0.65 µg were internalized and 38.64 ± 0.29 µg were found inside the EVs. The protein content in EV-AuNPs was higher compared to control EVs. LC-MS analysis showed that the AuNPs could alter the protein expression profile of the cancer cell. qPCR results revealed both EV-AuNPs-antimiR 135 b and EV-AuNPs-antimiR 135 b-Tf silenced target microRNA-135b, but higher efficacy was observed in the EV-AuNPs-antimiR 135 b-Tf group.
Obtained data proved EV-mediated transportation of biological AuNPs bearing effector RNA among tumor cells. We also found the efficacy of loaded EVs is higher using AuNPs decorated with a tumor-specific ligand such as transferrin.
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Parastoo Pourali; Milan Svoboda; Veronika Benson
|
Biological and Medicinal Chemistry; Nanoscience; Bioengineering and Biotechnology; Drug Discovery and Drug Delivery Systems
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-02-23
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d87f0266c138172953cef3/original/bio-produced-nanoparticles-load-into-extracellular-vesicles-and-support-horizontal-transfer-of-therapeutic-antimi-r.pdf
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641c485b91074bccd026d4b4
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10.26434/chemrxiv-2023-f1g2r-v2
|
BasisOpt: a Python package for quantum chemistry basis set optimization
|
The basis set used in quantum chemical calculations for molecular applications is vital to the accuracy and efficiency of the calculation, but the development of novel basis sets is hindered by an opaque process and inaccessibility of the tools required. We present here BasisOpt, a tool for the automated optimization of basis sets with an easy-to-use framework. It features an open and accessible workflow for basis set optimization that can be easily adapted to almost any quantum chemistry program, a standardized approach to testing basis sets, and visualization of both the optimized basis sets and the optimization process. We provide proof-of-concept examples where: (i) a density fitting basis set is optimized for He, Ne and Ar; (ii) the exponents of the def2-SVP basis are re-optimized for a set of molecules, rather than atoms; (iii) a large, almost saturated basis of sp primitives is automatically reduced to (10s5p) while achieving the lowest energy for such a basis set composition.
|
Robert Shaw; Grant Hill
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
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CC BY 4.0
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CHEMRXIV
|
2023-03-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641c485b91074bccd026d4b4/original/basis-opt-a-python-package-for-quantum-chemistry-basis-set-optimization.pdf
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6578f9c8fd283d7904ddc6b1
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10.26434/chemrxiv-2023-xrj86
|
Theory of the Relaxation of Trapped Spin-States in Spin Crossover Materials: Drosophila for Complex Dynamics
|
Understanding the underlying factors that give rise to complex kinetic processes is of fundamental interest to many research areas, such as protein folding, photochemistry, and quantum materials. Spin crossover (SCO) materials are relatively simple, highly tunable systems that offer a unique playground to study the universal aspects of complex dynamics. Experimentally, a diverse range of relaxation dynamics of trapped spin-states are observed in SCO materials, including exponential, sigmoidal, stretched exponential, multi-step, and mixed kinetics. Here we reproduce and explain this full range of relaxation behaviours using a semi-classical model that combines crystal field theory with elastic inter-molecular interactions. We show that frustrated intermolecular interactions lead to multiple energetically competitive ordered phases even in systems that contain only one crystallographically distinct SCO site. This rugged free energy landscape leads to dynamic disorder and thence complex dynamics. We show that the same frustrated interactions are responsible for multistep thermal transitions.
|
M. Nadeem; Ben Powell
|
Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Computational Chemistry and Modeling; Coordination Chemistry (Organomet.); Theory - Organometallic
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CC BY NC 4.0
|
CHEMRXIV
|
2023-12-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6578f9c8fd283d7904ddc6b1/original/theory-of-the-relaxation-of-trapped-spin-states-in-spin-crossover-materials-drosophila-for-complex-dynamics.pdf
|
635807da2e0c63447e3bb9f6
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10.26434/chemrxiv-2022-df8gb-v3
|
AN IMPROVED NON-TARGET ANALYSIS AND SUSPECT SCREENING WORKFLOW FOR ORGANIC ACID CONTAMINANTS IN DRINKING WATER
|
A novel and generalisable analytical workflow for non-target analysis (NTA) and suspect screening (SS) of potentially toxic organic acids in drinking water is presented, featuring selective extraction by silica-based strong anion exchange solid-phase extraction (SAX-SPE), mixed-mode liquid chromatography-high resolution mass spectrometric (LC-HRMS) analysis, non-targeted peak detection, features reduction and SS. To achieve this, a selection of 23 structurally diverse compounds with a broad range of polarities were evaluated. Importantly, the novel introduction of an elution solvent containing ammonium bicarbonate extended the current applicability of SAX-SPE for strong acids and subsequent mass spectrometry analysis. This new method performed with consistently higher recovery (88 ± 7 % at 500 ng L-1), improved selectivity and lower matrix interference (mean = 12%) over a generic mixed-mode weak anion exchange SPE method. In addition, a novel filter for reducing full-scan features from fulvic and humic acids was successfully introduced, reducing workload and potential for false positives. The workflow was then applied to NTA/SS of 10 London municipal drinking water samples, allowing the identification of 22 confirmed substances. Several poorly investigated and potentially harmful compounds were found. In particular, predicted mutagenicity and occurrence frequency indicated the need for further investigation of halogenated hydroxy-cyclopentene-diones (HCDs) and dibromomethanesulfonic acid in drinking water. Overall, this approach demonstrated that employing some selectivity for general molecular properties in NTA overall helped shortlist suspect and potentially toxic chemical contaminants with higher confidence, in this case for organic acids.
|
Davide Ciccarelli; Tim Marczylo; Paolo Vineis; Leon Barron
|
Analytical Chemistry; Environmental Analysis; Mass Spectrometry; Separation Science
|
CC BY 4.0
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CHEMRXIV
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2022-10-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635807da2e0c63447e3bb9f6/original/an-improved-non-target-analysis-and-suspect-screening-workflow-for-organic-acid-contaminants-in-drinking-water.pdf
|
61d3dc58d6dcc283f24ed648
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10.26434/chemrxiv-2022-6r8ml-v3
|
Predicting the Redox Potentials of Phenazine Derivatives using DFT Assisted Machine Learning
|
Here, four machine-learning models were employed to predict the redox potentials of phenazine derivatives in DME using DFT. A small dataset of 189 phenazine derivatives having only one type of functional group per molecule (20 unique groups) was used for the training. Models were validated on the external test-set containing new functional groups and diverse molecular structures and achieved reasonable accuracies (R2 > 0.57). Despite being trained on the molecules with a single type of functional group, models were able to predict the redox potentials of derivatives containing multiple and different types of functional groups with reasonable accuracy (R2 > 0.6). This type of performance for predicting redox potential from such a small and simple dataset of phenazine derivatives has never been reported before. Redox Flow Batteries (RFBs) are emerging as promising candidates for energy storage systems. However, new green and efficient materials are required for their widespread usage. We believe that the hybrid DFT-ML approach demonstrated in this report would help in accelerating the virtual screening of phenazine derivatives saving computational and experimental resources. This approach could potentially identify novel molecules for green energy storage systems such as RBF.
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Siddharth Ghule; Soumya Dash; Sayan Bagchi; Kavita Joshi; Kumar Vanka
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Theoretical and Computational Chemistry; Machine Learning
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CC BY NC ND 4.0
|
CHEMRXIV
|
2022-01-04
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d3dc58d6dcc283f24ed648/original/predicting-the-redox-potentials-of-phenazine-derivatives-using-dft-assisted-machine-learning.pdf
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67d0504e6dde43c9086c3e57
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10.26434/chemrxiv-2025-jf387
|
Enantio- and Diastereoselective Cyclopropanation of CF3-imidoyl sulfoxonium ylides Catalyzed by Chiral-at-Metal Rh(III) Complex
|
An enantio- and diastereoselective cyclopropanation of CF3-imidoyl sulfoxonium ylides with α,β-unsaturated 2-acyl imidazoles catalyzed by chiral-at-metal Rh(III) complex has been demonstrated for the first time. This work provides a practical approach for assembling 1,2,3-trisubstituted chiral cyclopropane with CF3-imidoyl structural units under mild reaction conditions, which has the advantages including broad substrates and good functional tolerance. In addition, a scale-up experiment and the synthetic transformations of the cycloadducts further highlight the synthetic utility.
|
Shi-Wu Li; Jixin Pian; Zhifei Zhao
|
Organic Chemistry; Organic Synthesis and Reactions
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CC BY NC ND 4.0
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CHEMRXIV
|
2025-03-14
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d0504e6dde43c9086c3e57/original/enantio-and-diastereoselective-cyclopropanation-of-cf3-imidoyl-sulfoxonium-ylides-catalyzed-by-chiral-at-metal-rh-iii-complex.pdf
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65732379cf8b3c3cd71b3e48
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10.26434/chemrxiv-2023-fql5t
|
Ligand Shell Thickness of PEGylated Gold Nanoparticles Controls Cellular Uptake and Radiation Enhancement
|
The drive to improve the safety and efficacy of radiotherapies for cancers has prompted the development of nanomaterials that can locally amplify the radiation dose at a tumor without damaging the surrounding healthy tissue. Gold nanoparticles (Au NPs), in particular, exhibit promising radiosensitizing properties under kilovolt X-ray exposure, although the precise mechanism behind this enhancement is not fully understood. While most studies recognize the involvement of factors such as core composition, size, shape, and ligand chemistry in the effectiveness of Au NPs for radiation-induced cancer treatment, there is a scarcity of direct assessments that connect the photophysical properties of the nanomaterial with the observed cellular or biological outcomes. Despite previous evidence of low energy electron (LEE) emission from Au NPs and their potential to initiate biological damage, to our knowledge, no studies directly correlate the LEE emission with radiation-induced cell death. In this study we assessed Au NPs functionalized with polyethylene glycol (PEG) ligands of varying molecular weights and lengths (1, 5, and 20 kDa PEG) as potential radiosensitizers of A549 lung cancer cells using kilovolt X- ray source potentials (33–130 kVp). We assessed NP internalization using mass cytometry, radiation dose enhancement using clonogenic survival assays, and LEE emission using a novel retarding field analyzer. Results reveal a statistically significant difference in cellular uptake and radiation dose enhancement for 5 kDa PEG-Au NPs compared to formulations using 1 and 20 kDa PEG, while analysis of LEE emission spectra demonstrated that differences in the length of the PEG ligand did not cause statistically significant attenuation of LEE flux. Consequently, we inferred that increased cellular uptake of NPs to be the cause for the observed enhancement in radiosensitivity for 5 kDa PEGylated Au NPs. The approach used in this study establishes a more complete workflow for designing and characterizing the performance of nanomaterial radiosensitizers, allowing for quantification of LEEs and cellular uptake and ultimately correlation with localized dose enhancement that leads to cell death.
|
Paul T. Lawrence; Avery S. Daniels; Allison J. Tierney; E. Charles H. Sykes; Charles R. Mace
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Physical Chemistry; Analytical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Photochemistry (Physical Chem.); Radiation
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-12-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65732379cf8b3c3cd71b3e48/original/ligand-shell-thickness-of-pe-gylated-gold-nanoparticles-controls-cellular-uptake-and-radiation-enhancement.pdf
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635b9e56aca1988ed2e8e982
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10.26434/chemrxiv-2022-x1d2t
|
Oxidation state dependent conjugation controls electrocatalytic activity in a two-dimensional di-copper metal-organic framework
|
Molecularly defined two dimensional conjugated metal-organic frameworks combine properties of molecular and material based electrocatalysts, enabling tunable active site and bandgap design. The rational optimization of these systems requires an understanding of the complex interplay between the various metal sites and their influence on catalysis. For this purpose, copper-phthalocyanine-based two-dimensional conjugated metal-organic framework (CuPc-CuO4 2D c-MOF) films with an edge-on layer orientation were transferred to (Ni-NTA) functionalised graphite electrodes and analyzed via electrochemical resonance Raman spectroscopy. With the help of Density Functional Theory (DFT) calculations for the first time a detailed assignment of the vibrational bands for different Cu oxidation states could be achieved and correlated to their electrocatalytic activity in respect to the oxygen reduction reaction (ORR). Potential dependent Raman spectroscopy made it possible to determine the redox potentials of the Cu in the CuPc moieties and the Cu-catecholate nodes individually with ECuPc= -0.04V and ECuO4= +0.33 V vs. Ag|AgCl. Albeit the Cu-catecholates are generally seen as the active site in these systems, electrocatalytic ORR was only observed below -0.1 V were both Cu units were present in their respective CuI state. DFT calculations of bandgaps and density of states (DOS) showed a significant decrease in bandgap and increase in π-conjugation upon transition from the inactive mixed CuII/CuI state to the active CuI/CuI state suggesting that slow electron supply in the mixed state limits catalysis at the Cu-catecholates. Our results indicate that the coupling between metal oxidation changes and π-conjugation of the 2D c-MOF is a key parameter towards achieving good electrocatalytic activity.
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Anna Maria Dominic; Zhiyong Wang; Agnieszka Kuc; Petko Petkov; Khoa Hoang Ly; Thi Lam Huong Pham; Martin Kutzschbach; Yuanyuan Cao; Julien Bachmann; Xinliang Feng; Renhao Dong; Inez Weidinger
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Physical Chemistry; Materials Science; Catalysis; Electrocatalysis; Redox Catalysis; Spectroscopy (Physical Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-11-02
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635b9e56aca1988ed2e8e982/original/oxidation-state-dependent-conjugation-controls-electrocatalytic-activity-in-a-two-dimensional-di-copper-metal-organic-framework.pdf
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6756924c085116a133d1e9ba
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10.26434/chemrxiv-2024-z046h
|
Specific Anion Effects on the Growth and Stability of Poly (2-ethyl-2-oxazoline)/Tannic Acid Layer by Layer Films
|
The control of pH responsiveness of hydrogen bonded (H-bonded) layer-by-layer films is especially important in biomedical applications. Specific anion effects are known to vary the cloud point temperature of poly(2-ethyl-2-oxazoline) (PEOX) solutions. By growing H-bonded multilayers of PEOX and Tannic Acid (TA) in the presence of nine different sodium salts at different salt concentrations, we show that the growth profile and pH stability of the multilayers can be controlled in a wide range. The observed changes in the average bilayer (BL) thickness and critical disintegration pH are in accordance with the Hofmeister series of anions. Going from the most kosmotropic (Na2CO3) to the most chaotropic (NaSCN), BL thickness decreases by ~11.5 nm while the critical disintegration pH increases up to 10. Conformational variations in PEOX chains from compact coils due to dehydration by kosmotropic anions to extended chains due to direct ion binding of chaotropic anions contribute to these changes. ITC investigation of PEOX/TA interaction in the presence of sodium salts in solution confirm the enhanced stability in the direction of the most chaotropic anion. The results clearly show that properties of H-bonded multilayers can be easily tuned by specific anion effects as desired by applications.
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Adem Levent Demirel; Elda Beruhil Bahar Adatoz
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Physical Chemistry; Polymer Science; Physical and Chemical Properties; Self-Assembly
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-12-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6756924c085116a133d1e9ba/original/specific-anion-effects-on-the-growth-and-stability-of-poly-2-ethyl-2-oxazoline-tannic-acid-layer-by-layer-films.pdf
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63b5cdd1518c16724f44718c
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10.26434/chemrxiv-2023-3sg08
|
Molecular design rules for imparting multiple damping modes in dynamic covalent polymer networks
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Imparting multiple, distinct dynamic processes at precise timescales in polymers is a grand challenge in soft materials design with implications for applications including electrolytes, adhesives, tissue engineering, and additive manufacturing. Many competing factors including the polymer architecture, molecular weight, backbone chemistry, and presence of solvent affect the local and global dynamics, and in many cases are interrelated. One approach to imparting distinct dynamic processes is through the incorporation of dynamic bonds with widely varying kinetics of bond exchange. Here, statistically crosslinked polymer networks are synthesized with mixed fast and slow dynamic bonds with four orders of magnitude different exchange kinetics. Oscillatory shear rheology shows that the single component networks (either fast or slow) exhibit a single relaxation peak, while mixing fast and slow crosslinkers in one network produces two peaks in the relaxation spectrum. This is in stark contrast to telechelic networks with the same mixture of dynamic bonds where only one mixed mode is observed, and here we develop the molecular design rules necessary to have each dynamic bond contribute a distinct relaxation mode. By controlling the polymer architecture and difference in the number of dynamic bonds per chain, we have elucidated the role of network architecture on imparting multimodal behavior in dynamic networks. A highly tunable and recyclable material has been developed with control of rubbery plateau modulus (through crosslink density), relaxation peak locations and ratio (through crosslinker selection and molar fractions), and tan δ (through the relationships of the rubbery plateau and relaxation peak locations).
|
Laura E. Porath; Nabil Ramlawi; Junrou Huang; M.T. Hossain; Maryanne Derkaloustian; Randy Ewoldt; Christopher M. Evans
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Materials Science; Polymer Science; Elastic Materials; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-01-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b5cdd1518c16724f44718c/original/molecular-design-rules-for-imparting-multiple-damping-modes-in-dynamic-covalent-polymer-networks.pdf
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62190d5c7c13f49f375e51cb
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10.26434/chemrxiv-2022-1hqfc
|
Singly- and Triply-Linked Magnetic Porphyrin Lanthanide Arrays
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The introduction of paramagnetic metal centers into a conjugated π-system is a promising approach towards engineering spintronic materials. Here, we report an investigation of two types of spin-bearing dysprosium(III) and gadolinium(III) porphyrin dimers: singly meso-meso-linked dimers with twisted conformations and planar edge-fused ,meso,-linked tapes. The rare-earth spin centers sit out of the plane of the porphyrin, so that the singly linked dimers are chiral, and their enantiomers can be resolved, whereas the edge-fused tape complexes can be separated into syn and anti stereoisomers. We compare the crystal structures, UV-vis-NIR absorption spectra, electrochemistry, EPR spectroscopy and magnetic behavior of these complexes. Low temperature SQUID magnetometry measurements reveal intramolecular antiferromagnetic exchange coupling between the GdIII centers in the edge-fused dimers (syn isomer: J = –51 ±2 MHz; anti isomer: J = –19 ±3 MHz), whereas no exchange coupling is detected in the singly-linked twisted complex. The phase memory times, Tm, are in the range 8–10 µs at 3 K, which is long enough to test quantum computational schemes using microwave pulses. The syn and anti Dy2 edge-fused tapes both exhibit single molecule magnetic hysteresis cycles at temperatures below 0.5 K with slow magnetization dynamics.
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Jeff Van Raden; Dimitris Alexandropoulos; Michael Slota; Simen Sopp; Taisuke Matsuno; Amber Thompson; Hiroyuki Isobe; Harry Anderson; Lapo Bogani
|
Organic Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Magnetism; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-02-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62190d5c7c13f49f375e51cb/original/singly-and-triply-linked-magnetic-porphyrin-lanthanide-arrays.pdf
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66d0a1a9a4e53c4876094198
|
10.26434/chemrxiv-2024-cxhpw
|
N–N Atropisomer Synthesis via Electrolyte- and Base-Free Electrochemical Cobalt-Catalysed C–H Annulation
|
Merging electrochemistry with asymmetric C−H activation has proven as an advantageous alternative to prepare valuable enantiopure molecules. However, established methods require a stoichiometric use of supporting electrolytes to promote electron transfer in solution and often additionally serve as a base to assist C−H bond cleavage, which are hazardous and would produce additional waste. Herein, we described an exogenous electrolyte- and base-free electrocatalytic atroposelective C–H annulation, providing facile and sustainable access to N–N axially chiral isoquinolinones in excellent enantioselectivities and good yields. This protocol is enabled by a combination of simple Co(OAc)2·4H2O and readily available chiral salicyloxazoline (Salox), proceeds well with 13 classes of alkynes, and tolerates a wealth of functional groups for streamlined transformations.
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Jiating Cai; Linzai Li; Chuitian Wang; Shi Qin; Shengdong Wang; Hui Gao; Zhi Zhou; Yugang Huang; Wei Yi; Zhongyi Zeng
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Organic Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-09-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d0a1a9a4e53c4876094198/original/n-n-atropisomer-synthesis-via-electrolyte-and-base-free-electrochemical-cobalt-catalysed-c-h-annulation.pdf
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64819d2e4f8b1884b70201a7
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10.26434/chemrxiv-2023-r4rxp-v2
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End-to-End Differentiable Force Field Generator with Crystal Structure Differentiation and Matching
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In this paper, we present a new force field (FF) parameterization method with direct matching of crystal structures and atomic charges optimization in end-to-end differentiable manner. The advancement of force field (FF) parameterization methods has been accelerated by differentiable programming. Automatic differentiation (AD) has facilitated energy and force matching by differentiating these quantities with respect to the FF parameters, which we mention as force differentiation and matching (FDM). Nevertheless, crystal structure matching with AD remains difficult due to the converged structures optimized by the iterative algorithm being non-differentiable with respect to the FF parameters. To overcome this limitation, we introduce structure differentiation and matching (SDM) technique for generating FFs of small organic molecules using reference data, including stable monomer structures, crystal structures, lattice energies, and potential energy surfaces (PESs) of dihedral angles. SDM employs implicit function differentiation (IFD) and differentiable Ewald techniques to optimize FF parameters and atomic charges correspondingly. Our case study of eight exemplified molecules demonstrates that SDM substantially outperforms the conventional FDM, with error factors reduced to less than one-quarter with the charge optimization method called SDM(q-opt). This strategy achieves remarkable precision in reproducing lattice constants, atomic configurations, lattice energies, and PESs. Furthermore, molecular dynamics simulations confirm the stability of the generated crystal structures. This method can be adapted to other FF categories, such as polarized FFs and those with explicit hydrogen bonding interactions. We foresee that SDM(q-opt) will emerge as a standard method for parameterizing FFs using crystal structures.
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Hiroshi Nakano; Shinnosuke Hattori; Hajime Kobayashi; Takumi Araki; Masakazu Ukita; Toshio Nishi; Yoshihiro Kudo
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Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning
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CC BY NC 4.0
|
CHEMRXIV
|
2023-06-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64819d2e4f8b1884b70201a7/original/end-to-end-differentiable-force-field-generator-with-crystal-structure-differentiation-and-matching.pdf
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66b8d5b601103d79c5a51898
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10.26434/chemrxiv-2024-5xf9v-v2
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Deposition of CdSe nanocrystals in highly porous SiO2 matrices – in-situ growth vs. infiltration methods
|
Embedding quantum dots into porous matrices is a very beneficial approach for generating hybrid nanostructures with unique properties. In this contribution we explore strategies to dope nanoporous SiO2 thin films made by atomic layer deposition and atomic etching with precise control over pore size with CdSe quantum dots. Two distinct strategies were employed for quantum dot deposition: in-situ growth of CdSe nanocrystals within the porous matrix via successive ionic layer adsorption reaction, and infiltration of pre-synthesized quantum dots. To address the impact of pore size layers with 10 nm and 30 nm average pore diameter were used as matrix. Our results show that though potentially also small pores are accessible for the in-situ approach, this strategy lacks controllability over the nanocrystal quality and size distribution. To dope layers with high quality quantum dots with well-defined size distribution and optical properties infiltration of preformed quantum dots is much more promising. It was observed that due to higher pore volume 30 nm porous silica shows higher loading after treatment than 10 nm porous silica matrix. This can be related to a better accessibility of the pores with higher pore size. The amount of infiltrated QDs can be influenced via drop casting of additional solvent on a pre-drop casted porous matrix as well as via varying the soaking time of a porous matrix in a QD solution. Luminescent QDs deposited via this strategy keep their luminescent properties upon deposition and the resulting thin films with immobilized quantum dots are suited for integration into optoelectronic devices.
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Raktim Baruah; Munira Dilshad; Marco Diegel; Jan Dellith; Jonathan Plentz; Andreas Undisz; Adriana Szeghalmi; Maria Wächtler
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Nanoscience; Nanofabrication; Nanostructured Materials - Nanoscience; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-08-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b8d5b601103d79c5a51898/original/deposition-of-cd-se-nanocrystals-in-highly-porous-si-o2-matrices-in-situ-growth-vs-infiltration-methods.pdf
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60c74a6d4c891933bfad321d
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10.26434/chemrxiv.12199610.v1
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Drug Repurposing Against SARS-CoV-2 Using E-Pharmacophore Based Virtual Screening and Molecular Docking with Main Protease as the Target
|
Since its first report in December 2019 from China the COVID-19 pandemic caused by the beta-coronavirus SARS-CoV-2 has spread at an alarming pace infecting about 26 lakh, and claiming the lives of more than 1.8 lakh individuals across the globe. Although social quarantine measures have succeeded in containing the spread of the virus to some extent, the lack of a clinically approved vaccine or drug remains the biggest bottleneck in combating the pandemic. Drug repurposing can expedite the process of drug development by identifying known drugs which are effective against SARS-CoV-2. The SARS-CoV-2 main protease is a promising drug target due to its indispensable role in viral multiplication inside the host. In the present study an E-pharmacophore hypothesis was generated using the crystal structure of the viral protease in complex with an imidazole carbaximide inhibitor as the drug target. Drugs available in the superDRUG2 database were used to identify candidate drugs for repurposing. The hits were further screened using a structure based approach involving molecular docking at different precisions. The most promising drugs were subjected to binding free energy estimation using MM-GBSA. Among the 4600 drugs screened 17 drugs were identified as candidate inhibitors of the viral protease based on the glide scores obtained from molecular docking. Binding free energy calculation showed that six drugs viz, Binifibrate, Macimorelin acetate, Bamifylline, Rilmazafon, Afatinib and Ezetimibe can act as potential inhibitors of the viral protease.
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arun kumar; Sharanya C.S; Abhithaj J; Dileep Francis; Sadasivan C
|
Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a6d4c891933bfad321d/original/drug-repurposing-against-sars-co-v-2-using-e-pharmacophore-based-virtual-screening-and-molecular-docking-with-main-protease-as-the-target.pdf
|
672226175a82cea2fa8400de
|
10.26434/chemrxiv-2024-vtg73
|
Skeletal editing of indoles and benzofurans to give indazoles, benzimidazoles, benzoxazoles and benzisoxazoles
|
Skeletal editing comprises the structural reorganization of compounds. Such editing can be achieved through atom swapping, atom insertion, atom deletion or reorganization of the compound's backbone structure. Conducted at a late stage in drug development campaigns, skeletal editing enables diversification of an existing pharmacophore, enhancing the efficiency of drug development. Instead of constructing a heteroarene classically from basic building blocks, structural variants are ready accessible directly starting from a lead compound or approved pharmacophore. Herein we present C to N atom swapping in indoles at the C2 position to give indazoles through oxidative cleavage of the indole heteroarene core and subsequent ring closure. Reactions proceed through ring-opened oximes as intermediates. Importantly, these ring deconstructed intermediates can also be diverted into benzimidazoles resulting in an overall C to N atom swapping with concomitant skeletal reorganization. The same structural diverting strategies are equally well applicable to benzofurans leading to either benzisoxazoles or benzimidazoles. All heteroarene classes accessible through these structural diversification processes belong to important compound classes.
|
Zhe Wang; Pengwei Xu; Shu-Min Guo; Constantin Gabriel Daniliuc; Armido Studer
|
Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-11-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672226175a82cea2fa8400de/original/skeletal-editing-of-indoles-and-benzofurans-to-give-indazoles-benzimidazoles-benzoxazoles-and-benzisoxazoles.pdf
|
65a1d3549138d23161cae4e7
|
10.26434/chemrxiv-2024-thvcv
|
A Computational Comparison Between Pomotrelvir and Nirmatrelvir Binding and Reactivity with SARS-CoV-2 Main Protease. Implications for Resistance Mechanisms
|
This study investigates the binding mode and reaction mechanism between pomotrelvir and the SARS-CoV-2 main protease using a combination of molecular mechanics and hybrid quantum mechanics / molecular mechanics simulations. Alchemical transformations where each Pi group of pomotrelvir was transformed into its counterpart in nirmatrelvir were performed to unravel the individual contribution of each group of the inhibitor to the binding and reaction processes. We have shown that while a gamma-lactam ring is preferred at position P1, a delta-lactam ring could be an alternative to be incorporated at this position in the design of inhibitors designed against wild-type main protease and for variants presenting mutations at position 166. For the P2 position, tertiary amines are clearly preferred with respect to secondary amines, because the ability to act as a hydrogen bond donor seem to favour more the interaction with the solvent than with the protein, decreasing the affinity for the enzyme. In addition, flexible groups at P2 position disfavour the formation of the covalent complex because they can disrupt the preorganization of the active site, favouring the exploration of non-reactive conformations. The substitution of the P2 group of pomotrelvir by that of nirmatrelvir resulted in a compound, here named as C2, that presents a notable improvement in the binding energy and a higher population of reactive conformations in the Michaelis complex. Analysis of the chemical reaction to form the covalent complex has shown a similar reaction mechanism and activation free energies for pomotrelvir, nirmatrelvir and C2. We hope that these findings could be useful to design better inhibitors to fight present and future variants of SARS-CoV-2 virus.
|
Johanna Schillings; Carlos A. Ramos-Guzmán; J. Javier Ruiz-Pernía; Iñaki Tuñón
|
Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Computational Chemistry and Modeling
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-01-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a1d3549138d23161cae4e7/original/a-computational-comparison-between-pomotrelvir-and-nirmatrelvir-binding-and-reactivity-with-sars-co-v-2-main-protease-implications-for-resistance-mechanisms.pdf
|
64aa8ed3ba3e99daefc5b107
|
10.26434/chemrxiv-2023-4g3xz
|
Rapid and Scalable Photocatalytic C(sp2)–C(sp3) Suzuki−Miyaura Cross-Coupling of Aryl Bromides with Alkyl Boranes
|
In recent years, there has been a growing demand for drug design approaches that incorporate a higher number of sp3-hybridized carbons, necessitating the development of innovative cross-coupling strategies to reliably introduce aliphatic fragments. Here, we present a novel and powerful approach for the light-mediated B-alkyl Suzuki−Miyaura cross-coupling between alkyl boranes and aryl bromides. Alkyl boranes can be easily generated via hydroboration from readily available alkenes, exhibiting excellent regioselectivity and enabling the selective transfer of a diverse range of primary alkyl fragments onto the arene ring. This methodology eliminates the need for expensive catalytic systems and sensitive organometallic compounds, operating efficiently at room temperature within just 30 minutes. Interestingly, our mechanistic studies reveal an unexpected mechanistic scenario that operates through transmetalation rather than alkyl radical formation, setting it apart from established metallaphotoredox protocols. Moreover, we demonstrate the advantageous translation of the present protocol to continuous-flow conditions, enhancing scalability, safety, and overall efficiency of the method. This versatile approach offers significant potential for accelerating drug discovery efforts by enabling the introduction of complex aliphatic fragments in a straightforward and reliable manner.
|
Ting Wan; Luca Capaldo; Jonas Djossou; Angela Staffa; Felix de Zwart; Bas de Bruin; Timothy Noel
|
Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Homogeneous Catalysis; Photocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2023-07-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64aa8ed3ba3e99daefc5b107/original/rapid-and-scalable-photocatalytic-c-sp2-c-sp3-suzuki-miyaura-cross-coupling-of-aryl-bromides-with-alkyl-boranes.pdf
|
666355ac12188379d8945d68
|
10.26434/chemrxiv-2024-kvdpq
|
Chemo-ribosomal synthesis of atropisomeric and macrocyclic peptides with embedded quinolines
|
Expanding the chemical and structural complexity of genetically encoded peptides remains a challenge in peptide therapeutics discovery. Here we report that linear peptides with a reactive β- or γ-keto amide at their N-termini can be synthesized ribosomally using in vitro translation methods. We show that peptides carrying an N-terminal β-keto amide can be converted into diverse heterocyclic quinoline-peptide hybrids via Friedländer reactions with a variety of 2-aminoarylcarbonyl co-substrates. Reactions with appropriately substituted 2-aminobenzophenones generated quinoline-peptide hybrids with stable biaryl atropisomeric axes. In vitro-translated peptides carrying both an N-terminal β-keto amide and an internal 2-aminoacetophenone motif undergo intramolecular Friedländer macrocyclization reactions that embed a quinoline pharmacophore directly within the macrocyclic backbone. The introduction of N-terminal ketide building blocks into genetically encoded materials and their post-translational derivatization with carbonyl chemistry simultaneously expands the chemical diversity and structural complexity of genetically encoded materials and provides a paradigm for the programmed synthesis of peptide-derived materials that more closely resemble complex natural products.
|
Isaac J. Knudson; Taylor L. Dover; Diondra A. Dilworth; Cameron Paloutzian; Hannah Cho; Alanna Schepartz; Scott J. Miller
|
Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Stereochemistry; Chemical Biology
|
CC BY 4.0
|
CHEMRXIV
|
2024-06-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666355ac12188379d8945d68/original/chemo-ribosomal-synthesis-of-atropisomeric-and-macrocyclic-peptides-with-embedded-quinolines.pdf
|
666aeee15101a2ffa87ff016
|
10.26434/chemrxiv-2024-qbncm
|
Enantioselective Synthesis of Alkyl Fluorides via Biocatalytic Reduction
|
Here we report the first biocatalytic asymmetric synthesis of alkyl fluorides via reduction of α-fluoroenones and α-fluoroenoates using ene reductase enzymes. The reduction of a wide range of (Z) or (E)-α-fluoroenones was shown to proceed in high yield and selectivity using ene reductases, with the different alkene geometries leading to opposite enantiomers of the chiral fluoroalkane. The reaction could also be successfully extended to α-fluoroenoates to access enantioenriched α-fluoroesters with only the E-alkene isomers under-going reduction, enabling mixtures of alkene geometries to be employed. The selectivity and substrate scope were rationalized using in silico substrate-enzyme molecular docking studies.
|
Helen Allan; Yu Wang; Bethan Winterson; Alexandra King; Abil Aliev; Rachel Szpara; Victor Laserna; Charlotte Coomber; John Ward; Jack Jeffries; Helen Hailes; Tom Sheppard
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Biocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2024-06-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666aeee15101a2ffa87ff016/original/enantioselective-synthesis-of-alkyl-fluorides-via-biocatalytic-reduction.pdf
|
6523bf178bab5d2055ef503b
|
10.26434/chemrxiv-2023-x6zhj
|
Aryne-based synthesis of cyclobutadiene-containing oligoacenes and related extended biphenylene derivatives
|
A novel aryne derived from a π-extended biphenylene, 2,3-didehydrobenzo[b]biphenylene, has been developed. The participation of this new aryne building block in [4+2] and palladium-catalyzed [2+2+2] cycloaddition reactions has been effectively applied to the synthesis of a variety of polycyclic conjugated hydrocarbons (PCHs) with appealing structures which combine (aromatic) benzene and (antiaromatic) cyclobutadiene (CBD) rings. Among them, a family of unsubstituted (or barely substituted) CBD-oligoacenes has been accessed by iterative Diels-Alder reactions of the new aryne wit furans and/or isobenzofurans, followed by deoxygenative aromatization of the resulting epoxy-derivatives. The experimental and computational study of the newly synthesized PCHs suggests an important degree of electron delocalization along the polycyclic skeleton, more pronounced in the linearly fused derivatives. Interestingly, the computed ACID plots reveal clockwise current density vectors at the peripheral bonds, originating from the sigma contributions of the antiaromatic cyclobutadiene rings.
|
Berta Álvarez; Jesús Janeiro; Agustín Cobas; Manuel A. Ortuño; Diego Peña; Enrique Guitián; Dolores Pérez
|
Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-11-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6523bf178bab5d2055ef503b/original/aryne-based-synthesis-of-cyclobutadiene-containing-oligoacenes-and-related-extended-biphenylene-derivatives.pdf
|
64a3ce67ba3e99daef7c599a
|
10.26434/chemrxiv-2023-pvkgc
|
CO2/13CO2 Dynamic Exchange in the Formate Complex [(2,9-(tBu)2-phen)Cu(O2CH)] and its Catalytic Activity in the Dehydrogenation of Formic Ac-id
|
Formate complexes of copper(I) are rare. We report here the synthesis, characterization, and crystal structure of the simple tricoordinate [(phen*)CuI(O2CH)] (1) supported with the bulky phenanthroline ligand 2,9-di-terbutyl-1,10-phenanthroline (phen*). Complex 1 decarboxylates at 100°C to give H2 and Cu(0) deposit with free phen*. To ensure that the degradation process goes through the hypothetical hydride [(phen*)CuH], Lewis acidic boron BR3 compounds (R = C6F5, Et) or organic scavengers have been introduced to trap it. In most case degradation occurs except with B(C6F5)3 that give the cationic complex [{(phen*)Cu}2(-HCO2)][(HCO2)B(C6F5)3] (2) which has been crystallized. While 1 does not react with CS2 when heated, it undergoes under 1 atm of 13CO2, a dynamic decarboxyla-tion/carboxylation process that indicates transient formation of the hydride. The catalytic activity of complex 1 in the dehydrogenation of formic acid is revealed.
|
Jean-Claude BERTHET; Kieu Phung; Pierre Thuéry; Thibault Cantat
|
Organometallic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-07-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a3ce67ba3e99daef7c599a/original/co2-13co2-dynamic-exchange-in-the-formate-complex-2-9-t-bu-2-phen-cu-o2ch-and-its-catalytic-activity-in-the-dehydrogenation-of-formic-ac-id.pdf
|
60c74db8337d6cb419e27e2b
|
10.26434/chemrxiv.12649730.v1
|
A Dual-Fluorophore Sensor Approach for Ratiometric Fluorescence Imaging of Potassium in Living Cells
|
Potassium is the most abundant intracellular
metal in the body, playing vital roles in regulating intracellular fluid volume,
nutrient transport, and cell-to-cell communication through nerve and muscle
contraction. On the other hand, aberrant alterations in K<sup>+</sup>
homeostasis contribute to a diverse array of diseases spanning cardiovascular
and neurological disorders to diabetes to kidney disease to cancer. Owing to
the large differences in intracellular versus extracellular K<sup>+</sup> concentrations
([K<sup>+</sup>]<sub>intra</sub> = 150 mM, [K<sup>+</sup>]<sub>extra</sub> =
3-5 mM), an unmet need for studies of K<sup>+</sup> physiology and pathology
remains a relative dearth of methods to reliably measure dynamic changes in
intracellular K<sup>+</sup> in biological specimens that meet the dual
challenges of low affinity and high selectivity for K<sup>+</sup>, particularly
over Na<sup>+</sup>, as currently available fluorescent K<sup>+</sup> sensors are
largely optimized with high-affinity receptors that are more amenable for
extracellular K<sup>+</sup> detection. We report the design, synthesis, and
biological evaluation of Ratiometric Potassium Sensor 1 (<b>RPS-1</b>), a dual-fluorophore
sensor that enables ratiometric fluorescence imaging of intracellular potassium
in living systems. <b>RPS-1</b> links a potassium-responsive fluorescent sensor
fragment (<b>PS525</b>) with a low-affinity, high-selectivity crown ether receptor
for K<sup>+</sup> to a potassium-insensitive reference fluorophore (<b>Coumarin
343</b>) as an internal calibration standard through ester bonds. Upon intracellular
delivery, esterase-directed cleavage splits these two dyes into separate
fragments to enable ratiometric detection of K<sup>+</sup>. <b>RPS-1</b>
responds to K<sup>+</sup> in aqueous buffer with high selectivity over
competing metal ions and is sensitive to potassium ions at steady-state intracellular
levels and can respond to decreases or increases from that basal set point.
Moreover, <b>RPS-1</b> was applied for comparative screening of K<sup>+</sup>
pools across a panel of different cancer cell lines, revealing elevations in basal
intracellular K<sup>+</sup> in metastatic breast cancer cell lines vs normal
breast cells. This work provides a unique chemical tool for the study of
intracellular potassium dynamics and a starting point for the design of other
ratiometric fluorescent sensors based on two-fluorophore approaches that do not
rely on FRET or related energy transfer designs.
|
Zeming Wang; Tyler C. Detomasi; Christopher Chang
|
Organic Synthesis and Reactions; Analytical Chemistry - General; Imaging; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74db8337d6cb419e27e2b/original/a-dual-fluorophore-sensor-approach-for-ratiometric-fluorescence-imaging-of-potassium-in-living-cells.pdf
|
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