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67c6f4f0fa469535b9e6e066
|
10.26434/chemrxiv-2025-5qf3p
|
Synthesis and Physicochemical Properties of Functionalized cis-2-((Fluoro)alkyl)cyclobutanes
|
Efficient decagram-scale synthesis of (fluoro)alkyl-containing cis-1,2-disubstited cyclobutane-derived building blocks is described. Starting from commercially available chemicals, target cyclobutylamines, carboxylic acids, and other valuable derivatives were obtained in 3–8 steps on up to 39 g scale. Physicochemical characterization of the prepared compounds and their model derivatives revealed the distinct features of cis-1,2-disubstituted cyclobutanes (namely, significantly lowered lipophilicity) as compared to their previously reported trans-isomeric counterparts. Computational analysis along with experimentally obtained structural properties suggested the decisive influence of the compounds’ conformation on the discussed properties.
|
Anton V. Chernykh; Oleksandr S. Liashuk; Kyrylo O. Kononenko; Artem Y. Michuda; Oleksandr S. Olifir; Dmytro Lesyk; Karina Turenko; Andrii V. Kozytskyi; Svitlana V. Shishkina; Petro Borysko; Serhiy V. Ryabukhin; Dmytro M. Volochnyuk; Oleksandr O. Grygorenko
|
Physical Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Stereochemistry
|
CC BY 4.0
|
CHEMRXIV
|
2025-03-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c6f4f0fa469535b9e6e066/original/synthesis-and-physicochemical-properties-of-functionalized-cis-2-fluoro-alkyl-cyclobutanes.pdf
|
60cbd754b912f8a3055a3728
|
10.26434/chemrxiv-2021-zj19k
|
Estimating the cooperativity of PROTAC-induced ternary complexes using 19F NMR displacement assay
|
Cooperativity is an important parameter to understand the ternary complexes formed by protein degraders. We developed fluorine NMR competition binding experiments to determine cooperativity of PROTACs. We show applicability to estimate both positive and negative cooperativity, also with homo-dimerizers, and highlight key features and considerations for optimal assay development.
|
Guilherme Castro; Alessio Ciulli
|
Biological and Medicinal Chemistry; Biochemistry; Biophysics; Chemical Biology
|
CC BY 4.0
|
CHEMRXIV
|
2021-06-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60cbd754b912f8a3055a3728/original/estimating-the-cooperativity-of-protac-induced-ternary-complexes-using-19f-nmr-displacement-assay.pdf
|
6466fa77f2112b41e9c960c5
|
10.26434/chemrxiv-2023-19v1v
|
Reactive Docking: a computational method for high-throughput virtual screenings of reactive species
|
We describe the formalization of the reactive docking protocol, a method developed to model and predict reactions between small molecules and biological macromolecules. The method has been successfully used in a number of applications already, including recapitulating large proteomics datasets, performing structure-reactivity target optimizations and prospective virtual screenings. By modeling a near-attack conformation-like state, no QM calculations are required to model ligand and receptor geometries. Here, we present its generalization using a large dataset containing more than 400 ligand-target complexes, 8 nucleophilic modifiable residue types, and more than 30 warheads. The method correctly predicts the modified residue in ~85% of complexes and shows enrichments comparable to standard focused virtual screenings in ranking ligands. This performance supports this approach for the docking and screening of reactive ligands in virtual chemoproteomics and drug design campaigns.
|
Giulia Bianco; Matthew Holcomb; Diogo Santos-Martins ; Andreas Tillack; Althea Hansel-Harris; Stefano Forli
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Biology; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-05-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6466fa77f2112b41e9c960c5/original/reactive-docking-a-computational-method-for-high-throughput-virtual-screenings-of-reactive-species.pdf
|
60c7504d842e65008fdb39d5
|
10.26434/chemrxiv.13019570.v1
|
A Bidentate iodine(III)-Based Halogen Bond Donor as Powerful Organocatalyst
|
<div>In contrast to iodine(I)-based halogen bond donors, </div><div>iodine(III)-derived ones have only been used as Lewis acidic organocatalysts in a handful of examples, and in all cases they acted in a monodentate fashion. Herein, we report the first application of a bidentate bis(iodolium) salt as organocatalyst in a Michael and a nitro-Michael addition reaction as well as in a Diels-Alder reaction that had not been activated by noncovalent organocatalysts before. In all cases, the performance of this bidentate XB donor distinctly </div><div>surpassed the one of arguably the currently strongest iodine(I)-based organocatalyst. Bidentate coordination to the substrate was corroborated by a structural analysis and by DFT calculations of the transition states. Overall, the catalytic activity of the bis(iodolium) system approaches that of strong Lewis acids like BF3.</div>
|
Flemming Heinen; Dominik Reinhard; Elric Engelage; Stefan Huber
|
Organic Synthesis and Reactions; Physical Organic Chemistry; Supramolecular Chemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-09-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7504d842e65008fdb39d5/original/a-bidentate-iodine-iii-based-halogen-bond-donor-as-powerful-organocatalyst.pdf
|
60c744fc702a9ba7c218a946
|
10.26434/chemrxiv.9944906.v1
|
Stereospecific Synthesis and Photophysical Properties of Propeller-Shaped C90H48 PAH
|
Highly twisted large PAHs offer, in addition to
physical properties, a feature of chirality, which results in non-super
imposable mirror-image structures of these compounds that can be resolved into
optically active enantiomers. This process, however, is cumbersome, which
largely restricts the available quantity of materials in optically active form
and represents a great hurdle for their applications. Herein, we have
synthesized an enantiomerically pure propeller-shaped PAH, C<sub>90</sub>H<sub>48</sub>,
possessing three [7]helicene and three [5]helicene subunits. This compound can
be obtained in gram quantities in a straight-forward manner. The photophysical
and chiroptical properties were investigated using UV−vis absorption and
emission, optical rotation and circular dichroism spectroscopy, supported by
DFT calculations. The non-linear optical properties were investigated by
two-photon absorption measurements using linearly and circularly polarized
light. The extremely twisted structure and packing of the homochiral compound
were investigated by single crystal X-ray diffraction analysis
|
Fangyuan Zhang; Evripidis Michail; Fridolin Saal; Ana-Maria Krause; Prince Ravat
|
Organic Synthesis and Reactions; Physical Organic Chemistry; Stereochemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-10-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744fc702a9ba7c218a946/original/stereospecific-synthesis-and-photophysical-properties-of-propeller-shaped-c90h48-pah.pdf
|
6148908ba7b2497fdf322865
|
10.26434/chemrxiv-2021-vmf6c
|
Thermoresponsive hydrogels for atmospheric water vapor harvesting
|
Currently, freshwater scarcity is a global challenge that is threatening four billion people across the world. To satisfy people’s increasing freshwater demand, harvesting atmospheric water from the air could be an alternative way. This work developed copolymer P(NIPAM-co-15%BzDMA) hydrogels to harvest atmospheric water vapor. Two methods were investigated to improve its adsorption performance: decreasing synthesis temperature below the LCST and copolymerizing with the optimum amount of quaternary ammonium salt (QAS). We found these two methods can effectively improve the water vapor uptake. After copolymerizing NIPAM with 15% QAS at 20°C, the water vapor uptake could be increased by almost 20% to 232 mg/g at 20°C and P/P0 of 0.75 compared with pure PNIPAM prepared at 60°C (194 mg/g). The significant increase can be attributed to the more uniform porous structure and the hygroscopicity of QAS. After coating PNIPAM onto the PESPU sponge skeleton, the PESPU-PNIPAM_60 could adsorb 180 mg/g gas water at 20°C and P/P0 of 0.75, and the modified sponges inherit the switchable wettability from PNIPAM. This research provides polymer processing parameters and their character for harvesting water vapor from the air with hydrogels.
|
Pavani Cherukupally; Boyuan Hao; Zhongshen Zhang; Daryl R Williams
|
Polymer Science; Hydrogels; Polymerization (Polymers); Polymer morphology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-09-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6148908ba7b2497fdf322865/original/thermoresponsive-hydrogels-for-atmospheric-water-vapor-harvesting.pdf
|
65ce884966c1381729bbb974
|
10.26434/chemrxiv-2024-v3dsv
|
Selective 1,4-syn-Carboamination of Cyclic 1,3-Dienes via Hybrid Palladium Catalysis
|
1,4-cis-disubstituted cyclic compounds play a pivotal role in pharmaceutical development, offering enhanced potency and bioavailability. However, their stereoselective and modular synthesis remains a long-standing challenge. Here, we report an innovative strategy for accessing these structures via mild conditions employing cyclic 1,3-dienes/alkyl(aryl)halides and amines. This procedure exhibits a wide substrate scope that tolerates various functional groups. The utility of this method is demonstrated in the efficient synthesis of a TRPV6 inhibitor, CFTR modulator and other bioactive molecules. Combined experimental and computational studies suggest that the hybrid palladium-catalyzed radical-polar crossover mechanism is crucial for achieving the exceptional 1,4-syn-addition selectivity (dr > 20:1).
|
Yan Liang; Tiancen Bian; Komal Yadav; Qixin Zhou; Liejin Zhou; rui sun; ZUXIAO ZHANG
|
Organic Chemistry; Catalysis; Organometallic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-02-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ce884966c1381729bbb974/original/selective-1-4-syn-carboamination-of-cyclic-1-3-dienes-via-hybrid-palladium-catalysis.pdf
|
60c73cc9bb8c1aead23d961d
|
10.26434/chemrxiv.14748879.v1
|
Prediction of Chameleonic Efficiency
|
<p>Prediction
of chameleonic properties from environment-dependent conformational ensembles generated by
molecular dynamics in explicit solvent is presented. This methodology yields
predictive models of overall polarity (experimentally determined EPSA) and
hydrogen bond donor exposure (experimentally measured <i>delta</i> log <i>P</i><sub>oct-tol</sub>) for 24
FDA-approved drug molecules. Two quantitative indices of chameleonic efficiency
are introduced to aid drug designers striving to combine sufficient
permeability and solubility.</p>
|
Laurent David; Mark Wenlock; Patrick Barton; Andreas Ritzén
|
Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-06-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc9bb8c1aead23d961d/original/prediction-of-chameleonic-efficiency.pdf
|
60c74700702a9be75f18ace7
|
10.26434/chemrxiv.9941627.v3
|
Structure–property Effects in the Generation of Transient Aqueous Benzoic Acid Anhydrides by Carbodiimide Fuels
|
<div>The design of dissipative systems, which operate out-of-equilibrium by consuming chemical fuels, is challenging. As yet, there are few examples of privileged fuel chemistries that can be broadly applied in abiotic systems in the same way that ATP hydrolysis is exploited throughout biochemistry. The key issue is that designing nonequilibrium systems is inherently about balancing the relative rates of coupled reactions. The use of carbodiimides as fuels to generate transient aqueous carboxylic anhydrides has recently been used in examples of new nonequilibrium materials and supramolecular assemblies. Here, we explore the kinetics of formation and decomposition of a series of benzoic anhydrides generated from the corresponding acids and EDC under typical conditions (EDC = <i>N</i>-(3-dimethylaminopropyl)-<i>N</i>′-ethylcarbodiimide hydrochloride). The reactions can be described by a simple mechanism that merges known behavior for the two processes independently. Structure–property effects in these systems are dominated by differences in anhydride decomposition rate. The kinetic parameters allow trends in concentration-dependent properties to be simulated, such as reaction lifetimes, peak anhydride concentrations, and yields. For key properties there are diminishing returns with the addition of increasing amounts of fuel. These results should provide useful guidelines for the design of functional systems making use of this chemistry. <br /></div>
|
Lasith Kariyawasam; Julie Kron; Run Jiang; André Sommer; Scott Hartley
|
Physical Organic Chemistry; Self-Assembly
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-12-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74700702a9be75f18ace7/original/structure-property-effects-in-the-generation-of-transient-aqueous-benzoic-acid-anhydrides-by-carbodiimide-fuels.pdf
|
618b909f98309bf1f8583556
|
10.26434/chemrxiv-2021-4m6b3-v2
|
Explaining and avoiding failures modes in goal-directed generation
|
Despite growing interest and success in automated in-silico molecular design, doubts remain regarding the ability of goal-directed generation algorithms to perform unbiased exploration of novel chemical spaces. A specific phenomenon has recently been highlighted: goal-directed generation guided with machine learning models produce molecules with high scores according to the optimization model, but low scores according to control models, even when trained on the same data distribution and the same target. In this work, we show that this worrisome behavior is actually due to issues with the predictive models and not the goal-directed generation algorithms. We show that with appropriate predictive models, this issue can be resolved, and molecules generated have high scores according to both the optimization and the control models.
|
Maxime Langevin; Rodolphe Vuilleumier; Marc Bianciotto
|
Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2021-11-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618b909f98309bf1f8583556/original/explaining-and-avoiding-failures-modes-in-goal-directed-generation.pdf
|
642e2ff00784a63aee9ad422
|
10.26434/chemrxiv-2022-n13d1-v8
|
Basic principle from electrospray ionization to soft ionization mass spectrometry and development of ion source: part Ⅱ
|
This paper continue talking about some questions in the experimental phenomenon and basic principle of soft ionization mass spectrometry, describe the forces between the charge and the analyte, ideal model of soft ionization technology, multi-charge and supercharging of proteins, mobility of gaseous ions in weak electric fields, the design of ion source and so on.
|
Jiehong Luo
|
Analytical Chemistry; Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642e2ff00784a63aee9ad422/original/basic-principle-from-electrospray-ionization-to-soft-ionization-mass-spectrometry-and-development-of-ion-source-part-ii.pdf
|
66c6f6eba4e53c4876394f49
|
10.26434/chemrxiv-2024-74qqp
|
Stereoselective Synthesis of Hexa-Aryl Borazines: Leaving Flatlands towards sp²-Based
3D Molecular Architectures
|
Borazine and its derivatives can be considered critical doping units for engineering hybrid C(sp2)-based molecules with tailored optoelectronic properties. Herein, we report the
first synthesis of hexaarylborazines that, bearing ortho-substituted aryl moieties, extend threedimensionally. Using a one-pot protocol, we first form an electrophilic chloroborazole and then react it with an aryl lithium (ArLi). By selecting the appropriate ortho-substituent, we can guide
the ArLi to add to the BN-core in a specific way, ultimately controlling the stereochemical outcome of the three-substitution reaction. Rationalization of the stereochemical model through computational analysis allowed us to show that when aryl lithium nucleophiles bearing rigid long-range ortho-substituents are used, i.e., stiff substituents. The ortho-substituent shields its side of the electrophilic B3N3 core, biasing the incoming ArLi to add anti at each addition step, forming the final tri-aryl borazine exclusively as cc-isomer. Leveraging this stereoselective approach, prototypical multichromophoric borazine derivatives were prepared, and we showcased how the stereochemical arrangement of these chromophores distinctly influences their redox behavior. This methodology paves the way for previously inaccessible borazines to serve as privileged precursors to transcend the conventional bidimensionality associated with graphenoid systems and pioneer the construction of new forms of three-dimensional C(sp2)-based architectures.
|
Vivek Wakchaure; María Mercedes Lorenzo-García; Francesco Fasano; Martina Crosta; Nicolas Biot; Nicola Demitri; Pradip Kumar Mondal; Benjamin D. Ward; Davide Bonifazi
|
Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-09-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c6f6eba4e53c4876394f49/original/stereoselective-synthesis-of-hexa-aryl-borazines-leaving-flatlands-towards-sp2-based-3d-molecular-architectures.pdf
|
62c6966ec79aca212b54a656
|
10.26434/chemrxiv-2022-4pw2n
|
Natural complex mixtures unequivocally defined in formulae difference space
|
Direct comparison of high-resolution mass spectrometry (HRMS) data acquired with different instrumentation or parameters remains difficult as the derived lists of molecular species via HRMS, even for the same sample, appear distinct. This inconsistency is the result of inherent inaccuracies caused by instrumental limitations and sample conditions. We propose a method that classifies HRMS data based on the differences in the number of elements between each pair of molecular formulae within the formulae list to preserve the essence of the given sample. The novel metric, Formulae Difference Chains Expected Length (FDCEL), allowed for comparing and classifying samples measured by different instruments. FDCEL metric was implemented for both spectrum quality control and for examination of samples of various nature. We also demonstrate a web application and a prototype for a uniform database for HRMS data serving as a benchmark for future biogeochemical applications.
|
Anastasia Sarycheva; Irina V. Perminova; Eugene N. Nikolaev; Alexander Zherebker
|
Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Geochemistry; Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-07-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c6966ec79aca212b54a656/original/natural-complex-mixtures-unequivocally-defined-in-formulae-difference-space.pdf
|
60c755f04c891980e6ad4784
|
10.26434/chemrxiv.14186174.v1
|
Titanocene Pnictinidene Complexes
|
The phospha-Wittig reagent <sup>Mes</sup>TerPPMe<sub>3</sub>
(<sup>Mes</sup>Ter = 2,6-{2,4,6-Me<sub>3</sub>-C<sub>6</sub>H<sub>2</sub>}-C<sub>6</sub>H<sub>3</sub>)
and arsa-Wittig reagent <sup>Dip</sup>TerAsPMe<sub>3</sub> (<sup>Dip</sup>Ter = 2,6-{2,6-<i>i</i>Pr<sub>2</sub>-C<sub>6</sub>H<sub>3</sub>}-C<sub>6</sub>H<sub>3</sub>)
have been employed to synthesize the titanocene complexes Cp<sub>2</sub>Ti(PMe<sub>3</sub>)PnAr
(Pn = P, As) with terminal phosphinidene or arsinidene ligands, respectively. <a><i>Ab initio</i> studies
show that the description as singlet biradicaloids in their ground state is
warranted.</a><br />
|
Malte Fischer; Fabian Reiß; Christian Hering-Junghans
|
Bonding; Coordination Chemistry (Inorg.); Ligands (Inorg.); Organometallic Compounds; Theory - Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755f04c891980e6ad4784/original/titanocene-pnictinidene-complexes.pdf
|
638e023b836cebf3bc749a78
|
10.26434/chemrxiv-2022-vfp1l
|
Cortical Bone under an Ultrahigh Magnetic Field: Relaxation, Spectroscopy and Micron-resolution Imaging
|
Compact, mineralized cortical bone tissues are often concealed on magnetic resonance (MR) images. Recent development of MR instruments and pulse techniques has yielded significant advances in acquiring anatomical and physiological information from cortical bone despite its poor 1H signals. This work demonstrates the first MR research on cortical bones under an ultrahigh magnetic field of 14 T. The 1H signals of different mammalian species exhibit multi-exponential decays of three characteristic T2 or T2* values: 0.1–0.5 ms, 1–4 ms, and 4–8 ms. Systematic sample comparisons attribute these T2/T2* value ranges to collagen-bound water, pore water, and lipids, respectively. Ultrashort echo time (UTE) imaging under 14 T yielded spatial resolutions of 20–80 microns, which resolves the three-dimensional anatomy of the Haversian canals. The T2* relaxation characteristics further allow spatial classifications of collagen, pore water and lipids in human specimens. Our study achieves a record of the spatial resolution for MR imaging in bone and shows that ultrahigh-field MR has the unique ability to differentiate the soft and organic compartments in bone tissues.
|
Tian He; Zhenfeng Pang; Yu Yin; Huadong Xue; Yichuan Pang; Haixin Song; Jianhua Li; Ruiliang Bai; An Qin; Xueqian Kong
|
Biological and Medicinal Chemistry; Analytical Chemistry; Imaging; Spectroscopy (Anal. Chem.); Bioengineering and Biotechnology; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-12-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638e023b836cebf3bc749a78/original/cortical-bone-under-an-ultrahigh-magnetic-field-relaxation-spectroscopy-and-micron-resolution-imaging.pdf
|
60c73e98702a9b0aa0189da1
|
10.26434/chemrxiv.6452828.v2
|
Air Quality in Puerto Rico in the Aftermath of Hurricane Maria: A Case Study on the Use of Lower-Cost Air Quality Monitors
|
In
the aftermath of Hurricane Maria, the electricity grid in Puerto Rico was
devastated, with over 90% of the island without electricity; as of December
2017, about 50% of the island lacked electricity, and power outages were common
elsewhere. Backup generators are widely used, sometimes as the main source of
electricity. The hurricane also damaged the island’s existing air monitoring
network and the University of Puerto Rico’s observing facilities. We deployed
four lower-cost air quality monitors (Real-time Affordable Multi-Pollutant or
RAMP monitors) and a black carbon (BC) monitor in the San Juan Metro Area in
November 2017. The first month of data collected with the RAMPs showed high
sulfur dioxide (SO<sub>2</sub>) and carbon monoxide (CO) concentrations of
varying magnitudes each night. SO<sub>2</sub> and CO are strongly correlated (r<sup>2</sup>
>0.9) at two sites ~5 km apart (University of Puerto Rico and an
industrial area, Puerto Nuevo), suggesting a single source type. BC measured at
the UPR site is also well correlated with CO and SO<sub>2</sub>. While the
RAMPs are not certified as a federal equivalent method, the RAMP SO<sub>2</sub>
data suggest that the EPA’s daily 1-hour threshold for SO<sub>2</sub>
(75 ppb) was exceeded on almost 80% of the first 30 days of deployment
(November-December 2017). The widespread reliance on generators for regular
electric supply in the aftermath of Hurricane Maria appears to have increased
air pollution in San Juan.
|
Subramanian Ramachandran; Aja Ellis; Elvis Torres-Delgado; Rebecca Tanzer; Carl Malings; Felipe Rivera; Maité Morales; Darrel Baumgardner; Albert Presto; Olga L. Mayol-Bracero
|
Atmospheric Chemistry; Environmental Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-07-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e98702a9b0aa0189da1/original/air-quality-in-puerto-rico-in-the-aftermath-of-hurricane-maria-a-case-study-on-the-use-of-lower-cost-air-quality-monitors.pdf
|
6468211da32ceeff2ded3003
|
10.26434/chemrxiv-2023-6vx14-v2
|
Bidirectional Elongation Strategy Using Ambiphilic Radical Linchpin for Modular Access to 1,4-Dicarbonyls via Sequential Photocatalysis
|
Organic molecules that can be connected with multiple substrates by sequential C−C bond formations can be utilized as linchpins in multicomponent processes. While they are useful for rapidly increasing molecular complexity, most of the reported linchpin coupling methods rely on the use of organometallic species as strong carbon nucleophiles to form C−C bonds, which narrows the functional group compatibility. Here, we describe a metal-free, radical-mediated coupling approach using a formyl-stabilized phosphonium ylide as a multifunctional linchpin under visible-light photoredox conditions. The present method uses the ambiphilic character of the phosphonium ylide, which serves both as a nucleophilic and an electrophilic carbon-centered radical source. The stepwise and controllable generation of these radical intermediates allows sequential photocatalysis involving two mechanistically distinct radical additions, both of which are initiated by the same photocatalyst in one pot with a high functional-group tolerance. The methodology enables a bidirectional assembly of the linchpin with two electronically differentiated alkene fragments and thus offers a rapid and modular access to 1,4-dicarbonyl compounds as versatile synthetic intermediates.
|
Akira Matsumoto; Natsumi Maeda; Keiji Maruoka
|
Organic Chemistry; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6468211da32ceeff2ded3003/original/bidirectional-elongation-strategy-using-ambiphilic-radical-linchpin-for-modular-access-to-1-4-dicarbonyls-via-sequential-photocatalysis.pdf
|
60c74f2c9abda26729f8d7bd
|
10.26434/chemrxiv.12847628.v1
|
Facilitation of Molecular Motion in Nanoparticles and Development of Turn-on Photoacoustic Bioprobe for in Vivo Detection of Nitric Oxide in Encephalitis
|
Nitric oxide (NO) is an important signaling molecule overexpressed in many diseases, thus the development of NO-activatable probes is of vital significance for monitoring related diseases. However, sensitive photoacoustic (PA) probes for detecting NO-associated complicated diseases (e.g., encephalitis), has yet to be developed. Herein, we report a NO-activated PA probe for in vivo detection of encephalitis by tuning the molecular geometry and energy transformation processes. A strong donor-acceptor structure with good conjugation can be obtained after NO treatment, along with the active intramolecular motion, significantly boosting “turn-on” near-infrared PA property. The molecular probe exhibits high specificity and sensitivity towards NO over interfering reactive species. Noninvasive in vivo imaging indicates that PA signal lights up in lipopolysaccharide-induced encephalitis with a high signal-to-background ratio of 15.7. Further studies reveal that the probe is also capable of differentiating encephalitis in different severities, being beneficial for understanding the disease evolution processes and drug screening. This work will inspire more insights into the development of high-performing NO-activated PA probes for advanced diagnosis by making full use of intramolecular motion and energy transformation processes.
|
Ji Qi; Leyan Feng; Xiaoyan Zhang; Haoke Zhang; Liwen Huang; Yutong Zhou; Zheng Zhou; zheng zhao; Xingchen Duan; Fei Xu; Ryan Tsz Kin Kwok; Jacky W. Y. Lam; Dan Ding; Xue Xue; Ben Zhong Tang
|
Aggregates and Assemblies; Dyes and Chromophores; Imaging Agents; Biochemical Analysis; Imaging; Nanostructured Materials - Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f2c9abda26729f8d7bd/original/facilitation-of-molecular-motion-in-nanoparticles-and-development-of-turn-on-photoacoustic-bioprobe-for-in-vivo-detection-of-nitric-oxide-in-encephalitis.pdf
|
60c7488e337d6c99d8e2758c
|
10.26434/chemrxiv.11929821.v1
|
DNA/TNA Mesoscopic Modeling of Melting Temperatures Suggest Weaker Hydrogen Bonding of CG than in DNA/RNA
|
TNA/DNA hybrids share several similarities to RNA/DNA, such as the tendency to form A-type helices and a strong dependency of their thermodynamic properties on purine/pyrimidine ratio. However, unlike RNA/DNA, not much is known about the base-pair properties of TNA. Here, we use a mesoscopic analysis of measured melting temperatures to obtain an estimate of hydrogen bonds and stacking interactions. Our results reveal that the AT base pairs in TNA/DNA have nearly identical hydrogen bond strengths than their counterparts in RNA/DNA, but surprisingly CG turned out to be much weaker despite similar stability.
|
Maria Izabel Muniz; Hershel Lackey; Jennifer Heemstra; Gerald Weber
|
Biophysical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-03-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7488e337d6c99d8e2758c/original/dna-tna-mesoscopic-modeling-of-melting-temperatures-suggest-weaker-hydrogen-bonding-of-cg-than-in-dna-rna.pdf
|
60c742249abda2e869f8bf67
|
10.26434/chemrxiv.8215715.v1
|
A New Four-Parameter Cubic Equation of State for Predicting Fluid Phase Behavior
|
<p>A new four-parameter
cubic equation of state (EoS) is generated by incorporating the critical
compressibility factor (Z<sub>c</sub>) apart from the critical pressure (P<sub>c</sub>)
and temperature (T<sub>c</sub>). One free parameter in the denominator of the
attractive term and two parameters in the alpha function are adjusted using the
experimental data of saturated liquid density, vapor pressure, and isobaric
liquid heat capacity of 48 components including hydrocarbons and
non-hydrocarbons. Applying this equation of state, saturated liquid density,
saturated vapor density, and vapor pressure of pure components are accurately
reproduced compared with experimental values. Furthermore, the predicted
properties including derivatives of alpha function, such as enthalpy of
vaporization, entropy of vaporization and isobaric heat capacity of liquid, also
have decent accuracy. The global average absolute relative deviation (AAD) of
saturated liquid density, saturated vapor density, saturated vapor pressure,
enthalpy of vaporization, entropy of vaporization, and isobaric heat capacity
of liquid in a wide reduced temperature (Tr) range of subcritical region reproduced
by this work are 4.33%, 4.18%, 3.19%, 2.26%, 2.27%, and 5.82%, respectively. Substantial
improvement has been achieved for the isobaric liquid heat capacity
calculation.</p>
|
zhiren he
|
Physical and Chemical Properties; Thermodynamics (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-06-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742249abda2e869f8bf67/original/a-new-four-parameter-cubic-equation-of-state-for-predicting-fluid-phase-behavior.pdf
|
65363f8d2431cc1dac59779c
|
10.26434/chemrxiv-2023-3sldd
|
A Sequential Transition Metal and Organocatalytic Approach to the Enantioselective Synthesis of C2-spiroindoline Systems
|
We report herein an organocatalyzed, enantioselective spirocyclization process for the construction of spiroindolines. This methodology creates a new avenue for the easy access to valuable C2-spiroindoline scaffolds bearing a quaternary stereocenter, via an aza-Michael addition reaction, wherein the acid additives play a role of dual functionality. The substrates for this key step were put together by an exo-selective, Pd-catalyzed gamma-arylation of silyldienol ethers of the corresponding cyclohexenones. A close alliance between a low catalyst loading and a sluggish reaction yields the spiroindolines in very good enantioselectivity.
|
Pooja Sah; Aakash Kumar Gond; Gaurav Saini; Manmohan Kapur
|
Organic Chemistry; Catalysis; Organometallic Chemistry; Stereochemistry; Organocatalysis; Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65363f8d2431cc1dac59779c/original/a-sequential-transition-metal-and-organocatalytic-approach-to-the-enantioselective-synthesis-of-c2-spiroindoline-systems.pdf
|
6780b710fa469535b96c9c46
|
10.26434/chemrxiv-2025-8mns1
|
Impact of molecular structure as sticker–spacer model on formation and internal environments of coacervates composed of low-molecular- weight compounds
|
Coacervates formed through liquid–liquid phase separation have been established as potential protocells. Unlike widely studied macromolecules, coacervates from low-molecular-weight compounds have recently gained importance because they provide simple but valuable in vitro models for biomolecular condensates and serve as promising platforms for the development of functional biomaterials. Herein, we present a modular molecular design for the phase separation of low-molecular-weight compounds containing two aromatic or cycloalkane stickers linked via a flexible hydrophilic spacer. These low-molecular-weight compounds self-assemble into micron-scale liquid-like coacervates at submillimolar concentrations. The coacervates provide a hydrophobic internal microenvironment that can selectively sequester hydrophobic guest molecules while excluding hydrophilic molecules. We demonstrate the controlled release of hydrophobic drugs encapsulated in reduction-responsive coacervates composed of nitrophenyl groups as stickers that are cleaved by the addition of a reductant to induce the disassembly of the coacervates. This research is based on a rational molecular design for the construction of simple coacervates composed of low-molecular-weight compounds and offers an opportunity to construct more complicated coacervate-based protocell models and biofunctional soft materials.
|
Sayuri Higashi; Ryutaro Fujimoto; Koichiro Hirosawa; Kenichi Suzuki; Masato Ikeda
|
Organic Chemistry; Nanoscience; Organic Compounds and Functional Groups; Supramolecular Chemistry (Org.); Nanostructured Materials - Nanoscience; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6780b710fa469535b96c9c46/original/impact-of-molecular-structure-as-sticker-spacer-model-on-formation-and-internal-environments-of-coacervates-composed-of-low-molecular-weight-compounds.pdf
|
65cce879e9ebbb4db95c0b2c
|
10.26434/chemrxiv-2024-7zbtf
|
Pyrene and Biochar (Raman Spectroscopy)
|
Pyrene is a polycyclic aromatic hydrocarbon (PAH) organic compound. Here we consider its Raman spectroscopy, and how it is revealing, when used to create nanograins (Gavilan et al., 2022), a spectrum which is like that we can observe when biochar is investigated. Besides the approach by Gavilan and coworkers, the research by Smith et al., 2016, based on the Raman spectra of several PAH compounds, and proposed to determine an assignment for the bands of char, will be considered too.
|
Amelia Carolina Sparavigna
|
Materials Science
|
CC BY 4.0
|
CHEMRXIV
|
2024-02-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cce879e9ebbb4db95c0b2c/original/pyrene-and-biochar-raman-spectroscopy.pdf
|
61128977424ea3707c87000f
|
10.26434/chemrxiv-2021-9q8zf-v2
|
Hot Exciplexes in U-Shaped TADF Molecules with Emission from Locally Excited States
|
Rapid reverse intersystem crossing and high color purity are vital characteristics of emitters with thermally activated delayed fluorescence in opto-electronic devices. We present a new approach, called “hot exciplexes” that enables access to both attributes at the same time. Hot exciplexes are produced by coupling facing donor and acceptor moieties to an anthracene bridge, yielding an exciplex with large T1 to T2 spacing. The hot exciplex model is investigated using optical spec-troscopy and quantum chemical simulations. Reverse intersystem crossing is found to occur preferentially from the T3 to the S1 state within only a few nanoseconds. Application and practi-cality of the model are shown by fabrication of organic light-emitting diodes with up to 32 % hot exciplex contribution and low efficiency roll-off.
|
A. Lennart Schleper; Kenichi Goushi; Christoph Bannwarth; Bastian Haehnle; Philipp Welscher; Chihaya Adachi; Alexander Kuehne
|
Organic Chemistry; Photochemistry (Org.); Physical Organic Chemistry; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-08-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61128977424ea3707c87000f/original/hot-exciplexes-in-u-shaped-tadf-molecules-with-emission-from-locally-excited-states.pdf
|
66fa3c1812ff75c3a1e99030
|
10.26434/chemrxiv-2024-jq33g
|
RNA-Based Aptamer Targeting Clusterin Protein as a Diabetes Biomarker
|
Clusterin protein is primarily used as a diabetes biomarker and can be used to detect cell density in diabetes. A lower β cells are an early sign of type 1 diabetes. Aptamers are single-stranded nucleotides that bind the target protein and are prevalent in disease diagnosis and targeted therapy. Recently, aptamer targeting clusterin protein has been developed as a biomarker of the β cells. We hypothesize that the rigid clusterin protein should have specific amino acids interacting with the particular aptamers. In this research work, we have performed in silico simulations to find the optimal aptamer capable of binding to the clusterin protein and can be used as a biomarker in diabetes. Specifically, we have performed molecular docking simulations to find the clusterin-aptamer binding complexes. These aptamers were selected based on their interactions with the clusterin protein. Phylogenetic analysis shows that the aptamers class is bifurcated into two sections. All the results were validated using the GrASP web server, which shows the aptamer binding region on the protein's surface. The finding indicates that the aptamer binds to clusterin and could potentially be used as a diabetes biomarker.
|
Irene Batta; Gaurav Sharma
|
Theoretical and Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-10-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fa3c1812ff75c3a1e99030/original/rna-based-aptamer-targeting-clusterin-protein-as-a-diabetes-biomarker.pdf
|
677eb1716dde43c908be8579
|
10.26434/chemrxiv-2025-r15f3
|
Current Approaches and Challenges in Advanced Oxidation Processes for Nanoplastic Degradation
|
The proliferation of plastic production has led to a surge in nanoplastics (NPs) pollution, posing significant environmental and health risks. Despite efforts to mitigate plastic waste, NPs persist as a significant challenge due to their small size, high surface-to-volume ratio, and complex nature. This review explores advanced oxidation processes (AOPs) as promising techniques for NP remediation, including ozonation, electrochemical, photocatalytic, and plasma-induced processes. Existing research is analyzed to investigate the performance of AOPs in NP degradation. Gaps in the development of effective processes and analytical methods are highlighted, and future directions are suggested. This review aims to enhance understanding and promote sustainable solutions for the remediation of NPs from contaminated water resources in alignment with the objectives outlined in the sixth Sustainable Development Goal set by the United Nations.
|
Arezou Fazli; Athanassia Athanassiou; Despina Fragouli
|
Materials Science; Polymer Science; Earth, Space, and Environmental Chemistry; Environmental Science
|
CC BY NC 4.0
|
CHEMRXIV
|
2025-01-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677eb1716dde43c908be8579/original/current-approaches-and-challenges-in-advanced-oxidation-processes-for-nanoplastic-degradation.pdf
|
614cb0f239ef6a0343278ae0
|
10.26434/chemrxiv-2021-4m2hs-v2
|
Gelation and Yielding Behavior of Polymer-Nanoparticle Hydrogels
|
Polymer-Nanoparticle hydrogels are a unique class of self-assembled, shear-thinning, yield-stress fluids which have demonstrated potential utility in many impactful applications. Here we present a thorough analysis of the gelation and yielding behavior of these materials with respect to the polymer and nanoparticle component stoichiometry. Through comprehensive rheological and diffusion studies, we reveal insights into the structural dynamics of the polymer nanoparticle network which identify that stoichiometry plays a key role in gelation and yielding, ultimately enabling the development of hydrogel formulations with unique shear-thinning and yield-stress behaviors. Access to these materials opens new doors for interest- ing applications in a variety of fields including tissue engineering, drug delivery, and controlled solution viscosity.
|
Abigail Grosskopf; Olivia Saouaf; Hector Lopez Hernandez; Eric Appel
|
Materials Science; Polymer Science; Biocompatible Materials; Drug delivery systems; Hydrogels
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-09-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614cb0f239ef6a0343278ae0/original/gelation-and-yielding-behavior-of-polymer-nanoparticle-hydrogels.pdf
|
60c757210f50db705f3981df
|
10.26434/chemrxiv.14125961.v2
|
The Early Steps of Molecule-to-Material Conversion in Chemical Vapor Deposition (CVD): A Case Study
|
Transition metal complexes with β-diketonate and
diamine ligands are valuable precursors for the chemical vapor deposition (CVD)
of metal oxide nanomaterials, but the metal-ligand bond dissociation mechanism
on the growth surface is not clarified yet. We address this question by Density
Functional Theory (DFT) and <i>ab initio</i> molecular dynamics (AIMD) in
combination with the Bluemoon (BM) statistical sampling approach. AIMD
simulations of the Zn β-diketonate-diamine complex Zn(hfa)<sub>2</sub>TMEDA
(hfa = 1,1,1,5,5,5-hexafluoro-2,4-pentanedionate; TMEDA = <i>N</i>,<i>N</i>,<i>N’</i>,<i>N’</i>-tetramethylethylenediamine)
show that rolling diffusion of this precursor at 500 K on a hydroxylated silica
slab leads to an octahedral-to-square pyramidal rearrangement of its molecular
geometry. The free energy profile of the octahedral-to-square pyramidal
conversion indicates that the process barrier (5.8 kcal/mol) is of the order of
magnitude of the thermal energy at the operating temperature. The formation of
hydrogen bonds with surface hydroxyls plays a key role in aiding the dissociation
of a Zn-O bond. In the square-pyramidal complex, the Zn center has a free
coordination position, which might promote the interaction with incoming
reagents on the deposition surface. These results provide a valuable atomistic
insight on the molecule-to-material conversion process which, in perspective,
might help to tailor by design the first nucleation stages of the target
ZnO-based nanostructures.<br />
|
Davide Barreca; Ettore Fois; Alberto Gasparotto; Chiara Maccato; Mario Oriani; gloria tabacchi
|
Materials Processing; Multilayers; Nanostructured Materials - Materials; Thin Films; Nanofabrication; Nanostructured Materials - Nanoscience; Organometallic Compounds; Solid State Chemistry; Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling; Theory - Computational; Interfaces; Physical and Chemical Processes; Surface; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757210f50db705f3981df/original/the-early-steps-of-molecule-to-material-conversion-in-chemical-vapor-deposition-cvd-a-case-study.pdf
|
63ff72a6937392db3d45adf3
|
10.26434/chemrxiv-2023-bjcxb
|
Biocidal polymer derived near white light-emitting carbonized polymeric dots for antibacterial and bioimaging applications
|
A growing antimicrobial crisis has increased demand for antimicrobial materials. It has become increasingly popular to convert polymeric macromolecules into carbonized polymer nanodots (CPDs) in order to achieve highly biocompatible materials with unique properties as a result of the ability to synthesize nanomaterials of the right size and add value to existing stable polymers. This work presents the tuning of polymeric carbon dots (PCDs) for antibacterial application by combining a biocidal polymer with one-pot solvothermal synthesis. PCDs displayed broad-spectrum antibacterial activity via various mechanisms, including inhibition of bacterial cell walls, ROS generation, and antibiotic resistance. Further, these biocidal PCDs were observed to show excitation-independent near-white light emission which on the other hand is generally possible due to mixed sizes, doping, and surface effects. As opposed to the parent biocidal polymer, CD added ROS-mediated bactericidal activity, increased cytocompatibility and nanofibers with anti-adhesive impact and the potential of imaging bacterial cells.
|
Shaifali Sartaliya; Raina Sharma; Anjana Sharma; Vianni Chopra; Neethu K M; Deepa Ghosh; Govindasamy Jayamurugan
|
Biological and Medicinal Chemistry; Polymer Science; Nanoscience; Biopolymers; Organic Polymers; Nanostructured Materials - Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ff72a6937392db3d45adf3/original/biocidal-polymer-derived-near-white-light-emitting-carbonized-polymeric-dots-for-antibacterial-and-bioimaging-applications.pdf
|
60c755e09abda2a788f8e457
|
10.26434/chemrxiv.14176646.v1
|
Time-Resolved UV-IR Experiments that Suggest Photoactivated Fe-Cu Dinuclear Catalyst
|
This work reports the synthesis of a triethylsilyl-substituted Fe-Cu complex that provided cyclohexane solubility to conduct time-resolved UV-IR studies. These studies suggest that UV light induces a photochemically active heterodinuclear species for arene borylation catalysis.<br />
|
Kyle Clark; Jacob Davis; Doo-Hyun Kwon; Erin E. Martinez; Michael R. Talley; David Michaelis; Daniel Ess; Matthew Asplund
|
Coordination Chemistry (Organomet.); Kinetics and Mechanism - Organometallic Reactions; Spectroscopy (Organomet.); Transition Metal Complexes (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755e09abda2a788f8e457/original/time-resolved-uv-ir-experiments-that-suggest-photoactivated-fe-cu-dinuclear-catalyst.pdf
|
667ec59bc9c6a5c07aae6cf4
|
10.26434/chemrxiv-2024-9trjb
|
Mechanistic Insights into the Potentiodynamic Electrosynthesis of PEDOT Thin Films at a Polarisable Liquid|Liquid Interface
|
Conducting polymer (CP) thin films find widespread use, for example in bioelectronic, energy harvesting and storage, and drug delivery technology. Electrosynthesis at a polarisable liquid|liquid interface using an aqueous oxidant and organic soluble monomer provides a route to free-standing and scalable CP thin films, such as poly(3,4-ethylenedioxythiophene) (PEDOT), in a single step at ambient conditions. Here, using the potentiodynamic technique of cyclic voltammetry, interfacial electrosynthesis involving ion-exchange, electron transfer, and proton adsorption charge transfer processes is shown to be mechanistically distinct from CP electropolymerisation at a solid electrode|electrolyte interface. The applied interfacial Galvani potential difference controls the interfacial concentration of the oxidant, EDOT monomers and oligomers, but not the CP redox state. Nevertheless, typical CP electropolymerisation electrochemical behaviours, such as steady charge accumulation with each successive cycle and the appearance of a nucleation loop, were observed. By combining (spectro)electrochemical measurements and theoretical models, this work identifies the underlying mechanistic origin of each feature on the cyclic voltammograms (CVs) due to charge accumulated from Faradaic and capacitive processes as the PEDOT thin film grows. The experimental methodology and theoretical models outlined in this article provide a broadly generic framework to understand evolving CVs during interfacial electrosynthesis using any suitable oxidant/monomer combination.
|
Rob A. Lehane; Alonso Gamero-Quijano; José A. Manzanares; Micheál D. Scanlon
|
Physical Chemistry; Materials Science; Polymer Science; Thin Films; Conducting polymers; Electrochemistry - Mechanisms, Theory & Study
|
CC BY 4.0
|
CHEMRXIV
|
2024-07-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667ec59bc9c6a5c07aae6cf4/original/mechanistic-insights-into-the-potentiodynamic-electrosynthesis-of-pedot-thin-films-at-a-polarisable-liquid-liquid-interface.pdf
|
60c75087bb8c1a587c3dbb19
|
10.26434/chemrxiv.13052360.v1
|
LC-MS/MS Validation for Drug of Abuse Testing Utilizing a Split Sample Oral Fluid Collection System.
|
<p>The Substance Abuse and Mental Health Services Administration (SAMHSA) recently authorized oral fluid (OF) as a preferable biofluid for drugs of abuse (DOA) screening compared to urine, and they required that each screening method be confirmed by a laboratory test. We developed a DOA mass spectrometry (MS) assay optimized for undiluted OF as a matching confirmatory test for the EZ-Saliva point of care (POC), split sample, rapid visual test. Using a double isotope ratio standardization, we achieved a limit of detection of <0.3 ng/mL for seven DOAs, with high precision in undiluted patient OF (CV<7.2%), linearity of R<sup>2</sup> = 0.99, lack of interference (<1.0%) by a panel of interfering compounds at 1000-fold excess, and a dynamic range of 0-850 ng/mL, from a consented population of N=84 self-reported THC users using the collection device (device yield >90%). Stability from degradation exceeded 72 hours. The lateral flow immunoassay strips of the POC exhibited a dose-dependent response, with a 90% sensitivity and 100% specificity for N=22 self-reported, THC patient OF, digitized for quantitation. We conclude that the split sample POC device in combination with the MS assay meets the SAMHSA stated requirements for a POC test with a laboratory confirmation. Split sample collection has significant advantages because it minimizes potential error created by taking a separate OF sample for laboratory confirmation. We recommend scaling to a larger validation study set and quantification of user OF THC levels that correlate with driver impairment levels. </p>
|
Marissa Howard; Paul Russo; Amanda N Haymond; Valerie Cruz Ortiz; Sydney R Andes; Virginia Espina; Alessandra Luchini; Lance Liotta; Raouf Guirguis
|
Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-10-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75087bb8c1a587c3dbb19/original/lc-ms-ms-validation-for-drug-of-abuse-testing-utilizing-a-split-sample-oral-fluid-collection-system.pdf
|
663163e021291e5d1d1dcc85
|
10.26434/chemrxiv-2024-856gt
|
A Bioorthogonal Precision Tool for human N-acetylglucosaminyltransferase V
|
Correct elaboration of N-linked glycans in the secretory pathway of human cells is essential in physiology. Early N-glycan biosynthesis follows an assembly line principle before undergoing crucial elaboration points that feature the sequential incorporation of the sugar N-acetylglucosamine (GlcNAc). The activity of GlcNAc transferase V (MGAT5) primes the biosynthesis of an N-glycan antenna that is heavily upregulated in cancer. Yet, the functional relevance and substrate choice of MGAT5 are ill-defined. Here, we employ a tactic termed bump-and-hole engineering to develop a bioorthogonal substrate analog for the activity of MGAT5. Chemoenzymatic synthesis is used to produce a collection of nucleotide-sugar analogs with bulky, bioorthogonal acylamide side chains. Protein engineering yields an MGAT5 variant that specifically uses one such substrate instead of the native nucleotide-sugar. We validate the enzymatic bump-and-hole system and show that the orthogonal enzyme-substrate pair is suitable to bioorthogonally tag glycoproteins. Through X-ray crystallography and molecular dynamic simulations, we establish the structural basis of bump-and-hole engineering, informing the design rules for bioorthogonal precision chemical tools.
|
Yu Liu; Ganka Bineva-Todd; Richard Meek; Laura Mazo; Beatriz Piniello; Olga Moroz; Nadima Begum; Andre Ohara; Chloe Roustan; Sara Tomita; Svend Kjaer; Karen Polizzi; Carme Rovira; Gideon Davies; Benjamin Schumann
|
Biological and Medicinal Chemistry; Cell and Molecular Biology; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663163e021291e5d1d1dcc85/original/a-bioorthogonal-precision-tool-for-human-n-acetylglucosaminyltransferase-v.pdf
|
6364efb6ac45c72280a52997
|
10.26434/chemrxiv-2022-wf3kf
|
High-Throughput Experimentation as an accessible technology for academic organic chemists in Europe and beyond.
|
For years now, High-Throughput Experimentation (HTE) have been applied to organic chemistry for reaction optimization and reaction discovery as a powerful tool for time and cost reduction. If this technology has been first developed by and for industry, and used as a routine method today, some academic researchers, including in Europe, are still challenging the accessibility of HTE as a general and daily used technology. One of the reasons is probably the expensive cost of such facilities development, which generally involves automation with robots, dedicated research teams, and expensive analytical instrumentation. This paper aims at bringing to light the accessibility of HTE with a minimum of instrumentation and cost, in order to help organic chemists to accelerate the discovery and optimization of new synthetic methodology, leading them to reduce their costs and empower their innovative research.
|
Xisco Caldentey; Eugénie Romero
|
Organic Chemistry; Catalysis; Organometallic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-11-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6364efb6ac45c72280a52997/original/high-throughput-experimentation-as-an-accessible-technology-for-academic-organic-chemists-in-europe-and-beyond.pdf
|
60f5c2707bf0c9634e5f66d8
|
10.26434/chemrxiv-2021-v0b70-v5
|
Drug Repurposing for Coronavirus (COVID-19): In Silico Screening of Known Drugs Against the SARS-CoV-2 Spike Protein Bound to Angiotensin Converting Enzyme 2 (ACE2) (6M0J)
|
In this study FDA approved HCV antiviral drugs and their structural analogues – several of them in clinical trials - were tested for their inhibitory properties towards the SARS-CoV-2 Spike protein bound to angiotensin converting enzyme 2 (ACE2) (6M0J) using a virtual screening approach and computational chemistry methods. The most stable structures and the corresponding binding affinities of thirteen such antiviral compounds were obtained. Frontier molecular orbital theory, global reactivity descriptors, molecular docking calculations and electrostatic potential (ESP) analysis were used to hypothesize the bioactivity of these drugs against 6M0J. It is found that increased affinity for the protein is shown by inhibitors with large compound volume, relatively higher electrophilicity index, aromatic rings and heteroatoms that participate in hydrogen bonding. Among the drugs tested, four compounds 10-13 showed excellent results – binding affinities -11.2 to -11.5 kcal.mol-1. These four top scoring compounds may act as lead compounds for further experimental validation, clinical trials and even for the development of more potent antiviral agents against the SARS-CoV-2.
|
Konstantinos Kalamatianos
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Chemoinformatics - Computational Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-07-20
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f5c2707bf0c9634e5f66d8/original/drug-repurposing-for-coronavirus-covid-19-in-silico-screening-of-known-drugs-against-the-sars-co-v-2-spike-protein-bound-to-angiotensin-converting-enzyme-2-ace2-6m0j.pdf
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60c746a4567dfe51cdec4677
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10.26434/chemrxiv.11365616.v1
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Covalent and Non-Covalent Strategies for the Immobilization of Tobacco Etch Virus (TEV) Protease on Superparamagnetic Nanoparticles
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<div>TEV protease fusion proteins were prepared and immobilized on superparamagnetic nanoparticles (SPIONs). Non-covalent (avidin-biotin) and covalent (HALOtag-chloroalkane) strategies were explored for TEV immobilization. HALOtag immobilized TEV protease provided enhance performance in both enzyme retention and reusability. SPION-immobilized proteases could be a convenient and cost-saving tool in the life sciences</div>
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Jessica L. Norris; Tulsi Patel; Anvesh K. R. Dasari; Thomas A. Cope; Kwang Hun Lim; Robert Hughes
|
Bioengineering and Biotechnology
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CC BY NC ND 4.0
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CHEMRXIV
|
2019-12-19
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746a4567dfe51cdec4677/original/covalent-and-non-covalent-strategies-for-the-immobilization-of-tobacco-etch-virus-tev-protease-on-superparamagnetic-nanoparticles.pdf
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67a65a8481d2151a028d3022
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10.26434/chemrxiv-2024-nb231-v2
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Unusual Directionality in Thioamide Hydrogen Bonds Can Stabilize β-Strands
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Though thioamides are considered weaker hydrogen-bond acceptors than oxoamides, recent calculations suggest they might enhance hydrogen bonds within the backbone of individual β-strands. We confirm this prediction through spectroscopic analysis of minimal amino-acid models. Further, incorporation of thioamides into the backbone of β-hairpin models high-lights opportunities to control β-strand stability.
|
Haoliang Zheng; Robert W Newberry
|
Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Physical Organic Chemistry; Chemical Biology
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CC BY NC 4.0
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CHEMRXIV
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2025-02-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a65a8481d2151a028d3022/original/unusual-directionality-in-thioamide-hydrogen-bonds-can-stabilize-strands.pdf
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643949ad08c86922fff7cf46
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10.26434/chemrxiv-2023-dt7vk-v2
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On the non-bonding valence band and the electronic properties of poly(triazine imide), a graphitic carbon nitride
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Graphitic carbon nitrides are covalently-bonded, layered, and crystalline semiconductors with high thermal and oxidative stability. These properties make graphitic carbon nitrides potentially useful in overcoming the limitations of 0D molecular and 1D polymer semiconductors. In this contribution, we study structural, vibrational, electronic and transport properties of nano-crystals of poly(triazine-imide) (PTI) derivatives with intercalated Li- and Br-ions and without intercalates. Intercalation-free poly(triazine-imide) (PTI-IF) is corrugated or AB stacked and partially exfoliated. We find that the lowest energy electronic transition in PTI is forbidden due to a non-bonding uppermost valence band and that its electroluminescence from the π-π* transition is quenched which severely limits their use as emission layer in electroluminescent devices. THz conductivity in nano-crystalline PTI is up to eight orders of magnitude higher than the macroscopic conductivity of PTI films. We find that the charge carrier density of PTI nano-crystals is among the highest of all known intrinsic semiconductors, however, macroscopic charge transport in films of PTI is limited by disorder at crystal-crystal interfaces. Future device applications of PTI will benefit most from single crystal devices that make use of electron transport in the lowest, π-like conduction band.
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David Burmeister; Michael Janus Bojdys; Alberto Eljarrat; Michele Guerrini; Eva Röck; Julian Plaickner; Christoph T. Koch; Natalie Banerji; Caterina Cocchi; Emil List-Kratochvil
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Physical Chemistry; Materials Science; Materials Processing; Physical and Chemical Processes; Structure; Materials Chemistry
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CC BY 4.0
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CHEMRXIV
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2023-04-17
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643949ad08c86922fff7cf46/original/on-the-non-bonding-valence-band-and-the-electronic-properties-of-poly-triazine-imide-a-graphitic-carbon-nitride.pdf
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60c755d50f50dbb98f397fad
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10.26434/chemrxiv.14156957.v1
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ChemPix: Automated Recognition of Hand-drawn Hydrocarbon Structures Using Deep Learning
|
<p>Inputting molecules into chemistry software, such as quantum chemistry packages, currently requires domain expertise, expensive software and/or cumbersome procedures. Leveraging recent breakthroughs in machine learning, we develop ChemPix: an offline, hand-drawn hydrocarbon structure recognition tool designed to remove these barriers. A neural image captioning approach consisting of a convolutional neural network (CNN) encoder and a long short-term memory (LSTM) decoder learned a mapping from photographs of hand-drawn hydrocarbon structures to machine-readable SMILES representations. We generated a large auxiliary training dataset, based on RDKit molecular images, by combining image augmentation, image degradation and background addition. Additionally, a small dataset of ~600 hand-drawn hydrocarbon chemical structures was crowd-sourced using a phone web application. These datasets were used to train the image-to-SMILES neural network with the goal of maximizing the hand-drawn hydrocarbon recognition accuracy. By forming a committee of the trained neural networks, we achieved a nearly 10 percentage point improvement of the molecule recognition accuracy and were able to assign a confidence value for the prediction based on the number of agreeing votes. The top ensemble model achieved a hand-drawn hydrocarbon recognition accuracy of 77% for the first prediction and 86% if the top 3 predictions were considered; in over 50% of cases, the model was at least 97% confident in the prediction, making it a promising tool for real-world use cases.</p>
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Hayley Weir; Keiran Thompson; Ben Choi; Amelia Woodward; Augustin Braun; Todd J. Martínez
|
Organic Compounds and Functional Groups; Chemical Education - General; Chemoinformatics; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-03-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755d50f50dbb98f397fad/original/chem-pix-automated-recognition-of-hand-drawn-hydrocarbon-structures-using-deep-learning.pdf
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60c7580b337d6c5aeae29154
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10.26434/chemrxiv.14494704.v1
|
A Fragment Diabatization Linear Vibronic Coupling Model for Quantum Dynamics of Multichromophoric Systems: Population of the Charge Transfer State in the Photoexcited Guanine Cytosine Pair
|
<div>We introduce a method (FrD-LVC) based on a fragment diabatization (FrD) for the parametrization of a Linear Vibronic Coupling (LVC) model suitable for studying the photophysics of multichromophore systems. In combination with effective quantum dynamics (QD) propagations with multilayer multiconfigurational time-dependent Hartree (ML-MCTDH), the FrD-LVC approach gives access to the study of the competition between intra-chromophore decays, like those at conical intersections, and inter-chromophore processes, like exciton localization/delocalization and the involvement of charge transfer (CT) states. We used FrD-LVC parametrized with TD-DFT calculations, adopting either CAM-B3LYP or ωB97X-D functionals, to study the ultrafast photoexcited QD of a Guanine-Cytosine (GC) hydrogen bonded pair, within a Watson-Crick arrangement, considering up to 12 coupled diabatic electronic states and the effect of all the 99 vibrational coordinates. The bright excited states localized on C and, especially, on G are predicted to be strongly coupled to the G->C CT state which is efficiently and quickly populated after an excitation to any of the four lowest energy bright local excited states. Our QD simulations show that more than 80% of the excited population on G and ~50% of that on C decays to this CT state in less than 50 fs. We investigate the role of vibronic effects in the population of the CT state and show it depends mainly on its large reorganization energy so that it can occur even when it is significantly less stable than the bright states in the Franck-Condon region. At the same time, we document that the formation of the GC pair almost suppresses the involvement of dark nπ* excited states in the photoactivated dynamics.</div>
|
James Green; Martha Yaghoubi Jouybari; Haritha Asha; Fabrizio Santoro; Roberto Improta
|
Computational Chemistry and Modeling; Theory - Computational; Photochemistry (Physical Chem.); Quantum Mechanics
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-04-28
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7580b337d6c5aeae29154/original/a-fragment-diabatization-linear-vibronic-coupling-model-for-quantum-dynamics-of-multichromophoric-systems-population-of-the-charge-transfer-state-in-the-photoexcited-guanine-cytosine-pair.pdf
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6744e0a3f9980725cfeb35f1
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10.26434/chemrxiv-2024-vwhv3
|
Development of 5-(5-Phenylthiophen-2-yl)-6-Azauridine as a Three-Prong Agent for Photodynamic Therapy, Cell Imaging, and Cancer Cell Inhibition
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The development of DNA and RNA nucleobase analogs as potential photodynamic therapy and cell imaging agents represents a significant breakthrough for prospective clinical applications relying on metal-free photosensitizers. The ability of these nucleobase analogs to inhibit cancer cell growth would add another dimension of sophistication and versatility. This study investigates the photophysical, electronic-structure, excited state dynamics, and cancer cell photodynamic and inhibitory properties of 5-(5-phenylthiophen-2-yl)-6-azauridine (PTAU). PTAU absorbs up to 425 nm and exhibits an intersystem crossing lifetime of 2.6 ± 0.2 ns in acetonitrile. Intersystem crossing leads to the population of a long-lived triplet state, which decays in 2.4 ± 0.3 µs. Furthermore, PTAU has fluorescence and singlet oxygen quantum yields of 43 ± 1% and 52 ± 2% in acetonitrile, and 12 ± 1% and 33 ± 2% in aqueous phosphate buffer solution, respectively. When applied to B16F10 murine melanoma cell lines, PTAU localizes primarily in mitochondria and exhibits excellent photodynamic efficacy with an IC50 of 125 ± 5 µM at a low dose of 5 J cm-2 of photoactivation. No dark toxicity is observed. Notably, PTAU also inhibits cell proliferation of B16F10 murine melanoma and A431 human epidermoid carcinoma by more than 95% at a concentration of 250 µM in the absence of light. Therefore, PTAU stands out as the first DNA/RNA nucleobase derivative capable of acting as a multipurpose agent for photodynamic therapy, bioimaging, and inhibition of cancer cell proliferation. These findings pave the way for developing modified 6-azauridine analogs absorbing visible to infrared light for their use as cell imaging-assisted PDT agents and cancer cell inhibitors.
|
Sourav Seth; Chris Acquah; Liraz Levi; Steffen Jockusch; Carlos Crespo-Hernández
|
Physical Chemistry; Organic Chemistry; Chemical Kinetics; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.)
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CC BY NC 4.0
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CHEMRXIV
|
2024-11-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6744e0a3f9980725cfeb35f1/original/development-of-5-5-phenylthiophen-2-yl-6-azauridine-as-a-three-prong-agent-for-photodynamic-therapy-cell-imaging-and-cancer-cell-inhibition.pdf
|
67d08e68fa469535b9e3ad1c
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10.26434/chemrxiv-2025-7bfzh
|
Stabilisation and functional enhancement of a metal-organic framework purinate-glass composite
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The development of metal-organic framework (MOF) crystal-glass composites (CGCs) has been hindered by the scarcity of MOF glass matrices with low glass transition temperatures (Tgs). Here, we investigate a CGC consisting of a low-Tg MOF glass, (agZIF-UC-7) and UiO-66. Powder X-ray diffraction and stability tests in phosphate buffer saline solution showed UiO-66 was stabilised in the glass matrix. Additionally, the composite exhibited enhanced dye uptake and gas adsorption relative to agZIF-UC-7.
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Celia Castillo-Blas; Ashleigh Chester; Yujun Rong; Bethan Turner; Georgina P. Robertson; Ayano Kono; Philip A Chater; Lauren McHugh; David A. Keen; Thomas D. Bennett
|
Materials Chemistry
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CC BY 4.0
|
CHEMRXIV
|
2025-03-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d08e68fa469535b9e3ad1c/original/stabilisation-and-functional-enhancement-of-a-metal-organic-framework-purinate-glass-composite.pdf
|
66fa69f0cec5d6c142a90485
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10.26434/chemrxiv-2024-0jxrg-v2
|
Fingerprint Analysis of X-Ray Absorption Spectra of Catalysts: From Linear Combination Fit to Machine-Learning Trained on Multielement Experimental Library
|
X-ray absorption near edge structure (XANES) spectroscopy is a powerful method to probe the oxidation state and local structure of metals in catalytic materials. However, it suffers from the lack of unbiased data analysis protocols. Machine learning (ML) overcomes human-related factors by uncovering relevant spectrum-structure relationships and subsequent cross-validation analysis. The bottlenecks in the automatic processing of experimental data are the lack of chemically diverse XANES reference libraries and systematic differences between theory and experiment. Therefore, compiling experimental reference libraries across the periodic table and rational application of ML methodology to small (in terms of data science) training datasets becomes increasingly important. This work revises the classical XANES fingerprint analysis by database augmentation, feature extraction, cross-validation, and uncertainty analysis. We apply the developed methodology to decipher the oxidation state and local coordination of supported vanadium-oxo species (VOx), which change their structure participating in oxidative dehydrogenation catalysis. The developed library and instruments for analysis may serve as a starting point for a unified platform of fingerprint XANES data analysis.
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Bogdan Protsenko; Yuya Kakiuchi; Sergey Guda; David Trummer; Anna Zabilska; Svetlana Shapovalova; Alexander Soldatov; Olga Safonova; Christophe Coperet; Alexander Guda
|
Theoretical and Computational Chemistry; Materials Science; Catalysis; Catalysts; Machine Learning; Heterogeneous Catalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-10-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fa69f0cec5d6c142a90485/original/fingerprint-analysis-of-x-ray-absorption-spectra-of-catalysts-from-linear-combination-fit-to-machine-learning-trained-on-multielement-experimental-library.pdf
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60c73e574c891972e0ad1d98
|
10.26434/chemrxiv.6894833.v1
|
Diverse Cyclopentenes via Enantioselective Cu-Catalyzed Desymmetrization
|
<div>
<div>
<div>
<p>A highly regio-, diastereo- and enantioselective Cu-catalyzed
desymmetrization of diverse meso-bisphosphates with alkyl zirconium nucleophiles has been
developed. The reaction allows access to a broad range of functionalized cyclopentenes with
up to three contiguous stereogenic centers, including quaternary centers and spirocyclic ring
systems.</p></div></div></div>
|
Reece Jacques; Robert D. C. Pullin; Stephen P. Fletcher
|
Organic Compounds and Functional Groups; Stereochemistry; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-08-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e574c891972e0ad1d98/original/diverse-cyclopentenes-via-enantioselective-cu-catalyzed-desymmetrization.pdf
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637d06bf6b4e814d0c7b49b3
|
10.26434/chemrxiv-2022-4wr1m-v2
|
An Automated Variable E-Field DFT Application (A.V.E.D.A.) for Evaluation of Optimally Oriented Electric Fields on
Chemical Reactivity
|
Recent theoretical work and experiments at molecular junctions have provided a strong conceptualization for the effects of oriented electric fields (OEFs) on organic reactions. Depending upon the axis of application, OEFs can increase (or decrease) reaction rate or distinguish between isomeric pathways. Despite the conceptual elegance of OEFs, which may be applied externally or induced locally, as tools for catalyzing organic reactions, implementation in synthetically relevant systems has been hampered by inefficiencies in evaluating reaction sensitivity to field effects. Herein we describe the development of the Automated Variable Electric-Field DFT Application (A.V.E.D.A.) for streamlined evaluation of a reaction’s susceptibility to OEFs. This open-source software was designed to be accessible for non-expert users of computational and programming tools. Following initiation by a single command (and with no subsequent intervention) the Linux workflow manages a series of density functional theory (DFT) calculations and mathematical manipulations to optimize local-minimum and transition-state structures in oriented electric fields of increasing magnitude. The resulting molecular and reaction dipole moments, field-perturbed geometries, and net effective activation energies are compiled for user interpretation. Ten representative pericyclic reactions that showcase the development and evaluation of A.V.E.D.A. are described.
|
Dalton Hanaway; Rose Kennedy
|
Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Computational Chemistry and Modeling
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-11-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637d06bf6b4e814d0c7b49b3/original/an-automated-variable-e-field-dft-application-a-v-e-d-a-for-evaluation-of-optimally-oriented-electric-fields-on-chemical-reactivity.pdf
|
6577acbdfd283d7904cb1e98
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10.26434/chemrxiv-2023-q3cmz
|
Jahn-Teller distortions and phase transitions in LiNiO2: Insights from ab initio molecular dynamics and variable-temperature X-ray diffraction
|
The atomistic structure of lithium nickelate (LiNiO2), the parent compound of Ni-rich layered oxide cathodes for Li-ion batteries, continues to elude a comprehensive understanding. The common consensus is that the material exhibits local Jahn-Teller distortions that dynamically reorient, resulting in a time-averaged undistorted R3 ̅m structure. Through a combination of ab initio molecular dynamics (AIMD) simulations and variable-temperature X-ray diffraction (VT-XRD), we explore Jahn-Teller distortions in LiNiO2 as a function of temperature. Static Jahn-Teller distortions are observed at low temperatures (T < 250 K), followed by a broad phase transition occurring between 250 K and 350 K, leading to a highly dynamic, displacive phase at high temperatures (T > 350 K), which does not show the four short and two long bonds characteristic of local Jahn-Teller distortions. This transition is seen in AIMD simulations via abrupt changes in the calculated pair distribution function and the bond-length distortion index, and in X-ray diffraction via the monoclinic lattice parameter ratio amon/bmon and angle, the fit quality of an R3 ̅m-based structural refinement, and a peak-sharpening of the diffraction peaks on heating consistent with the loss of distorted domains. Between 250 K and 350 K, a mixed-phase regime is found via the AIMD simulations where distorted and undistorted domains coexist. The repeated change between the distorted and undistorted states in this mixed phase regime allows the Jahn-Teller long axes to change direction, these pseudorotations of the Ni-O long axes being a side effect of the onset of the displacive phase transition. Antisite defects, involving Li ions in the Ni layer and Ni ions in the Li layer, are found to pin the undistorted domains at low temperatures, impeding cooperative ordering at a longer length scale.
|
Annalena R. Genreith-Schriever; Alexandra Alexiu; George S. Phillips; Chloe S. Coates; Liam A. V. Nagle-Cocco; Joshua D. Bocarsly; Farheen N. Sayed; Siân E. Dutton; Clare P. Grey
|
Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Energy Storage; Materials Chemistry
|
CC BY NC ND 4.0
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CHEMRXIV
|
2023-12-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6577acbdfd283d7904cb1e98/original/jahn-teller-distortions-and-phase-transitions-in-li-ni-o2-insights-from-ab-initio-molecular-dynamics-and-variable-temperature-x-ray-diffraction.pdf
|
60c74c62ee301c263fc7a079
|
10.26434/chemrxiv.12473375.v1
|
Luminescence, Chiroptical, Magnetic and Ab-Initio Crystal-Field Characterizations of an Enantiopure Helicoidal Yb(III) Complex: The Van Vleck Rennaissance
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<p>The electronic structure of a chiral Yb(III)-based complex is fully determined by taking advantage of experimental magnetic, luminescence, and chiroptical characterizations in combination with ab-initio wavefunction calculations. The combined use of these techniques allows determining with high resolution the electronic structure diagram as well as the nature of the different states involved in the magnetic and chiroptical properties of the investigated complex. The different crystal-field pictures deduced from spectroscopic measurements are re-conciliated in light of the magnetic properties and ab-initio results in the frame of the van Vleck initial vision. Advanced ab-initio calculations demonstrate that global chiroptical spectra correspond to the sum of intricated transitions with similar or opposite polarizations.</p>
|
Frédéric Gendron; Sebastiano Di Pietro; Laura Abad Galan; François Riobé; Virginie Placide; Laure Guy; Francesco Zinna; Lorenzo Di Bari; Amina Bensalah-Ledoux; Yannick Guyot; Guillaume Pilet; Fabrice Pointillart; Bruno Baguenard; Stephan Guy; Olivier Cador; Olivier MAURY; Boris Le Guennic
|
Lanthanides and Actinides; Magnetism; Theory - Computational; Spectroscopy (Physical Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-06-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c62ee301c263fc7a079/original/luminescence-chiroptical-magnetic-and-ab-initio-crystal-field-characterizations-of-an-enantiopure-helicoidal-yb-iii-complex-the-van-vleck-rennaissance.pdf
|
661b097191aefa6ce18226d8
|
10.26434/chemrxiv-2024-j13hj-v2
|
Hydrogen-Atom Binding Energy of Structurally Well-defined Cerium Oxide Nodes at the Metal−Organic Framework-Liquid Interfaces
|
Redox-active metal oxides are prevalent in the fields of thermal, photo-, and electrocatalysis. Thermodynamics of proton-coupled electron transfer (PCET) reactions at their surfaces are critical as they scale with their activity as a catalyst. The structural heterogeneity and ambiguity of surface sites have largely precluded structural understanding of the exact redox-active sites, challenging chemists to design the catalyst structure down to the atomic level. Here, we report electrochemically determined stoichiometry and thermodynamics of PCET reactions of the cerium-based metal−organic framework (MOF), Ce-MOF-808. Cyclic voltammograms (CVs) of the MOF-deposited electrodes in aqueous buffers at various pHs revealed a Faradaic couple that can be ascribed to Ce4+/3+ redox. Plotting the half-wave potential (E½) against the electrolyte pH resulted in a Pourbaix diagram with a slope of 65 ± 9 mV/pH, suggesting a 1H+/1e- stoichiometry. Using the thermochemical analogy between 1H+/1e- and one H-atom (H∙), the H-atom binding energy on the hexanuclear Ce6 node, the Ce3+O−H bond dissociation free energy (BDFE), was calculated to be 77 ± 2 kcal mol-1. In-silico calculations quantitatively corroborated our BDFE measurements. Furthermore, multiple proton topologies were computationally elucidated to exhibit similar BDFEs to the experimental values, agreeing with the wide Faradaic features of all CVs, implicating that the system has a substantial BDFE distribution. To the best of our understanding, this is the first thermochemical measurement of H-atom binding on MOFs. Implications of the presented thermochemical measurements on catalysis using metal oxides and MOFs are discussed.
|
Zachary Ingram; Chance Lander; Madeleine Oliver; Nazmiye Gokce Altincekic; Liangliang Huang; Yihan Shao; Hyunho Noh
|
Inorganic Chemistry; Catalysis; Electrochemistry; Supramolecular Chemistry (Inorg.); Heterogeneous Catalysis; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-04-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661b097191aefa6ce18226d8/original/hydrogen-atom-binding-energy-of-structurally-well-defined-cerium-oxide-nodes-at-the-metal-organic-framework-liquid-interfaces.pdf
|
639a42f6dadddcd0ae8ea5a0
|
10.26434/chemrxiv-2022-d3jl7
|
A “non-magnetic” triplet bismuthinidene enabled by relativity
|
Isolation and stabilization of main group diradical species have posed a synthetic challenge over the years due to their intrinsic high reactivity. Herein we report on a large-scale synthesis and isolation of a mono-coordinate bismuthinidene featuring a rigid and bulky ligand, which protects the Bi(I) center. The compound was characterized by its unique spectroscopic features (UV-vis and NMR), but more prominently, by its magnetic properties. Multiconfigurational quantum chemical calculations predict the ground state of the compound to be dominated by a spin-triplet. Further support for this electronic structure description was obtained through correlation of theory to experimental XRD, XAS, and UV-Vis data. However, all magnetic measurements (EPR, NMR and SQUID) point to a diamagnetic compound. This apparent discrepancy can be explained by an extremely large spin-orbit coupling (SOC) that leads to an unprecedented zero-field splitting of more than 8000 cm‒1, thus leaving a MS = 0 magnetic sublevel thermally isolated in the electronic ground state. The extremely large SOC effect is a result of the low-coordination number of the bismuth center in interplay with its heavy element nature.
|
Yue Pang; Nils Nöthling; Markus Leutzsch; Liqun Kang; Eckhard Bill; Maurice van Gastel; Edward Reijerse; Richard Goddard; Lucas Wagner; Daniel SantaLucia; Serena DeBeer; Frank Neese; Josep Cornella
|
Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Magnetism; Main Group Chemistry (Organomet.); Spectroscopy (Organomet.)
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-12-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639a42f6dadddcd0ae8ea5a0/original/a-non-magnetic-triplet-bismuthinidene-enabled-by-relativity.pdf
|
65bd313466c1381729d3fa2c
|
10.26434/chemrxiv-2024-qv8jh
|
Synthesis and Reactivity of the [NCCCO]– Cyanoketenate Anion
|
Cyanoketene is a fundamental molecule that is actively being searched for in the interstellar medium. Its deprotonated form (cyanoketenate) is a heterocumulene that is isoelectronic to carbon suboxide whose structure has been the subject of debate. These research questions are hampered by a lack of useful synthetic pathways to these molecules. We report the first synthesis of the cyanoketenate anion in [K(18-crown-6)][NCCCO] (1) as a stable molecule on a multigram scale in excellent yields (>90%). The structure of this molecule is probed crystallographically and computationally. We also explore the protonation of 1, and its reaction with triphenylsilylchloride and carbon dioxide. In all cases, anionic dimers are formed. The cyanoketene could be synthesized and crystallographically characterized when stabilized by a N-heterocyclic carbene. The cyanoketenate is a very useful unsaturated building block containing N, C and O atoms that can now be explored with relative ease and will undoubtedly unlock more interesting reactivity.
|
Tongtong Wang; Zhuangzhuang Guo; Laura English; Douglas Stephan; Andrew Jupp; Maotong Xu
|
Inorganic Chemistry; Main Group Chemistry (Inorg.); Reaction (Inorg.); Small Molecule Activation (Inorg.)
|
CC BY 4.0
|
CHEMRXIV
|
2024-02-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bd313466c1381729d3fa2c/original/synthesis-and-reactivity-of-the-nccco-cyanoketenate-anion.pdf
|
60c73d0e0f50db6a3339540a
|
10.26434/chemrxiv.5393944.v1
|
Explaining the magnetism of gold
|
<p>In
the present work, a computational study is performed in order to clarify the
possible magnetic nature of gold. For such purpose, gas phase Au<sub>2</sub>
(zero charge) is modelled, in order to calculate its gas phase formation
enthalpy. The calculated values were compared with the experimental value
obtained by means of Knudsen
effusion mass spectrometric studies [5]. Based on the obtained
formation enthalpy values for Au<sub>2</sub>, the compound with two unpaired
electrons is the most probable one. The calculated ionization energy of
modelled Au<sub>2</sub> with two unpaired electrons is 8.94 eV and with zero
unpaired electrons, 11.42 eV. The difference (11.42-8.94 = 2.48 eV = 239.29
kJmol<sup>-1</sup>), is in very good agreement with the experimental value of
226.2 ± 0.5 kJmol<sup>-1</sup> to the
Au-Au bond<sup>7</sup>. So, as expected, in the specie with none unpaired
electrons, the two 6s<sup>1</sup> (one of each gold atom) are paired, forming a
chemical bond with bond order 1. On the other hand, in Au<sub>2</sub> with two
unpaired electrons, the s-d hybridization prevails, because the relativistic
contributions. A molecular orbital energy diagram for gas phase Au<sub>2</sub>
is proposed, explaining its paramagnetism (and, by extension, the paramagnetism
of gold clusters and nanoparticles).</p>
|
Robson de Farias
|
Magnetism
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2017-09-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0e0f50db6a3339540a/original/explaining-the-magnetism-of-gold.pdf
|
64dded8769bfb8925a11f9bf
|
10.26434/chemrxiv-2023-57hwb
|
Vinylic C–H Activation of Styrenes by an Iron–Aluminum Complex
|
The oxidative addition of sp2 C–H bonds of alkenes to single-site transition metal complexes is complicated by the compet-ing π-coordination of the C=C double bond, limiting the examples of this type of reactivity and onwards applications. Here we report the C–H activation of styrenes by a well-defined bimetallic Fe–Al complex. These reactions are highly selective resulting in the (E)-β-metalation of the alkene. For this bimetallic system, alkene binding appears to be essential for the reaction to occur. Experimental and computational insight suggests an unusual reaction pathway in which a (2+2) cycloaddi-tion intermediate is directly converted into the hydrido vinyl product via an intramolecular sp2 C–H bond activation across the two metals. The key C–H cleavage step proceeds through a highly asynchronous transition state near the boundary be-tween a concerted/stepwise mechanism influenced by the resonance stabilization ability of the aryl substituent.
|
NIkolaus Gorgas; Benedek Stadler; Andrew White; Mark Crimmin
|
Organometallic Chemistry; Bond Activation; Kinetics and Mechanism - Organometallic Reactions; Transition Metal Complexes (Organomet.)
|
CC BY 4.0
|
CHEMRXIV
|
2023-08-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64dded8769bfb8925a11f9bf/original/vinylic-c-h-activation-of-styrenes-by-an-iron-aluminum-complex.pdf
|
60c74c5df96a00c3b72877aa
|
10.26434/chemrxiv.12463946.v1
|
Binding Mechanism and Structural Insights into the Identified Protein Target of Covid-19 with In-Vitro Effective Drug Ivermectin
|
<p>While an FDA approved drug Ivermectin was reported to dramatically reduce the cell line of SARS-CoV-2 by ~5000 folds within 48 hours, the precise mechanism of action and the COVID-19 molecular target involved in interaction with this in-vitro effective drug are unknown yet. Among 12 different COVID-19 targets studied here, the RNA dependent RNA polymerase (RdRp) with RNA and Helicase NCB site show the strongest affinity to Ivermectin amounting -10.4 kcal/mol and -9.6 kcal/mol, respectively. Molecular dynamics of corresponding protein-drug complexes reveals that the drug bound state of RdRp with RNA has better structural stability than the Helicase NCB site, with MM/PBSA free energy of -135.2 kJ/mol, almost twice that of Helicase (-76.6 kJ/mol). The selectivity of Ivermectin to RdRp is triggered by a cooperative interaction of RNA-RdRp by ternary complex formation. Identification of the target and its interaction profile with Ivermectin can lead to more powerful drug designs for COVID-19 and experimental exploration. </p>
|
Parth Sarthi Sen Gupta; Satyaranjan Biswal; Saroj Kumar Panda; Abhik Kumar Ray; Malay Kumar Rana
|
Bioengineering and Biotechnology; Bioinformatics and Computational Biology; Biophysics; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c5df96a00c3b72877aa/original/binding-mechanism-and-structural-insights-into-the-identified-protein-target-of-covid-19-with-in-vitro-effective-drug-ivermectin.pdf
|
67c0e5306dde43c908c6f7ce
|
10.26434/chemrxiv-2025-f7cmz
|
Lanthanum and Gadolinium Complexes with Neutral Tertiary Phosphine Ligands: Synthesis, Structures, Magnetism and Bonding
|
The coordination chemistry of lanthanoids with neutral tertiary phosphine ligands is still largely underdeveloped, with only few examples and none for some of the lanthanoids, such as gadolinium. Therefore, the formation of organometallic lanthanum and gadolinium phosphine complexes was investigated. Solvent-free precursors [Ln(COT)I] and [LnCp3] (Ln = La, Gd) were reacted with the bisphosphines 1,2-bis(dimethylphosphino)ethane (dmpe) and 1,2- bis(dimethylphosphino)methane (dmpm). The resulting complexes [Gd(COT)I(dmpe)], [{Gd(COT)(μ-I)}2(μ-dmpm)], [{LnCp3}2(μ-dmpe)] (Ln = La, Gd) and the precursor [Gd(COT)I(thf)2] could be isolated and were characterized by single crystal x-ray diffraction. Depending on the ancillary ligands and bisphosphines backbone, chelating and bridging coordination modes were observed for the bisphosphine ligands. The magnetism of the dimeric gadolinium complexes was investigated via SQUID magnetometry. A weak antiferromagnetic coupling was found between the Gd3+ ions in [{Gd(COT)(μ-I)}2(μ-dmpm)]. A DFT study was performed on the isolated complexes to study the nature of the Ln-P bonds. Quantum theory of atoms in molecules analysis showed a correlation between the (overall small) bond covalency and the Ln-P bond length.
|
Jan Locher; Sophie Jana Gross; Sebastian Dechert; Serhiy Demeshko; Lisa Vondung
|
Organometallic Chemistry; Coordination Chemistry (Organomet.); Theory - Organometallic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c0e5306dde43c908c6f7ce/original/lanthanum-and-gadolinium-complexes-with-neutral-tertiary-phosphine-ligands-synthesis-structures-magnetism-and-bonding.pdf
|
6345793ae0a4835d03fb3fb9
|
10.26434/chemrxiv-2022-n9lzd
|
Comprehensive Structure-Activity Relationship Studies of Cepafungin Enabled by Biocatalytic C–H Oxidations
|
The cepafungins are a class of highly potent and selective eukaryotic proteasome inhibitor natural products with potential to treat refractory multiple myeloma and other cancers. The structure-activity relationship of the cepafungins is not fully understood. This account chronicles the development of a chemoenzymatic approach to cepafungin I. A failed initial route involving derivatization of pipecolic acid prompted us to examine the biosynthetic pathway for the production of 4-hydroxylysine, which culminated in the development of a 9-step synthesis of cepafungin I. An alkyne-tagged analog enabled chemoproteomic studies of cepafungin and comparison of its effects on global protein expression in human multiple myeloma cells to the clinical drug bortezomib. A preliminary series of analogs elucidated critical determinants of potency in proteasome inhibition. Herein we report the chemoenzymatic syntheses of 13 additional analogs of cepafungin I guided by a proteasome-bound crystal structure, 5 of which are more potent than the natural product. Enzymatic strategies enabled the facile synthesis of oxidized amino acids in the macrocycle warhead as well as the tail fragment. Additional analogs were prepared by chemical methods to further explore the SAR at other regions of the scaffold. These studies reveal the criticality of the macrocyclic L-lysine oxidation regio-/stereochemistry introduced in the natural product biosynthesis relative to other possible lysine oxidation patterns found in nature. The lead analog was found to have seven-fold greater proteasome b5 subunit inhibitory activity and has been evaluated against several multiple myeloma and mantle cell lymphoma cell lines in comparison to the clinical drug bortezomib.
|
Alexander Amatuni; Anton Shuster; Daniel Abegg; Alexander Adibekian; Hans Renata
|
Organic Chemistry; Natural Products; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6345793ae0a4835d03fb3fb9/original/comprehensive-structure-activity-relationship-studies-of-cepafungin-enabled-by-biocatalytic-c-h-oxidations.pdf
|
6494035f24989702c2c4307d
|
10.26434/chemrxiv-2023-69m82-v2
|
Finite-size Effects on the Calculation of X-ray Scattering from Molecular Dynamics Simulations
|
Structural studies using x-ray scattering methods for investigating molecules in solution are shifting focus towards describing the role and effects of the surrounding solvent. However, forward models based on molecular dynamics (MD) simulations to simulate structure factors and x-ray scattering from interatomic distributions such as radial distribution functions (RDFs) face limitations imposed by simulations, particularly at low values of the scattering vector q. In this work, we show how the value of the structure factor at q = 0 calculated from RDFs sampled from finite MD simulations is effectively dependent on the size of the simulation cell. To eliminate this error, we derive a new scheme to renormalize the sampled RDFs based on a model of the excluded volume of the particle-pairs they were sampled from, to emulate sampling from an infinite system. We compare this new correction method to two previous RDF- correction methods, developed for Kirkwood-Buff theory applications. We present a quantitative test to assess the reliability of the simulated low-q scattering signal, and show that our RDF-correction successfully recovers the correct q = 0 limit for neat water. We investigate the effect of MD-sampling time on the RDF-corrections, before advancing to a molecular example system, comprised of a transition metal complex solvated in a series of water cells with varying densities. We show that our correction recovers the correct q = 0 behaviour for all densities. Furthermore, we employ a simple continuum scattering model to dissect the total scattering signal from the solvent-solvent structural correlations in a solute-solvent model system to find two distinct contributions: a non-local density-contribution from the finite, fixed cell size in NVT simulations, and a local contribution from the solvent shell. We show how the second contribution can be approximated without also including the finite-size contribution. Finally, we provide a ’best-practices’-checklist for experimentalists planning to incorporate explicit solvation MD simulations in future work, offering guidance for improving the accuracy and reliability of structural studies using x-ray scattering methods in solution.
|
Asmus Ougaard Dohn; Verena Isabell Markmann; Amke Nimmrich; Kristoffer Haldrup; Klaus Braagaard Møller; Martin Meedom Nielsen
|
Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Radiation; Statistical Mechanics
|
CC BY 4.0
|
CHEMRXIV
|
2023-06-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6494035f24989702c2c4307d/original/finite-size-effects-on-the-calculation-of-x-ray-scattering-from-molecular-dynamics-simulations.pdf
|
60c75262ee301ce80bc7abbc
|
10.26434/chemrxiv.13293356.v1
|
Concise asymmetric syntheses of streptazone A and abikoviromycin
|
Streptazone A and abikoviromycin are related alkaloids that both feature an unusual arrangement of reactive functionalities within an underlying compact tricyclic ring system. Here, we report a highly concise asymmetric synthesis of both natural products. The developed route first constructs another member of the streptazones, streptazone B1, using a rhodium-catalyzed distal selective allene-ynamide Pauson-Khand reaction as the key transformation. A regio- and enantioselective epoxidation under chiral phase-transfer catalytic conditions was then achieved to directly make streptazone A in 8 steps overall. A chemoselective, iridium-catalyzed reduction of the enaminone-system was employed to make abikoviromycin in one additional step. Studies of the intrinsic reactivity of streptazone A towards the cysteine mimic, <i>N</i>-acetylcysteamine, revealed unanticipated transformations, resulting in thiol conjugation to both the hindered tertiary carbon of the double allylic epoxide and in bis-thiol conjugation which may proceed via formation of a cyclopentadienone intermediate. With flexible access to these compounds, studies aimed to identify their direct biological targets are now possible.
|
Gustav J. Wørmer; Nikolaj
L. Villadsen; Peter Nørby; Thomas Poulsen
|
Natural Products; Organic Synthesis and Reactions; Homogeneous Catalysis; Organocatalysis; Catalysis; Reaction (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-11-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75262ee301ce80bc7abbc/original/concise-asymmetric-syntheses-of-streptazone-a-and-abikoviromycin.pdf
|
60c75251469df422ddf44b52
|
10.26434/chemrxiv.13285847.v1
|
Simple Acridan-Based Multi-Resonance Structures Enable Highly-Efficient Narrowband Green TADF Electroluminescence
|
Multi-resonance thermally activated delayed fluorescence (MR-TADF) offered
exceptional solution for narrowband organic light emitting diode (OLED) devices in
terms of color purity and luminescence efficiency, while the development of new MR
skeleton remained an exigent task, especially for long wavelength region. We hereby
demonstrate that a simple modification of the B (boron)-N (nitrogen) framework by
sp3
-carbon insertion would significant bathochromic shift the short-range chargetransfer emission and improve the device performances. The bis(acridan)phenylenebased skeleton developed in this contribution presented a non-planar conformation and
allowed facile introduction of isolating units to prevent triplet-involved quenching,
deriving two luminophores with quantum yields approaching 90% and narrow FWMHs
below 30 nm in film state. Corresponding green-emissive devices realized superior
performances comparing to the planar carbazolyl-based MR-TADF analogues, with a
maximum external quantum efficiency (EQEmax) up to 28.2% and small efficiency rolloff without the involvement of any sensitizing host
|
pengcheng jiang; Lisi Zhan; Xiaosong Cao; Xialei Lv; Shaolong Gong; Changjiang Zhou; Zhongyan Huang; Fan Ni; Yang Zou; Chuluo Yang
|
Optical Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-11-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75251469df422ddf44b52/original/simple-acridan-based-multi-resonance-structures-enable-highly-efficient-narrowband-green-tadf-electroluminescence.pdf
|
62a8b54af5524aa5c3121f63
|
10.26434/chemrxiv-2022-tqbw0
|
Two color imaging of different hypoxia levels in cancer cells
|
Hypoxia (low oxygen levels) exists in a wide range of biological contexts, including plants roots, bacterial biofilms, and solid tumors. In all cases, hypoxia elicits responses affecting the biological system that is experiencing low oxygen that impact on its survival. In the case of bacterial biofilms and tumors, hypoxia makes treating these conditions more difficult and has a negative impact on patient prognosis. Therefore, chemical probes that enable the study of biological hypoxia are valuable tools to help increase understanding of disease-related conditions that involve low oxygen levels, ultimately leading to improved diagnosis and treatment. While a number of small molecule-based hypoxia-sensing probes exist, the majority of these image only very severe hypoxia (≥1% O2), and therefore do not give a full picture of biological hypoxia, which is heterogenous. Commonly used antibody-based imaging tools for hypoxia are less convenient than small molecules, as secondary detection steps involving immunostaining are required. Here we report the synthesis, electrochemical properties, photophysical analysis, and biological validation of a range of indolequinone-based bioreductive fluorescent probes. We show that these compounds can image different levels of hypoxia in 2D and 3D cell culture. The resorufin-based probe 2 was activated in conditions of 4% O2 and lower, while the Tokyo green-based probe 4 was only activated in severe hypoxia – 0.5% O2 and less. Simultaneous application of these compounds in spheroids revealed that compound 2 images similar levels of hypoxia to pimonidazole, while compound 4 images more extreme hypoxia in a manner analogous to EF5. Compounds 2 and 4 are therefore useful tools to study hypoxia in a cellular setting and represent convenient alternatives to antibody-based imaging approaches.
|
Antoine Wallabregue; Hannah Bolland; Stephen Faulkner; Ester Hammond; Stuart Conway
|
Biological and Medicinal Chemistry; Chemical Biology
|
CC BY 4.0
|
CHEMRXIV
|
2022-06-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a8b54af5524aa5c3121f63/original/two-color-imaging-of-different-hypoxia-levels-in-cancer-cells.pdf
|
60c746baee301c4791c7957a
|
10.26434/chemrxiv.11371611.v1
|
Bidentate Chiral Bis(imidazolium)-Based Halogen Bond Donors: Synthesis and First Applications in Enantioselective Recognition and Catalysis
|
Even though halogen bonding – the noncovalent interaction between
electrophilic halogen substituents and Lewis bases – has now been established
in molecular recognition and catalysis, its use in enantioselective processes
is still very little explored. Herein, we present the synthesis of chiral
bidentate halogen bond donors based on two iodoimidazolium units with rigidly
attached chiral sidearms. With these Lewis acids, chiral recognition of a
racemic diamine is achieved in NMR studies. DFT calculations support a 1:1
interaction of the halogen bond donor with both enantiomers and indicate that
the chiral recognition is based on a different spatial orientation of the Lewis
bases in the halogen bonded complexes. In addition, moderate enantioselectivity
is achieved in a Mukaiyama aldol reaction with a preorganized variant of the chiral
halogen bond donor. This represents the first case in which asymmetric
induction was realized with a pure halogen bond donor lacking any additionally
active functional groups.
|
Revannath L. Sutar; Elric Engelage; Raphael Stoll; Stefan Huber
|
Organic Synthesis and Reactions; Physical Organic Chemistry; Supramolecular Chemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-12-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746baee301c4791c7957a/original/bidentate-chiral-bis-imidazolium-based-halogen-bond-donors-synthesis-and-first-applications-in-enantioselective-recognition-and-catalysis.pdf
|
60c73f5f9abda2955cf8ba98
|
10.26434/chemrxiv.7364225.v1
|
Selective Generation of Singlet Oxygen in Chloride Accelerated Copper Fenton Chemistry
|
<p>Singlet oxygen (<sup>1</sup>O<sub>2</sub>), a widely used reactive oxygen species (ROS) in industry and biomedical applications, plays a fundamental role throughout nature. We report a novel method to generate <sup>1</sup>O<sub>2</sub>selectively and efficiently through copper-based Fenton chemistry under circumneutral conditions enhanced by chloride as co-catalyst, with reactivity completely different than that observed in classical iron-based Fenton chemistry. The mechanism of its formation was elucidated through the kinetic studies of orthogonally reactive reporter molecules, i.e., singlet oxygen sensor green, 4-hydroxy-2,2,6,6-tetramethylpiperidine, and phenol, and selective ROS quenchers. This method selectively generates <sup>1</sup>O<sub>2</sub><i>in situ</i>neither relying on photosensitization nor resulting in side reactions, and together with the mechanistic understanding of the Cu-Fenton reaction, not only opens new possibilities in many industries, such as organic synthesis and antimicrobial treatments, but also provides insight into Cu and H<sub>2</sub>O<sub>2</sub>containing chemical, environmental, and biological systems.</p>
|
Andrew Carrier; Collins Nganou; David Oakley; Yongli Chen; Ken Oakes; Stephanie MacQuarrie; Xu Zhang
|
Redox Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-11-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f5f9abda2955cf8ba98/original/selective-generation-of-singlet-oxygen-in-chloride-accelerated-copper-fenton-chemistry.pdf
|
60c74374ee301cee20c78fdf
|
10.26434/chemrxiv.8966297.v2
|
Reusable Chemically-Micropatterned Substrates via Sequential Photoinitiated Thiol-Ene Reactions as Template for Perovskite Thin-Film Microarrays
|
<p>Patterning semiconducting materials are
important for many applications such as microelectronics, displays, and
photodetectors. Lead halide perovskites are an emerging class of semiconducting
materials that can be patterned via solution-based methods. Here we report an
all-benchtop patterning strategy by first generating a patterned surface with
contrasting wettabilities to organic solvents that have been used in the
perovskite precursor solution then spin-coating the solution onto the patterned
surface. The precursor solution only stays in the area with higher affinity
(wettability). We applied sequential sunlight-initiated thiol-ene reactions to
functionalize (and pattern) both glass and conductive fluorine-doped tin oxide
(FTO) transparent glass surfaces. The functionalized surfaces were measured
with the solvent contact angles of water and different organic solvents and
were further characterized by XPS, selective fluorescence staining, and
selective DNA adsorption. By simply spin-coating and baking the perovskite
precursor solution on the patterned substrates, we obtained perovskite
thin-film microarrays. The spin-coated perovskite arrays were characterized by
XRD, AFM, and SEM. We concluded that Patterned substrate prepared via
sequential sunlight-initiated thiol-ene click reactions is suitable to
fabricate perovskite arrays via the benchtop process. In addition, the same
patterned substrates can be reused several times until a favorable perovskite
microarray is acquired. Among a few conditions we have tested, DMSO solvent and
modified FTO surfaces with alternatively carboxylic acid and alkane is the best
combination to obtain high-quality perovskite microarrays. The solvent contact
angle of DMSO on carboxylic acid-modified FTO surface is nearly zero and 65±3<sup>o</sup>
on octadecane modified FTO surface.</p>
|
Kurt Waldo E. Sy Piecco; Juvinch R. Vicente; Joseph R. Pyle; David C. Ingram; Martin E. Kordesch; Jixin Chen
|
Nanostructured Materials - Materials; Thin Films
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-07-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74374ee301cee20c78fdf/original/reusable-chemically-micropatterned-substrates-via-sequential-photoinitiated-thiol-ene-reactions-as-template-for-perovskite-thin-film-microarrays.pdf
|
6135833466dedd536d04a02f
|
10.26434/chemrxiv-2021-j1m8l
|
Sustainable Hybrid Route to Renewable Methacrylic Acid via Biomass-Derived Citramalate
|
Combined chemical technologies of microbial fermentation and thermal catalysis provides a hybrid process for sustainable manufacturing of biorenewable sugar-derived monomers for plastics. In this work, methacrylic acid (MAA), a target molecule for the polymer industry, was produced from biomass-derived glucose through the intermediate molecule, citramalic acid. The biosynthetic pathway engineered in E. coli produced citramalic acid intermediate with a high yield (91% of theoretical maximum) from glucose by overexpressing citramalate synthase, removing downstream degradation enzyme 3-isopropylmalate dehydratase, and optimizing the fermentation medium. Thermal heterogeneous catalysis converted the citramalate intermediate to methacrylic acid (MAA) via decarboxylation and dehydration. A selectivity of ~71% for the production of MAA and its intermediate α-hydroxybutyric acid was achieved at a temperature of 250 oC and an acidity of 1.0 mol acid/mol citramalate. An alumina catalyst was found to enhance selectivity to MAA in a single reactor pass from 45.6% in the absence of catalyst to 63.2%. This limited selectivity to MAA was attributed to equilibrium between MAA and α-hydroxybutyric acid, but overall process selectivity to MAA was shown to be higher upon separation and recycle of reaction intermediates. A process flow diagram was proposed of the hybrid route for the conversion of glucose to the final end product, methacrylic acid, for poly(methyl methacrylate) (PMMA).
|
Yuxiao Wu; Manish Shetty; Kechun Zhang; Paul Dauenhauer
|
Biological and Medicinal Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Reaction Engineering; Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-09-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6135833466dedd536d04a02f/original/sustainable-hybrid-route-to-renewable-methacrylic-acid-via-biomass-derived-citramalate.pdf
|
6707ad3051558a15efafde42
|
10.26434/chemrxiv-2024-jd8vk
|
CO2 utilization in a micellar system: synthesis of cyclic carbonates
|
Fixation of carbon dioxide from its waste streams into value added products, in organic synthesis processes, whilst challenging, would lead to great ecological benefits. To this end, a CO2 cycloaddition to epoxides seems most promising as it is a 100% atom economic reaction leading to valuable cyclic carbonates. However, many of the reaction systems utilized for their synthesis employ organic solvents, high temperatures, and high pressure. Thus, the micellar conditions reported here achieve a metal and organic solvent free approach, giving access to not only carbonates but also carbamates without the need for pressurization or heating. Extensive studies of interactions between micelles and carbon dioxide opens up pathways to use this gaseous reagent in aqueous media.
|
Wojciech J. Depa; Souvik Majumder; Mariana Nadirova; Piotr Cmoch; Wojciech Chaładaj; Martin P. Andersson; Dorota Gryko
|
Organic Chemistry; Catalysis; Organocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6707ad3051558a15efafde42/original/co2-utilization-in-a-micellar-system-synthesis-of-cyclic-carbonates.pdf
|
65d3c450e9ebbb4db9b80cb4
|
10.26434/chemrxiv-2024-gt53w
|
A Strategy for the Controllable Generation of Organic Superbases from Benchtop-Stable Salts
|
Organic superbases are a distinct class of strong Brønsted base that enable numerous modern reaction applications. However, despite their great synthetic potential, widespread use and study of superbases are limited by their air sensitivity and difficult preparation. To address this, we report air-stable carboxylate salts of BTPP and P2-t-Bu phosphazene superbases that, when added to solution with an epoxide, spontaneously generate freebase. These systems function as effective precatalysts and stoichiometric prereagents for superbase-promoted addition, substitution and polymerization reactions. In addition to improving the synthesis, shelf stability, handling and recycling of phosphazenes, this approach enables precise regulation of the rate of base generation in situ. The activation strategy effectively mimics manual slow addition techniques, allowing for control over a reaction’s rate or induction period and improvement of reactions that require strong base but are also sensitive to its presence, such as Pd-catalyzed coupling reactions.
|
Stephen Sujansky; Garrett Hoteling; Jeffrey Bandar
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Base Catalysis; Organocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-02-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d3c450e9ebbb4db9b80cb4/original/a-strategy-for-the-controllable-generation-of-organic-superbases-from-benchtop-stable-salts.pdf
|
66de04e812ff75c3a1cbc63d
|
10.26434/chemrxiv-2024-299w9
|
Constrained TACC3 peptidomimetics for a non-canonical protein-protein interface elucidate allosteric communication in Aurora-A Kinase
|
Peptidomimetic design for non-canonical interfaces is less well established than for α-helix and β-strand mediated protein-protein interactions. Using the TACC3/Aurora-A kinase interaction as a model, we developed a series of constrained TACC3 peptide variants with 10-fold increased binding potencies (Kd) towards Aurora-A in comparison to the parent peptide. High-affinity is achieved in part by restricting the accessible conformational ensemble of the peptide leading to a more favourable entropy of binding. In addition to acting as potent orthosteric TACC3/Aurora-A inhibitors, these peptidomimetics were shown to activate the kinase and inhibit the N-Myc/Aurora-A interaction at a distal site. Thus, the potency of these tools uniquely allowed us to unveil new insight into the role of allosteric communication in the kinase.
|
Diana Gimenez; Martin Walko; Jennifer Miles; Megan Wright; Richard Bayliss; Wilson Andrew
|
Biological and Medicinal Chemistry; Biochemistry; Biophysics; Chemical Biology
|
CC BY 4.0
|
CHEMRXIV
|
2024-09-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66de04e812ff75c3a1cbc63d/original/constrained-tacc3-peptidomimetics-for-a-non-canonical-protein-protein-interface-elucidate-allosteric-communication-in-aurora-a-kinase.pdf
|
626b29f9ed4d8830581c6ed6
|
10.26434/chemrxiv-2022-f01l4
|
Solvent Organization and Electrostatics Tuned by Solute Electronic Structure: Amide vs. Non-Amide Carbonyls
|
The ability to exploit carbonyl groups to measure electric fields in enzymes and other complex reactive environments using the vibrational Stark effect has inspired growing interest in how these fields can be measured, tuned, and ultimately designed. Previous studies have concentrated on the role of the solvent in tuning the fields exerted on the solute. Here, we explore instead the role of the solute electronic structure in modifying the local solvent organization and electric field exerted on the solute. By measuring the infrared absorption spectra of amide-containing molecules, as prototypical peptides, and contrasting them with non-amide carbonyls in a wide range of solvents, we show that these solutes experience notable differences in their frequency shifts in polar solvents. Using vibrational Stark spectroscopy and molecular dynamics simulations, we demonstrate that while some of these differences can be rationalized using the distinct intrinsic Stark tuning rates of the solutes, the larger frequency shifts for amides and dimethylurea primarily result from the larger solvent electric fields experienced by their carbonyl groups. These larger fields arise due to their stronger p-π conjugation, which results in larger C=O bond dipole moments that further induce substantial solvent organization. Using electronic structure calculations, we decompose the electric fields into contributions from solvent molecules that are in the first solvation shell and those from the bulk and show that both of these contributions are significant and become larger with enhanced conjugation in solutes. These results show that structural modifications of a solute can be used to tune both the solvent organization and electrostatic environment, indicating the importance of a solute-centric paradigm in modulating and designing the electrostatic environment in condensed-phase chemical processes.
|
Steven Fried; Chu Zheng; Yuezhi Mao; Thomas Markland; Steven Boxer
|
Theoretical and Computational Chemistry; Physical Chemistry; Solution Chemistry; Spectroscopy (Physical Chem.)
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-05-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626b29f9ed4d8830581c6ed6/original/solvent-organization-and-electrostatics-tuned-by-solute-electronic-structure-amide-vs-non-amide-carbonyls.pdf
|
60c74fed0f50dbb3bf3974c1
|
10.26434/chemrxiv.12377648.v2
|
Mechanism of the Highly Effective Peptide Bond Hydrolysis by MOF808 Catalyst Under Biologically Relevant Conditions
|
Efficient and selective hydrolysis of inert peptide bonds is of paramount importance. MOF-808, a metal-organic framework based on Zr6 nodes, can hydrolyze peptide bonds efficiently under biologically relevant conditions. However, the details of the catalyst structure and of the underlying catalytic reaction mechanism are challenging to establish. By means of DFT calculations we first investigate the speciation of the Zr6 nodes and identify the nature of ligands that bind to the Zr6O8H4-x core in aqueous conditions. The core is predicted to strongly prefer a Zr6O8H4 protonation state and to be predominantly decorated by bridging formate ligands, giving Zr6(μ3-O)4(μ3-OH)4(BTC)2(HCOO)6 and Zr6(μ3-O)4(μ3-OH)4(BTC)2(HCOO)5(OH)(H2O) as the most favorable structures at physiological pH. The GlyGly peptide can bind MOF in several different ways, with the preferred structure involving coordination through the terminal carboxylate analogously to the binding mode of formate ligand. The pre-reactive binding mode in which the amide carbonyl oxygen coordinates the metal core lies 7 kcal higher in free energy. The preferred reaction pathway is predicted to have two close-lying transition states, either of which could be the rate-determining step: nucleophilic attack on the amide carbon atom and C-N bond breaking, with calculated relative free energies of 31 and 32 kcal/mol, respectively. Replacement of formate by water and hydroxide at the Zr6 node is predicted to be possible, but does not appear to play a role in the hydrolysis mechanism.
|
Dragan Conic; Kristine Pierloot; Tatjana Parac-Vogt; Jeremy Harvey
|
Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-09-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fed0f50dbb3bf3974c1/original/mechanism-of-the-highly-effective-peptide-bond-hydrolysis-by-mof808-catalyst-under-biologically-relevant-conditions.pdf
|
651e5bbbbda59ceb9ae73e43
|
10.26434/chemrxiv-2023-2mf82
|
Oxide Ion Dynamics in Hexagonal Perovskite Mixed Conductor Ba7Nb4MoO20: A Comprehensive Ab Initio Molecular Dynamics Study
|
Hexagonal perovskite Ba7Nb4MoO20-related materials are very promising solid electrolytes with high oxide ion conductivity and redox stability, making them potentially applicable in solid oxide fuel cells. Optimizing the properties of this family of materials necessitates atomic-level understanding of the oxide ion dynamics leading to high conductivity. Here we report extensive ab initio molecular dynamics simulations of Ba7Nb4MoO20 investigating oxide ion motions, which allowed the observation of a continuous diffusion pathway for oxide ions in the (ab) plane, but also revealed significant contribution of the oxygen atoms from crystallographic sites located outside this plane, to the long-range dynamics. To probe the timescale of oxide ion diffusion, complementary quasielastic neutron scattering experiments were carried out, and showed that oxide ion dynamics in Ba7Nb4MoO20, even at 950 oC, are too slow to be observable on a nanosecond timescale. Based on the atomic-level understanding of structure-property relationships afforded by this detailed computational study, we propose new materials design strategies with potential to significantly increase oxide ion conductivity in Ba7Nb4MoO20-related hexagonal perovskites, which target to simultaneously increase the number of oxide ion charge carriers and rotational flexibility of the (Nb/Mo)Ox polyhedra.
|
Bettina Schwaighofer; Markus Appel; Miguel Angel Gonzalez; Ivana Radosavljevic Evans
|
Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Fuel Cells; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651e5bbbbda59ceb9ae73e43/original/oxide-ion-dynamics-in-hexagonal-perovskite-mixed-conductor-ba7nb4mo-o20-a-comprehensive-ab-initio-molecular-dynamics-study.pdf
|
60c750330f50db3bd6397528
|
10.26434/chemrxiv.11903112.v2
|
Molecular dynamics approach for capturing calixarenes--proteins interactions: the case of cytochrome c
|
Here, we propose a molecular dynamics investigation of the supramolecular association of sulfonatedcalix-[8]-arenes to cytochrome c. The binding sites prone to interactions with sulfonated calixarenescan be identified without prior knowledge of the X-ray structure, and the binding free energiesestimated by molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) post-analysis arefound to be in neat agreement with the isothermal titration calorimetry (ITC) measurements The per-residuedecomposition reveals the detailed picture of this electrostatically-driven association and notably therole of the arginine R13 as a bridge residue between the two main anchoring sites. In addition,the analysis of the residue behavior by means of a supervised machine learning protocol unveils the formation of an hydrogen bond network far from the binding sites, increasing the rigidity of theprotein.
|
Alessio Bartocci; florence szczepaniak; Tao Jiang; Natacha Gillet; Elise Dumont
|
Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-09-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750330f50db3bd6397528/original/molecular-dynamics-approach-for-capturing-calixarenes-proteins-interactions-the-case-of-cytochrome-c.pdf
|
678fcb3481d2151a02235cba
|
10.26434/chemrxiv-2025-nn3vj
|
Enhanced Crystallinity of Tetrahalopyridyl (THP) Derivatized Compounds
|
Promoting the formation of ordered crystalline material is a fundamental challenge in the fields of organic synthesis, crystal engineering and wider material science. Traditional approaches typically employ strong, unidirectional intermolecular interactions as the core princi-ples for tecton and synthon design. In contrast, the interactions between complex biomolecules, such as proteins, take advantage of the cooperativity of multiple, weak, polyaxial non-covalent interactions (NCIs), working in concert, to generate strongly associated super-structures. Such design principles have yet to be successfully applied to small molecule crystal engineering. Here we show that the tetra-halopyridyl (THP) unit fulfils these tectonic criteria. Firstly, vast and varied THP based NCIs are identified within the Cambridge Struc-tural Database (CSD). The diversity of NCIs is then validated through manual interrogation of a model library and quantified through quantum topological analyses using Bader’s Atoms In Molecules (QTAIM), non-covalent interactions – reduced density gradient (NCI-RDG) and natural bond orbital (NBO) approaches. Furthermore, the critical importance of F···F interactions is revealed through analysis of 17 pairs of interactions in a diverse library of 12 related scaffolds. The utility of the approach is then shown across a wide variety of substrates including promoting natural product crystallinity and for application in absolute structural determination
|
Callum Begg; Viktoriya Dragomanova; Dmitry Yufit; Toby Blundell; Steven Cobb; Mark Fox; Matthew Kitching; William Brittain
|
Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Crystallography – Organic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678fcb3481d2151a02235cba/original/enhanced-crystallinity-of-tetrahalopyridyl-thp-derivatized-compounds.pdf
|
653be8c948dad2312083d784
|
10.26434/chemrxiv-2023-8d22n
|
Johnson-Mehl-Avrami-Kolmogorov model applied to describe the site blocking effect in interstitial solid solution
|
Interstitial solid solutions, such as carbon in steels or hydrogen in metal and alloys, are important materials for many applications. Thermodynamic models that accurately predict the behavior of interstitial solid solution are essential for designing new materials and to improve computational materials tools. In this work, we revisited the problem of calculating the configurational entropy of interstitial solid solutions when site blocking effect occurs. Using an unprecedented approach, we propose a new site blocking model that uses the Johson-Mehl-Avrami-Kolmogorov (JMAK) equation to calculate the fraction of blocked sites. The proposed model (to be called JMAK model) allows to estimate the number of blocked sites considering the site blocking overlapping phenomenon in a simple and direct way. The JMAK model was validated by comparing the calculated values of configurational entropy
with both numerical simulation and experimental data.
|
Otávio Pedroso; Yannick Champion; Walter Botta; Guilherme Zepon
|
Physical Chemistry; Materials Science; Alloys; Hydrogen Storage Materials; Thermodynamics (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653be8c948dad2312083d784/original/johnson-mehl-avrami-kolmogorov-model-applied-to-describe-the-site-blocking-effect-in-interstitial-solid-solution.pdf
|
66b7552f5101a2ffa8d89bc4
|
10.26434/chemrxiv-2024-glhqn-v2
|
Singlet-Triplet Inversion in Triangular Boron Carbon Nitrides
|
The discovery of singlet-triplet (ST) inversion in some π-conjugated triangle-shaped boron carbon nitrides is a remarkable breakthrough that defies Hund’s first rule. Deeply rooted in strong electron-electron interactions, ST inversion has garnered significant interest due to its potential to revolutionize triplet harvesting in organic LEDs. Using the well-established Pariser-Parr-Pople model for correlated electrons in π-conjugated systems, we employ a combination of CISDT and RASCI calculations to investigate the photophysics of several triangular boron carbon nitrides. Our findings reveal that ST inversion in these systems is primarily driven by a network of alternating electron- donor and electron-acceptor groups in the molecular rim, rather than by the triangular molecular structure itself.
|
Matteo Bedogni; Francesco Di Maiolo
|
Theoretical and Computational Chemistry; Physical Chemistry; Energy; Computational Chemistry and Modeling; Theory - Computational; Spectroscopy (Physical Chem.)
|
CC BY 4.0
|
CHEMRXIV
|
2024-08-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b7552f5101a2ffa8d89bc4/original/singlet-triplet-inversion-in-triangular-boron-carbon-nitrides.pdf
|
67d2c8436dde43c908a42e65
|
10.26434/chemrxiv-2025-j5szt
|
Tracking the enzymatic activity of Hexokinase
with 2D-IR spectroscopy
|
Hexokinase catalyzes the first step of glycolysis, transferring a phosphate group from adenosine triphosphate (ATP) to glucose (Glc) to produce glucose-6-phosphate (Glc-6P) and adenosine diphosphate (ADP). This enzymatic reaction is crucial in biochemistry and medical diagnostics, such as Glc level assessments using the hexokinase/glucose-6-phosphate dehydrogenase method.
In this study, we employ two-dimensional infrared (2DIR)
spectroscopy to monitor hexokinase activity in real time
by observing the asymmetric stretching vibrations of the
(PO2)−-groups in ATP and ADP. Compared to Fouriertransform infrared (FTIR), 2D-IR offers enhanced structural resolution and reduced solvent interference. Our results reveal distinct cross-peaks in the ATP spectrum absent in ADP, attributed to intramolecular coupling of (PO2)−- groups. This work highlights the advantages of 2D-IR spectroscopy for studying enzymatic processes.
|
Till Stensitzki; Philip Gasse; Tibor Fuhrmann; Henrike Müller-Werkmeister
|
Physical Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Biophysical Chemistry; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d2c8436dde43c908a42e65/original/tracking-the-enzymatic-activity-of-hexokinase-with-2d-ir-spectroscopy.pdf
|
66594f6221291e5d1db65cdd
|
10.26434/chemrxiv-2024-bf6pw
|
Accurate prediction of antibody deamidations by combining high-throughput automated peptide mapping and protein language model-based deep learning
|
Therapeutic antibodies such as monoclonal antibodies (mAbs), bispecific and multispecific antibodies are pivotal in therapeutic protein development and have transformed disease treatments across various therapeutic areas. The integrity of therapeutic antibodies, however, is compromised by sequence liabilities, notably deamidation, where asparagine (N) and glutamine (Q) residues undergo chemical degradations. Deamidation negatively impacts the efficacy, stability, and safety of diverse classes of antibodies, thus necessitating the critical need for early and accurate identification of vulnerable sites. In this article, a comprehensive antibody deamidation-specific dataset (n = 2285) of varied modalities was created by using high- throughput automated peptide mapping, followed by supervised machine learning to predict the deamidation propensities as well as extents throughout the entire antibody sequences. We propose a novel chimeric deep-learning model, integrating protein language model (pLM)- derived embeddings with local sequence information for enhanced deamidation predictions. Remarkably, this model requires only sequence inputs, eliminating the need for laborious feature engineering. Our approach demonstrates state-of-the-art performance, offering a streamlined workflow for high-throughput automated peptide mapping and deamidation prediction, with potential of broader applicability to other antibody sequence liabilities.
|
Ben Niu; Benjamin Lee; Lili Wang; Wen Chen; Jeffrey Johnson
|
Biological and Medicinal Chemistry; Analytical Chemistry; Mass Spectrometry; High-throughput Screening; Biochemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66594f6221291e5d1db65cdd/original/accurate-prediction-of-antibody-deamidations-by-combining-high-throughput-automated-peptide-mapping-and-protein-language-model-based-deep-learning.pdf
|
64a331899ea64cc167630afe
|
10.26434/chemrxiv-2023-5b4hl-v2
|
Quantum Diamonds at the Beach: Chemical insights into silica growth on nanoscale diamond using multimodal characterization and simulation
|
Surface chemistry of materials that host quantum bits such as diamond are an important avenue of exploration as quantum computation and quantum sensing platforms mature. Interfacing diamond in general, and nanoscale diamond (ND) in particular with silica is a potential route to integrate the quantum bit into a photonic device, fiber optic, cells or tissues with flexible functionalization chemistry. While silica growth on ND cores has been used successfully for quantum sensing and biolabeling, the surface mechanism to initiate growth was unknown. This report describes the surface chemistry responsible for silica bond formation on diamond and uses X-ray absorption spectroscopy (XAS) to probe the diamond surface chemistry and its electronic structure with increasing silica thickness. A modified Stöber (Cigler) method was used to synthesize 2–35 nm thick shells of SiO2 onto carboxylic acid rich ND cores and the diamond features and surface structure were characterized by overlapping techniques including electron microscopy. Importantly, we discovered that SiO2 growth on carboxylated NDs eliminates the presence of carboxylic acids and that basic ethanolic solutions converts the ND surface to an alcohol-rich surface prior to silica growth. The data supports a mechanism that alcohols on the ND surface generate silyl-ether (ND-O-Si-(OH)3) bonds due to rehydroxylation by ammonium hydroxide in ethanol. Additionally, resonant inelastic X-ray scattering (RIXS) maps produced by the transition edge sensor supports the chemical analysis provided by XAS. The suppression of the diamond electronic structure as a function of SiO2 thickness was observed, and the Auger electron escape depth was modeled using the NIST database for the Simulation of Electron Spectra for Surface Analysis (SESSA) to support our experimental results. Researchers using high-pressure high temperature (HPHT) NDs or any alcohol-terminated material (metal oxides, oxidized silicon carbide or cubic-boron nitride) for quantum sensing applications may exploit these results to design new core-shell quantum sensors with base-catalyzed reactions and metal oxide precursors.
|
Perla J. Sandoval; Karen Lopez; Andres Arreola; Anida Len; Pomaikaimaikalani Yamaguchi; Rina Kawamura; Camron X. Stokes; Cynthia Melendrez; Davida Simpson; Sang-Jun Lee; Charles Titus; Virginia Altoe; Sami Sainio; Dennis Nordlund; Kent Irwin; Abraham Wolcott
|
Physical Chemistry; Nanoscience; Spectroscopy (Physical Chem.); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-07-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a331899ea64cc167630afe/original/quantum-diamonds-at-the-beach-chemical-insights-into-silica-growth-on-nanoscale-diamond-using-multimodal-characterization-and-simulation.pdf
|
611d83321d1cc20b9bc7981e
|
10.26434/chemrxiv-2021-4j0f0
|
Natural Products-based drug design from Bahia Semi-Arid region against SARS-CoV-2 Mpro (3Clpro)
|
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), receives global attention due to the serious threat that affect public health. Since December 2019, its incidence affecting millions of patients and its rapid dissemination on a worldwide scale have led the searching for its treatment. To discover hit compounds that can be used alone or in combination with repositioned drugs, we initiated a structure-assisted drug design program including Virtual Screening, Docking, pharmacokinetic and toxicological analysis (ADMET) and Molecular Dynamics Simulation (MD) from Natural Products Database of the Bahia Semi-Arid region (NatProDB). We also aimed to identify novel scaffolds that target the SARS-CoV-2 Main Protease (Mpro, 3Clpro) since this protein plays a pivotal role in mediating viral replication and transcription, which makes it an attractive drug target for coronaviruses. Here, we selected 10 molecules that could be studied in vitro to lead discovery in response to this infectious diseases. The best SARS-CoV-2 Mpro complexes interactions revealed that some enzyme sites were accessed thereby confirming that this method can be employed as a suitable starting method for the identification of novel SARS-CoV-2 Mpro inhibitors. Two compounds (b01 and b02) suggest a better potential for interaction with SARS-CoV-2 main protease (Mpro) and could be further studied.
|
Rai Silva; Humberto Freitas; Njogu Kimani; Cleydson Santos; Samuel Silva da Pita
|
Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-08-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611d83321d1cc20b9bc7981e/original/natural-products-based-drug-design-from-bahia-semi-arid-region-against-sars-co-v-2-mpro-3clpro.pdf
|
66db1543cec5d6c14252b757
|
10.26434/chemrxiv-2024-nrpgz
|
Modulating Peptide Self-Assembly via Triblock Chiral Patterning
|
The suprastructural integrity of peptide self- assemblies is driven by an intricate array of cohesive interactions that guide and maintain hierarchical order. Seemingly minor alterations to atomic arrangement, such as substitution with D- amino acids, can dramatically affect assembly potential and resultant architecture. When a primary sequence is comprised of consecutive identical motifs, “block heterochiral” peptides can be generated by partitioning chiral inversions according to these underlying elementary units. In this work, we present a combinatorial exploration of all triblock chiral patterns for the model β-sheet-forming peptide KFE12 (Ac-(FKFE)3-NH2). Analysis of the four resulting enantiomer pairs reveals that each produces a unique morphology, ranging from minimal 4-nm-wide fibrils to micron-scale semi-structured aggregates. Our investigation of these variants illustrates a combination of conserved and divergent hierarchical features, reflecting complex interplay between persistent fundamental forces and the unique spatial implications of blockwise intramolecular chiral interfaces.
|
Conor O'Neill; Jonathan Fascetti; Zoe Clapacs; Lauren Kaplita; Chih-Yun Liu; Darren Kim; Mark White; Jai Rudra
|
Materials Science; Nanoscience; Aggregates and Assemblies; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-09-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66db1543cec5d6c14252b757/original/modulating-peptide-self-assembly-via-triblock-chiral-patterning.pdf
|
60c744724c8919321bad27cb
|
10.26434/chemrxiv.9791477.v1
|
Potassium Pre-Inserted K1.04Mn8O16 Cathode Materials for Aqueous Li-Ion and Na-Ion Hybrid Capacitors
|
For
the applications of aqueous Li-ion hybrid capacitors and Na-ion hybrid
capacitors, potassium
ions are pre-inserted into MnO<sub>2</sub>
tunnel structure, the as-prepared K<sub>1.04</sub>Mn<sub>8</sub>O<sub>16</sub>
materials consist of <a>nanoparticles</a> and nanorods were prepared by facile high-temperature solid-state reaction. <a></a>The
as-prepared materials were
well studied
andthey show outstanding
electrochemical behavior. We
assembled hybrid supercapacitors with commercial activated carbon (YEC-8A) as anode
and K<sub>1.04</sub>Mn<sub>8</sub>O<sub>16 </sub>as cathode. It has high energy densities and
power densities. Li-ion capacitors reach a high energy density of 127.61
Wh kg<sup>-1 </sup>at the power density of 99.86 W kg<sup>-1</sup> and Na-ion capacitor
obtains
170.96 Wh kg<sup>-1 </sup>at 133.79 W kg<sup>-1</sup>. In addition, the <a>hybrid supercapacitor</a>s demonstrate excellent cycling performance which
maintain 97 % capacitance retention for Li-ion capacitor and 85 % for Na-ion capacitor
after 10,000 cycles.
|
Yamin Zhang; Lina Chen; Chongyang Hao; Xiaowen Zheng; Yixuan Guo; Long Chen; Kangrong Lai; Yinghe Zhang; Lijie Ci
|
Composites
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-09-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744724c8919321bad27cb/original/potassium-pre-inserted-k1-04mn8o16-cathode-materials-for-aqueous-li-ion-and-na-ion-hybrid-capacitors.pdf
|
60c7536e9abda20f8df8dfb4
|
10.26434/chemrxiv.13490199.v1
|
Planar Tetracoordinate Fluorine Atoms
|
Unlike other atoms, planar tetracoordinate fluorines are elusive. So far, there are no theoretical or experimental reports suggesting their existence. Herein, we introduce the first six combinations, whose global minima contain a planar tetracoordinate fluorine. All of them are surrounded exclusively by atoms of group 13. The bonding scheme shown by these species is entirely different from analogous systems with carbon, nitrogen, or oxygen atoms. The magnetic response characterizes these systems mostly σ-aromatic. The planar form is somewhat stabilized by subtle ionic interactions of the fluorine with the peripheral atoms, forming an adequately sized cavity. <br />
|
Gabriela Castillo-Toraya; Mesías Orozco-Ic; Eugenia Dzib; Ximena Zarate; Filiberto Ortiz-Chi; jorge barroso; Gabriel Merino
|
Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-12-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7536e9abda20f8df8dfb4/original/planar-tetracoordinate-fluorine-atoms.pdf
|
61342ca0d5f0803838bb0578
|
10.26434/chemrxiv-2021-jfpj4-v2
|
Photosynthetic Reaction Center Variants Made via Genetic Code Expansion Show Tyr at M210 Tunes the Initial Electron Transfer Mechanism
|
Photosynthetic reaction centers (RCs) from Rhodobacter sphaeroides were engineered to vary the electronic properties of a key tyrosine close to an essential electron transfer component (M210) via its replacement with site-specific genetically encoded noncanonical amino acid tyrosine analogs. High fidelity of noncanonical amino acid incorporation was verified with mass spectrometry and x-ray crystallography and demonstrated that RC variants exhibit no significant structural alterations relative to wild-type. Ultrafast transient absorption spectroscopy indicates the excited primary electron donor, P*, decays via an approximately 4 ps and 20 ps population to produce the charge-separated state P+HA- in all variants. Global analysis indicates that in the 4 ps population P+HA- forms through a 2-step process P* –> P+BA– –> P+HA-, while in the 20 ps population it forms via a 1-step P* –> P+HA– superexchange mechanism. The percentage of P* population that decays via the superexchange route varies from approximately 25% to 45% among variants while in wild-type this percentage is approximately 15%. Increases in the P* population which decays via superexchange correlates with increases in free energy of the P+BA– intermediate caused by a given M210 tyrosine analog. This was experimentally estimated through resonance Stark spectroscopy, redox titrations, and near-infrared absorption measurements. As the most energetically perturbative variant, 3-nitrotyrosine at M210 creates an approximately 110 meV increase in the free energy of P+BA– along with a dramatic diminution of the 1030 nm transient absorption band indicative of P+BA– formation. Collectively this work indicates the tyrosine at M210 tunes the mechanism of primary electron transfer in the RC.
|
Jared Weaver; Chi-Yun Lin; Kaitlyn M. Faries; Irimpan Mathews; Silvia Russi; Dewey Holten; Christine Kirmaier; Steven Boxer
|
Physical Chemistry; Biophysical Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-09-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61342ca0d5f0803838bb0578/original/photosynthetic-reaction-center-variants-made-via-genetic-code-expansion-show-tyr-at-m210-tunes-the-initial-electron-transfer-mechanism.pdf
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6756fc297be152b1d06b6058
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10.26434/chemrxiv-2024-bhcdp
|
Visible-Light-Induced Synergistic W/Cr Catalyzed gem-Difluoroallylation of Unactivated Alkanes
|
Currently, the scope of Nozaki−Hiyama−Kishi (NHK) reaction is limited to aldehydes and ketones to construct alcohol de-rivatives. Moreover, most NHK reactions focus on the use of pre-activated electrophilic partners and generally require hygroscopic and easily oxidized CrCl2, which typically necessitates the use of a glove box to prevent the formation of detrimental aqueous CrCl3. Herein, we have described a visible-light-induced synergistic W/Cr(III) catalyzed NHK-type gem-difluoroallylation reaction of unactivated cyclic and linear alkanes. The reaction merits feedstock materials, mild reaction conditions, and wide functionality tolerance. Mechanistic studies imply the favorable reduction of CrCl3 to CrCl2 by reduced decatungstate W10O325-, thus closing the catalytic cycle.
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Zhijie Zhang; Yue Zhang; Xinyu Xie; Hua-Wei Liu; Tianshuai Zhu; Jing-Jing Zhang; Meng-Yang Hu; zhen chen
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Organic Chemistry
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CC BY 4.0
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CHEMRXIV
|
2024-12-12
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6756fc297be152b1d06b6058/original/visible-light-induced-synergistic-w-cr-catalyzed-gem-difluoroallylation-of-unactivated-alkanes.pdf
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60c7447d4c89197b3bad2806
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10.26434/chemrxiv.9846083.v1
|
An Alkyne Linchpin Strategy for Drug:Pharmacophore Conjugation: Experimental and Computational Realization of a meta-Selective Inverse Sonogashira Coupling
|
<div>
<div>
<div>
<div>
<div>
<div>
<p>The late-stage functionalization (LSF) of pharmaceutical and agrochemical compounds
by the site-selective activation of C-H bonds offers immediate access to diverse structural analogs
and expands the accessible chemical space. We report an C-H functionalization LSF strategy that
hinges on the use of an alkyne linchpin to assemble conjugates of sp2-rich marketed
pharmaceuticals and agrochemicals with sp3-rich 3D-fragments and natural products. This is
accomplished through a template-assisted inverse Sonogashira reaction that displays high levels
of selectivity for the meta-position. This protocol is also amenable to distal structural modifications
of a-amino acids. The transformation of alkyne functionality to other functional groups further
highlights the applicative potential. Computational and experimental mechanistic studies shed
light on the detailed mechanism. Turnover-limiting 1,2-migratory insertion of the bromoalkyne
coupling partner occurs after relatively fast C-H activation. While this insertion occurs
unselectively, regioconvergence results from one of the adducts undergoing a 1,2-trialkylsilyl migration to form the alkynylated product. A heterobimetallic Pd–Ag TS, which is essential for
product formation, is explicitly implicated in the β-bromide elimination step. </p></div></div></div></div></div></div><div><div><div>
</div>
</div>
</div>
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Sandeep Porey; Xinglong Zhang; Suman Bhowmick; Vikas Kumar Singh; Srimanta Guin; Robert Paton; Debabrata Maiti
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Organic Synthesis and Reactions; Computational Chemistry and Modeling; Homogeneous Catalysis
|
CC BY NC ND 4.0
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CHEMRXIV
|
2019-09-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7447d4c89197b3bad2806/original/an-alkyne-linchpin-strategy-for-drug-pharmacophore-conjugation-experimental-and-computational-realization-of-a-meta-selective-inverse-sonogashira-coupling.pdf
|
65ef1edc66c1381729bf5d1d
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10.26434/chemrxiv-2024-srxbm
|
Synergetic enhancing effects between platinum nano-sensitizers and clinically approved stabilizing ligands in proton therapy, causing high-yield double-strand breaks of plasmid DNA at relevant dose
|
Proton therapy is used to eradicate tumors in sensitive areas by targeted delivery of energy. Its effectiveness can be amplified using nanoparticles as sensitizers, due to the production of reactive oxygen species (ROS) at the nanoparticle´s catalytically active surface, causing the cleavage of DNA. However, the impact of stabilizing macromolecular ligands capping the particles, needed for nanosensitizer dispersion in physiological fluids, is underexplored. In this work, we use initially ligand-free colloidal platinum nanoparticles (PtNP) fabricated by scalable laser synthesis in liquids, which allows studying particle and ligand effects separately. PtNP are incubated with stabilizing concentrations of the clinically approved ligands albumin, Tween, and polyethylene glycol, and irradiated with proton beams at clinically relevant doses (2 Gy and 5 Gy). At these doses, plasmid DNA cleavage larger than 55% of clustered DNA damage is achieved. BSA, Tween, and polyethylene glycol on the NP surface work as double strand breaking (DSB) enhancers and synergetic effects occur even at low and clinically relevant particle concentrations and irradiation doses. Here, DSB enhancement by ligand-capped PtNP even exceeds the sum of the individual ligand and particle effects. The presented fundamental correlations provide selection rules for nanosensitizer design in proton therapy.
|
Sandra Zwiehoff; Astrid Hensel; Ramin Rishmawi; Parisa Shakibaei; Carina Behrends; Katrin Hommel; Christian Bäumer; Shirley K. Knauer; Beate Timmermann; Christoph Rehbock; Stephan Barcikowski
|
Biological and Medicinal Chemistry; Nanoscience; Nanofabrication; Biophysics; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ef1edc66c1381729bf5d1d/original/synergetic-enhancing-effects-between-platinum-nano-sensitizers-and-clinically-approved-stabilizing-ligands-in-proton-therapy-causing-high-yield-double-strand-breaks-of-plasmid-dna-at-relevant-dose.pdf
|
60c74a02bb8c1a7b383daf2f
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10.26434/chemrxiv.12137550.v1
|
Anodic Oxidation of Dithiane Carboxylic Acids: A Rapid, Mild and Practical Way to Access Functionalised Orthoesters
|
A new electrochemical methodology has been developed for the preparation of a wide variety of functionalised orthoesters under mild and green conditions from easily accessible dithiane derivatives. The new methodology also offers an unprecedented way to access tri(fluorinated) orthoesters, a class of compound that has never been studied before. This provides the community with a rapid and general method to prepare libraries of functionalised orthoesters from simple and readily available starting materials.
|
Anthony Garcia; Matthew Leech; Alessia Petti; Camille Denis; Iain C. A. Goodall; Adrian Dobbs; Kevin Lam
|
Organic Synthesis and Reactions; Electrochemistry; Electrochemistry - Mechanisms, Theory & Study
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a02bb8c1a7b383daf2f/original/anodic-oxidation-of-dithiane-carboxylic-acids-a-rapid-mild-and-practical-way-to-access-functionalised-orthoesters.pdf
|
63bf74632b3d4e91d78e3252
|
10.26434/chemrxiv-2023-sgs1k
|
Shock-Induced Cooling in Liquid Nitrogen Revisited
|
Evolution of nitrogen under shock compression up to 100 GPa is revisited via molecular dynamics simulations using a machine-learned interatomic model. Our model is shown capable of recovering the structure, dynamics, speciation and kinetics in hot compressed liquid nitrogen predicted by first- principles molecular dynamics, as well as the experimentally determined principal shock Hugoniot. We find that a purely molecular dissociation description of nitrogen chemistry provides an incomplete picture, and that short oligomers form in non-negligible quantities; no evidence is found for shock- induced cooling upon re-shocking.
|
Rebecca Lindsey; Sorin Bastea; Sebastien Hamel; Yanjun Lyu; Nir Goldman; Laurence Fried
|
Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties; Thermodynamics (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-01-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bf74632b3d4e91d78e3252/original/shock-induced-cooling-in-liquid-nitrogen-revisited.pdf
|
67422b587be152b1d08789ed
|
10.26434/chemrxiv-2024-f1nsj
|
Glycan Mixture Analysis by Kernel Component Composition for Matrix Factorization
|
A major challenge in structural glycomics is the presence of isomeric glycan structures, which may not be fully resolved by separation techniques such as liquid chromatography (LC) and ion mobility spectrometry (IMS). Tandem mass spectrometry (MS/MS) can be employed following on-line separation to distinguish unresolved features, as the temporal profiles of various fragment ions reflect different combinations of those from their respective precursor ions. However, traditional principal component analysis can produce negative signals that are unrealistic for real data, and classic non-negative matrix factorization (NMF) methods may result in factors that include contributions from multiple components.
This paper introduces a new variation of NMF, termed kernel component composition (KCC), which enables users to impose domain-specific prior knowledge about the components as parametric kernels. These kernel parameters are then learned directly from the data. We developed a theoretically guaranteed algorithm based on proximal gradient descent to solve the optimization problem posed by KCC and derived detailed parameter update rules when using Gaussian kernels. The effectiveness of the KCC algorithm is demonstrated through simulation tests and its application to deconvoluting chemical datasets, including LC- and IM-MS/MS analysis of isomeric glycan mixtures.
|
Pengyu Hong; Chaoshuang Xia; Yang Tang; Juan Wei; Cheng Lin
|
Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67422b587be152b1d08789ed/original/glycan-mixture-analysis-by-kernel-component-composition-for-matrix-factorization.pdf
|
646a49b7f2112b41e9eb483d
|
10.26434/chemrxiv-2023-v5snr
|
Understanding Antiferromagnetic and Ligand Field Effects on Spin Crossover in a Triple-decker Dimeric Cr(II) Complex
|
Two possible explanations for the temperature-dependence of spin crossover (SCO) behavior in the dimeric triple-decker Cr(II) complex ([(C5Me5)Cr(P5)Cr(C5Me5)]+) have been offered. One invokes variations in antiferromagnetic interactions between the two Cr(II) ions, while the other posits the development of a strong ligand-field effect favoring the low-spin ground state. We perform multireference electronic structure calculations based on multiconfiguration pair-density functional theory to resolve these effects. We find quintet, triplet, and singlet electronic ground states, respectively, for the experimental geometries at high, intermediate, and low temperatures. The ground-state transition from quintet to triplet at intermediate temperature derives from increased antiferromagnetic interactions between the two Cr(II) ions. By contrast, the ground-state transition from triplet to singlet at low temperature is attributable to increased ligand-field effects, which dominate with continued variations in antiferromagnetic coupling. This study provides quantitative detail for the degree to which these two effects can act in concert for the observed SCO behavior in this complex and others subject to temperature dependent variations in geometry.
|
Arup Sarkar; Matthew Hermes; Chris Cramer; John Anderson; Laura Gagliardi
|
Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Magnetism; Transition Metal Complexes (Inorg.); Theory - Computational
|
CC BY 4.0
|
CHEMRXIV
|
2023-05-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646a49b7f2112b41e9eb483d/original/understanding-antiferromagnetic-and-ligand-field-effects-on-spin-crossover-in-a-triple-decker-dimeric-cr-ii-complex.pdf
|
60c73f61337d6c4a5de26518
|
10.26434/chemrxiv.7367708.v1
|
Flow Imaging Microscopy as a Novel Tool for High-Throughput Evaluation of Elastin-like Polymer Coacervates
|
<div>Biological and bioinspired polymer microparticles have broad biomedical and industrial applications, including drug delivery, tissue engineering, surface modification, environmental remediation, imaging, and sensing. Full realization of the potential of biopolymer microparticles will require methods for rigorous characterization of particle sizes, morphologies, and dynamics, so that researchers may correlate particle characteristics with synthesis methods and desired functions. Toward this end, we evaluated biopolymer microparticles using flow imaging microscopy. This technology is widely used in the biopharmaceutical industry but is not yet well-known among the materials community. Our polymer, a genetically engineered elastin-like polypeptide (ELP), self-assembles into micron-scale coacervates. We performed flow imaging of ELP coacervates using two different instruments, one with a lower size limit of approximately 2 microns, the other with a lower size limit of approximately 300 nanometers. We validated flow imaging results by comparison with dynamic light scattering and atomic force microscopy analyses. We explored the effects of various solvent conditions on ELP coacervate size, morphology, and behavior, such as the dispersion of single particles versus aggregates. We found that flow imaging is a superior tool for rapid and thorough particle analysis of ELP coacervates in solution. We anticipate that researchers studying many types of microscale protein or polymer assemblies will be interested in flow imaging as a tool for quantitative, solution-based characterization.<br /></div>
|
Laura Marvin; Wynter Paiva; Nicole Gill; Marissa A. Morales; Jeffrey Mark Halpern; James Vesenka; Eva Rose Balog
|
Aggregates and Assemblies; Biological Materials; Biopolymers; Drug delivery systems; Microscopy; Bioengineering and Biotechnology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-11-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f61337d6c4a5de26518/original/flow-imaging-microscopy-as-a-novel-tool-for-high-throughput-evaluation-of-elastin-like-polymer-coacervates.pdf
|
60c7598b469df4bcd8f4588e
|
10.26434/chemrxiv.14493846.v2
|
Antioxidant and UV-radiation absorption activity of aaptamine derivatives – Potential application for natural organic sunscreens
|
Antioxidant and UV absorption activities of three marine product originated - aaptamine derivatives including piperidine[3,2-b]demethyl(oxy)aaptamine (<b>C1</b>), 9-amino-2-ethoxy-8-methoxy-3H-benzo[de][1,6]naphthyridine-3-one (<b>C2</b>), and 2-(sec-butyl)-7,8-dimethoxybenzo[de]imidazo[4,5,1-ij][1,6]-naphthyridin-10(9H)-one (<b>C3</b>) were theoretically studied by density functional theory (DFT). Direct antioxidant activities of C1–C3 were firstly evaluated via their intrinsic thermochemical properties and radical scavenging activity of the potential antioxidants with the HOO●/HO● radicals via four mechanisms, including: hydrogen atom transfer (HAT), single electron transfer (SET), proton loss (PL) and radical adduct formation (RAF). Kinetic calculation reveals that HOO● scavenging in water is occurred via HAT mechanism with C1 (kapp, 7.13x10<sup>6</sup> M-1 s-1) while RAF is more dominant with C2 (k<sub>app</sub>, 1.40x10<sup>5</sup> M-1 s-1) and C3 (kapp, 2.90x10<sup>5</sup> M-1 s-1). Antioxidant activity of aaptamine derivatives can be classified as <b>C1 </b>> <b>C3 </b>> <b>C2</b>. Indirect antioxidant properties based on Cu(I) and Cu(II) ions chelating activity were also investigated in aqueous phase. All three studied compounds show spontaneous and favorable Cu(I) ion chelating activity with DG0 being -15.4, -13.7, and -15.7 kcal.mol-1, whereas DG0 for Cu(II) chelation are -10.4, -10.8, and -2.2 kcal.mol-1 for C1, C2 and C3, respectively. In addition, all compounds show UVA and UVB absorption; in which the excitations are determined mostly as π-π* transition. Overall, the results suggest the potential applications of the aaptamines in pharmaceutics and cosmetics, i.e. as sunscreen and antioxidant ingredient.<br />
|
Thi Le Anh Nguyen; Thi Hoai Nam Doan; Dinh Hieu Truong; Nguyen Thi Ai Nhung; Duong Tuan Quang; Dorra Khiri; Florent Louis; Abderrahman El Bakali; Sonia Taamalli; Duy Quang Dao
|
Chemical Kinetics; Thermodynamics (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7598b469df4bcd8f4588e/original/antioxidant-and-uv-radiation-absorption-activity-of-aaptamine-derivatives-potential-application-for-natural-organic-sunscreens.pdf
|
6521ad3345aaa5fdbb80057c
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10.26434/chemrxiv-2023-fr5tg
|
Interphase formation on Al2O3-coated carbon negative electrodes in lithium-ion batteries
|
Interfacial coatings show promise in stabilizing carbon negative electrodes for lithium-ion batteries. For example, applying nanometer scale Al2O3 coatings on carbon can improve fast-charging, low-temperature battery performance, and cycle life. However, the exact mechanism by which these interfacial films stabilize negative electrodes in lithium-ion batteries remains poorly understood. Here, we show that Al2O3 coatings on carbon negative electrodes undergo structural and chemical changes during the formation of the solid-electrolyte interphase (SEI) at low potentials. During formation, we find a conformal bilayer SEI on Al2O3-coated carbon electrodes, with each layer exhibiting distinct chemistry. Importantly, the SEI structure, chemistry, and uniformity differ substantially between Al2O3-coated carbon electrodes and uncoated carbon electrodes. Our results suggest that performance improvements are not solely due to the presence of the Al2O3 coating. Instead, we propose that the improved SEI structure, chemistry, and uniformity after formation are the key factors contributing to improvements in battery performance.
|
Rafael Vilá; Solomon Oyakhire; Yi Cui
|
Nanoscience; Energy; Nanostructured Materials - Nanoscience; Energy Storage; Materials Chemistry
|
CC BY NC ND 4.0
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CHEMRXIV
|
2023-10-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6521ad3345aaa5fdbb80057c/original/interphase-formation-on-al2o3-coated-carbon-negative-electrodes-in-lithium-ion-batteries.pdf
|
61679782a3d2c9b9f0d615aa
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10.26434/chemrxiv-2021-frhb5
|
Electrochemical nano-roughening of gold microstructured electrodes for the enhanced detection of copper and glucose
|
One of the main challenges for electrochemical sensor miniaturization is the fabrication of electrodes with a smaller footprint, while maintaining, or even increasing, their sensitivity for the targeted application. Our research group has previously demonstrated the enhancement of the electroactive surface area of gold electrodes up to 6-fold, relative to planar gold electrodes with the same footprint, through the generation of a wrinkled thin film surface via thermal shrinking. In this work, the electroactive surface area of wrinkled gold electrodes was further enhanced up to 5-fold (30-fold over flat electrodes) using a chronoamperometric pulsing technique. Scanning electron microscopy images showed progressive increase of surface roughness in response to an increasing number of applied pulses. The resulting nanoroughened electrodes present several advantages in addition to the enhanced electroactive surface area. These electrodes offer superior fouling resistance compared to that of wrinkled and flat electrodes when submerged in a solution containing bovine serum albumin at high concentrations. Cyclic voltammetry data also revealed greater sensitivity of nanoroughened electrodes toward anodic copper stripping, where the limit of quantification of copper by the nano-roughened electrodes was 0.3 ppm. Nano-roughened electrodes also allowed the highly sensitive enzyme-free detection of glucose through chronoamperometry, with a limit of detection of 0.5 mM, whereas planar electrodes did not demonstrate any ability to oxidize glucose. We foresee that this methodology to fabricate nanostructured electrodes will accelerate the development of simple, cost-effective and high sensitivity electrochemical platforms.
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Eduardo Gonzalez Martinez; Sokunthearath (Kevin) Saem; Nadine Beganovic; Jose Moran-Mirabal
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Materials Science; Analytical Chemistry; Nanoscience; Nanostructured Materials - Materials; Electrochemical Analysis; Nanofabrication
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-10-15
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61679782a3d2c9b9f0d615aa/original/electrochemical-nano-roughening-of-gold-microstructured-electrodes-for-the-enhanced-detection-of-copper-and-glucose.pdf
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60c75745bb8c1aa55d3dc7c1
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10.26434/chemrxiv.14387495.v1
|
Stereochemical Effect of the Small Ring Unit in 7-R-3,4-Cyclopropano- and 7-R-3,4-Epoxy-bicyclo[4.2.0]octan-1,5-Dienes on Conrotatory Ring Opening Torquoselectivity
|
Application
of the differential activation energy approach suggests that the strong inward
opening tendency of the formyl group in 3,4-cyclopropano-7-formyl-bicyclo[4.2.0]octan-1,5-diene
and also 3,4-epoxy-7-formyl-bicyclo[4.2.0]octan-1,5-diene is either counter
balanced to a level that the reaction turns torquo-neutral or it rotates
outward, depending upon the stereo-relationship of the small ring unit with the
formyl substituent. The NBO interaction approach, however, predicts inward
selectivity throughout. These molecules, therefore, can be used as excellent
test examples to judge the validity of one approach over the other.
|
Veejendra Yadav
|
Physical Organic Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-04-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75745bb8c1aa55d3dc7c1/original/stereochemical-effect-of-the-small-ring-unit-in-7-r-3-4-cyclopropano-and-7-r-3-4-epoxy-bicyclo-4-2-0-octan-1-5-dienes-on-conrotatory-ring-opening-torquoselectivity.pdf
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6604224666c1381729f7f36c
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10.26434/chemrxiv-2024-882hh
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OM-DIFF: INVERSE-DESIGN OF ORGANOMETALLIC CATALYSTS WITH GUIDED EQUIVARIANT DENOISING DIFFUSION
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Organometallic complexes are ubiquitous in homogeneous catalysis and other technological applications. Optimization of such complexes for specific applications is challenging due to the large variety of possible metal-ligand combinations and ligand-ligand interactions. Here we present OM-Diff, an inverse design framework based on a diffusion generative model for in-silico design of such complexes from scratch. Given the importance of the spatial structure of a catalyst, the model directly operates on all-atom (including hydrogen) representations in 3D space. To handle the symmetries inherent to that data representation, OM-Diff combines an equivariant diffusion model and an equivariant property predictor to drive sampling at inference time. The model can conditionally generate novel ligands beyond those in the training dataset. We demonstrate the potential of the proposed approach by designing catalysts for a family of cross-coupling reactions, and validating a selection of novel proposed compounds with DFT calculations.
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François Cornet; Bardi Benediktsson; Bjarke Hastrup; Mikkel N. Schmidt; Arghya Bhowmik
|
Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry; Machine Learning; Artificial Intelligence; Transition Metal Complexes (Organomet.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-03-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6604224666c1381729f7f36c/original/om-diff-inverse-design-of-organometallic-catalysts-with-guided-equivariant-denoising-diffusion.pdf
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6375e68774b7b61f3f013e76
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10.26434/chemrxiv-2022-vtg5f
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Molecular Manipulation of Micro-Environment of Au Active Sites on Mesoporous Silica for Enhanced Catalytic Reduction of 4-Nitrophenol
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At the confined nanospace and/or nanoscale interface, the catalytic nature of active sites on the molecule level still remains elusive. Herein, with the catalytic hydride reduction of 4-nitrophenol (4-NP) over gold nanoparticles (NPs) catalysts as a prototype reaction, the influence of delicate change of microenvironment of catalytic active site on the reaction kinetics of 4-NP to 4-aminophenol (4-AP) with the introduction of varied alkali-metal ion (AM+) salt, have been deeply investigated. We demonstrate that structural water (SW) adsorbed on Au NPs in the form of {OH-·H2O@Au NPs} is the real catalytic active sites (not alone Au NPs), and in the presence of lithium chloride (LiCl), it shows the best catalytic performance. In addition, the isotope labeling and kinetic isotope effect (KIE) experiments evidences that, the reduction of 4-NP does not follow the classical Langmuir-Hinshelwood (L-H) bimolecular mechanism, but an interfacial SW dominated electron and proton transfer mechanism. The proposed mechanism answers why the dissociation of O-H bond of water is the rate-determining step (RDS) of 4-NP reduction, and, counter-intuitively, the solvent water is the hydrogen source of final product 4-AP, instead of sodium borohydride (NaBH4) reducer. Importantly, the co-existence of Li+ and Cl- ions synergistically stabilizes the transition state of reaction and accelerates the interfacial electron and proton transfer, consequently enhancing the reaction kinetics. The model of structural water as a bridge to transfer electron and proton at nanoscale interface is the reminiscent of working mechanism of photosystem two (PSII) for water splitting on Mn4CaO5 cluster.
|
Meng Ding; Bo Peng; Jia-Feng Zhou; Hui Chen; Yi-Song Zhu; En-Hui Yuan; Belén Albela; Laurent Bonneviot; Peng Wu; kun zhang
|
Catalysis; Heterogeneous Catalysis
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CC BY NC ND 4.0
|
CHEMRXIV
|
2022-11-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6375e68774b7b61f3f013e76/original/molecular-manipulation-of-micro-environment-of-au-active-sites-on-mesoporous-silica-for-enhanced-catalytic-reduction-of-4-nitrophenol.pdf
|
63523abcecdad534ade69582
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10.26434/chemrxiv-2022-v073h
|
Evaluation of the vacuum effect on headspace solid-phase microextraction of volatile organic compounds from aqueous samples using finite element analysis modeling
|
Headspace solid-phase microextraction (HSSPME) of volatile organic compounds (VOCs) from aqueous samples under vacuum conditions (Vac-HSSPME) allows increasing extraction rates and decreasing detection limits compared to HSSPME under atmospheric pressure. The positive effect of the vacuum on HSSPME of an analyte can be quickly estimated using its Henry’s law constant (HLC). Substantial positive effect of the vacuum can be expected for analytes with HLC lower than 1.6·10-4 atm m3 mol−1 (0.065 at 25 °C). This conclusion was made using a two-layer model of evaporation, which does not consider possible effects of other parameters of HSSPME. This research was aimed at a detailed evaluation of the possible effect of vacuum on the equilibration time and extracted amounts of analytes with various HLC and coating-headspace distribution constants (Kfh) using the computational model recently developed in COMSOL Multiphysics software. It has been proven that HSSPME under vacuum provides faster equilibration of VOCs with all studied Kfh and HLC. Drop in the equilibration time can reach 33.7 times. The largest vacuum impact on the extracted analyte was 3.9-4.0 times at Kfh = 106 and HLC = 10-6-10-3. The substantial (<1.5 times) vacuum impact should not be expected for analytes with Kfh < 105 for 15-min extraction and Kfh < 105.5 for 30-min extraction. For greater Kfh, HLC values should be lower than 0.1. The obtained results and the developed model can be recommended for the evaluation whether HSSPME is reasonable to conduct under vacuum conditions.
|
Bulat Kenessov; Aset Muratuly
|
Analytical Chemistry; Environmental Analysis; Separation Science
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-10-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63523abcecdad534ade69582/original/evaluation-of-the-vacuum-effect-on-headspace-solid-phase-microextraction-of-volatile-organic-compounds-from-aqueous-samples-using-finite-element-analysis-modeling.pdf
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639dffcab9c5f6252bd68c76
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10.26434/chemrxiv-2022-p98xq
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Accessing 3D molecular diversity via benzylic C–H cross coupling
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Pharmaceutical and agrochemical discovery efforts rely on robust methods for chemical synthesis that rapidly access diverse molecules. Cross-coupling reactions are the most widely used synthetic methods, but these methods typically form bonds to C(sp2)-hybridized carbon atoms (e.g., amide coupling, biaryl coupling) and lead to a prevalence of "flat" molecular structures with suboptimal physicochemical and topological properties. Benzylic C(sp3)–H cross-coupling methods offer an appealing strategy to address this limitation by directly forming bonds to C(sp3)-hybridized carbon atoms, and emerging methods exhibit synthetic versatility that rivals conventional cross-coupling methods to access products with drug-like properties. Here, we use a virtual library of >350,000 benzylic ethers and ureas derived from benzylic C–H cross-coupling to test the widely held view that coupling at C(sp3)-hybridized carbon atoms affords products with improved three-dimensionality. The results show that the conformational rigidity of the benzylic scaffold strongly influences the product dimensionality. Products derived from flexible scaffolds often exhibit little or no improvement in three-dimensionality, unless they adopt higher energy conformations. This outcome introduces an important consideration when designing routes to topologically diverse molecular libraries. The concepts elaborated herein are validated experimentally through an informatics-guided synthesis of selected targets and the use of high-throughput experimentation to prepare a library of three-dimensional products that are broadly distributed across drug-like chemical space.
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Si-Jie Chen; Cyndi Qixin He; May Kong; Jun Wang; Shishi Lin; Shane W. Krska; Shannon S. Stahl
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Organic Chemistry; Catalysis; Combinatorial Chemistry; Organic Synthesis and Reactions; Redox Catalysis
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CC BY NC ND 4.0
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CHEMRXIV
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2022-12-21
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639dffcab9c5f6252bd68c76/original/accessing-3d-molecular-diversity-via-benzylic-c-h-cross-coupling.pdf
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60c74bb7702a9bb14d18b4e3
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10.26434/chemrxiv.12368486.v1
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Van Der Waals Epitaxy of Soft Twisted Bilayers: Lattice Relaxation and Static Distortion Waves
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Interfaces comprising incommensurate or twisted hexagonal lattices are ubiquitous and of great interest in the materials science and physics communities. Here we demonstrate 2D crystalline domains of soft block copolymers (BCPs) on patterned hard hexagonal lattices that provide fundamental insights into van der Waals heteroepitaxy. At moderate registration forces, it is experimentally found that these BCP-hard lattice incommensurate arrays do not adopt a simple Moiré superstructure, but instead adopt local structural deformations called static distortion waves (SDWs) a primary route to energy minimization.
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Cong Jin; Brian Olsen; Erik Luber; Jillian Buriak
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Aggregates and Assemblies; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience
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CC BY NC ND 4.0
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CHEMRXIV
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2020-05-28
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bb7702a9bb14d18b4e3/original/van-der-waals-epitaxy-of-soft-twisted-bilayers-lattice-relaxation-and-static-distortion-waves.pdf
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65a545f5e9ebbb4db936e0ea
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10.26434/chemrxiv-2023-g4jsc-v2
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NMR Analyses of-1,3-Bridged Calix[4]arene
Conformations
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Calix[4]arenes are cyclic oligomers known for their unique molecular architecture
that provides a versatile platform for various applications in supramolecular chemistry.
When strategically coupled with fluorescent molecules, their molecular recognition enables highly selective and sensitive chemosensors. The introduction of bridging groups at 1,3 phenolic positions within the calix[4]arene framework has the potential to yield distinctive structural features and enhanced functional properties. Despite their opportunities, calix[4]arene preparation requires careful characterization of conformationally restricted rotomers. We used a combination of experimental and computational techniques to elucidate the three-dimensional structure and conformational dynamics of a 1,3-bridged calix[4]arene derivative. Nuclear magnetic resonance (NMR) spectroscopy, Density Functional Theory (DFT) based optimization, and Boltzmann-weighted NMR chemical shift calculations are used to determine the precise molecular structure of the binding domain in our novel calix[4]arene derivative, including conformation, bond
distance, and angle details.
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Ryan P Madigan; Brandon B Fulton; Whitney E Gerro; Paula F Nino; Bryce Vilaysane; Narda R Dominguez; Austin J Carlson; Benjamin J P Jones; Carl J Lovely; Frank W Foss Jr.
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Theoretical and Computational Chemistry; Organic Chemistry; Analytical Chemistry; Organic Synthesis and Reactions; Stereochemistry; Computational Chemistry and Modeling
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CC BY NC 4.0
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CHEMRXIV
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2024-01-17
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a545f5e9ebbb4db936e0ea/original/nmr-analyses-of-1-3-bridged-calix-4-arene-conformations.pdf
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62eacc60d131b753d70b68ed
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10.26434/chemrxiv-2022-n7b06
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Elucidation of the O-antigen structure of Escherichia coli O93 and biosynthetic aspects thereof
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The structure of the O-antigen from the international reference strain Escherichia coli O93:−:H16 has been determined. A nonrandom modal chain-length distribution was observed for the lipopolysaccharide, a pattern which is typical when long O-specific polysaccharides are expressed. By a combination of (i) bioinformatics information on the gene cluster related to O-antigen synthesis including putative function on glycosyl transferases, (ii) the magnitude of NMR coupling constants of anomeric protons and (iii) unassigned 2D 1H,13C-HSQC and 1H,1H-TOCSY NMR spectra it was possible to efficiently elucidate the structure of the carbohydrate polymer in an automated fashion using the computer program CASPER. The polysaccharide also carries O-acetyl groups and their locations were determined by 2D NMR experiments showing that ~½ of the population was 2,6-di-O-acetylated, ~¼ was 2-O-acetylated, whereas ~¼ did not carry O-acetyl groups at one of the mannosyl residues. The structure of the tetrasaccharide repeating unit of the O-antigen is given by: →2)-b-D-Manp-(1→3)-b-D-Manp2Ac6Ac-(1→4)-b-D-GlcpA-(1→3)-a-D-GlcpNAc-(1→, which should also be the biological repeating unit and it shares structural elements with capsular polysaccharides from E. coli K84 and K50. The structure of the acidic O-specific polysaccharide from Cellulophaga baltica strain NN015840T differs to that of the O-antigen from E. coli O93 by lacking the O-acetyl group at O6 of the O-acetylated mannosyl residue.
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Axel Furevi; Jonas Ståhle; Claudio Muheim; Spyridon Gkotzis; Daniel Daley; Klas Udekwu; Göran Widmalm
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Biological and Medicinal Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2022-08-04
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62eacc60d131b753d70b68ed/original/elucidation-of-the-o-antigen-structure-of-escherichia-coli-o93-and-biosynthetic-aspects-thereof.pdf
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