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60c74e8cee301c0608c7a4fa
|
10.26434/chemrxiv.12765410.v1
|
Reinforcing the Supply Chain of COVID-19 Therapeutics with Expert-Coded Retrosynthetic Software
|
Supply chains become stressed when demand for essential products increases rapidly in times of crisis. This year, the
scourge of coronavirus highlighted the fragility of diverse supply chains, affecting the world’s pipeline of hand sanitizer,
1
toilet paper,2 and pharmaceutical starting materials.
3 Many drug repurposing studies are now underway.
4 If a winning
therapeutic emerges, it is unlikely that the existing inventory of the medicine, or even the chemical raw materials needed
to synthesize it,5 will be available in the quantities required to satisfy global demand. We show the use of a retrosynthetic
artificial intelligence (AI)
6-10 to navigate multiple parallel synthetic sequences, and arrive at plausible alternate reagent
supply chains for twelve investigational COVID-19 therapeutics. In many instances, the AI utilizes C–H functionalization
logic,
11-13 and we have experimentally validated several syntheses, including a route to the antiviral umifenovir that
requires functionalization of six C–H bonds. This general solution to chemical supply chain reinforcement will be useful
during global disruptions, such as during a pandemic.
|
Yingfu Lin; Zirong Zhang; Babak Mahjour; Di Wang; Rui Zhang; Eunjae Shim; Andrew McGrath; Yuning Shen; Nadia Brugger; Rachel Turnbull; Shashi Jasty; Sarah Trice; Tim Cernak
|
Organic Synthesis and Reactions; Process Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e8cee301c0608c7a4fa/original/reinforcing-the-supply-chain-of-covid-19-therapeutics-with-expert-coded-retrosynthetic-software.pdf
|
6562157329a13c4d47f72ce8
|
10.26434/chemrxiv-2023-w7vzl
|
A microfluidic bio membrane for flow rate metering
|
This study describes the function, optimization, and demonstration of a new class of passive, low-cost microfluidic flow meters based on birefringent chitosan membranes analyzed by polarized microscopy. We subjected an optimally synthesized membrane to dynamic flow conditions while monitoring the real-time response of its optical properties. We obtained figures of merit, including the linear response operating range (0 to 65 uL min-1), minimum response time (250 ms), sensitivity (2.03 % ×10-3 uL-1 min), and minimum sensor longevity (1 week). In addition, possible sources of interference were identified. Finally, we demonstrate the membrane as a low-cost flow rate measurement device for the close loop control of a commercial pressure-driven pump. Preliminary experiments using a basic PID controller with the membrane-based flow rate measurement device showed that stable control could be achieved and the system could reach steady-state behavior in less than 15 seconds.
|
Nan Jia; Tianyang Deng; Charles Larouche; Tigran Galstian; André Bégin-Drolet; Jesse Greener
|
Analytical Chemistry; Analytical Apparatus; Biochemical Analysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-11-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6562157329a13c4d47f72ce8/original/a-microfluidic-bio-membrane-for-flow-rate-metering.pdf
|
60c74ed64c89192f27ad3ad7
|
10.26434/chemrxiv.12808295.v1
|
Engineering Protein Dynamics of Ancestral Luciferase
|
<p>Insertion-deletion
mutations are sources of major functional innovations in naturally evolved proteins,
but directed evolution methods rely primarily on substitutions. Here, we report
a powerful strategy for engineering backbone dynamics based on InDel
mutagenesis of a stable and evolvable template, and its validation in
application to a thermostable ancestor of haloalkane dehalogenase and <i>Renilla</i> luciferase. First, extensive
multidisciplinary analysis linked the conformational flexibility of a
loop-helix fragment to binding of the bulky substrate coelenterazine. The
fragment’s key role in extant <i>Renilla</i>
luciferase was confirmed by transplanting it into the ancestor. This increased
its catalytic efficiency 7,000-fold, and fragment-containing mutants showed
highly stable glow-type bioluminescence with 100-fold longer half-lives than
the flash-type <i>Renilla</i> luciferase <i>RLuc8</i>,<i> </i>thereby addressing a
limitation of a popular molecular probe<i>.</i> Thus, our three-step approach: (i) constructing a robust
template, (ii) mapping functional regions by backbone mutagenesis, and (iii) transplantation
of a dynamic feature, provides a potent strategy for discovering protein
modifications with globally disruptive but functionally innovative effects.</p>
|
Andrea Schenkmayerova; Gaspar Pinto; Martin Toul; Martin Marek; Lenka Hernychova; Joan Planas-Iglesias; Veronika Liskova; Daniel Pluskal; Michal Vasina; Stephane Emond; Mark Doerr; Radka Chaloupková; David Bednar; Zbynek Prokop; Florian Hollfelder; Uwe T. Bornscheuer; Jiri Damborsky
|
Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ed64c89192f27ad3ad7/original/engineering-protein-dynamics-of-ancestral-luciferase.pdf
|
60c74918469df430f7f43b4a
|
10.26434/chemrxiv.11494398.v2
|
Efficient targeted degradation via reversible and irreversible covalent PROTACs
|
<p>PROteolysis Targeting Chimeras (PROTACs) represent an exciting inhibitory modality with many advantages, including sub-stoichiometric degradation of targets. Their scope, though, is still limited to-date by the requirement for a sufficiently potent target binder. A solution that proved useful in tackling challenging targets is the use of electrophiles to allow irreversible binding to the target. However, such binding will negate the catalytic nature of PROTACs. Reversible covalent PROTACs potentially offer the best of both worlds. They possess the potency and selectivity associated with the formation of the covalent bond, while being able to dissociate and regenerate once the protein target is degraded. Using Bruton’s tyrosine kinase (BTK) as a clinically relevant model system, we show efficient covalent degradation by non-covalent, irreversible covalent and reversible covalent PROTACs, with <10 nM DC50’s and >85% degradation. Our data suggests that part of the degradation by our irreversible covalent PROTACs is driven by reversible binding prior to covalent bond formation, while the reversible covalent PROTACs drive degradation primarily by covalent engagement. The PROTACs showed enhanced inhibition of B cell activation compared to Ibrutinib, and exhibit potent degradation of BTK in patients-derived primary chronic lymphocytic leukemia cells. The most potent reversible covalent PROTAC, RC-3, exhibited enhanced selectivity towards BTK compared to non-covalent and irreversible covalent PROTACs. These compounds may pave the way for the design of covalent PROTACs for a wide variety of challenging targets.</p>
|
Ronen Gabizon; Amit Shraga; Paul Gehrtz; Ella Livnah; Yamit Shorer; Neta Gurwicz; Liat Avram; Tamar Unger; Hila Aharoni; Shira Albeck; Alexander Brandis; Ziv Shulman; Ben- Zion Katz; Yair Herishanu; Nir London
|
Chemical Biology
|
CC BY 4.0
|
CHEMRXIV
|
2020-03-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74918469df430f7f43b4a/original/efficient-targeted-degradation-via-reversible-and-irreversible-covalent-prota-cs.pdf
|
6193e70a78db4e47f810560a
|
10.26434/chemrxiv-2021-jh6cj
|
Global analysis of crystal energy landscapes: applying the threshold algorithm to molecular crystal structures
|
We describe the implementation of the Monte Carlo threshold algorithm for molecular crystals as a method to provide an estimate of the energy barriers separating crystal structures. By sampling the local energy minima accessible from multiple starting structures, the simulations yield a global picture of the crystal energy landscapes. This provides valuable information on the depth of the energy minima associated with crystal structures and adds to the information available from crystal structure prediction methods that are used for anticipating polymorphism. We present results from applying the threshold algorithm to four polymorphic organic molecular crystals, examine the influence of applying space group symmetry constraints during the simulations, and discuss the relationship between the structure of the energy landscape and the intermolecular interactions present in the crystals.
|
Shiyue Yang; Graeme Day
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Structure; Materials Chemistry; Crystallography
|
CC BY 4.0
|
CHEMRXIV
|
2021-11-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6193e70a78db4e47f810560a/original/global-analysis-of-crystal-energy-landscapes-applying-the-threshold-algorithm-to-molecular-crystal-structures.pdf
|
60c73d0e702a9b1269189ae2
|
10.26434/chemrxiv.5375101.v1
|
A minimalist approach to protein identification
|
This work demonstrates a minimal single-molecule proteolysis-free approach that requires very small samples, is non-destructive, and can be translated with currently available technology into a portable device for possible use in the field or in an academic setting, or in a pre-screening step preceding conventional mass spectrometry.<br />
|
G. Sampath
|
Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2017-09-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0e702a9b1269189ae2/original/a-minimalist-approach-to-protein-identification.pdf
|
6660a914418a5379b0281018
|
10.26434/chemrxiv-2024-fppl4
|
Synchronized Photoluminescence and Electrical Mobility Enhancement in 2D WS2 through Sequence-Specific Chemical Passivation
|
Two-dimensional (2D) semiconducting dichalcogenides hold exceptional promise as optoelectronic materials for next-generation electronic and photonic devices, as well as their hybrid circuits. Despite this potential, the pervasive presence of defects in 2D dichalcogenides results in carrier mobility and photoluminescence (PL) that fall significantly short of theoretical predictions. Although defect passivation offers a potential solution, its effects have been inconsistent. This inconsistency arises from the current materials and methods, which fail to achieve the desired binding chemistry and band structure engineering necessary to enhance optical and electrical properties simultaneously. In this work, we uncover new binding chemistry using a sequence-specific chemical passivation (SSCP) protocol based on 2-furanmethanothiol (FSH) and bis(trifluoromethane) sulfonimide lithium salt (Li-TFSI), which allows us to demonstrate a synchronized 100-fold enhancement in both carrier mobility and photoluminescence (PL) in WS2 monolayers. We propose a novel synergistic defect passivation mechanism, supported by ultrafast transient absorption spectroscopy (TA), Hard X-ray photoelectron spectroscopy (HAXPES), and density functional theory (DFT) calculations. Our findings establish a new performance benchmark for the optical and electronic properties of WS2 monolayers, paving the way for the development of more efficient and sustainable 2D semiconductor technologies.
|
Zhaojun Li; Ulrich Noumbe; Elin Berggren; Henry Nameirakpam; Takashi Kimura; Eito Asakura; Victor Gray; Tomas Edvinsson; Andreas Lindblad; Makoto Kohda; Rafael Araujo; Akshay Rao; M. Venkata Kamalakar
|
Materials Science; Nanoscience; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-06-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6660a914418a5379b0281018/original/synchronized-photoluminescence-and-electrical-mobility-enhancement-in-2d-ws2-through-sequence-specific-chemical-passivation.pdf
|
66789ff201103d79c5f59711
|
10.26434/chemrxiv-2024-65x2m-v4
|
Extracellular vesicles of different cellular origin feature distinct biomolecular corona dynamics
|
Initially observed on synthetic nanoparticles, biomolecular corona existence and role in determining nanoparticle identity and function are now beginning to be acknowledged in biogenic nanoparticles, particularly in extracellular vesicles. We have developed here a methodology based on Fluorescence Correlation Spectroscopy to track biomolecular corona formation on extracellular vesicles derived from red blood cells and placental mesenchymal stromal cells when these vesicles are dispersed in human plasma. The methodology allows for the study of corona dynamics in situ in physiological conditions. Results evidence that the two extracellular vesicle populations feature distinct corona dynamics, with red blood cell-derived extracellular vesicles exchanging a higher number of proteins. These findings indicate that the dynamics of the biomolecular corona may ultimately be linked to the cellular origin of the extracellular vesicles, revealing an additional level of heterogeneity, and possibly of bionanoscale identity, that characterizes circulating extracellular vesicles.
|
Angelo Musicò; Andrea Zendrini; Santiago Gimenez Reyes; Valentina Mangolini; Lucia Paolini; Miriam Romano; Andrea Papait; Antonietta Rosa Silini; Paolo Di Gianvincenzo; Arabella Neva; Marina Cretich; Ornella Parolini; Camillo Almici; Sergio Moya; Annalisa Radeghieri; Paolo Bergese
|
Physical Chemistry; Biological and Medicinal Chemistry; Nanoscience; Bioengineering and Biotechnology; Interfaces; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66789ff201103d79c5f59711/original/extracellular-vesicles-of-different-cellular-origin-feature-distinct-biomolecular-corona-dynamics.pdf
|
6687ccbf01103d79c5182638
|
10.26434/chemrxiv-2024-96463
|
Consolidating LC×LC-HRMS/MS Technique for the Non-targeted Analysis of Poly- And Perfluorinated Substances: a Trial on Aqueous-Film Forming Foams.
|
To date, poly- and perfluoroalkyl substances (PFASs) represent a real threat for both their environmental persistence, wide physicochemical variability, and their potential toxicity. Thus far a large portion of these chemicals remain structurally unknown. These chemicals, therefore, require the implementation of complex non-targeted analysis workflows using high resolution mass spectrometry coupled with liquid chromatography (LC-HRMS) for their comprehensive detection and monitoring. This approach, even though comprehensive, does not always provide the much needed analytical resolution for the analysis of complex PFAS mixtures such as fire-fighting aqueous-film forming foams (AFFFs). This study consolidates the advantages of LC×LC technique hyphenated with high-resolution tandem mass spectrometry (HRMS/MS) for the identification of PFASs in AFFF mixtures. A total of 57 PFAS homologue series (HSs) were identified in 3M and Orchidee AFFF mixtures thanks to the (i) high chromatographic peak capacity (n’2D,c~300) and the (i) increased mass domain resolution provided by the “remainder of Kendrick Mass” (RKM) analysis on the HRMS data. Then, we attempted to annotate PFASs of each HSs exploiting the available reference standards and the FluoroMatch workflow in combination with the RKM defect by different fluorine repeating units, such as CF2, CF2O, and C2F4O. This approach resulted in 12 identified PFAS HSs, including compounds belonging to the HSs of PFACAs, PFASAs, SF5-PFASAs, N-SPAmP-FASA, and N-CMAmP-FASA. The annotated categories of perfluoroalkyl aldehydes, and chlorinated PFASAs represent a first record of PFAS HSs in the investigated AFFF samples.
|
Lapo Renai; Massimo Del Bubba; Andrea F. G. Gargano; Saer Samanipour
|
Analytical Chemistry; Mass Spectrometry; Separation Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6687ccbf01103d79c5182638/original/consolidating-lc-lc-hrms-ms-technique-for-the-non-targeted-analysis-of-poly-and-perfluorinated-substances-a-trial-on-aqueous-film-forming-foams.pdf
|
626cddceed4d881c1f1e01cf
|
10.26434/chemrxiv-2022-vprhs
|
Increased CO2 affinity and adsorption selectivity in MOF-801 fluorinated analogues
|
The novel ZrIV-based PerFluorinated Metal-Organic Framework (PF-MOF) [Zr6O4(OH)4(TFS)6] (ZrTFS) was prepared under solvent-free conditions using the commercially available tetrafluorosuccinic acid (H2TFS) as bridging ditopic linker. Since H2TFS can be seen as the fully aliphatic and perfluorinated C4 analogue of fumaric acid, ZrTFS was found to be isoreticular to zirconium fumarate (MOF-801). The structure of ZrTFS was solved and refined from X-ray Powder Diffraction data. Despite this analogy, the gas adsorption capacity of ZrTFS is much lower than that of MOF-801; in the former, the presence of bulky fluorine atoms causes a considerable windows size reduction. In order to have PF-MOFs with more accessible porosity, Post-Synthetic Exchange (PSE) reactions on (defective) MOF-801 suspended in H2TFS aqueous solutions were carried out. Despite the different H2TFS concentrations used in the PSE process, the exchanges yielded two mixed-linker materials of similar minimal formulae [Zr6O4(μ3-OH)4(μ1-OH)2.08(H2O)2.08(FUM)4.04(HTFS)1.84] (PF-MOF1) and [Zr6O4(μ3-OH)4(μ1-OH)1.83(H2O)1.83(FUM)4.04(HTFS)2.09] (PF-MOF2) (FUM2- = fumarate), where the perfluorinated linker was found to fully replace the capping acetate in the defective sites of pristine MOF-801. CO2 and N2 adsorption isotherms collected on all samples reveal that both CO2 thermodynamic affinity (isosteric heat of adsorption at zero coverage, Qst) and CO2/N2 adsorption selectivity increase with the amount of incorporated TFS2-, reaching the maximum values of 30 kJ mol-1 and 41 (IAST), respectively, in PF-MOF2. This confirms the beneficial effect coming from the introduction of fluorinated linkers in MOFs on their CO2 adsorption ability. Finally, solid-state density functional theory calculations were carried out to cast light on the structural features and on the thermodynamics of CO2 adsorption in MOF-801 and ZrTFS. Due to the difficulties in modelling a defective MOF, an intermediate structure containing both linkers in the framework was also designed. In this structure, the preferential CO2 adsorption site is the tetrahedral pore in the “UiO-66-like” structure. The extra energy stabilization stems from a hydrogen bond interaction between CO2 and a hydroxyl group on the inorganic cluster.
|
Diletta Morelli Venturi; Maria Sole Notari; Roberto Bondi; Edoardo Mosconi; Waldemar Kaiser; Giorgio Mercuri; Giuliano Giambastiani; Andrea Rossin; Marco Taddei; Ferdinando Costantino
|
Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Compounds; Theory - Inorganic; Materials Chemistry; Crystallography – Inorganic
|
CC BY 4.0
|
CHEMRXIV
|
2022-05-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626cddceed4d881c1f1e01cf/original/increased-co2-affinity-and-adsorption-selectivity-in-mof-801-fluorinated-analogues.pdf
|
63cb19afbb08ed7d9e11b9fd
|
10.26434/chemrxiv-2022-rsm6s-v2
|
Effects of Epitranscriptomic RNA Modifications on the Catalytic Activity of SARS-CoV-2 Replication Complex
|
Like other viruses, SARS-CoV-2 causes different symptoms and different degrees of harmfulness to different individuals. Potential reasons include an individual’s viral dose exposure, the affinity of an individual’s ACE2 to the spike protein of the virus, and the ability of the individual’s induced immune system to neutralize the virus. Beyond these, an individual’s epitranscriptomic system could be among the causes as well. The viral RNA genome, once inside the host cell, can be subject to modifications by the host’s epitranscriptomic machinery. Because the machinery is different in different individuals, it is reasonable to believe that RNA modifications are different among different individuals, and can positively or negatively affect downstream events that involve the RNA such as replication of viral genome, generation of viral mRNAs, viral protein production, RNA recognition by host’s immune system, and packaging of RNA genome into new viral particles. In this context, we studied the effects of several RNA modifications including pseudouridine (Ψ), 5-methylcytosine (m5C), N6-methyladenosine (m6A), N1-methyladenosine (m1A) and N3-methylcytosine (m3C) on the catalytic activity of SARS-CoV-2 replication complex (SC2RC), which included RNA dependent RNA polymerase (RdRp). We found that Ψ, m5C, m6A and m3C had little effects on the activity, while m1A severely inhibited the enzyme. Both m1A and m3C disrupt canonical base pairing. It is interesting one of them inhibits the enzyme while the other does not. The fact that m1A inhibits SC2RC may imply that the modification can be difficult to identify using any method even though it may exist and play a critical role. Putting aside other mechanisms by which the modifications cause individualized symptoms, the results indicated that individuals with a higher chance of m1A modification may stop viral replication and have less severe symptoms. However, this contradicts the observations that individuals with clinical conditions such as cancer, obesity and diabetes, who have upregulated m1A modifications, are more vulnerable to COVID-19. This contradiction may be explained by the importance of the dynamic nature of epitranscriptomic modifications for viral survival.
|
Alexander Apostle; Yipeng Yin; Komal Chillar; Adikari M. D. N. Eriyagama; Reed Arneson; Emma Burke; Shiyue Fang; Yinan Yuan
|
Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Chemical Biology; Microbiology
|
CC BY 4.0
|
CHEMRXIV
|
2023-01-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63cb19afbb08ed7d9e11b9fd/original/effects-of-epitranscriptomic-rna-modifications-on-the-catalytic-activity-of-sars-co-v-2-replication-complex.pdf
|
60c740e39abda2479ff8bd95
|
10.26434/chemrxiv.7862006.v1
|
Photocatalytic Proximity Labelling of MCL-1 by a BH3 Ligand
|
Ligand-directed protein labelling can be used to introduce diverse chemical functionalities onto proteins without the need for incorporation of genetically encoded tags. Here we report a method for the rapid and efficient labelling of a protein using a ruthenium-bipyridyl (Ru(II)(bpy)3) modified peptide designed to mimic an interacting BH3 ligand within a BCL-2 family protein-protein interaction (PPI). Using sub-stoichiometric quantities of (Ru(II)(bpy)3)-modified NOXA-B and irradiation with visible light for 1 minute, the anti-apoptotic protein MCL-1 was photolabelled in a ligand-dependent manner with a variety of functional tags, as determined by in-gel fluorescence, affinity purification, and ESIMS analysis. In contrast with previous reports on Ru(II)(bpy)3-catalysed photolabelling, tandem MS experiments revealed that the dominant labelling occurred on a cysteine residue of MCL-1. Labelling of MCL-1 occurred selectively in mixtures with other proteins, including the structurally related BCL-2 member, BCL-xL. These results improve methodology for proximity-induced photolabelling of proteins, demonstrate the approach is applicable to interfaces that mediate PPIs, and pave the way towards future use of ligand-directed proximity labelling for dynamic analysis of the localisation and interactome of BCL-2 family proteins.<br />
|
Hester Beard; Rachel George; Andrew Wilson; Robin Bon
|
Chemical Biology; Photocatalysis; Ligand Design
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-03-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e39abda2479ff8bd95/original/photocatalytic-proximity-labelling-of-mcl-1-by-a-bh3-ligand.pdf
|
61c2d98202c214f30d2e0f2d
|
10.26434/chemrxiv-2021-bg20x
|
Access tetracoordinate boron-doped polycyclic aromatic hydrocarbons with aggregation-induced emission under mild conditions
|
The boron-doped polycyclic aromatic hydrocarbons (PAHs) have attracted ongoing attention in the field of optoelectronic materials due to their unique optical and redox properties. To investigate the effect of tetracoordinate boron in PAHs bearing N-heterocycles (indole and carbazole), a facile approach to four-coordinate boron-doped PAHs was developed, which does not require elevated temperature and pre-synthesized functionalized boron reactants. Five tetracoordinate boron-doped PAHs (NBNN-1 – NBNN-5) were synthesized with different functional groups. Two of them (NBNN-1 and NBNN-2) could further undergo oxidative coupling reactions to form fused off-plane tetracoordinate boron-doped PAHs NBNN-1f and NBNN-2f. Compared to the three-coordinate boron-doped counterparts, the UV/Vis absorption and fluorescent emission are significantly red-shift. Unlike the distinct impact of coordination number of boron on optoelectronic properties, the difference of functional groups on the boron atom has negligible impact on their optical and electrochemical properties. The compounds NBNN-1f and NBNN-2f show aggregation-induced emission.
|
Long Jiang; Dehui Tan; Xiaobin Chen; Tinghao Ma; Baoliang Zhang; Deng-Tao Yang
|
Organic Chemistry; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2021-12-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c2d98202c214f30d2e0f2d/original/access-tetracoordinate-boron-doped-polycyclic-aromatic-hydrocarbons-with-aggregation-induced-emission-under-mild-conditions.pdf
|
66b308a501103d79c5fd9b91
|
10.26434/chemrxiv-2024-r4wnq
|
CrySPR: A Python interface for implementation of crystal structure pre-relaxation and prediction using machine-learning interatomic potentials
|
The functional properties of crystalline inorganic materials in a variety of applications including, but not limited to, catalysts, batteries, solar cells, electronics, fundamentally depend on their crystal structures. Discovery of novel materials could be transformative for these fields. In the past few decades, the computational science community has developed crystal structure prediction (CSP) methods with the goal to find the exact symmetry-constrained atomic arrangements in the periodic unit cell, which are globally and/or locally energetically favorable: finding the globally minimal or locally minimal crystal structure for a given chemical formula. The implementation of CSP typically involves an iteration procedure with at least two components: the sampling of the potential energy surface (PES) for generating raw/unrelaxed crystal structures, and the subsequent local energy minimization of generated structures. The latter part is typically carried out through computationally expensive density functional (DFT) calculations. A non-exhaustive but representative list of available CSP codes includes USPEX, CALYPSO, AIRSS, XtalOpt, IM2ODE; due to the nature of DFT calculations, this CSP process can be very time-consuming. Recent rapid advances of pre-trained machine-learning interatomic potentials (ML-IAPs) based on data from DFT calculations, such as, M3GNet, CHGNet and MACE (amongst others) have significantly accelerated the process of local energy minimization but have not thoroughly been tested on CSP tasks. The realization of local energy minimization using ML-IAPs, referred to as pre-relaxation when compared with using DFT calculations, plays a critical role in the CSP implementation. We present here, CrySPR, which stands for Crystal Structure Pre-Relaxation and PRediction, which is specifically designed to serve as a Python package that provides user-friendly application programming interfaces (APIs), functionalities and utilities for crystal structure generation, pre-relaxation of structures using ML-IAPs and structure prediction. The codes are open-source and have been released to the Python Package Index (PyPI).
|
Wei Nong; Ruiming Zhu; Kedar Hippalgaonkar
|
Theoretical and Computational Chemistry; Materials Science; Inorganic Chemistry; Theory - Inorganic; Theory - Computational; Crystallography – Inorganic
|
CC BY 4.0
|
CHEMRXIV
|
2024-08-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b308a501103d79c5fd9b91/original/cry-spr-a-python-interface-for-implementation-of-crystal-structure-pre-relaxation-and-prediction-using-machine-learning-interatomic-potentials.pdf
|
60c74cfd469df478fff441ed
|
10.26434/chemrxiv.12464120.v2
|
Zwitterionic AIEgens: Rational Molecular Design for NIR-II Fluorescence Imaging-Guided Synergistic Phototherapy
|
Fluorescence
imaging in the second near-infrared region (NIR-II) can penetrate tissue at centimeter depths
and obtain high fidelity of images. However, facile synthesis of small-molecule fluorescent photosensitizers for efficient NIR-II fluorescence imaging as well as photodynamic and photothermal
combinatorial therapies (PDT-PTT) is still a challenging
task. Herein, we reported a rational design and facile
synthesis protocol for a series of novel NIR-emissive zwitterionic luminogens with aggregation-induced emission (AIE) features for cancer
phototheranostics.
|
wei zhu; Miaomiao Kang; qian wu; Zhijun Zhang; yi wu; Chunbin Li; Kai LI; Lei Wang; Dong Wang; Ben Zhong Tang
|
Bioorganic Chemistry; Photosensitizers
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-24
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cfd469df478fff441ed/original/zwitterionic-ai-egens-rational-molecular-design-for-nir-ii-fluorescence-imaging-guided-synergistic-phototherapy.pdf
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671d320598c8527d9e79d3ce
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10.26434/chemrxiv-2024-plh2j
|
Alkane Dehydrogenation and H/D Exchange by a Cationic Pincer-Ir(III) Hydride:
A Novel Mechanism of C-H Addition and 𝛽-H Elimination Leads to Unprecedented Selectivity
|
We report that the cationic iridium complex (iPrPCP)IrH+ undergoes addition of alkane C-H bonds, which is manifested by catalytic alkane transfer-dehydrogenation to give alkenes and by hydrogen isotope (H/D) exchange (HIE). Contrary to established selectivity trends found for C-H activation by transition metal complexes, strained cycloalkanes, including cyclopentane, cycloheptane, and cyclooctane, undergo C-H addition much more readily than n-alkanes which in turn are much more reactive than cyclohexane. Aromatic C-H bonds also undergo H/D exchange much less rapidly than those of the strained cycloalkanes, but much more favorably than cyclohexane. The order of reactivity toward dehydrogenation correlates qualitatively with the reaction thermodynamics, but the magnitude is much greater than can be explained by thermodynamics. Accordingly, the cycloalkenes corresponding to the strained cycloalkanes undergo hydrogenation much more readily than cyclohexene, despite the less favorable thermodynamics of such hydrogenations. Computational (DFT) studies allow rationalization of the origin of reactivity and the unusual selectivity. Specifically, the initial C-H addition is strongly assisted by 𝛽-agostic interactions, which are particularly favorable for the strained cycloalkanes. Subsequent to 𝛼-C-H addition, the H atom of the 𝛽-agostic C-H bond is transferred to the hydride ligand of (iPrPCP)IrH+, to give a dihydrogen ligand. The overall processes, C-H addition and 𝛽-H-transfer to hydride, generally show intermediates on the IRC surface but they are extremely shallow, such that the 1,2-dehydrogenations are presumed to be effectively concerted although asynchronous.
|
Ashish Parihar; Thomas J. Emge; Faraj Hasanayn; Alan S. Goldman
|
Organic Chemistry; Catalysis; Organometallic Chemistry; Bond Activation; Kinetics and Mechanism - Organometallic Reactions; Theory - Organometallic
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-10-29
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671d320598c8527d9e79d3ce/original/alkane-dehydrogenation-and-h-d-exchange-by-a-cationic-pincer-ir-iii-hydride-a-novel-mechanism-of-c-h-addition-and-h-elimination-leads-to-unprecedented-selectivity.pdf
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653ed4d8c573f893f165b671
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10.26434/chemrxiv-2023-1dmql
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MolecularWebXR: Multiuser discussions about chemistry and biology in immersive and inclusive VR
|
MolecularWebXR is our new website for education, science communication and scientific peer discussion in chemistry and biology built on WebXR. It democratizes multi-user, inclusive virtual reality (VR) experiences that are deeply immersive for users wearing high-end headsets, yet allow participation by users with consumer devices such as smartphones, possibly inserted into cardboard goggles for immersivity, or even computers or tablets. With no installs as it is all web-served, MolecularWebXR enables multiple users to simultaneously explore, communicate and discuss chemistry and biology concepts in immersive 3D environments, manipulating objects with their bare hands, either present in the same real space or scattered throughout the globe thanks to built-in audio features. A series of preset rooms cover educational material on chemistry and structural biology, and an empty room can be populated with material prepared ad hoc using moleculARweb's VMD-based PDB2AR tool. We verified ease of use and versatility by users aged 12-80 in entirely virtual sessions or mixed real-virtual sessions at science outreach events, student instruction, scientific collaborations, and conference lectures. MolecularWebXR is available for free use without registration at https://molecularwebxr.org, and a blog post version of this preprint with embedded videos is available at https://go.epfl.ch/molecularwebxr-blog-post.
|
Fabio Cortes Rodriguez; Gianfranco Frattini; Fernando Teixeira Pinto Meireless; Danae Terrien; Sergio Cruz-Leon; Matteo Dal Peraro; Eva Schier; Diego Moreno; Luciano Abriata
|
Biological and Medicinal Chemistry; Chemical Education; Chemical Education - General; Biochemistry; Biophysics
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CC BY NC ND 4.0
|
CHEMRXIV
|
2023-11-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653ed4d8c573f893f165b671/original/molecular-web-xr-multiuser-discussions-about-chemistry-and-biology-in-immersive-and-inclusive-vr.pdf
|
60c7494e702a9bd73c18b10b
|
10.26434/chemrxiv.12015792.v2
|
Energetics Based Modeling of Hydroxychloroquine and Azithromycin Binding to the SARS-CoV-2 Spike (S)Protein - ACE2 Complex
|
The use of hydroxychloroquine to aid in the disruption of the SARS-CoV-2 virus and to cure or at least treat the COVID-19 disease is recently being reviewed in various clinical trials worldwide, but with insufficient examination of the binding of human ACE2 to the viral spike. In order to understand and assess the efficacy of the drug or drug combination, this paper looks at the effect of the pharmaceutical drug hydroxychloroquine, as well as a common co-drug, azithromycin, on the SARS-CoV-2 spike-ACE2 complex by using virtualized quantum mechanical modeling to better characterize binding sites on the complex, assess the binding between these sites and the drug compounds, and enhance community PDB files. <br />
|
Samarth Sandeep; Kirk McGregor
|
Bioinformatics and Computational Biology; Chemical Biology
|
CC BY 4.0
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CHEMRXIV
|
2020-03-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7494e702a9bd73c18b10b/original/energetics-based-modeling-of-hydroxychloroquine-and-azithromycin-binding-to-the-sars-co-v-2-spike-s-protein-ace2-complex.pdf
|
60c75405bdbb896316a3a55e
|
10.26434/chemrxiv.12980927.v2
|
Green Synthesis: A Novel Method for Bromination of 7-AminoPhthalide
|
<div>A novel method for preparing a bromo substituted 7-Amino-phthalides and 7-</div><div>Amino-3-hydroxy-phthalides via the bromonium ion intermediate under acidic conditions at</div><div>higher temperature were developed. The results will illustrate the potential utility of this</div><div>method as an environment-friendly process for synthesis of bromo substituted aryl amines,</div><div>along with conservation of half mole equivalent of halides.</div>
|
Sudershan Reddy Gondi
|
Organic Compounds and Functional Groups; Organic Synthesis and Reactions
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CC BY 4.0
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CHEMRXIV
|
2021-01-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75405bdbb896316a3a55e/original/green-synthesis-a-novel-method-for-bromination-of-7-amino-phthalide.pdf
|
6401d7f09789de3dd9d8b55d
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10.26434/chemrxiv-2023-9msp2
|
Temporal Differentiation of Extracellular Vesicles by Metabolic Glycan Labeling-Assisted Microfluidics
|
Extracellular vesicle (EV)/exosome secretion is a dynamic process that tunes the cellular communication for response to internal and external cues. The selective enrichment of a newly synthesized EV/exosome has been hindered by the basic fact that all EVs/exosomes, new and old, share the similar inherent parameters and thus are indistinguishable. Here, we developed a method by cotranslational introduction of azide groups into EV/exosome proteins as a timestamp and label them with biotin tag by click chemistry, to separate the newly synthesized EVs/exosomes from preexisting populations by streptavidin-modified herringbone microfluidic chip. For mouse model of anti-PD-L1 immunotherapy, the level of newly synthesized PD-L1+ EVs detected by the developed approach was superior to the total PD-L1+ EVs from mixed time sources (quantified by classical method) for tumor progression. This method makes it possible to address the temporal characteristics of newly synthesized EVs/exosomes in cell and in vivo, for studying EV/exosome secretion to respond to specific stimuli.
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Qiuyue Wu; Wencheng Wang; Chi Zhang; Zhenlong You; Yinyan Zeng; Yinzhu Lu; Suhui Zhang; Xingrui Li; Chaoyong Yang; Yanling Song
|
Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Bioengineering and Biotechnology; Chemical Biology
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-03-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6401d7f09789de3dd9d8b55d/original/temporal-differentiation-of-extracellular-vesicles-by-metabolic-glycan-labeling-assisted-microfluidics.pdf
|
66a07c20c9c6a5c07ab47e80
|
10.26434/chemrxiv-2024-zt155-v2
|
Imaging and quantifying the biological uptake and distribution of nanoplastics using a dual-functional model material
|
Nanoplastics (NPs) are invisible to human eyes yet pose significant concerns to human health due to their wide environmental presence and high potential for biological uptake, transport, and accumulation. Conventional analytical methods suffer from low accuracy and precision in NP detection due to their limited reliability and quantitative ability. To address these challenges, we developed a dual-functional model NP that allows for in-situ imaging by surface-enhanced Raman spectroscopy (SERS) and ex-situ quantification by inductively coupled plasma-mass spectrometry (ICP-MS). In this study, the model NP has a core-shell structure with Raman reporter-functionalized gold nanoparticles as the core and a layer of plastic as the shell. The gold core can enhance the Raman reporter signals and make model PS detectable, which can be used to visualize the uptake of the model NP in plant tissue by SERS. Meanwhile, the model NP particle numbers in the collected plants can be quantified by ICP-MS based on the presence of gold in the core. The model PS demonstrated stability in structure, size, and surface charges over one year, with no indication of chemical leaching. In this study, garlic plants were used as our experimental matrix to evaluate the potential of the dual-functional model PS for application in living organisms. Our aim was to determine whether the model PS in the garlic plants could be effectively quantified and qualified by SERS and ICP-MS. Garlic plants were grown in various concentrations of model NP suspensions for a 30-day period. The results showed that the NP uptake was concentration-dependent with higher concentrations of model NP leading to higher uptake by the garlic roots. The study also investigated the changes in NP uptake over time, showing that longer NP exposure resulted in more NP uptake in garlic roots. The study also demonstrated the effective coordination between SERS and ICP-MS. In cases where SERS had limitations in detecting the presence of model PS, ICP-MS proved capable of facilitating detection in garlic tissue. This study demonstrates the potential use of this dual-functional model NP for studying NP behavior with SERS and ICP-MS in living organisms, which holds significant implications for better understanding their impact on crops for future studies.
|
Mingjiu Liu; Anupam Das; Nubia Zuverza-Mena; Jason White; Huiyuan Guo
|
Analytical Chemistry; Earth, Space, and Environmental Chemistry; Agriculture and Food Chemistry; Environmental Analysis; Imaging; Microscopy
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-07-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a07c20c9c6a5c07ab47e80/original/imaging-and-quantifying-the-biological-uptake-and-distribution-of-nanoplastics-using-a-dual-functional-model-material.pdf
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6454e4fb1ca6101a45d1a67d
|
10.26434/chemrxiv-2022-hvnx1-v2
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RNA-protein complexes and force field polarizability
|
Molecular dynamic (MD) simulations offer a way to study biomolecular interactions and their dynamics at the atomistic level. There are only a few studies of RNA-protein complexes in MD simulations, and here we wanted to study how force fields differ when simulating RNA-protein complexes: 1) argonaute 2 with bound guide RNA and a target RNA, 2) CasPhi-2 bound to CRISPR RNA and 3) Retinoic acid-inducible gene I C268F variant in complex with double-stranded RNA. We tested three non-polarizable force fields: Amber protein force fields ff14SB and ff19SB with RNA force field OL3, and the all-atom OPLS4 force field. Due to the highly charged and polar nature of RNA, we also tested the polarizable AMOEBA force field and the ff19SB and OL3 force fields with a polarizable water model OPC3-pol. Our results show that the non-polarizable force fields lead to compact and stable complexes. The polarizability in the force field or in the water model allows significantly more movement from the complex, but in some cases, this results in the disintegration of the complex structure, especially if the protein contains longer loop regions. Thus, one should be cautious when running long-scale simulations with polarizability. As a conclusion, all the tested force fields can be used to simulate RNA-protein complexes and the choice of the optimal force field depends on the studied system and research question.
|
Hanna Baltrukevich; Piia Bartos
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Computational Chemistry and Modeling
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CC BY 4.0
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CHEMRXIV
|
2023-05-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6454e4fb1ca6101a45d1a67d/original/rna-protein-complexes-and-force-field-polarizability.pdf
|
67a5cb45fa469535b95e8de5
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10.26434/chemrxiv-2024-zz9pw-v2
|
Assigning the Stereochemistry of Natural Products by Machine Learning
|
Nature has settled for L-chirality for proteinogenic amino acids and D-chirality for the carbohydrate backbone of nucleotides. Here we asked the question whether stereochemical patterns might also exist among natural products (NPs) such that their stereochemistry could be assigned automatically. Indeed, we report that a language model can be trained to assign the stereochemistry of NPs using the open access NP database COCONUT. In detail, our language model, called NPstereo, translates an NP structure written as absolute SMILES into the corresponding isomeric SMILES notation containing stereochemical information with 80.1% per-stereocenter accuracy for full assignments and 86.3% per-stereocenter accuracy for partial assignments across various NP classes including secondary metabolites such as alkaloids, polyketides, lipids and terpenes. NPstereo might be useful to assign or correct the stereochemistry of newly discovered NPs.
|
Markus Orsi; Jean-Louis Reymond
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY NC 4.0
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CHEMRXIV
|
2025-02-07
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a5cb45fa469535b95e8de5/original/assigning-the-stereochemistry-of-natural-products-by-machine-learning.pdf
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63f70d6432cd591f1259b36f
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10.26434/chemrxiv-2023-wzdrs-v2
|
FleX: a computer vision program to evaluate strain in flexible crystals
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The program FleX (Flexural deformation for Xtals) has been developed for a quick, easy and accurate evaluation of the maximum deformation reached in flexible crystals from a simple optical microscope picture. The program takes advantage of computer vision libraries to find a bent crystals contours and fit the contours to semicircles. It can, then, calculate its theoretical maximum deformation along its long axis using equations from the Euler-Bernoulli beam theory.
|
Benjamin Hsieh; Lai-Chin Wu; Arnaud Grosjean
|
Materials Science
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-02-23
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f70d6432cd591f1259b36f/original/fle-x-a-computer-vision-program-to-evaluate-strain-in-flexible-crystals.pdf
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60c740930f50db2317395980
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10.26434/chemrxiv.7765241.v1
|
Probing the Substrate Promiscuity of Isopentenyl Phosphate Kinase as a Platform for Hemiterpene Analogue Production
|
Isoprenoids are a large class of natural products with wide-ranging applications. Synthetic biology approaches to the manufacture of isoprenoids and their new-to-nature derivatives are limited due to the provision in Nature of just two hemiterpene building blocks for isoprenoid biosynthesis. To address this limitation, artificial chemo-enzymatic pathways such as the alcohol-dependent hemiterpene pathway (ADH) serve to leverage consecutive kinases to convert exogenous alcohols to pyrophosphates that could be coupled to downstream isoprenoid biosynthesis. To be successful, each kinase in this pathway should be permissive of a broad range of substrates. For the first time, we have probed the promiscuity of the second enzyme in the ADH pathway, isopentenyl phosphate kinase from Thermoplasma acidophilum, towards a broad range of acceptor monophosphates. Subsequently, we evaluate the suitability of this enzyme to provide non-natural pyrophosphates and provide a critical first step in characterizing the rate limiting steps in the artificial ADH pathway.<br />
|
Sean Lund; Taylor Courtney; Gavin Williams
|
Biochemistry; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-02-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740930f50db2317395980/original/probing-the-substrate-promiscuity-of-isopentenyl-phosphate-kinase-as-a-platform-for-hemiterpene-analogue-production.pdf
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60c741b2469df435c7f42e9e
|
10.26434/chemrxiv.8123648.v1
|
Quantum-Induced Symmetry-Breaking in the Deuterated Dihydroanthracenyl Radical
|
The hydrogen-atom adduct with anthracene, 9-dihydroanthracenyl radical (C<sub>14</sub>H<sub>11</sub>), and its deuterated analogue, have been identified by laser spectroscopy coupled to time-of-flight mass spectrometry, supported by time-dependent density functional theory calculations. The electronic spectrum of 9-dihydroanthracenyl radical exhibits an origin band at 19115 cm<sup>-1</sup> and its ionization energy was determined to be 6.346(1) eV. The spectra reveal a low-frequency vibrational progression corresponding to a mode described by a butterfly-inversion. In the deuterated analogue, a zero-point-energy imbalance along this coordinate is found to lead to a doubling of the observed spectral lines in the progression. This is attributed to quantum-induced symmetry breaking as previously observed in isotopologues of CH<sub>5</sub><sup>+</sup>.
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Olha Krechkivska; Callan Wilcox; Klaas Nauta; Scott Kable; Timothy Schmidt
|
Space Chemistry; Theory - Computational; Quantum Mechanics; Spectroscopy (Physical Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2019-05-15
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741b2469df435c7f42e9e/original/quantum-induced-symmetry-breaking-in-the-deuterated-dihydroanthracenyl-radical.pdf
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66e82ed212ff75c3a1803059
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10.26434/chemrxiv-2024-67549
|
Machine Learning for Microscopy Data Analysis: Toward Real-time Optical and
Electrical Characterization of Sub-micron Materials
|
(Micro)spectroscopy often generates various output signals due to intrinsic inhomogeneity of material arrangement at low dimensions or machinery drift, albeit the bulk composition and experimental parameters remain constant. In fact, such diversity can be harnessed to measure material’s purity, unveiling various concealed features via statistical inspection of heterogeneous signals acquired from several microscopy scans. However, the approach requires efficient categorization of a substantial number of signals, which is currently encumbered by
laborious calculations, computational hurdles, and manual intervention. This necessitates a programmed interface to perform time-efficient big data analytics, lack of which has perpetually widened the schism between laboratory and industrial-scale microscopy-based assessment of
nanomaterials. We present a robust technique - an unsupervised machine learning driven module for automatic clustering and class-wise power spectral density calculation of real-time microscopy signals. Our methodology has been tested across different aspects of wide-field fluorescence imaging and scanning tunnelling spectroscopy, demonstrating the versatility. Additionally, we investigated the impact of data-processing on the clustering efficiency and optimized the methodology. We anticipate that our futuristic workflow package for contemporary microscopes is the initial endeavor toward fast data analytics and instant
material characterization, spanning a diverse spectrum of interests.
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Amitrajit Mukherjee; Robby Reynaerts; Bapi Pradhan; Sudipta Seth; Andreas T. Rösch ; Tamali Banerjee; Lata Chouhan; Handong Jin; Christian Sternemann; Michael Paulus; Luca Leoncino; Kunal S. Mali; Steven De Feyter; Maarten Roeffaers; Egbert Willem Meijer; Johan Hofkens; Elke Debroye
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Materials Science; Analytical Chemistry; Nanoscience; Microscopy; Spectroscopy (Anal. Chem.); Nanostructured Materials - Nanoscience
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-09-17
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e82ed212ff75c3a1803059/original/machine-learning-for-microscopy-data-analysis-toward-real-time-optical-and-electrical-characterization-of-sub-micron-materials.pdf
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60c74cf3bb8c1a778b3db4ec
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10.26434/chemrxiv.12203240.v2
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Kinetic Prediction of Reverse Intersystem Crossing in Organic Donor–Acceptor Molecules
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Reverse intersystem crossing (RISC), the uphill spin-flip process from a triplet to a singlet excited state, plays a key role in a wide range of photochemical applications. Understanding and predicting the kinetics of such processes in vastly different molecular structures would facilitate the rational design of new materials. Here, we demonstrate a theoretical expression that successfully reproduces experimental RISC rate constants ranging over five orders of magnitude in twenty different molecules. We show that the spin flip occurs across the singlet–triplet crossing seam involving a higher-lying triplet excited state where the semi-classical Marcus parabola is no longer valid. The present model explains the counterintuitive substitution effects of bromine on the RISC rate constants of newly synthesized molecules, providing a predictive tool for material design.<br />
|
Naoya Aizawa; Yu Harabuchi; Satoshi Maeda; Yong-Jin Pu
|
Photochemistry (Physical Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-06-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cf3bb8c1a778b3db4ec/original/kinetic-prediction-of-reverse-intersystem-crossing-in-organic-donor-acceptor-molecules.pdf
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677d47f181d2151a0234f815
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10.26434/chemrxiv-2025-t65dj
|
Accurate calculation of electron paramagnetic resonance parameters for molybdenum compounds
|
Paramagnetic molybdenum compounds are of great interest in 4d-metal inorganic chemistry and metalloenzyme catalysis. Electron paramagnetic resonance (EPR) spectroscopies that determine hyperfine coupling parameters and g values are essential tools for investigating the local and global electronic structure of these compounds. Such studies require support from accurate quantum chemical approaches to establish reliable structure–spectroscopy correlations. Here we present a curated database of 22 molecular Mo complexes with well-defined structures and EPR parameters and investigate quantum chemical approaches to determine optimal protocols for computing 95Mo hyperfine coupling constants (HFCs) and g values of Mo(V) compounds. It is shown that the SARC all-electron basis sets developed for the Douglas–Kroll–Hess (DKH) Hamiltonian can be used without any adaptation also for the exact-2-component (X2C) Hamiltonian and require no modifications to produce excellent and converged results for both HFCs and g values. The dependence of EPR parameters on the functional is studied in detail. Double-hybrid functionals and global hybrids with high percentage of exact exchange are top performers for 95Mo HFCs, with PBE0-DH achieving the best agreement with experiment. The DFT results on HFCs are compared with values obtained by coupled cluster theory with the domain-based local pair natural orbital approach (DLPNO-CCSD) and we show that the latter falls short in terms of accuracy and consistency compared to the best performing functionals for the preset set of compounds. Smaller differentiation among functionals is observed for the calculation of g tensors, with double hybrids being surpassed by several global and range-separated hybrid functionals, although PBE0-DH is still a top performer and can thus be recommended as the most reliable DFT approach overall for both valence and core properties of Mo compounds.
|
Maria Drosou; Iris Wehrung; Dimitrios A. Pantazis; Maylis Orio
|
Theoretical and Computational Chemistry; Inorganic Chemistry; Bioinorganic Chemistry; Spectroscopy (Inorg.); Theory - Computational
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CC BY NC ND 4.0
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CHEMRXIV
|
2025-01-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677d47f181d2151a0234f815/original/accurate-calculation-of-electron-paramagnetic-resonance-parameters-for-molybdenum-compounds.pdf
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6458651507c3f02937633db5
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10.26434/chemrxiv-2023-8gd8z
|
Photochromism and Photomagnetism in 1,4-bis(4,5-diphenyl-imidazolyl)benzene Chromophores: Water Assisted π-stacks for the Generation of Stable Free Radicals in Solid State
|
Photochromism and photomagnetism are two important
features for the generation of smart materials that are of utility for optical switches and memory devices. Very few materials that exhibit both the features at room temperature are known to date, the reported ones mostly contain metal-ions to assist the electron transfer with photo stimuli. Herein, we report a new class of organic materials that show photochromism and photomagnetism at room temperature due to the generation of free radicals in the solid-state. 1,4-bis(4,5-diphenyl-1H-imidazol-2-yl)benzene (BDPI) was found to acts as organic photomagnet without use of any traditional photochromic couplers or radical containing moieties. Solvent molecules (eg. water and DMSO) form hydrogen bonds with the imidazole rings which act as binding glue in stacking of 1,4-bis(imidazolyl)benzene moieties via π···π interactions. These interactions found to play a significant role in promoting strong spin-spin interaction in the solid-state which can be inferred from the appearance of broad EPR signal, whereas a sharp signal appeared only after irradiation. The sharp signal indicates formation of
paramagnetic free radicals which influence antiferromagnetic exchange interactions with weakening of the magnetic susceptibility significantly. This work provides a new direction in the ongoing research of photochromic and photomagnetic materials, where a simple 1,4- bis(imidazolyl)benzene system changes its color, radical
activity and magnetic behavior with photoirradiation.
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Subhajit Saha; Sudipta Khamurai; Rajib Moi; Anakuthil Anoop; Vladimir Chernyshev; Debamalya Banerjee; Kumar Biradha
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Organic Chemistry; Materials Science; Photochemistry (Org.); Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-05-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6458651507c3f02937633db5/original/photochromism-and-photomagnetism-in-1-4-bis-4-5-diphenyl-imidazolyl-benzene-chromophores-water-assisted-stacks-for-the-generation-of-stable-free-radicals-in-solid-state.pdf
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61f1762b63acbabdc41ada62
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10.26434/chemrxiv-2022-nrv2z
|
How much technological progress is needed to make solar hydrogen cost-competitive?
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Cost-effective production of green hydrogen is a major challenge for global adoption of a hydrogen economy. Technologies such as photoelectrochemical (PEC) or photocatalytic (PC) water splitting and photovoltaic + electrolysis (PV+E) allow for sustainable hydrogen production from sunlight and water, but are not yet competitive with fossil fuel-derived hydrogen. Herein, open-source software for techno-economic analysis (pyH2A) along with a Monte Carlo-based methodology for modelling of technological progress are developed. Together, these tools allow for the study of required technological improvement to reach a competitive target cost. They are applied to PEC, PC and PV+E to identify required progress for each and derive actionable research targets. For PEC, it is found that cell lifetime improvements (> 2 years) and operation under high solar concentration (> 50-fold) are crucial, necessitating systems with high space-time yields. In case of PC, solar-to-hydrogen efficiency has to reach at least 6% and lowering catalyst concentration (< 0.2 g/L) by improving absorption properties is identified as a promising path to low-cost hydrogen. PV+E requires ca. 2 or 3-fold capital cost reductions for photovoltaic and electrolyzer components. We hope that these insights can inform materials research efforts to improve these technologies in the most impactful ways.
|
Jacob Schneidewind
|
Materials Science; Catalysis; Energy; Photocatalysis; Fuels - Energy Science; Photovoltaics
|
CC BY 4.0
|
CHEMRXIV
|
2022-01-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f1762b63acbabdc41ada62/original/how-much-technological-progress-is-needed-to-make-solar-hydrogen-cost-competitive.pdf
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612839bab817b405680b98f1
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10.26434/chemrxiv-2021-68zn8
|
Predicting spike protein NTD mutations of SARS-CoV-2 causing immune escape by molecular dynamics simulations
|
The emergence of coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been bringing the world to a standstill. Beyond all doubt, the most striking therapeutic target for antibody development is the spike (S) protein on the surface of virus. In contrast with an immunodominant receptor-binding domain (RBD) of the spike protein, little is known about neutralizing antibodies binding mechanisms of N-terminal domain (NTD), let alone the effect of NTD mutation on antibody binding and risk of immune evasion. Employing various computational approaches in this study, we investigated critical residues for NTD-antibody bindings and their detailed mechanism. The results showed that some residues on NTD including Y144, K147, R246 and Y248 are critically involved in the direct interaction of NTD with many monoclonal antibodies (mAbs), indicating that the viruses harboring these residue mutations may have high risk of immune evasion. Binding free energy calculations and the interaction mechanism study revealed that R246I, which is present in Beta (B.1.351) variant, may decrease or even abrogate the efficacies of many antibodies. Therefore, special attention should be paid to the mutations of the 4 residues for future antibody design and development.
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Liping Zhou; Leyun Wu; Cheng Peng; Yanqing Yang; Yulong Shi; Zhijian Xu; Weiliang Zhu
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Theoretical and Computational Chemistry; Computational Chemistry and Modeling
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CC BY 4.0
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CHEMRXIV
|
2021-09-01
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612839bab817b405680b98f1/original/predicting-spike-protein-ntd-mutations-of-sars-co-v-2-causing-immune-escape-by-molecular-dynamics-simulations.pdf
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66168097418a5379b08999b3
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10.26434/chemrxiv-2024-3236v
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Fuel-Driven Dynamic Combinatorial Peptide Libraries
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Dynamic combinatorial chemistry (DCC) creates libraries of molecules that are constantly interchanging in a dynamic combinatorial library. When a library member self-assembles, it can displace the equilibria, leading to emergent phenomena like its selection or even its replication. However, such dynamic combinatorial libraries typically operate in or close to equilibrium. This work introduces a new dynamic combinatorial chemistry fueled by a catalytic reaction cycle that forms transient, out-of-equilibrium peptide-based macrocycles. The products in this library exist out of equilibrium at the expense of fuel and are thus regulated by kinetics and thermodynamics. By creating a chemically fueled dynamic combinatorial library with the vast structural space of amino acids, we explored the liquid-liquid phase separation behavior of the library members. The new versatile chemistry enables simple and complex coacervation and creates structures with significantly longer lifetimes than other chemically fueled examples.
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Fabian Späth; Michele Stasi; Héctor Soria-Carrera; Judit Sastre; Brigitte Kriebisch; Job Boekhoven
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Physical Chemistry; Organic Chemistry; Combinatorial Chemistry; Supramolecular Chemistry (Org.); Chemical Kinetics; Materials Chemistry
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CC BY 4.0
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CHEMRXIV
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2024-04-12
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66168097418a5379b08999b3/original/fuel-driven-dynamic-combinatorial-peptide-libraries.pdf
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672a014f7be152b1d00b1263
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10.26434/chemrxiv-2024-2k85w
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Timed formation and aging of complex coacervates using a volatile salt
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Biomolecular condensates are liquid droplets formed by liquid-liquid phase separation, which play a role in a variety of cellular processes. In the last decade, there has been a growing interest in their study, often by using complex coacervates as models. Despite their similar properties, a limitation of complex coacervates is their inability to show time-dependent behavior such as aging, as they are typically structures in thermodynamic equilibrium. Here, we present a simple protocol to trigger delayed formation and aging in coacervates. We use ammonium carbonate for this protocol, a volatile salt which decreases the ionic strength of the solution as it decomposes. Using this salt, we have been able to program coacervate formation after delays ranging from hours to days. This process can be repeated multiple times, as the decomposition of ammonium carbonate leaves no waste-products. The mechanical properties of the coacervate phase also change over time with this protocol, showing a steady increase in viscosity reminiscent of aging in condensates. Since the element that causes temporal evolution is the salt and not the coacervates, this protocol does not require any synthesis and can be easily adapted to multiple complex coacervates.
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Lunan Yan; Weiwei Zheng; Enola Muller; Philippe Carl; Thomas Hermans; Guillermo Monreal Santiago
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Materials Science; Polymer Science; Polyelectrolytes - Materials; Polyelectrolytes - Polymers
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CC BY NC 4.0
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CHEMRXIV
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2024-11-07
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672a014f7be152b1d00b1263/original/timed-formation-and-aging-of-complex-coacervates-using-a-volatile-salt.pdf
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67817bf881d2151a029fb76a
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10.26434/chemrxiv-2025-pqmcc
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How Local is `Local'? Deep Learning Reveals Locality of the Induced Magnetic Field of Polycyclic Aromatic Hydrocarbons
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We investigate the locality of magnetic response in polycyclic aromatic molecules using a novel deep-learning approach. Our method employs graph neural networks (GNNs) with a graph-of-rings representation to predict Nucleus-Independent Chemical Shifts in the space around the molecule. We train a series of models, each time reducing the size of the largest molecules used in training. The accuracy of prediction remains high (MAE < 0.5 ppm), even when training the model only on molecules with up to 4 rings, thus providing strong evidence for the locality of magnetic response. To overcome the known problem of generalization of GNNs, we implement a k-hop expansion strategy and succeed in achieving accurate predictions for molecules with up to 15 rings (almost 4 times the size of the largest training example). Our findings have implications for understanding the magnetic response in complex molecules and demonstrate a promising approach to overcoming GNN scalability limitations. Furthermore, the trained models enable rapid characterization, without the need for more expensive DFT calculations.
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Yair Davidson; Aviad Philipp; Sabyasachi Chakraborty; Alex M. Bronstein; Renana Gershoni-Poranne
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Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Computational Chemistry and Modeling; Machine Learning
|
CC BY NC 4.0
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CHEMRXIV
|
2025-01-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67817bf881d2151a029fb76a/original/how-local-is-local-deep-learning-reveals-locality-of-the-induced-magnetic-field-of-polycyclic-aromatic-hydrocarbons.pdf
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60c74331337d6c54c4e26b6b
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10.26434/chemrxiv.8969684.v1
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A Robust, Porous and Solution-Processable Molecular Crystal Containing Multiple Donor-Acceptor Units
|
We report a curious porous molecular
crystal that is devoid of the common traits of related systems. Namely, the molecule
does not rely on directional hydrogen bonds to enforce open packing; and it
offers neither large concave faces (i.e., high internal free volume) to
frustrate close packing, nor any inherently built-in cavity like in the class
of organic cages. Instead, the permanent porosity (as unveiled by the X-ray
crystal structure and CO<sub>2</sub> sorption studies) arises from the strong
push-pull units built into a Sierpinski-like molecule that features four
symmetrically backfolded (<b>SBF</b>) side
arms. Each side arm consists of the 1,1,4,4-tetracyanobuta-1,3-diene acceptor
(TCBD) coupled with the dimethylaminophenyl donor, which is conveniently installed
by a cycloaddition-retroelectrocyclization (CA-RE) reaction. Unlike the poor/fragile
crystalline order of many porous molecular solids, the molecule here readily
crystallizes and the crystalline phase can be easily deposited into thin films
from solutions. Moreover, both the bulk sample and thin film exhibit excellent
thermal stability with the porous crystalline order maintained even at 200 °C. The intermolecular forces underlying this robust porous molecular crystal likely
include the strong dipole interactions and the multiple C···N and C···O short
contacts afforded by the strongly donating and accepting groups integrated
within the rigid molecular scaffold.
|
Shengxian Cheng; Xiaoxia Ma,; Yonghe He; Jun He; Matthias Zeller; Zhengtao Xu
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Crystallography – Organic
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CC BY NC ND 4.0
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CHEMRXIV
|
2019-07-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74331337d6c54c4e26b6b/original/a-robust-porous-and-solution-processable-molecular-crystal-containing-multiple-donor-acceptor-units.pdf
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67ae589a81d2151a02548c9c
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10.26434/chemrxiv-2025-hn2j6
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Structure-guided design of ISOX-DUAL-based Degraders targeting BRD4 and CBP/EP300. A case of Degrader collapse
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Degraders with dual activity against BRD4 and CBP/EP300 were designed. A structure-guided design approach was taken to assess and test potential exit vectors on the dual BRD4 and CBP/EP300 inhibitor, ISOX-DUAL. Candidate Degrader panels revealed that VHL-recruiting moieties could mediate dose-responsive ubiquitination of BRD4. A panel of CRBN-recruiting thalidomide-based Degraders were unable to induce ubiquitination or degradation of target proteins. High-resolution protein co-crystal structures revealed an unexpected interaction between the thalidomide moiety and Trp81 on the first bromodomain of BRD4. The inability to form a ternary complex provides a potential rationale for the lack of Degrader activity with these compounds, some of which have remarkable affinities close to those of (+)-JQ1, as low as 65 nM in a biochemical assay, vs 1.5 M for their POI ligand, ISOX-DUAL. Such a “Degrader collapse” may represent an under-reported mechanism by which some putative Degrader molecules are inactive with respect to target protein degradation.
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Anthony Edmonds; Dimitrios-Ilias Balourdas; Graham Marsh; Robert Felix; Bradley Basher; Jeff Cooper; Cari Grabl-Feesl; Madhu Kollareddy; Karim Malik; Helen Stewart; Timothy Chevassut; Ella Lineham; Simon Morley; Oleg Fedorov; James Bennett; Mohan Rajasekaran; Samuel Ojeda; Drew Harrison; Christopher Ott; Andreas Joerger; Hannah Maple; John Spencer
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Biological and Medicinal Chemistry; Organic Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems; Crystallography – Organic
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CC BY 4.0
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CHEMRXIV
|
2025-02-18
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ae589a81d2151a02548c9c/original/structure-guided-design-of-isox-dual-based-degraders-targeting-brd4-and-cbp-ep300-a-case-of-degrader-collapse.pdf
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60c7409cbb8c1a6d2c3d9de2
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10.26434/chemrxiv.7663124.v2
|
Long-wavelength Fluorophores for Voltage Sensing
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<p>We present the design, synthesis, and applications of a new
class of voltage-sensitive fluorescent indicators built on a modified
carbofluorescein scaffold. Carbofluoresceins are an attractive target for
responsive probes because they maintain oxygen substitution patterns at the 3'
and 6' positions, similar to fluorescein, while simultaneously possessing excitation
and emission profiles red-shifted nearly 50 nm compared to fluorescein.
However, the high p<i>K</i><sub>a</sub> of
carbofluorescein dyes, coupled with their tendency to cyclize to
non-fluorescent configurations precludes their use in voltage-imaging
applications. Here, we overcome the limitations of carbofluoresceins via
chlorination to lower the p<i>K</i>a by 2
units to 5.2 and sulfonation to prevent cyclization to the non-absorbing form.
To achieve this, we devise a synthetic route to halogenated sulfonated
carbofluoresceins from readily available, inexpensive starting materials. New,
chlorinated sulfone carbofluoresceins have low p<i>K</i><sub>a</sub> values (5.2) and can be incorporated into
phenylenevinylene molecular wire scaffolds to create carboVoltage-sensitive
Fluorophores (carboVF dyes). The best of the new carboVF dyes,
carboVF2.1(OMe).Cl, possesses excitation and emission profiles >560 nm,
displays high voltage sensitivity (>30% ΔF/F per 100 mV), and can be used in
the presence of other blue-excited fluorophores like green fluorescent protein
(GFP). Because carboVF2.1(OMe).Cl contains a phenolic oxygen, it can be
incorporated into fluorogenic labeling strategies. Alkylation with a sterically
bulky cyclopropylmethyl-derived acetoxymethyl ether renders carboVF weakly
fluorescent; we show that fluorescence can be restored by the action of porcine
liver esterase (PLE) both <i>in vitro</i>
and on the surface of living cells and neurons. Together, these results suggest
chlorinated sulfone carbofluoresceins can be promising candidates for hybrid
chemical-genetic voltage imaging at wavelengths beyond typical fluorescein
excitation and emission.</p>
|
Gloria Ortiz; Pei Liu; Su Naing; Vikram Muller; Evan Miller
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Bioorganic Chemistry; Organic Synthesis and Reactions; Biophysics; Cell and Molecular Biology; Chemical Biology
|
CC BY NC ND 4.0
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CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7409cbb8c1a6d2c3d9de2/original/long-wavelength-fluorophores-for-voltage-sensing.pdf
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61636d71fb86194484f4235f
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10.26434/chemrxiv-2021-pxgsq
|
Glenthenamines A–F: Enamine pyranonaphthoquinones from the Australian pasture plant-derived Streptomyces sp. CMB-PB042
|
Chemical investigations into solid phase cultivations of an Australian sheep station pasture plant-derived Streptomyces sp. CMB-PB042, yielded the rare enamine
naphthopyranoquinones BE-54238A (1) and BE-54238B (2), together with four new analogues, glenthenamines B–D (4–6) and F (8), and two handling artifacts, glenthenamines A (3) and E (7). Single crystal X-ray analyses of 1–2 resolved
configurational ambiguities in the scientific literature, while detailed spectroscopic analysis and biosynthetic considerations assigned structures inclusive of absolute
configuration to 3–8. We propose a plausible sequence of biosynthetic transformations linking structural and configurational features of 1–8, and apply a novel Schiff base "fishing" approach to detect a key deoxyaminosugar precursor. These enamine naphthopyranoquinone disclose a new P-gp inhibitory pharmacophore capable of reversing doxorubicin resistance in P-gp overexpressing colon carcinoma cells.
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Taizong Wu; Angela Salim; Hui Cui; Zeinab Khalil; Paul Bernhardt; Robert Capon
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Organic Chemistry; Natural Products
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-10-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61636d71fb86194484f4235f/original/glenthenamines-a-f-enamine-pyranonaphthoquinones-from-the-australian-pasture-plant-derived-streptomyces-sp-cmb-pb042.pdf
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646bbd94b3dd6a6530906847
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10.26434/chemrxiv-2023-gqmrq
|
Novel coumarin-nucleobase hybrids with potential anticancer activity: Synthesis, in-vitro cell-based evaluation, and molecular docking
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A new series of compounds planned by molecular hybridization of the nucleobases uracil and thymine, or the xanthine theobromine, with coumarins, and linked through 1,2,3-triazole heterocycles were evaluated for their in vitro anticancer activity against the human tumor cell lines: colon carcinoma (HCT116), laryngeal tumor cells (Hep-2), and lung carcinoma cells (A549). The hybrid compound 7a exhibited better activity in the series, showing an IC50 of 24.19 ± 1.39 μM against the HCT116 cells, with a selectivity index (SI) of 6, when compared to the cytotoxicity against the non-tumor cell line HaCat. Molecular docking studies were performed on all active compounds and suggested that the synthesized compounds possess a high affinity to DNA Topoisomerase-1 protein, supporting their antitumor activity. The in silico toxicity prediction studies suggest that the compounds present a low risk of causing theoretical mutagenic and tumorigenic effects. These findings indicate that the molecular hybridization from natural derivative molecules is an interesting approach to seek new antitumor candidates.
|
Maiara Correa de Moraes; Rafaele Frassini; Mariana Roesch-Ely; Favero Reisdorfer de Paula; Thiago Barcellos
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Organic Synthesis and Reactions; Chemoinformatics - Computational Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-05-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646bbd94b3dd6a6530906847/original/novel-coumarin-nucleobase-hybrids-with-potential-anticancer-activity-synthesis-in-vitro-cell-based-evaluation-and-molecular-docking.pdf
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6510296660c37f4f765ceb3e
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10.26434/chemrxiv-2023-f8gk3
|
Asymmetric q-Gaussian functions to fit the Raman LO mode band in Silicon Carbide
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Previous studies (Sparavigna, 2023) have demonstrated the Tsallis q-Gaussian functions suitable for the analysis of Raman spectra. Here we consider two asymmetric forms of them, with the aim of further improving the fitting of Raman spectra. The first asymmetric form, that we are here proposing for the first time, is a generalization of the Breit-Wigner-Fano function. The other profile is that made by two different half q-Gaussian functions, chosen to fit the two sides of a Raman band. The case study that we will discuss in detail is that of the Raman LO mode of Silicon Carbide.
|
Amelia Carolina Sparavigna
|
Materials Science
|
CC BY 4.0
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CHEMRXIV
|
2023-09-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6510296660c37f4f765ceb3e/original/asymmetric-q-gaussian-functions-to-fit-the-raman-lo-mode-band-in-silicon-carbide.pdf
|
63810d2b0058eb333865255a
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10.26434/chemrxiv-2022-4x475
|
Effect of Particulate Reinforcing Agents on Shore Hardness and Scratch Hardness of Polymeric Hybrid Blend Composites
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This paper explores the use of Wollastonite, Cloisite 20A, Hollow Glass Micro Spheres and Precipitated Silica as reinforcing fillers in PE-BA-GMA compatibilized blends of Hytrel with HDPE (60:40). Wollastonite has been treated with 3-glycidyloxypropyl trimethoxysilane (GPTMS), and its effect on dispersion and hardness has been studied via SEM. I have tried to understand how the aspect ratio, size and surface property of the filler affect its tendency to cause nucleation, or reinforce the composites. These effects have been corroborated with the shore hardness, scratch hardness, other mechanical properties and flammability. Additionally, DSC has been used to study the degree of crystallinity of the composites, which has been correlated with the mechanical properties of these composites.
|
Manoj Praharaj Bhatnagar
|
Materials Science; Polymer Science; Composites; Polymer blends; Polymer morphology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-11-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63810d2b0058eb333865255a/original/effect-of-particulate-reinforcing-agents-on-shore-hardness-and-scratch-hardness-of-polymeric-hybrid-blend-composites.pdf
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669d250e01103d79c5e691c7
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10.26434/chemrxiv-2024-4vrx9-v2
|
A Correlated Flat-bottom Elastic Network Model for Improved Bond Rearrangement in Reaction Paths
|
This study introduces correlated flat-bottom elastic network model (CFB-ENM), an extension of our recently developed flat-bottom elastic network model (FB-ENM) for generating plausible reaction paths. While FB-ENM improved upon the widely used image-dependent pair potential (IDPP) by addressing unintended structural distortion and bond breaking, it still struggled with regulating the timing of series of bond breaking and formation. CFB-ENM overcomes this limitation by incorporating structure-based correlation terms. These terms impose constraints on pairs of atom pairs, ensuring immediate formation of new bonds after breaking of existing bonds. We optimized paths for 121 reactions using the direct MaxFlux method to find that CFB-ENM significantly improves reaction paths. Compared to FB-ENM, CFB-ENM paths exhibited lower maximum DFT energies along the paths in 82\% of reactions, with an average decrease of 30.0 kcal/mol. In cases where CFB-ENM produced higher energies, most increases were below 10 kcal/mol and often involved quasi-four-membered ring formation, which can be omitted beforehand. CFB-ENM generates collision-free paths that preserve non-reactive structural elements and regulate bond rearrangements, potentially reducing computational costs in subsequent precise reaction path or transition state searches. An implementation of CFB-ENM based on the Atomic Simulation Environment is available on GitHub, facilitating its use in computational chemistry research.
|
Shin-ichi Koda; Shinji Saito
|
Theoretical and Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-07-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669d250e01103d79c5e691c7/original/a-correlated-flat-bottom-elastic-network-model-for-improved-bond-rearrangement-in-reaction-paths.pdf
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638532b5ebc1c73549d62b6a
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10.26434/chemrxiv-2023-81b7f
|
Modeling the Coulomb barrier and fusion reaction with alternating/unequal electromagnetic fields
|
The Coulomb barrier occurs at the quantum interface between the strong and the electromagnetic fundamental forces. Overcoming the Coulomb barrier is the central goal of nuclear fusion, and an effective model of the barrier can only accelerate the achievement of this potential source of clean and abundant energy. A recently introduced magnetic “Coulomb” barrier model provides a visual and tactile representation of the fusion potential curve, including the counterintuitive combination of far-range repulsion and close-range attraction (https://youtu.be/FzEHs47nylA). The model contains a pair of opposing circular magnet arrays, each array comprising a series of double north-oriented magnets alternating in regular sequence with single south-oriented magnets. This configuration generates complex magnetic fields between the arrays, with the result that the net force between them (attractive or repulsive) depends on the degree of separation. The close-range dynamic simulates the behavior of the strong nuclear force within the Coulomb barrier, and the plot of magnetic force versus distance reproduces the familiar fusion potential curve. Given Maxwell’s unification of electricity and magnetism within the electromagnetic fundamental force, the question arises as to whether alternating and unequal electric fields might also demonstrate a potential barrier. In this exercise, the circular alternating and unequal magnet sequences of each magnet array are replaced by theoretical alternating +1 and -2 coulomb electrostatic charges to produce a pair of opposing electrostatic arrays. The centimeter scale and essential geometry are preserved. Coulomb’s law is then used to calculate component forces at incremental distances between the arrays. The theoretical electrostatic analog of the magnetic "Coulomb" barrier apparatus generates a force/distance curve that is nearly identical to the magnetic barrier curve but differing only in magnitude. Combinations of opposite and unequal charges also have the capacity to emulate or model quark “confinement.” Like the Coulomb barrier, confinement is a quantum mechanical phenomenon. Nothing like it exists in the classical domain. And like the Coulomb barrier, confinement forces may be modeled with an appropriately configured sequence of alternating and unequal charges, as shown in Figure 3(a).
Here, the six alternating +1 and -2 coulomb charges are assumed to occupy fixed positions 1 cm apart. A displacement force is applied to an internal -2 charge in a direction orthogonal to the linear sequence. The orthogonal force component between the internal -2 charge and each of the other charges in the sequence is then determined using Coulomb's law. The sum of these forces is plotted versus the distance between the displaced charge and its original in-line position (see Figure 3(b)). The plot is undeniably electrostatic and yet bears no resemblance to the inverse square plot normally associated with the force between a pair of charged particles. In fact, this electrostatic force/distance curve more closely resembles published quark “confinement" force behavior.
|
Raymond Walsh
|
Physical Chemistry; Energy; Chemical Education; Quantum Mechanics; Structure
|
CC BY 4.0
|
CHEMRXIV
|
2023-05-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638532b5ebc1c73549d62b6a/original/modeling-the-coulomb-barrier-and-fusion-reaction-with-alternating-unequal-electromagnetic-fields.pdf
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60c73cc9bdbb89f789a37b7a
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10.26434/chemrxiv.14743914.v1
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Morphogenesis of Magnetite Mesocrystals: Interplay Between Nanoparticle Morphology and Solvation Shell
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In this study, faceted mesocrystals have been assembled from the dispersion of truncated cubic-shaped iron oxide nanoparticles stabilized by oleic acid (OA) molecules using the non-solvent “gas phase diffusion technique” into an organic solvent. The effects of synthesis conditions as well as of the nanoparticle size and shape on the structure and morphogenesis of mesocrystals were examined. The interactions of OA capped iron oxide nanoparticles with solvent molecules were probed by analytical ultracentrifugation and double difference pair distribution function analysis. It was shown that the structure of the organic shell significantly depends on the nature and polarity of solvent molecules.
|
Julian Brunner; Britta Maier; Sabrina L. J. Thomä; Felizitas Kirner; Igor Baburin; Dmitry Lapkin; Rose Rosenberg; Sebastian Sturm; Dameli Assalauova; Jerome Carnis; Young Yong Kim; Zhe Ren; Fabian Westermeier; Sebastian Theiss; Horst Borrmann; Sebastian Polarz; Alexander Eychmüller; Axel Lubk; Ivan Vartanyants; Helmut Cölfen; Mirijam Zobel; Elena Sturm; Elena Sturm (née Rosseeva)
|
Nanostructured Materials - Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-06-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc9bdbb89f789a37b7a/original/morphogenesis-of-magnetite-mesocrystals-interplay-between-nanoparticle-morphology-and-solvation-shell.pdf
|
679bd448fa469535b9795471
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10.26434/chemrxiv-2025-2v2p7
|
Statistical Analysis of the Dynamic Behavior of Individual Discharges During the Ignition and Continuous Phases of Contact Glow Discharge Electrolysis
|
Contact Glow Discharge Electrolysis (CGDE) denotes a plasma inside a vapor layer surrounding a gas-evolving electrode immersed in an aqueous electrolyte and operated at high voltages. We used a high-speed camera to image the formation of the vapor layer as well as its dynamic behavior during continuous CGDE on a Au wire cathode. The plasma ignites with a spark within a large bubble at the tip, which expands along the wire to the top, leaving a stable glow within the vapor layer behind. Using an in-house developed open-source Python-based software we deduced, from a thorough statistical analysis of images taken during continuous CGDE, a vapor layer thickness between 0.1 and 0.4 mm. Furthermore, we provide information on the dynamic behavior of individual discharges through the vapor layer from a series of images. The discharges are confined within the vapor layer and, thus, the extent of the discharges is similar to the vapor layer thickness. We find that the discharges have approximately the shape of oblate spheroids, which appear either as circles or ellipses in the camera images, depending on the orientation of the discharge with respect to the camera. We discuss the relevance of our results for the fundamental understanding of atomic scale surface structural changes and products formed in the solution in the presence of the plasma.
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Lukas Forschner; Jan-Luca Gembus; Lars Schücke; Peter Awakowicz; Andrew R. Gibson; Timo Jacob; Albert Kilian Engstfeld
|
Physical Chemistry; Materials Science; Catalysis; Interfaces; Physical and Chemical Properties
|
CC BY 4.0
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CHEMRXIV
|
2025-02-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679bd448fa469535b9795471/original/statistical-analysis-of-the-dynamic-behavior-of-individual-discharges-during-the-ignition-and-continuous-phases-of-contact-glow-discharge-electrolysis.pdf
|
60c7548a567dfeb605ec60bd
|
10.26434/chemrxiv.13674277.v1
|
Stability of Calcium Ion Battery Electrolytes: Predictions from Ab Initio Molecular Dynamics Simulations
|
<p>Multivalent
batteries, such as magnesium-ion, calcium-ion, and zinc-ion batteries, have
attracted significant attention as next-generation electrochemical energy
storage devices to complement conventional lithium-ion batteries (LIBs). Among
them, calcium-ion batteries (CIBs) are the least explored due to the difficult
reversible Ca deposition-dissolution. In this work, we examined the stability
of four different Ca salts with weakly coordinating anions and three different
solvents commonly employed in existing battery technologies to identify
suitable candidates for CIBs. By employing Born-Oppenheimer molecular dynamics
(BOMD) simulations on salt-Ca and solvent-Ca interfaces, we find that the
tetraglyme solvent and carborane salt are promising candidates for CIBs. Due to
the strong reducing nature of the calcium surface, the other salts and solvents
readily decompose. We explain the microscopic mechanisms of salt/solvent
decomposition on the Ca surface using time-dependent projected density of
states, time-dependent charge-transfer plots, and climbing-image nudged elastic
band calculations. Collectively, this work presents the first mechanistic
assessment of the dynamical stability of candidate salts and solvents on a Ca
surface using BOMD simulations, and provides a predictive path toward designing
stable electrolytes for CIBs. </p>
<p> </p>
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Sharma Yamijala; Hyuna Kwon; Juchen Guo; Bryan Wong
|
Fuels - Materials; Computational Chemistry and Modeling; Theory - Computational; Reaction Engineering; Electrochemistry - Organometallic; Kinetics and Mechanism - Organometallic Reactions; Energy Storage; Fuels - Energy Science; Fuel Cells; Electrochemistry - Mechanisms, Theory & Study; Physical and Chemical Processes; Physical and Chemical Properties; Quantum Mechanics; Solution Chemistry; Structure; Surface; Thermodynamics (Physical Chem.); Materials Chemistry
|
CC BY NC ND 4.0
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CHEMRXIV
|
2021-02-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7548a567dfeb605ec60bd/original/stability-of-calcium-ion-battery-electrolytes-predictions-from-ab-initio-molecular-dynamics-simulations.pdf
|
60c751fe567dfe5f0eec5b7b
|
10.26434/chemrxiv.13238708.v1
|
Brittle Behaviour in Aspirin Crystals: Evidence of Spalling Fracture
|
<div>
<div>
<div>
<p>Single crystals of aspirin form I were cleaved and indented on their dominant face. Upon
inspection, it was possible to observe strongly anisotropic shallow lateral cracks due to the
extreme low surface roughness after cleavage. Atomic Force Microscopy (AFM) imaging
showed spalling fractures nucleating from the indent corners, forming terraces with a height
of one or two interplanar spacings d100. The formation of such spalling fractures in aspirin was
rationalised using basic calculations of attachment energies, showing how (100) layers are
poorly bonded when compared to their relatively higher intralayer bonding. An attempt at
explaining the preferential propagation of these fractures along the [010] direction is
discussed.
</p>
</div>
</div>
</div>
|
Benjamin
P. A. Gabriele; Craig J. Williams; Douglas Stauffer; Brian Derby; Aurora J. Cruz-Cabeza
|
Physical Organic Chemistry; Nanostructured Materials - Materials; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-11-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751fe567dfe5f0eec5b7b/original/brittle-behaviour-in-aspirin-crystals-evidence-of-spalling-fracture.pdf
|
66fac76151558a15ef9a0bb2
|
10.26434/chemrxiv-2024-45x6c
|
Development of ionically crosslinked network in metal oxide based carboxylated acrylonitrile butadiene copolymer with self-healing characteristics
|
Ionic clusters produced during the crosslinking of elastomers with zinc oxide influence the overall mechanical performance of ionic elastomers such as carboxylated nitrile rubber (XNBR). The composition of these ionic aggregates is investigated for the first time in this work by maintaining time as variable and other factors constant. Lower temperature healing properties by formation of ionic crosslink has been observed. Detailed analysis by Fourier Transform Infrared spectroscopy revealed that interaction between Zn2+ and COO1- actually affects the bonding structures and Universal Testing Machine proved that ionic crosslink shows better healing efficiency than a combination of covalent and ionic crosslink due to sulphur and zinc oxide, for the first time. The inability to heal the rubber compound at all due to the presence of Carbon Black filler was also observed for the first time.
|
ADRINEEL ROY
|
Polymer Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fac76151558a15ef9a0bb2/original/development-of-ionically-crosslinked-network-in-metal-oxide-based-carboxylated-acrylonitrile-butadiene-copolymer-with-self-healing-characteristics.pdf
|
66bdc06020ac769e5faa23be
|
10.26434/chemrxiv-2024-w8nbl
|
Discovering Covalent Cyclic Peptide Inhibitors of Peptidyl Arginine Deiminase 4 (PADI4) Using mRNA-Display with a Genetically Encoded Electrophilic Warhead
|
Covalent drugs can achieve high potency with long dosing intervals. However, concerns remain about side-effects associated with off-target reactivity. Combining macrocyclic peptides with covalent warheads provides a solution to minimise off-target reactivity: the peptide enables highly specific target binding, positioning a weakly reactive warhead proximal to a suitable residue in the target. Here we demonstrate direct discovery of covalent cyclic peptides using encoded libraries containing a weakly electrophilic cysteine-reactive fluoroamidine warhead. We combine direct incorporation of the warhead into peptide libraries using the flexible in vitro translation system with a peptide selection approach that identifies only covalent target binders. Using this approach, we identify potent covalent inhibitors of the peptidyl arginine deiminase, PADI4 or PAD4, that react exclusively at the active site cysteine. We envisage this approach will enable covalent peptide inhibitor discovery for a range of related enzymes and expansion to alternative warheads in the future.
|
Isabel Mathiesen; Ewen Calder; Simone Kunzelmann; Louise Walport
|
Biological and Medicinal Chemistry; Organic Chemistry; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems
|
CC BY 4.0
|
CHEMRXIV
|
2024-08-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66bdc06020ac769e5faa23be/original/discovering-covalent-cyclic-peptide-inhibitors-of-peptidyl-arginine-deiminase-4-padi4-using-m-rna-display-with-a-genetically-encoded-electrophilic-warhead.pdf
|
6267bac6ef2ade6be73db71b
|
10.26434/chemrxiv-2022-h2g6d
|
Halide Perovskites as Disposable Epitaxial Templates for the Phase-Selective Synthesis of Lead Sulfochloride Nanocrystals
|
Colloidal chemistry grants access to a wealth of materials through simple and mild reactions. However, even few elements can combine in a variety of stoichiometries and structures, potentially resulting in impurities or even wrong products. Similar issues have been long addressed in organic chemistry by using reaction-directing groups, that are added to a substrate to promote a specific product and are later removed. Inspired by such approach, we demonstrate the use of CsPbCl3 perovskite nanocrystals to drive the phase-selective synthesis of two novel lead sulfochlorides: Pb3S2Cl2 and Pb4S3Cl2. When homogeneously nucleated in solution, lead sulfochlorides form Pb3S2Cl2 nanocrystals. Conversely, the presence of CsPbCl3 triggers the formation of Pb4S3Cl2/CsPbCl3 epitaxial heterostructures. The phase selectivity is guaranteed by the continuity of the cationic subnetwork across the interface, a condition not met in a hypothetical Pb3S2Cl2/CsPbCl3 heterostructure. The perovskite domain is then etched, delivering phase-pure Pb4S3Cl2 nanocrystals that could not be synthesized directly.
|
Stefano Toso; Muhammad Imran; Enrico Mugnaioli; Anna Moliterni; Rocco Caliandro; Nadine J. Schrenker; Andrea Pianetti; Juliette Zito; Francesco Zaccaria; Ye Wu; Mauro Gemmi; Cinzia Giannini; Sergio Brovelli; Ivan Infante; Sara Bals; Liberato Manna
|
Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-04-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6267bac6ef2ade6be73db71b/original/halide-perovskites-as-disposable-epitaxial-templates-for-the-phase-selective-synthesis-of-lead-sulfochloride-nanocrystals.pdf
|
60c749d2702a9b7a7918b1ca
|
10.26434/chemrxiv.12108546.v1
|
Battle Against Coronavirus: Repurposing Old Friends (Food Borne Polyphenols) for New Enemy (COVID-19)
|
<p>In
the era of extreme scientific development where the scientific community have
reached beyond moon, the entire world today is facing an immense problem due to
deadly effect of COVID-19 (coronavirus disease), originated in Wuhan.
Coronavirus is having dexterity to target immune compromised people very easily
and swiftly get transmitted to healthy individuals from infected ones.
Coronavirus infections are spreading very rapidly, and almost all the countries
around the world are having corona positive people and asymptomatic carriers. This
pandemic has created havoc both to human health and economy in lack of an
effective treatment against this disease. Due to time limitations and urgency
to find cure for COVID 19 we have undertaken the help of structure assisted
drug design approach which mainly involves virtual screening program which
identifies the structural leads which can target COVID-19 main protease (M<sup>pro</sup>).
This protease is the key enzyme of coronavirus which plays crucial role in
virus replication and transcription, which can be targeted to retard the growth
of virus inside the host. In the
present work, the Phenol explorer database (version 3.6) containing 751
different food borne polyphenols were screened against the (M<sup>pro</sup>) to identify suitable structural leads
with potential to inhibit this protease though High throughput modelling and
molecular docking approach. We identified six potential polyphenols belonging
to Sanguiin, Theaflavin gallate, Theaflavin digallate, Kaempferol,
Punicalagin and Protocatechuic acid chemical classes. All the six polyphenols
have much higher docking scores ≥ -9.8 kcal/mol as compared to peptidomimetic
inhibitor (N3) of COVID 19 virus M<sup>pro</sup>. Pharmacokinetic and Drug
likeness predictions of these polyphenols were done using SwissADME web tool
where Protocatechuic acid shown fairly good results (1 Lipinski violation). The
studies suggest the dietary intake of <b>“<i>black tea</i></b>” can improve the
resistance to fight against COVID 19 virus in early stages of human infection. Importantly though, the enriched subset of six
compounds identified from the larger library has to be validated experimentally. </p>
|
sonam bhatia; Sabeena Giri; Arnica F Lal; Shaminder Singh
|
Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749d2702a9b7a7918b1ca/original/battle-against-coronavirus-repurposing-old-friends-food-borne-polyphenols-for-new-enemy-covid-19.pdf
|
64c7e2099ed5166e93cc7195
|
10.26434/chemrxiv-2023-d22xj-v2
|
Electrochemical Chlor-Iron Process for Iron Production from Iron Oxide and Seawater
|
The iron and steel industry accounts for ~ 8% of global greenhouse gas emissions. Electrochemical reduction of iron ore to metal for electric arc furnaces can enable sustainable steel production, but existing electrochemical processes require expensive capital or electrolytes. We report a low-temperature, electrochemical cell that consumes low-cost and abundant iron oxide and seawater, while co-producing NaOH and Cl2 with industrially relevant current densities reaching 300 mA cm-2 and current efficiencies >90 %. Freestanding films of phase-pure iron were formed after 4 h of continuous, stable electrolysis. The process can lead to levelized costs of iron that are competitive with iron produced in fossil-fuel-powered blast furnaces (< $500 per metric tonne) and the co-produced NaOH can be used for CO2 mineralization from the air or ocean, creating a net negative-emission process.
|
Berkley Noble; Louka Moutarlier; Paul Kempler
|
Materials Science; Energy; Chemical Engineering and Industrial Chemistry; Materials Processing; Industrial Manufacturing; Reaction Engineering
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-08-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c7e2099ed5166e93cc7195/original/electrochemical-chlor-iron-process-for-iron-production-from-iron-oxide-and-seawater.pdf
|
62d960575819878ab74a7b2b
|
10.26434/chemrxiv-2022-tlczl
|
Total Synthesis of Peshawaraquinone
|
A concise synthesis of a stereochemically complex meroterpenoid, peshawaraquinone, via the unsymmetrical dimerization of its achiral precursor, dehydro-alpha-lapachone, is reported. Enabled by reversible oxa-6pi-electrocyclizations of (2H)-pyran intermediates, the base-catalyzed dimerization sets up an intramolecular (3+2) cycloaddition, with the formation of six stereocenters during the cascade. Combining the synthesis and in situ dimerization of dehydro-alpha-lapachone allows a one-step total synthesis of peshawaraquinone from lawsone and prenal.
|
Tomas de Castro; David Huang; Christopher Sumby; Andrew Lawrence; Jonathan George
|
Organic Chemistry; Natural Products; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-07-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d960575819878ab74a7b2b/original/total-synthesis-of-peshawaraquinone.pdf
|
65304519c3693ca993699513
|
10.26434/chemrxiv-2023-lxlmf
|
A Sensitive Temperature Sensor with a Large Dynamic Spectral Range Based on a Dual-emissive Thermally Activated Delayed Fluorescence Dendrimer System
|
Dual emission from organic thermally activated delayed fluorescence (TADF) emitters is often difficult to observe, especially in the solution-state, because most compounds adhere to Kasha’s rule where emission originates from the lowest energy excited state. Two TADF dendrimers with different rigid and planar N-doped polycyclic aromatic hydrocarbons (PAH) as acceptors were designed and synthesized. By modulating the molecular geometry, compound 2GCzBPN that possesses a strongly twisted geometry exhibits TADF, while 2GCzBPPZ, possessing a less twisted geometry, shows dual emission with an emission peak at 475 nm associated with the monomer and one at 575 nm linked to aggregates that is TADF. This dual emission is both concentration-dependent and temperature-dependent in solution. This is the first observation of aggregate emission from TADF dendrimers in solution. The control of the contributions from intramolecular and intermolecular charge-transfer states permits a wide color tuning from sky blue through white to yellow light emission. We demonstrate how 2GCzBPPZ can serve as a temperature sensor and exhibits excellent temperature sensitivity across a very wide temperature range (70 °C to 70 °C) in n-hexane, accompanied by a significant spectral response, ranging from yellow to white, and then blue emission, which is the widest detected temperature range and color response reported for an organic luminescent material in solution and also to the best of our knowledge the first small molecule TADF compound used for colorimetric temperature sensing. By embedding 2GCzBPPZ into paraffin, we demonstrated a spatio-temperature sensor that showed a noticeable emission shift from yellow to green and ultimately to blue as the temperature increased from 20 °C to 200 °C. Finally, solution-processed organic light-emitting diodes (OLEDs) using these two dendrimer emitters showed divergent performance, with a three-times higher maximum external quantum efficiency (EQEmax) of 15.0% for the device with 2GCzBPPZ compared to the device with 2GCzBPN (5.3%).
|
Changfeng Si; Dianming Sun; Eli Zysman-Colman
|
Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Spectroscopy (Physical Chem.); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65304519c3693ca993699513/original/a-sensitive-temperature-sensor-with-a-large-dynamic-spectral-range-based-on-a-dual-emissive-thermally-activated-delayed-fluorescence-dendrimer-system.pdf
|
66e96d7f12ff75c3a198c983
|
10.26434/chemrxiv-2024-5dk2f
|
Effect of minor differences in sequences of huntingtin peptides on their interactions with sucrose and trehalose: in silico investigation
|
In this work the behavior of two Huntingtin (Htt) peptides in mixtures with water and either sucrose or trehalose were investigated by classical molecular dynamics (MD) simulations. Structures of those peptides are listed in the Protein Databank as 2LD2 (Biophys. J., 2013, 105, 699-710) and 6N8C (Proc. Natl. Acad. Sci., 2019, 116, 9, 3562-3571). The principal difference between those peptides is in their C- and N-terminals. Since Huntington’s disease is related to the aggregation of proteins containing consecutive polyglutamine in their amino acid chains, the aim was to investigate if smaller amounts of disaccharides could reduce aggregation of two peptides from the Htt protein. Computational results revealed that both sugars alter the secondary structures of peptides and decrease the total number of contacts (the sum of hydrophobic contacts and hydrogen bonds) between these biomolecules. However, regarding only the number of hydrogen bonds, the disaccharides reduced this value for peptide-peptide interactions for 6N8C, while for 2LD2 sucrose and trehalose instead promoted an increase of this number. Such a difference in behaviors of peptides could be related to dissimilarities in their sequences, pointing out the importance to consider amino-acid residues in C- and N-terminal when developing drugs. Furthermore, both disaccharides demonstrated abilities to slow down the dynamics of simulated mixtures, which was concluded from rotational correlation and self-intermediate scattering functions. Amino-acid residues MET(1), GLU(5), LYS(6), LYS(9), GLU(12), LYS(15), PHE(17) and GLN(18) are identified as the main candidate amino acids involved in interpeptide binding and binding to disaccharides, where the glutamic acid residues (GLU(5) and GLU(12)) had the highest number of hydrogen bonds with sucrose and trehalose.
|
Inna Ermilova; Linnea Ögren; Olivia Borg; Maria Weber; Elinor Einarsson; Erik Podda Grahn; Jan Swenson
|
Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-09-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e96d7f12ff75c3a198c983/original/effect-of-minor-differences-in-sequences-of-huntingtin-peptides-on-their-interactions-with-sucrose-and-trehalose-in-silico-investigation.pdf
|
60c74720f96a0077e1286e85
|
10.26434/chemrxiv.11536392.v1
|
σ-Bond Hydroboration of Cyclopropanes
|
Hydroboration of alkenes is a classical reaction in organic synthesis, in which alkenes react with boranes to give alkylboranes, with subsequent oxidation resulting in alcohols. The double bond (π-bond) of alkenes can be readily reacted with boranes owing to its high reactivity. However, the single bond (σ-bond) of alkanes has never been reacted. To pursue the development of σ-bond cleavage, we selected cyclopropanes as model substrates since they present a relatively weak σ-bond. Herein, we describe an iridium-catalyzed hydroboration of cyclopropanes, resulting in β-methyl alkylboronates. These unusually branched boronates can be derivatized by oxidation or cross-coupling chemistry, accessing “designer” products that are desired by practitioners of natural product synthesis and medicinal chemistry. Furthermore, mechanistic investigations and theoretical studies revealed the enabling role of the catalyst.
|
Hiroki Kondo; Shin Miyamura; Chisa Kobayashi; Arifin; Stephan Irle; Kenichiro Itami; Daisuke Yokogawa; Junichiro Yamaguchi
|
Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-01-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74720f96a0077e1286e85/original/bond-hydroboration-of-cyclopropanes.pdf
|
6629a1bc418a5379b0a3c829
|
10.26434/chemrxiv-2024-5fwnd
|
Fluorescence imaging using deep-red Indocyanine Blue (ICB) a complementary partner for near infrared Indocyanine Green (ICG)
|
Indocyanine Blue (ICB) is the deep-red, pentamethine analogue of the widely used clinical near-infrared heptamethine cyanine dye, Indocyanine Green (ICG). The two fluorophores have the same number of functional groups and molecular charge and vary only by a single vinylene unit in the polymethine chain which produces a predictable difference in spectral and physicochemical properties. We find that the two dyes can be employed as a complementary pair in diverse types of fundamental and applied fluorescence imaging experiments. A fundamental fluorescence spectroscopy study used ICB and ICG to test a recently proposed FRET mechanism for enhanced fluorescence brightness in heavy water (D2O). The results support two important corollaries of the proposal, (a) the strategy of using heavy water to increase the brightness of fluorescent dyes for microscopy or imaging is most effective when the dye emission band is above 650 nm, and (b) the magnitude of the heavy water florescence enhancement effect for near-infrared ICG is substantially diminished when the ICG surface is dehydrated due to binding by albumin protein. Two applied fluorescence imaging studies demonstrated how deep-red ICB can be combined with a near-infrared fluorophore for paired agent imaging in the same living subject. One study used dual-channel mouse imaging to visualize increased blood flow in a model of inflamed tissue, and a second mouse tumor imaging study simultaneously visualized the vasculature and cancerous tissue in separate fluorescence channels. The results suggest that ICB and ICG can be incorporated within multicolor fluorescence imaging methods for perfusion imaging and hemodynamic characterization in a wide range of diseases.
|
Rananjaya Gamage; Bradley Smith
|
Biological and Medicinal Chemistry; Chemical Biology
|
CC BY 4.0
|
CHEMRXIV
|
2024-04-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6629a1bc418a5379b0a3c829/original/fluorescence-imaging-using-deep-red-indocyanine-blue-icb-a-complementary-partner-for-near-infrared-indocyanine-green-icg.pdf
|
66ba1d4a01103d79c5bda60a
|
10.26434/chemrxiv-2024-lwpz2
|
High-Throughput Automated Data Analysis workflow for ADC Biotransformation Characterization
|
Antibody-drug conjugates (ADCs) have garnered renewed attention after decades of research to fine-tune their components, maximizing efficacy while minimizing toxicity. Understanding structural integrity of ADCs in vivo is critical for lead optimization. Despite of its importance, currently ADC biotransformation has not been broadly studied. High resolution accurate mass data analysis of biotransformed products has been a major bottleneck because of manual and time-consuming analyte identification process which can take days to weeks of analysis time by expert users. We developed a streamlined data analysis workflow that enables automated peak identification using various commercial software tools significantly improving data processing efficiency. A linker-payload biotransformation library was created for each new molecule and then combined with antibody sequence information for peak matching. As a proof of concept, we tested this workflow across different payload and linker types: an example using a topoisomerase I inhibitor-conjugated ADC and a comparison to a historical in vivo ADC biotransformation dataset for a pyrrolobenzodiazepine-conjugated ADC. Using this automated workflow, we were able to rapidly identify major biotransformation species that were previously found manually including loss of linker-payload, maleimide ring hydrolysis, cysteinylation at deconjugated site and partial linker-payload cleavage. Overall, this improved data-analysis workflow has demonstrated its superb effectiveness in streamlining ADC biotransformation identification and enabled quantification that was highly comparable to previously obtained results, thus demonstrating its comparability. This advancement can now positively impact drug development by substantially reducing data analysis time thus enabling faster design-test-analyze cycle times which are critical in early drug discovery setting.
|
Kate Liu; Yongling Ai; Hui Yin Tan; Jiaqi Yuan; John K. Meissen; Yue Huang; Anton I. Rosenbaum
|
Analytical Chemistry; Chemoinformatics; Mass Spectrometry
|
CC BY 4.0
|
CHEMRXIV
|
2024-08-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ba1d4a01103d79c5bda60a/original/high-throughput-automated-data-analysis-workflow-for-adc-biotransformation-characterization.pdf
|
634fe8853e8d99ef08204c71
|
10.26434/chemrxiv-2022-vtj1s
|
Solar E→Z photoisomerization of azo switches
|
By absorbing light energy, molecular photoswitches can undergo structural changes, store chemical energy, and perform dynamic work, which has profound impacts on the development of stimuli-responsive systems, energy storage/conversion materials, artificial molecular machines, etc. Developing photoswitches that can be fueled by natural sunlight will bring great benefits to their applications in the context of carbon neutrality. Here, we show that solar photoswitching can be realized by reshaping the absorption spectral profile, i.e., rendering the absorption of parent isomer overwhelmingly stronger than that of metastable isomer across the UV–Vis spectra. Solar E→Z photoisomerization of azo molecules—the most widely used class of photoswitches—are achieved by implementing this spectral tuning principle. A simple yet tunable molecular design strategy to meet this spectral requirement is established and a variety of solar photoisomerizable heteroaryl-based azo-switches are developed. Photoswitching under natural sunlight in place of the traditional artificial lights represents a crucial step towards sustainable light-driven processes.
|
Zhao-Yang Zhang; Dongfang Dong; Tongtong Dang; Tao Li
|
Physical Chemistry; Photochemistry (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634fe8853e8d99ef08204c71/original/solar-e-z-photoisomerization-of-azo-switches.pdf
|
6164b87aa3d2c9f436d3a6ec
|
10.26434/chemrxiv-2021-lnbml-v2
|
Capillaric - Field Effect Transistors
|
Controling fluid flow in capillaric circuits is a key requirement to increase their uptake for assay applications. Capillary action off-valves provide such functionality by pushing an occluding bubble into the channel using a difference in capillary pressure. Previously, we utilised the binary switching mode of this structure to develop a powerful set of fundamental fluidic valving operations. In this work we provide evidence that these structures are in fact functionally complementary to electronic Junction Field Effect Transistors and thus warrant the use of the new term of capillaric- Field Effect Transistor to describe these types of valves. To support this conclusion, we present a theoretical description, experimental characterisation, and practical application of analog flow resistance control. In addition, we demonstrate that the valves can also be re-opened. These are two key capabilities previously missing for a full analogy to electronic transistors. We show modulation of the flow resistance from fully open to pinch-off, determine the flow rate – trigger channel volume relationship and demonstrate that the latter can be modelled using Shockley’s equation for electronic transistors. Finally, we provide a first example of how the valves can be opened and closed repeatedly.
|
Robert Claude Meffan; Julian Menges; Fabian Dolamore; Daniel Mak; Conan Fee; Renwick Dobson; Volker Nock
|
Analytical Chemistry; Analytical Apparatus
|
CC BY NC 4.0
|
CHEMRXIV
|
2021-10-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6164b87aa3d2c9f436d3a6ec/original/capillaric-field-effect-transistors.pdf
|
66d23e4820ac769e5f665f23
|
10.26434/chemrxiv-2024-f54pl
|
Proving the Potential: External Validation of STopTox as in Silico Alternative to Animal Toxicity Testing
|
Over the past several decades, reducing, refining, and replacing animal testing (three R’s) has been a prominent goal in chemical toxicology.1 The STopTox (Systemic and Topical chemical Toxicity) platform was developed for this objective as an innovative in-silico alternative to conventional animal testing for acute systemic and topical toxicity testing.2 STopTox utilizes quantitative structure-activity relationship (QSAR) models to predict the toxicity of chemicals, providing a comprehensive, accessible, and user-friendly tool for hazard identification.2 STopTox models were rigorously validated during its initial development using extensive publicly available data sets, ensuring compliance with the Organisation for Economic Co-operation and Development (OECD) principles. These models boasted high internal accuracy and substantial external predictive power.2,3 Despite these promising results, continued validation with novel compounds is integral in establishing the robustness and reliability needed for STopTox to be used as a substitute for in vivo animal testing. In this research letter, we aim to evaluate the predictive performance of STopTox using independent data sets across the six major endpoints of acute toxicity: acute oral, dermal, and inhalation systemic toxicity, as well as skin sensitization, skin irritation/corrosion, and eye irritation/corrosion through external validation. The outcomes of this validation underscore the potential of STopTox to reliably predict toxicity, thereby supporting STopTox as a reliable regulatory decision-making tool that contributes to reducing animal testing in toxicological assessments.
|
Ricardo Scheufen Tieghi; Cleber Melo Filho; Holli-Joi Martin; Jose Teofilo Morera Filho; Tripp LaPratt; Dave Allen; Judy Strickland; Alexander Tropsha; Nicole Kleinstreuer; Eugene Muratov
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Agriculture and Food Chemistry; Bioinformatics and Computational Biology; Artificial Intelligence
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-09-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d23e4820ac769e5f665f23/original/proving-the-potential-external-validation-of-s-top-tox-as-in-silico-alternative-to-animal-toxicity-testing.pdf
|
65faf0d2e9ebbb4db91ba174
|
10.26434/chemrxiv-2024-76633
|
Electrowinning for room-temperature ironmaking: Mapping the electrochemical aqueous iron interface
|
A promising route towards room-temperature ironmaking is electrowinning, where iron ore dissolution is coupled with cation electrodeposition to grow pure iron. However, poor faradaic efficiencies against the hydrogen evolution reaction (HER) is a major bottleneck. To develop a mechanistic picture of this technology, we conduct a first-principles thermodynamic analysis of the Fe110 aqueous electrochemical interface. Constructing a surface Pourbaix diagram, we predict that the iron surface will always drive towards adsorbate coverage. We calculate theoretical overpotentials for terrace and step sites and predict growth at the step sites are likely to dominate. Investigating the hydrogen surface phases we model several hydrogen absorption mechanisms, all of which are predicted to be endothermic. Additionally, for HER we identify step sites as being more reactive than on the terrace, and with competitive limiting potentials to iron plating. The results presented here further motivate electrolyte design towards HER suppression.
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Lance Kavalsky; Venkatasubramanian Viswanathan
|
Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Computational Chemistry and Modeling; Electrochemistry - Mechanisms, Theory & Study; Surface
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-03-21
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65faf0d2e9ebbb4db91ba174/original/electrowinning-for-room-temperature-ironmaking-mapping-the-electrochemical-aqueous-iron-interface.pdf
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60c75739f96a00132b288c20
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10.26434/chemrxiv.14382056.v1
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Multiplexed Small Molecule Ligand Binding Assays by Affinity Labeling and DNA Sequence Analysis
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<p>Small molecule binding assays to target proteins are a core component of drug discovery and development. While a number of assay formats are available, significant drawbacks still remain in cost, sensitivity, and throughput. To improve assays by capitalizing on the power of DNA sequence analysis, we have developed an assay method that combines DNA encoding with split-and-pool sample handling. The approach involves affinity labeling of DNA-linked ligands to a protein target. Critically, the labeling event assesses ligand binding and enables subsequent pooling of several samples. Application of a purifying selection on the pool for protein-labeled DNAs allows detection of ligand binding by quantification of DNA barcodes. We demonstrate the approach in both ligand displacement and direct binding formats and demonstrate its utility in determination of relative ligand affinity, profiling ligand specificity, and high-throughput small molecule screening.</p>
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Bo Cai; Casey Krusemark
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Chemical Biology; Drug Discovery and Drug Delivery Systems
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CC BY NC ND 4.0
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CHEMRXIV
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2021-04-08
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75739f96a00132b288c20/original/multiplexed-small-molecule-ligand-binding-assays-by-affinity-labeling-and-dna-sequence-analysis.pdf
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657552c45bc9fcb5c97b17c9
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10.26434/chemrxiv-2023-q235j-v2
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Ring Opening Metathesis Polymerization (ROMP) of the Dewar Isomer of 1,2-Azaborinine, a B-N Isostere of Benzene
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The successful polymerization of the Dewar isomer of an azaborinine heterocycle is reported. Controlled ring-opening metathesis polymerization was accomplished with Grubbs and Hoveya-Grubbs 2nd generation catalysts (G2, HG2), as well as a Z-selective Ru catalyst (HGM2001). The structure of the polymers containing 4-membered B-N heterocycles was verified by GPC, multinuclear and 2D NMR. Differences in regiochemistry of polymers derived from G2/HG2 versus the Z-selective catalyst HGM2001 were substantiated by 2D NOESY, FT-IR and Raman analyses. The incorporation of B-N heterocycles into these polymer structures is promising as a route to functional polymers that contain polar side groups.
|
Huina Lin; Xinyu Yang; Shih-Yuan Liu; Frieder Jaekle
|
Inorganic Chemistry; Polymer Science; Inorganic Polymers; Main Group Chemistry (Inorg.)
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CC BY 4.0
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CHEMRXIV
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2023-12-11
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657552c45bc9fcb5c97b17c9/original/ring-opening-metathesis-polymerization-romp-of-the-dewar-isomer-of-1-2-azaborinine-a-b-n-isostere-of-benzene.pdf
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61664d298b620d712c4da94e
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10.26434/chemrxiv-2021-h2bmc
|
Multi-State Density Functional Theory for Ground and Excited States
|
We report a rigorous formulation of multi-state density functional theory (MSDFT) that extends
the Kohn-Sham (KS) energy functional for the ground state to a Hamiltonian matrix functional
H[D] of the density matrix D in the space spanned by the lowest N adiabatic states. We establish
a variational principle of MSDFT, which guarantees that the variational optimization results in a
Hamiltonian matrix, whose eigenvalues are the lowest N eigen-energies of the system. We present an
explicit expression of H[D] and introduce the correlation matrix functional. Akin to KS-DFT
for the ground state, a universal multi-state correlation potential is derived for a two-state
system as an illustrative example. This work shows that MSDFT is an exact density functional
theory that treats the ground and excited states on an equal footing and provides a framework for
practical applications and future developments of approximate functionals for excited states.
|
Yangyi Lu; Jiali Gao
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Processes
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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/61664d298b620d712c4da94e/original/multi-state-density-functional-theory-for-ground-and-excited-states.pdf
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60c75300337d6c1ef3e287e8
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10.26434/chemrxiv.13377119.v1
|
Small Molecules to Destabilize the ACE2-RBD Complex: A Molecular Dynamics Study for Potential COVID-19 Therapeutics
|
The ongoing COVID-19 pandemic has infected millions of people, claimed hundreds of thousands of lives, and made a worldwide health emergency. Understanding the SARS-CoV-2 mechanism of infection is crucial in the development of potential therapeutics and vaccines. The infection process is triggered by direct binding of the SARS-CoV-2 receptor-binding domain (RBD) to the host cell receptor, Angiotensin-converting enzyme 2 (ACE2). Many efforts have been made to design or repurpose therapeutics to deactivate RBD or ACE2 and prevent the initial binding. In addition to direct inhibition strategies, small chemical compounds might be able to interfere and destabilize the meta-stable, pre-fusion complex of ACE2-RBD. This approach can be employed to prevent the further progress of virus infection at its early stages. In this study, Molecular docking is employed to analyze the binding of two chemical compounds, SSAA09E2 and Nilotinib, with the druggable pocket of the ACE2-RBD complex. The structural changes as a result of the interference with the ACE2-RBD complex are analyzed by molecular dynamics simulations. Results show that both Nilotinib and SSAA09E2 can induce significant conformational changes in the ACE2-RBD complex, intervene with the hydrogen bonds, and influence the flexibility of proteins. Moreover, essential dynamics analysis suggests that the presence of small molecules can trigger large-scale conformational changes that may destabilize the ACE2-RBD complex.
|
Meghdad Razizadeh; Mehdi Nikfar; Yaling Liu
|
Biochemistry; Bioinformatics and Computational Biology; Biophysics; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
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CHEMRXIV
|
2020-12-16
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75300337d6c1ef3e287e8/original/small-molecules-to-destabilize-the-ace2-rbd-complex-a-molecular-dynamics-study-for-potential-covid-19-therapeutics.pdf
|
66f2f400cec5d6c1421354f9
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10.26434/chemrxiv-2024-k7kn2-v2
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Trogocytosis targeting chimeras (TrogoTACs) for targeted protein transfer
|
Cell surface proteins contribute to cellular identity and mediate a myriad of pathological and normal physiological processes. Multiple induced proximity strategies have emerged to manipulate the cell surface proteome, wherein a protein of interest can be depleted in a targeted manner. These strategies can be applied to diseases marked by the presence of a pathogenic protein. However, many pathologies result from the absence of critical cell surface proteins.1–4 Restoring deficient cell-surface proteins without genetic intervention remains a formidable challenge. We sought to address this problem by exploiting a natural process for cell-to-cell transfer of membrane proteins known as trogocytosis. Here we report the development of Trogocytosis-TArgeting Chimeras (TrogoTACs), bispecific molecules capable of inducing protein transfer between distinct cells. We designed TrogoTACs that bind the B cell receptor CD22 through a synthetic small molecule ligand chemically linked to an antibody that recognizes a cell surface molecule expressed on a target cell. These CD22-targeted TrogoTACs induce cell surface protein transfer from the target cell to B cells by redirecting trogocytosis in a targeted fashion. We show that the process depends on cell-cell contact, expression of CD22, and requires high-affinity CD22 binding. We demonstrate the utility of TrogoTACs across several cell models, achieving efficient transfer of therapeutically relevant proteins such as PD-1, CD25, EGFR, and HER2. Finally, we show that trogocytosed MHC class I can elicit T cell activation and cell killing. This technology offers a new avenue for non-genetic cell surface modification, therapeutic interventions, and a platform for targeted modulation of the cell surface proteome.
|
Nicholas Till; Muthukumar Ramanathan; Kang Yong Loh; Carolyn Bertozzi
|
Biological and Medicinal Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-09-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f2f400cec5d6c1421354f9/original/trogocytosis-targeting-chimeras-trogo-ta-cs-for-targeted-protein-transfer.pdf
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61c534ddf52bc4b626cb9b57
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10.26434/chemrxiv-2021-ds0ml
|
Towards a Quantitative Cartography of the Grain Boundary Energy Landscape: Paths and Correlations
|
We apply a newly developed Voronoi fundamental zone (VFZ) framework to gain insights about grain boundary (GB) structure-property relationships in the five degree-of-freedom (5DOF) space of cubic GBs. We analyze the shape and size of a 5DOF fundamental zone (FZ), molecular statics energy uncertainty, property similarity of GBs that are crystallographically \close" (i.e. correlations), and energy pathways through 5DOF space. Considered together, these insights are important for managing tradeoffs between accuracy, complexity, and design considerations for electron backscatter diffraction/serial sectioning, high-energy diffraction microscopy, molecular statics, and density-functional theory. In terms of the shape and size of a 5DOF FZ, we discover that a FZ is smaller than expected at only ∼65° in the largest principal component. Thus, a 10° difference between two GBs, which may have previously been considered small, is actually quite large. We represent a GB by five transformed Cartesian coordinates equipped with a Euclidean distance metric. Using this representation, we find that the FZ has a low aspect-ratio shape (i.e. width, length, height, etc. are similar) which is important for 5DOF numerical differentiation. Semivariogram and numerical optimization methods reveal that grain boundary energy (GBE) in Ni and Fe are globally correlated within ∼6° to 8° in the grain boundary octonion (GBO) sense (multiply by 2 to convert to misorientation angle). For local correlation lengths of high-symmetry GBs of interest, we notice significant variation relative to global correlation lengths and an inverse relationship with the Brandon criterion. We suggest that property data with no more than ± ∼3 % error and point sets with GBs that are no more than ∼3−4° apart should be used and then paired with high-fidelity interpolation strategies. Finally, in terms of dynamic material behavior, geodesic paths through 5DOF space for Ni suggest that, under appropriate conditions, a certain low-energy Σ7 GB may transform into the frequently observed Σ3 coherent-twin GB which may be interesting to verify by experiment or simulation.
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Sterling G. Baird; Eric R. Homer; David T. Fullwood; Oliver K. Johnson
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Materials Science
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CC BY 4.0
|
CHEMRXIV
|
2021-12-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c534ddf52bc4b626cb9b57/original/towards-a-quantitative-cartography-of-the-grain-boundary-energy-landscape-paths-and-correlations.pdf
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6339f43d114b7ef85125ae10
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10.26434/chemrxiv-2022-8z7rv
|
Direct Detection of Hydrogen Bonds in Supramolecular Systems Using 1H-15N HMQC
|
Hydrogen-bonded supramolecular systems are usually characterized in solution through analysis of NMR data such as complexation induced shifts and nuclear Overhauser effects (nOe). Routine direct detection of hydrogen-bonding particularly in multicomponent mixtures, even with the aid of 2D NMR experiments for full assignment, is more challenging. We describe an elementary rapid 1H-15N HMQC NMR experiment which addresses these challenges without the need for complex pulse sequences. Under readily accessible conditions, (243/263 K, 50 mmol solutions) and natural 15N abundance, un-ambiguous assignment of 15N resonances facilitates direct detection of intra- and intermolecular hydro-gen-bonds in mechanically interlocked structures and quadruply hydrogen-bonded dimers – of dialkylureidopyrimidinones (AUPy), Ureidopyrimidinones (UPy), and diamidonaphthyridines (DAN) – in single or multicomponent mixtures to establish tautomeric configuration, conformation, and, to resolve self-sorted speciation.
|
Michael Jinks; Mark Howard; Federica Rizzi; Stephen Goldup; Andrew Burnett; Wilson Andrew
|
Organic Chemistry; Analytical Chemistry; Supramolecular Chemistry (Org.); Spectroscopy (Anal. Chem.)
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CC BY 4.0
|
CHEMRXIV
|
2022-10-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6339f43d114b7ef85125ae10/original/direct-detection-of-hydrogen-bonds-in-supramolecular-systems-using-1h-15n-hmqc.pdf
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6260533988636cc26019768d
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10.26434/chemrxiv-2022-srqt9
|
Dipolar Heteronuclear Correlation Solid-State NMR Experiments Between Half-Integer Quadrupolar Nuclei: The Case of 11B-17O
|
With 73 % of all NMR-active nuclei being quadrupolar, there is great interest in the development of NMR experiments that can probe the proximity between quadrupolar spins. Here, several pulse sequences for magic angle spinning (MAS) 11B-17O Resonance-Echo Saturation-Pulse DOuble-Resonance (RESPDOR) and dipolar Heteronuclear Multiple Quantum Correlation (D-HMQC) solid-state NMR experiments were investigated. In these pulse sequences, Rotational-Echo Double-Resonance (REDOR) recoupling with central transition (CT) selective 180 pulses were applied to either the 11B or 17O spins to recouple the 11B-17O dipolar interactions. 11B{17O} RESPDOR experiments on model 17O-enriched boronic acids showed that application of dipolar recoupling on the 11B channel yielded more signal dephasing than when recoupling is applied on the 17O channel; however, short effective 11B transverse relaxation time constants (T2’) hinders the acquisition of dephasing curves out to long recoupling durations. Application of REDOR recoupling to 17O spins was found to produce significant dephasing without compromising the 11B T2’. Comparison of experimental 11B{17O} RESPDOR curves to that of numerical simulations enabled the 17O isotopic enrichment to be estimated. 2D 11B{17O} D-HMQC spectra were recorded with either 11B or 17O REDOR recoupling at a variety of radio frequency field conditions. Lastly, 2D 11B{17O} and 23Na{17O} D-HMQC spectra of a 17O-enriched sodium borate glass were acquired to demonstrate the practical application of these heteronuclear correlation experiments to probe structural connectivity between two quadrupolar spins. Importantly, the high-field 2D 11B-17O D-HMQC NMR spectrum revealed two unique 17O sites correlating to 4-coordinate BO4 (B[4]), which were attributed to the expected B[3]-O-B[4] and unexpected B[4]-O-B[4] bridging O atoms. The heteronuclear correlation experiments outlined here should be applicable to a variety of quadrupolar spin pairs.
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Rick Dorn; Alexander Paterson; Ivan Hung; Peter Gor'kov; Austin Thompson; Aaron Sadow; Zhehong Gan; Aaron Rossini
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Physical Chemistry; Catalysis; Spectroscopy (Physical Chem.); Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-04-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6260533988636cc26019768d/original/dipolar-heteronuclear-correlation-solid-state-nmr-experiments-between-half-integer-quadrupolar-nuclei-the-case-of-11b-17o.pdf
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60c74ed59abda27318f8d737
|
10.26434/chemrxiv.12808091.v1
|
Chemically Fueled Transient Geometry Changes in Diphenic Acids
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Transient changes in molecular geometry are key to the function of many important biochemical systems. Here, we show that diphenic acids undergo out-of-equilibrium changes in dihedral angle when reacted with a carbodiimide chemical fuel. Treatment of appropriately functionalized diphenic acids with EDC (<i>N</i>-(3-dimethylaminopropyl)-<i>N</i>′-ethylcarbodiimide hydrochloride) yields the corresponding diphenic anhydrides, reducing the torsional angle about the biaryl bond by approximately 45°, regardless of substitution. In the absence of steric resistance, the reaction is well-described by a simple mechanism; the resulting kinetic parameters can be used to derive important properties of the system, such as yields and lifetimes. The reaction tolerates steric hindrance ortho to the biaryl bond, although the competing formation of (transient) byproducts complicates quantitative analysis.
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Isuru Jayalath; Hehe Wang; Georgia Mantel; Lasith S. Kariyawasam; Scott Hartley
|
Physical Organic Chemistry
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CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ed59abda27318f8d737/original/chemically-fueled-transient-geometry-changes-in-diphenic-acids.pdf
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64c8bdee9ed5166e93d81f43
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10.26434/chemrxiv-2022-8hnrh-v2
|
Homo-BacPROTAC-induced degradation of ClpC1 as a strategy against drug-resistant mycobacteria
|
Antimicrobial resistance is a global health threat that requires development of new treatment concepts. These should not only overcome existing resistance, but be designed to slow down emergence of new resistance mechanisms. Targeted protein degradation, whereby a drug redirects cellular proteolytic machinery towards degrading a specific target, is an emerging concept in drug discovery. We developed proteolysis targeting chimeras active in bacteria (BacPROTACs) that bind to ClpC1, a component of the mycobacterial protein degradation machinery. The anti-Mycobacterium tuberculosis (Mtb) BacPROTACs were derived from cyclomarins, natural products known to bind to ClpC1, which were dimerized resulting in compounds that recruit and degrade ClpC1. The resulting Homo-BacPROTACs reduced levels of endogenous ClpC1 in Mycobacterium smegmatis, as well as displayed minimum inhibitory concentrations in the low micro- to nanomolar range in mycobacterial strains, including multiple drug resistant Mtb isolates. The compounds also killed Mtb resident in macrophages. Thus, Homo-BacPROTACs that degrade ClpC1 represent a different strategy for targeting Mtb and overcoming drug resistance.
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Lukas Junk; Volker Martin Schmiedel; Somraj Guha; Katharina Fischel; Peter Greb; Kristin Schwechel; Violetta Krisilia; Lasse van Geelen; Klaus Rumpel; Parvinder Kaur; Ramya V. Krishnamurthy; Shridhar Narayanan; Christiane Kofink; Andreas Mantoulidis; Philipp Biber; Gerhard Gmaschitz; Uli Kazmaier; Anton Meinhart; Julia Leodolter; David Hoi; Sabryna Junker; Francesca Ester Morreale; Tim Clausen; Rainer Kalscheuer; Harald Weinstabl; Guido Boehmelt
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Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Chemical Biology; Drug Discovery and Drug Delivery Systems
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-08-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c8bdee9ed5166e93d81f43/original/homo-bac-protac-induced-degradation-of-clp-c1-as-a-strategy-against-drug-resistant-mycobacteria.pdf
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6701a41bcec5d6c1424946be
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10.26434/chemrxiv-2024-zvbvw
|
Binary CO2/H2O adsorption on CO2 capture metal-organic frameworks CALF-20, Al-Fumarate and CAU-10H using microscale dynamic column breakthrough
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This study reports the development of a quantitative microscale dynamic column breakthrough instrument to measure the competitive equilibrium loadings of CO2 and H2O isotherms on small quantities (≈ 200 mg) of metal-organic framework (MOF) samples. The binary CO2 and H2O equilibria were measured on CALF-20, Al-Fumarate and CAU-10-H, three MOFs of interest for post-combustion CO2 capture at 30 °C. For Al-Fumarate and CAU-10-H, pure CO2 and H2O competition was measured at 30 °C. For CALF-20, extensive mapping of the impact of CO2 concentration and various water concentrations was performed at 30 °C. All three MOFs feature an S-shape H2O isotherm and a type-I CO2 isotherm. In all three MOFs, the CO2 capacity is generally retained towards the left of the inflection point of the H2O isotherm. Water capacity drops after the inflection point, and the magnitude of the drop depends on the sharpness of the H2O isotherm. On the one hand, for Al-Fumarate and CAU-10-H the H2O isotherm was unaffected by CO2. On the other hand, for CALF-20, the presence of CO2 impacts the H2O water isotherm, extending the relative humidity range over which the CO2 capacity is retained. Using the ideal adsorbed solution theory to predict the binary equilibria revealed deviations from ideality for all three MOFs.
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Noelie Constant; Gwyneth Liske; Shanmuk Ravuru; Anjana Puliyanda; Veronique Pugnet; Alejandro Orsikowsky; Sayali-Ramdas Chavan; Philip Llewellyn; James Sawada; Arvind Rajendran
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Energy; Chemical Engineering and Industrial Chemistry; Thermodynamics (Chem. Eng.); Transport Phenomena (Chem. Eng.); Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-10-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6701a41bcec5d6c1424946be/original/binary-co2-h2o-adsorption-on-co2-capture-metal-organic-frameworks-calf-20-al-fumarate-and-cau-10h-using-microscale-dynamic-column-breakthrough.pdf
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62b991f358b3d609d3611c13
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10.26434/chemrxiv-2022-3c782-v2
|
Regularized CASPT2: an intruder-state-free approach
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In this work we present a new approach to fix the intruder state problem (ISP) in CASPT2 based on σp regularization. The resulting $σ^p$-CASPT2 method is compared to previous techniques, namely the real and imaginary level shifts, on a theoretical basis and by performing a series of systematic calculations. The analysis is focused on two aspects, the effectiveness of $σ^p$-CASPT2 in removing the ISP and the sensitivity of the approach with respect to the input parameter. We found that σp-CASPT2 compares favorably with respect to previous approaches, and that different versions, $σ^1$-CASPT2 and $σ^2$-CASPT2, have different potential application domains. This analysis also reveals the unsuitability of the real level shift technique as a general way to avoid the intruder state problem.
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Stefano Battaglia; Lina Fransén; Ignacio Fdez. Galván; Roland Lindh
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational
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CC BY 4.0
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CHEMRXIV
|
2022-06-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b991f358b3d609d3611c13/original/regularized-caspt2-an-intruder-state-free-approach.pdf
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67bd5057fa469535b9ceadf7
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10.26434/chemrxiv-2025-np2hv
|
Rh-catalyzed mechanochemical transfer hydrogenation for the synthesis of periphery-hydrogenated polycyclic aromatic compounds
|
Hydrogenated nanographene has attracted attention as a new class of nanocarbon material owing to its potential applications in various research fields. However, the synthesis of periphery-hydrogenated nanographenes or polycyclic aromatic hydrocarbons (PAHs) is a significant challenge because of the harsh conditions and poor solubility of the starting materials. Conventional solution-state conditions require high-pressure hydrogen gas and a lengthy reaction time. In this study, we developed a novel approach utilizing rhodium-catalyzed mechanochemical transfer hydrogenation, which enables hydrogenation without using hydrogen gas. Various hydrogenated PAHs were rapidly obtained using a simple protocol under ambient atmosphere and air, with one PAH showcasing intriguing properties such as aggregation-induced emission. Thus, the demonstrated mechanochemical hydrogenation method is expected to contribute to the rapid and efficient synthesis of a novel class of sp2/sp3-carbon-conjugated hydrocarbons.
|
Yoshifumi Toyama; Takumu Nakamura; Yushin Horikawa; Yuta Morinaka; Yohei Ono; Akiko Yagi; Kenichiro Itami; Hideto Ito
|
Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Heterogeneous Catalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2025-02-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bd5057fa469535b9ceadf7/original/rh-catalyzed-mechanochemical-transfer-hydrogenation-for-the-synthesis-of-periphery-hydrogenated-polycyclic-aromatic-compounds.pdf
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611a30b04cb479b8843032b9
|
10.26434/chemrxiv-2021-2930x
|
Self-assembled Structures Formed by Fmoc modified aliphatic amino acids
|
We report the self-assembled structures formed by Fmoc modified aliphatic uncharged single amino acids. The self-assembling properties of (((9H-fluoren-9-yl)methoxy)carbonyl)-L-alanine (Fmoc-Ala-OH), (((9H-fluoren-9-yl)methoxy)carbonyl)-L-leucine (Fmoc-Leu-OH), (((9H-fluoren-9-yl)methoxy)carbonyl)-L-isoleucine (Fmoc-Ile-OH), and (((9H-fluoren-9-yl)methoxy)carbonyl)-L-valine (Fmoc-Val-OH) were studied under varying conditions such as concentration and temperature. Fmoc-Ala-OH shows flower-like self-assembled structure at both low and high concentration under room temperature as well as on heating at 70ºC. We also studied self-assembly of the modified branched chain amino acids (BCAA) i.e. Fmoc-Leu-OH, Fmoc-Ile-OH, and Fmoc-Val-OH. Fmoc-Leu-OH forms flower-like morphology at both low and high concentration under room temperature which changes to small tube-like structure on heating. Fmoc-Ile-OH on the other hand shows fibres-like self-assembly at lower and higher concentration at room temperature. While, on heating at lower concentration they formed a tube like self-assembled structure and at higher concentration they formed a fibres-like morphology. In the case of Fmoc-Val-OH they form a flower-like morphology at lower concentration at room temperature and at higher concentration they formed fibres-like assembly at room temperature. On the other hand, on heating Fmoc-Val-OH shows a fibres-like assembly at lower and higher concentration. Once the self-assembled structure of all Fmoc single amino acid characterized through the optical microscopy then our future aims to characterized those self-assembled structure through sophisticated microscopy and spectroscopy techniques and understand the mechanisms of self-assembled structure. Hence, the modified amino acids may pave the way for the design of novel self-assembled architectures which can be controllable manipulated to impart desired function..
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Nidhi Gour; Bharti Koshti; Soumick Naskar; Vivekshinh Kshtriya; Hanuman Narode
|
Biological and Medicinal Chemistry; Organic Chemistry; Nanoscience; Bioorganic Chemistry; Nanofabrication; Chemical Biology
|
CC BY NC ND 4.0
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CHEMRXIV
|
2021-08-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611a30b04cb479b8843032b9/original/self-assembled-structures-formed-by-fmoc-modified-aliphatic-amino-acids.pdf
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64a41894ba3e99daef7f16f0
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10.26434/chemrxiv-2023-qxlgg
|
Towards Copper(I) Clusters for Photo-Induced Oxidation of Biological Thiols in Living Cells
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The cell redox balance can be disrupted by the oxidation of biological peptides and lead to the cell death, which paves the way for a new class of cytotoxic drugs. With the aim of developing compounds capable of specifically inducing fatal redox reactions upon irradiation, we have developed a library of copper compounds. This metal is abundant and considered essential for human health, making it particularly attractive for the development of new anticancer drugs. Copper(I) clusters with thiol ligands (including 5 novel ones) have been synthesized and characterized. Structures were elucidated by X-ray diffraction and show that the compounds are oligomeric clusters. The clusters display high photooxidation capacity towards cysteine – an essential amino acid – upon irradiation in the visible range (450 nm), while remaining completely inactive in the dark. This photoredox activity against a biological thiol was very encouraging for the development of an anticancer photoredox drug. However, the in vitro assay on murine cancer cells did not show any toxicity – whether in the dark or when exposed to 450 nm light, likely because of the poor solubility of the complexes in biological medium.
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Lisa Gourdon-Grünewaldt; Olivier Blacque; Gilles Gasser; Kevin Cariou
|
Biological and Medicinal Chemistry; Inorganic Chemistry; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-07-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a41894ba3e99daef7f16f0/original/towards-copper-i-clusters-for-photo-induced-oxidation-of-biological-thiols-in-living-cells.pdf
|
65f83fc966c13817293c98ab
|
10.26434/chemrxiv-2024-mfkpv
|
Solar light CO2 photoreduction enhancement by mononuclear rhenium(I) complexes: Characterization and mechanistic insights
|
The photocatalytic efficacy of a novel mononuclear rhenium(I) complex in CO2 reduction is remarkable, with a turnover number (TONCO) of 1517 in three hours, significantly outperforming previous Re(I) catalysts. This complex, synthesized via a substitution reaction on an aromatic ring to form a bromo-bipyridine derivative, L1 = 2-Bromo-6-(1H-pyrazol-1-yl)pyridine, and further reacting with [Re(CO)5Cl], results in the facial-tricarbonyl complex [ReL1(CO)3Cl] (1). The light green solid was obtained with an 80% yield and thoroughly characterized using cyclic voltammetry, NMR, FTIR and UV-vis spectroscopy. Cyclic voltammetry under CO2 atmosphere revealed three distinct redox processes, suggesting the formation of new electroactive compounds. The studies on photoreduction highlighted the ability of the catalyst to reduce CO2, while NMR, FTIR, and ESI mass spectrometry provided insights into the mechanism, revealing the formation of solvent-coordinated complexes and new species under varying conditions. Additionally, computational studies (DFT) were undertaken to better understand the electronic structure and reactivity patterns of 1, focusing on the role of the ligand, spectroscopic features, and redox behavior. This comprehensive approach provides insights on the intricate dynamics of CO2 photoreduction, showcasing the potential of Re(I) complexes in catalysis.
|
Marcos Bento; Nuno Bandeira; Haralampos Miras; Artur Moro; João Carlos Lima; Sara Realista; Michael Gleeson; Edwin Devid; Paula Brandão; João Rocha; Paulo Martinho
|
Inorganic Chemistry; Catalysis; Coordination Chemistry (Inorg.); Photocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f83fc966c13817293c98ab/original/solar-light-co2-photoreduction-enhancement-by-mononuclear-rhenium-i-complexes-characterization-and-mechanistic-insights.pdf
|
6321665f0429d6bbca9ddf8d
|
10.26434/chemrxiv-2022-mxtb3-v3
|
Mitigating the non-specific rolling circle amplification: a comprehensive assessment of the role of ligation and digestion methods
|
Rolling circle amplification (RCA) has been utilized for detecting a diverse range of analytes, molecular pathways, and in cellular imaging. However, non-specific amplification (NSA, amplification in absence of a target analyte) in RCA assays, especially those involving pre-synthesized circular DNA (cDNA), affects its sensitivity and specificity. NSA could originate from inefficient ligation or the succeeding cDNA purification steps. To quantify the NSA in RCA here, cDNA substrates were prepared using either self-annealing, splint-padlock, or cohesive end ligations. The cDNAs were then each subjected to nine different exonuclease digestion steps and quantified for NSA under both linear and hyperbranched RCA conditions. We investigated buffer composition, divalent ion concentration, single or dual enzyme digestion, overhang length in cohesive end ligation, and splint length in splint-padlock ligation. When applied in tandem, the conditions successfully mitigated the NSA end-fluorescence 30 – 100 fold while reducing the relative NSA (with respect to primer assisted RCA) to ~5%. Besides understanding the mechanistic origin of NSA, novel aspects of enzyme-substrate selectivity, buffer composition, and the role of divalent ions in enzyme activity were discovered. With increasing analytical applications, this study will help standardize NSA-free RCA assays involving pre-synthesized cDNA.
|
Vandana Kuttappan Nair; Chandrika Sharma; Souradyuti Ghosh
|
Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Chemistry - General; Biochemistry; Chemical Biology
|
CC BY 4.0
|
CHEMRXIV
|
2022-09-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6321665f0429d6bbca9ddf8d/original/mitigating-the-non-specific-rolling-circle-amplification-a-comprehensive-assessment-of-the-role-of-ligation-and-digestion-methods.pdf
|
62f2bb1e1ea5f644e76e8b05
|
10.26434/chemrxiv-2022-4c5q9-v2
|
Conformational dynamics of mCherry variants: a link between sidechain motions and fluorescence brightness
|
We recently developed the red fluorescent protein (RFP) mCherry-XL, which is threefold brighter than its predecessor, mCherry, with a directed evolution approach using fluorescence-lifetime flow cytometry selections. The enhanced brightness is due to a significant decrease in the non-radiative decay rate underlying its increase in fluorescence quantum yield. To examine the dynamic role of the four mutations that distinguish the two RFPs and closely-related variants, we employed microsecond-timescale, all-atom molecular dynamics simulations to sample their ground state conformational landscapes. The simulations revealed the significance of the I197R mutation, which leads to the formation of multiple hydrogen-bonded contacts. The triad of interactions observed between residues K70, E148 and 197R is also seen in mScarlet, another RFP of unrelated origin, but of comparably high brightness. These substitutions in mCherry-XL increased the rigidity of the β-barrel, for example as shown by increased hydrogen-bonding in the chromophore region and decreased root-mean-square backbone deviations. Furthermore, mCherry-XL showed significantly less ns-timescale breathing of the gap between β-7 and β-10 strands. This gap was previously shown to be the most flexible region of mCherry, permitting entry of O2 into the barrel. We also characterize the role played by the sidechain of residue 161 using a combination of MD simulations and in-vitro experimental characterization. We find this position is critical to the steric interactions that perturb the chromophore electronic structure. MD simulations also help us to recognize a network of hydrogen-bonded interactions between the chromophore, the residue 143, 163 and 59, which can potentially impact the electron distribution of the chromophore. Finally, we shed light on the conformational dynamics of the conserved residues R95 and S146, which are hydrogen bonded to the chromophore, and provide physical insights into the observed photophysics. To the best of our knowledge, this is the first study that evaluates the conformational space for a set of closely related FPs generated by directed evolution.
|
Srijit Mukherjee; Premashis Manna; Nancy Douglas; Prem P. Chapagain; Ralph Jimenez
|
Physical Chemistry; Biophysical Chemistry; Spectroscopy (Physical Chem.); Statistical Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-08-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f2bb1e1ea5f644e76e8b05/original/conformational-dynamics-of-m-cherry-variants-a-link-between-sidechain-motions-and-fluorescence-brightness.pdf
|
60c756d8469df45e66f45393
|
10.26434/chemrxiv.14332589.v1
|
Peptidomimetic Polyurethanes Disrupt Surface Established Bacterial Biofilms and Prevent Biofilm Formation
|
Over
80% of all chronic bacterial infections in humans are associated with biofilms,
which are surface-associated bacterial communities encased within a secreted
exopolysaccharide matrix that can provide resistance to environmental and
chemical insults. Biofilm formation triggers broad adaptive changes in the
bacteria, allowing them to be almost a thousand-fold more resistant to
conventional antibiotic treatments and host immune responses. The failure of
antibiotics to eliminate biofilms leads to persistent chronic infections and
can promote the development of antibiotic-resistant strains. Therefore, there
is an urgent need to develop agents that effectively prevent biofilm formation
and eradicate established biofilms. Herein, we present water-soluble synthetic
peptidomimetic polyurethanes that can disrupt surface established biofilms of <i>Pseudomonas
aeruginosa, Staphylococcus aureus, </i>and <i>Escherichia coli</i>, all of
which show tolerance to the conventional antibiotics polymyxin B and ciprofloxacin.
Furthermore, these polyurethanes prevent bacterial attachment and stimulate
bacterial surface motility to inhibit biofilm formation of both Gram-positive
and Gram-negative bacteria at sub-inhibitory concentrations, without being
toxic to mammalian cells. Our results show that these polyurethanes show
promise as a platform for the development of therapeutics that target biofilms
and modulate surface interactions of bacteria for the treatment of chronic
biofilm-associated infections and as antibiofilm agents.
|
Apoorva Vishwakarma; Francis Dang; Allison Ferrell; Hazel A. Barton; Abraham Joy
|
Biocompatible Materials; Microbiology; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756d8469df45e66f45393/original/peptidomimetic-polyurethanes-disrupt-surface-established-bacterial-biofilms-and-prevent-biofilm-formation.pdf
|
60c74802bb8c1a2bf23dabbc
|
10.26434/chemrxiv.11828928.v1
|
Elimination of Ethylene from Cyclobutyl Groups Characterised by X-ray Crystallography in a Metal-Organic Framework Matrix
|
<p>We herein describe a series of breakthroughs in synthetic and structural chemistry. We have developed a novel strategy for the preparation and atomic-level characterisation of aromatic compounds with vinyl functional groups. Such compounds are highly sought after since they make exceptional polymers. Until now, however, deliberate synthetic methods and precise structural details have eluded researchers. We addressed this challenge by using a metal-organic framework as a matrix to isolate the vinyl groups. Cyclobutyl rings serve as synthetic precursors. The expulsion of ethylene from them delivers the desired compounds. This transformation is unprecedented in the literature. The framework is unperturbed by the high temperature required for thermolysis, which itself is a startling observation. We further show how the inherent reactivity of the vinyl groups can be harnessed to deliver addition products in quantitative yields. The two transformations take place in a single-crystal-to-single-crystal manner without changing the overall network structure of the parent framework. This manuscript defines a new strategy for preparing and studying an important class of compound using site-isolation in a framework matrix. It will thus appeal to synthetic chemists, materials scientists and crystallographers. Looking ahead, there are opportunities for the strategy to be extended to related compounds to produce other sought-after targets.</p>
|
Adil Alkas; Laurine E. S. Friche; Shikeale N. Harris; Shane G. Telfer
|
Hybrid Organic-Inorganic Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-02-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74802bb8c1a2bf23dabbc/original/elimination-of-ethylene-from-cyclobutyl-groups-characterised-by-x-ray-crystallography-in-a-metal-organic-framework-matrix.pdf
|
60c74983ee301c1d18c79a7c
|
10.26434/chemrxiv.11345063.v2
|
Single Crystal Growth of High-Pressure Phases of Ice and Salt Hydrate Far Below the Original Melting Point by Mixing Alcohol: Crystal Structure Determination of Magnesium Chloride Heptahydrate
|
An crystal-growth technique for single crystal x-ray structure analysis of high-pressure forms of hydrogen-bonded crystals is proposed. We used alcohol mixture (methanol: ethanol = 4:1 in volumetric ratio), which is a widely used pressure transmitting medium, inhibiting the nucleation and growth of unwanted crystals. In this paper, two kinds of single crystals which have not been obtained using a conventional experimental technique were obtained using this technique: ice VI at 1.99 GPa and MgCl<sub>2</sub>·7H<sub>2</sub>O at 2.50 GPa at room temperature. Here we first report the crystal structure of MgCl2·7H2O. This technique simultaneously meets the requirement of hydrostaticity for high-pressure experiments and has feasibility for further in-situ measurements.
|
Keishiro Yamashita; Kazuki Komatsu; Hiroyuki Kagi
|
Crystallography – Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-03-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74983ee301c1d18c79a7c/original/single-crystal-growth-of-high-pressure-phases-of-ice-and-salt-hydrate-far-below-the-original-melting-point-by-mixing-alcohol-crystal-structure-determination-of-magnesium-chloride-heptahydrate.pdf
|
60c74e6c337d6c7d69e27f9c
|
10.26434/chemrxiv.12746948.v1
|
Machine Learning in Prediction of Intrinsic Aqueous Solubility of Drug-like Compounds: Generalization, Complexity or Predictive Ability?
|
<div>Here, we present a collection of publicly available<br />intrinsic aqueous solubility data of 829 drug-like<br />compounds. Four different machine learning algorithms<br />(random forest, light GBM, partial least squares and<br />LASSO) coupled with multi-stage permutation<br />importance for feature selection and Bayesian hyperparameter optimization were employed for the<br />prediction of solubility based on chemical structural<br />information. Our results have shown that LASSO<br />yielded the best predictive ability on an external test set<br />with and RMSE(test) of 0.70 log points and 105 features<br />in the model. Taking into account the number of<br />descriptors as well, an RF model achieved the best<br />balance between complexity and predictive ability with<br />an RMSE(test) of 0.72 with only 17 features. We<br />propose a ranking score for choosing the best model, as<br />test set performance is only one of the factors in creating<br />an applicable model. The ranking score is a weighted<br />combination of generalization, number of features<br />involved and test set performance
<br /></div><div><br /></div><div><br /></div><div><br /></div><div>The data related to this paper can be downloaded from 10.5281/zenodo.3968754</div>
|
Mario Lovric; Kristina Pavlović; Petar Žuvela; Adrian Spataru; Bono Lučić; Roman Kern; Richard Ming Wah Wong
|
Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e6c337d6c7d69e27f9c/original/machine-learning-in-prediction-of-intrinsic-aqueous-solubility-of-drug-like-compounds-generalization-complexity-or-predictive-ability.pdf
|
65390f38c573f893f10b962c
|
10.26434/chemrxiv-2023-vt5cw
|
Nuclear quantum effects in hydroxide hydrate along the H-bond bifurcation pathway
|
Path integral simulations are used to explore nuclear quantum effects (NQEs) in hydroxide hydrate and its perdeuterated isotopomer along the H-bond bifurcation pathway. Towards this, a new PES using the symmetric gradient domain machine learning method with ab initio data at the CCSD(T)/aug-cc-pVTZ level is built. From path integral umbrella sampling simulations, free energy profiles along the bifurcation coordinate are explored as a function of temperature. At ambient temperature, the bifurcation barrier is increased upon the inclusion of NQEs. At low temperatures in the deep tunneling regime, the barrier is strongly decreased and flattened. These trends are examined and the role of the O-O distance is also investigated through two-dimensional umbrella sampling.
|
Mrinal Arandhara; Sai G. Ramesh
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65390f38c573f893f10b962c/original/nuclear-quantum-effects-in-hydroxide-hydrate-along-the-h-bond-bifurcation-pathway.pdf
|
621ca9a891a2e6aa19df8f51
|
10.26434/chemrxiv-2022-t1kbb
|
RanDepict - Random Chemical Structure Depiction Generator
|
The development of deep learning-based optical chemical structure recognition (OCSR) systems has led to a need for datasets of chemical structure depictions. The diversity of the features in the training data is an important factor for the generation of deep learning systems that generalise well and are not overfit to a specific type of input. In the case of chemical structure depictions, these features are defined by the depiction parameters such as bond length, line thickness, label font style and many others.
Here we present RanDepict, a toolkit for the creation of diverse sets of chemical structure depictions. The diversity of the image features is generated by making use of all available depiction parameters in the depiction functionalities of the CDK, RDKit, and Indigo. Furthermore, there is the option to enhance and augment the image with features such as curved arrows, chemical labels around the structure, or other kinds of distortions.
Using depiction feature fingerprints, RanDepict ensures diversely picked image features. Here, the depiction and augmentation features are summarised in binary vectors and the MaxMin algorithm is used to pick diverse samples out of all valid options.
By making all resources described herein publicly available, we hope to contribute to the development of deep learning-based OCSR systems.
|
Henning Otto Brinkhaus; Kohulan Rajan; Achim Zielesny; Christoph Steinbeck
|
Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2022-03-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621ca9a891a2e6aa19df8f51/original/ran-depict-random-chemical-structure-depiction-generator.pdf
|
656dea18cf8b3c3cd7c3ed3a
|
10.26434/chemrxiv-2023-shx8j
|
Direct Synthesis of CuPd Icosahedra Supercrystals studied by in situ X-ray Scattering
|
Nanocrystal self-assembly into supercrystals provides a versatile platform for creating novel materials and devices with tailored properties. While common self-assembly strategies imply the use of purified nanoparticles after synthesis, conversion of chemical precursors directly into nanocrystals and then supercrystals in simple procedures has been rarely reported. Here we study the nucleation and growth of CuPd icosahedra and their consecutive assembly into extended closed-packed face-centered cubic (fcc) supercrystals. To this end, we simultaneously and in situ measure X-ray total scattering with pair-distribution function analysis (TS-PDF) and small-angle X-ray scattering (SAXS). We find that the supercrystals formation is preceded by an intermediate dense phase of nanocrystals displaying short-range order (SRO). We further show that the organization of oleic acid/oleylamine surfactants into lamellar structures likely drives the emergence of the SRO phase and later of the supercrystals by creating an excluded volume to particle diffusion. The supercrystal formation as well as their disassembly are triggered by temperature. Our study demonstrates that depletion effects can be crucial in the direct synthesis of supercrystals. We also provide a general approach to investigate novel preparation routes of supercrystals in situ and across several length scales via X-ray scattering.
|
Davide Derelli; Kilian Frank; Lukas Grote; Federica Mancini; Ann-Christin Dippel; Olof Gutowski; Bert Nickel; Dorota Koziej
|
Materials Science; Nanoscience; Aggregates and Assemblies; Alloys; Nanostructured Materials - Nanoscience; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656dea18cf8b3c3cd7c3ed3a/original/direct-synthesis-of-cu-pd-icosahedra-supercrystals-studied-by-in-situ-x-ray-scattering.pdf
|
66fef29312ff75c3a15431c1
|
10.26434/chemrxiv-2024-45q9k
|
Molecular Engineering of Emissive Molecular Qubits Based on Spin-Correlated Radical Pairs
|
Spin chemistry of photogenerated spin-correlated radical pairs (SCRPs) offers a practical approach to control chemical reactions and molecular emissions using weak magnetic fields. This capability to harness magnetic field effects (MFEs) paves the way for developing SCRPs-based molecular qubits. Here, we introduce a new series of donor-chiral bridge-acceptor (D-χ-A) molecules that demonstrate significant MFEs on fluorescence intensity and lifetime in solution at room temperature – critical for quantum sensing. By precisely tuning the donor site through torsional locking, distance extension, and planarization, we achieved remarkable control over key quantum properties, including field-response range and linewidth. In the most responsive systems, emission lifetimes increased by over 200%, and total emission intensity was modulated by up to 30%. This level of tunability, and rational design principle of optically addressable molecular qubits, represents a major leap toward functional synthetic molecular qubits, advancing the field of molecular quantum technologies.
|
Neo Lin; Miu Tsuji; Isabella Bruzzese; Angela Chen; Michael Vrionides; Noen Jian; Farhan Kittur; Thomas Fay; Tomoyasu Mani
|
Theoretical and Computational Chemistry; Physical Chemistry; Chemical Kinetics; Photochemistry (Physical Chem.); Quantum Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fef29312ff75c3a15431c1/original/molecular-engineering-of-emissive-molecular-qubits-based-on-spin-correlated-radical-pairs.pdf
|
60c74feb4c8919396bad3c9f
|
10.26434/chemrxiv.12959945.v1
|
Quantum Mechanics / Extremely Localized Molecular Orbital Embedding Strategy for Excited-States. 2. Coupling to the Equation-of-Motion Coupled Cluster Method
|
Equation-of-Motion Coupled Cluster with single and double excitations (EOM-CCSD) is currently one of the most accurate quantum chemical methods for the investigation of excited-states, but its non-negligible computational cost unfortunately limits its application to small molecules. To extend its range of applicability, one possibility consists in its coupling with the so-called multi-scale embedding techniques. Along this line, in this work we propose the interface of the EOM-CCSD method with the recently developed quantum mechanics / extremely localized molecular orbital (QM/ELMO) strategy, an approach where the chemically relevant region of the investigated system is treated at fully quantum chemical level (QM region), while the remaining part (namely, the chemical environment) is described through transferred and frozen extremely localized molecular orbitals (ELMO subsystem). In order to determine capabilities and limitations of the novel EOM-CCSD/ELMO approach, some validation tests were properly designed and carried out. They indicated that the new approach is particularly useful and efficient in describing local electronic transitions in relatively large systems, for both covalently and non-covalently bonded QM and ELMO regions. In particular, it has been shown that, including only a limited number of atoms in the chemically active subunit, the ELMO-embedded computations enable the reproduction of excitation energies and oscillator strengths resulting from full EOM-CCSD calculations within the limit of chemical accuracy, but with a significantly reduced computational cost. Furthermore, despite the approximation of an embedding potential given by frozen extremely localized molecular orbitals, it was observed that the new strategy is able to satisfactorily account for the effects of the environment.
|
Giovanni Macetti; Alessandro Genoni
|
Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-09-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74feb4c8919396bad3c9f/original/quantum-mechanics-extremely-localized-molecular-orbital-embedding-strategy-for-excited-states-2-coupling-to-the-equation-of-motion-coupled-cluster-method.pdf
|
60c7428cbb8c1acb613da155
|
10.26434/chemrxiv.8307419.v1
|
Self-Assembled Fluid Phase Floating Membranes with Tuneable Water Interlayers
|
<p>We present a reliable method for the fabrication of fluid phase
unsaturated bilayers which are readily self-assembled on charged self-assembled
monolayer (SAM) surfaces producing high coverage floating supported bilayers
where the membrane to surface distance could be controlled with nanometer
precision. Vesicle fusion was used to deposit the bilayers onto anionic SAM coated
surfaces. Upon assembly the bilayer to SAM solution interlayer thickness was
7-10 Å with evidence suggesting that this layer was present due to SAM
hydration repulsion of the bilayer from the surface. This distance could be increased
using low concentrations of salts which caused the interlayer thickness to
enlarge to ~33 Å. Reducing the salt concentration resulted in a return to a
shorter bilayer to surface distance. These accessible and controllable membrane models are well suited to a
range of potential applications in biophysical studies, bio-sensors and
Nano-technology.</p><br />
|
Luke Clifton; Nicoló Paracini; Arwel
V. Hughes; Jeremy H. Lakey; Nina-Juliane Seinke; Joshaniel F. K. Cooper; Martynas Gavutis; Maximilian W. A. Skoda
|
Biocompatible Materials; Biological Materials; Thin Films; Nanofabrication; Nanostructured Materials - Nanoscience; Biophysical Chemistry; Self-Assembly; Surface
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-06-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7428cbb8c1acb613da155/original/self-assembled-fluid-phase-floating-membranes-with-tuneable-water-interlayers.pdf
|
60c74c72337d6c6ce7e27c5c
|
10.26434/chemrxiv.12480452.v1
|
Identification of Potent Inhibitors of ATP Synthase Subunit C (AtpE) from Mycobacterium Tuberculosis Using in Silico Approach
|
<p>ATP
synthase subunit c (AtpE) is an enzyme that catalyzes the production of ATP
from ADP in the presence of sodium or proton gradient from <i>Mycobacterium tuberculosis</i> (MTB). This enzyme considered an
essential target for drug design and its shares the same pathway with the
target of Isoniazid. Thus, this enzyme would serve as an alternative target of
the Isoniazid. The 3D model structure of the AtpE was constructed based on the
principle of the homology modeling using the Modeller9.16. The developed model
was subjected to the energy minimization and refinement using molecular dynamic
(MD) simulation. The minimized model structure was searched against Zinc and
PubChem database to determine ligands that bind to the enzyme with minimum
binding energy using RASPD and PyRx tool. A total of 4776 compounds capable of
binding to AtpE with minimum binding energies were selected. These compounds
further screened for physicochemical properties (Lipinski rule of five). All
the compounds that possessed the desirable properties selected and used for
molecular docking analysis. Five (5) compounds with minimum binding energies
ranged between ─8.69, and ─8.44kcal/mol, less than the free binding energy of
ATP were selected. These compound further screened for the absorption,
distribution, metabolism, excretion, and toxicity (ADME and toxicity)
properties. Of the five compounds, three (ZINC14732869, ZINC14742188, and
ZINC12205447) fitted all the ADME and toxicity properties and subjected to MD
simulation and Molecular Mechanics Generalized Born and Surface Area (MM-GBSA)
analyses. The results indicated that the ligands formed relatively stable
complexes and had free binding energies, less than the binding energy of the
ATP. Therefore, these ligands considered as prospective inhibitors of MTB after
successful experimental validation</p>
|
Mustafa Alhaji Isa
|
Biochemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Microbiology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c72337d6c6ce7e27c5c/original/identification-of-potent-inhibitors-of-atp-synthase-subunit-c-atp-e-from-mycobacterium-tuberculosis-using-in-silico-approach.pdf
|
67290b47f9980725cf1587e6
|
10.26434/chemrxiv-2024-b5wjj
|
Photo-swing CO2 capture using aminopolymers as sorbents and TiN light absorber
|
Using aminopolymers as the sorbent material for dilute CO2 capture, a photo-swing method is demonstrated in an industrially relevant contactor architecture using titanium nitride (TiN) nanosized light absorbers coupled with low-power LEDs with irradiances up to 420 mW/cm². The photo-driven desorption process is applied to dry and humid CO2 streams. Consistent with known sorption mechanisms for aminopolymers, humid CO2 streams increased the CO2 uptake, in our case by ~30%. The photo-swing CO2 capture desorbed ~83% and ~100% CO2 compared to thermally-driven desorption over the same period for a dry and humid CO2 stream, respectively. The photo-swing CO2 capture exhibits robust performance over > 90 cycles without significant signs of photo(thermal) induced sorbent degradation. This work lays the groundwork for photo-swing DAC technology as a scalable, energy-efficient solution for CO2 capture, well-suited for modular systems in remote locations utilizing intermittent renewable energy sources.
|
Noemi Leick; Sawyer Halingstad; James Crawford; Michael Carroll; Matthew Yung; Randy Cortright; Wade Braunecker
|
Materials Science; Energy; Chemical Engineering and Industrial Chemistry; Nanostructured Materials - Materials; Optical Materials
|
CC BY 4.0
|
CHEMRXIV
|
2024-11-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67290b47f9980725cf1587e6/original/photo-swing-co2-capture-using-aminopolymers-as-sorbents-and-ti-n-light-absorber.pdf
|
60c7463abdbb89226ba38ba7
|
10.26434/chemrxiv.11164796.v1
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Quantum Control of Ultrafast Internal Conversion using Nano-Confined Virtual Photons
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<div>
<div>
<div>
<p>The rational control of non-radiative relaxation remains an unfulfilled goal for synthetic
chemistry. In this study, we show strongly coupling an ensemble of molecules to the virtual
photons of an electromagnetic cavity provides a rational handle over ultrafast, non-radiative
dynamics. Specifically, we control the concentration of zinc tetraphenyl porphyrin molecules
within nano-scale Fabry-Perot cavity structures to show a variable collective vacuum Rabi
splitting between the polaritons coincides with changes in internal conversion rates. We find
these changes obey a power law dependence on the collective vacuum Rabi splitting, but de-
viate from the predictions of so-called gap laws. We also show simple theories of structural
changes caused by polariton formation cannot explain discrepancies between our results and
established theoretical predictions. Our results demonstrate a mechanism by which cavity
polariton formation controls the fundamental photo-physics of light harvesting and photo-
catalytic molecular moieties and the gap remaining in our fundamental understanding of these
mechanisms.
</p>
</div>
</div>
</div>
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Aleksandr Avramenko; Aaron Rury
|
Chemical Kinetics; Optics; Photochemistry (Physical Chem.); Quantum Mechanics; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-11-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7463abdbb89226ba38ba7/original/quantum-control-of-ultrafast-internal-conversion-using-nano-confined-virtual-photons.pdf
|
634199c0114b7e5c512e23a5
|
10.26434/chemrxiv-2022-fldj9
|
Enhancing Dynamic Spectral Diffusion in Metal-Organic Frameworks Through Defect Engineering
|
The crystal packing of organic chromophores has a profound impact on their photophysical properties. Molecular crystal engineering is generally incapable of producing precisely spaced arrays of molecules for use in photovoltaics, light-emitting diodes, and sensors. A promising alternative strategy is the incorporation of chromophores into crystalline metal-organic frameworks (MOFs), leading to matrix coordination-induced emission (MCIE) upon confinement. However, it remains unclear how the precise arrangement of chromophores and defects dictates photophysical properties in these systems, limiting the rational design of well-defined photoluminescent materials. Herein, we report new, robust Zr-based MOFs constructed from the linker tetrakis(4-carboxyphenyl)ethylene (TCPE4−) that exhibit an unexpected structural transition in combination with a prominent shift from green to blue photoluminescence (PL) as a function of the amount of acid modulator (benzoic, formic, or acetic acid) used during synthesis. Time-resolved PL (TRPL) measurements provide full spectral information and reveal that the observed hypsochromic shift arises due to a higher concentration of linker substitution defects at higher modulator concentrations, leading to broader excitation transfer-induced spectral diffusion. Spectral diffusion of this type has not been reported in a MOF to date, and its observation provides structural information that is otherwise unobtainable using traditional crystallographic techniques. Our findings suggest that defects have a profound impact on the photophysical properties of MOFs, and that their presence can be readily tuned to modify energy transfer processes within these materials.
|
Arjun Halder; David Bain; Julia Oktawiec; Matthew Addicoat; Stavrini Tsangari; Jose Fuentes-Rivera; Tristan Pitt; Andrew Musser; Phillip Milner
|
Physical Chemistry; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634199c0114b7e5c512e23a5/original/enhancing-dynamic-spectral-diffusion-in-metal-organic-frameworks-through-defect-engineering.pdf
|
60c7554c567dfe4c22ec626c
|
10.26434/chemrxiv.14061680.v1
|
Assembly and Application of a Low Budget Photo Reactor
|
Photochemistry is a fast growing research field and many transformations previously not accessible to chemists now have become part of an ever growing standard repertoire. The limiting factors for a photo reactor system however is the possibility to perform stirring, removal of excess heat and the irradiation with UV or visible light – all that within a secure surrounding. Systems for starters may be as expensive as several thousand Euro. Here we design and assemble a LED photo reactor using scrap and standard materials, only spending less than 30 € for a LED. The system may be adjusted to any required wave length and its assembly is shown for the use of a 400 nm wave length lamp. To demonstrate its application, we then exemplarily use the reactor in the removal of a photo labile protection group during the synthesis of a SARS-CoV-2 spike protein glyco peptide.<br />
|
Olov Wallner; Kirill Mamonov; Florian Ortis; Dana Michel; Maurice Michel
|
Organic Synthesis and Reactions; Photochemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-02-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7554c567dfe4c22ec626c/original/assembly-and-application-of-a-low-budget-photo-reactor.pdf
|
60c758aa702a9b240b18cd89
|
10.26434/chemrxiv.14573712.v1
|
A Self-Immolative Molecular Beacon for Amplified Nucleic Acid Detection
|
Fluorogenic hybridization probes allow the detection of RNA and DNA sequences in homogeneous solution. Typically, one target molecule is activating the fluorescence of a single probe molecule. This limits the sensitivity of nucleic acid detection. Herein, we report a self-immolative Molecular Beacon (iMB), which escapes the one-target-one-probe dogma. The iMB probe includes a photoreductively cleavable N-alkylpicolinium (NAP) linkage within the loop region. A fluorophore at the 5'-end serves, on the one hand, as a reporter group and, on the other hand, as a photosensitizer of a NAP-linker cleavage reaction. In the absence of a target, the iMB adopts a hairpin shape. Quencher proups prevent photo-induced cleavage. The iMB opens upon hybridization with target, and both fluorescent emission as well as photo-inductive cleavage of the NAP-linker can occur. In contrast to previous chemical amplification probes, iMBs are unimolecular. Cleavage leads to products that have lower target affinity than the probes before reaction. Aided by catalysis, the method allowed the detection of 5 pM RNA target within 100 min. <br />
|
Magdalena Roth; Oliver Seitz
|
Bioorganic Chemistry; Biochemical Analysis; Biophysics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758aa702a9b240b18cd89/original/a-self-immolative-molecular-beacon-for-amplified-nucleic-acid-detection.pdf
|
60c747490f50db78ac3965a1
|
10.26434/chemrxiv.11618202.v1
|
Time-Resolved Decarboxylative Alkyl Coupling Promoted by NADH and Blue Light
|
<div><div><div><p>Flexible, small and strong alkyl ligations created upon external light stimuli can open new avenues for medicinal and biological research. Herein, we have found that NADH and analogues can drive photo-couplings without auxiliary photocatalysts. The time- resolved alkyl photo-ligation between redox-active carboxylate derivatives and electron-poor olefins displays a surprising moisture and air-tolerance, and unusually high coupling rates in dilute conditions. This work sets the conceptual basis for further biocompatible C-C coupling reactions promoted by visible-light in combination with NADH, the ubiquitous reductant of biological systems.</p></div></div></div>
|
Rajdip Chowdhury; Zhunzhun Yu; Stefanie V. Kohlhepp; Xiang Yin; Abraham Mendoza
|
Bioorganic Chemistry; Natural Products; Organic Synthesis and Reactions; Photochemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-01-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747490f50db78ac3965a1/original/time-resolved-decarboxylative-alkyl-coupling-promoted-by-nadh-and-blue-light.pdf
|
67818b4d6dde43c9080b1d81
|
10.26434/chemrxiv-2025-xlxcp
|
High-Speed Cyclic Voltammetry Regressions Using Machine Learning
|
The ability to rapidly regress the kinetic parameters from cyclic voltammograms is important for many laboratory automation endeavors. Inspired by how expert electrochemists can rapidly interpret cyclic voltammograms simply by their shape, here we show that convolutional neural networks (similar to those used in handwriting analysis) can successfully regress both the kinetic rate constant and transfer coefficient of cyclic voltammetry data. This type of machine learning models obtained 93.6% five fold cross validation accuracy, and could obtain both the kinetic rate constant and transfer coefficient in a few milliseconds. This is in comparison to over 3000 seconds using an optimization protocol with finite elemental analysis to regress the kinetic parameters via solving the governing differential equations. This advancement will be very useful for many electrochemical applications where high-throughput experimentation is necessary.
|
Darik Rosser; Kevin Leonard
|
Analytical Chemistry; Energy; Chemical Engineering and Industrial Chemistry; Electrochemical Analysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67818b4d6dde43c9080b1d81/original/high-speed-cyclic-voltammetry-regressions-using-machine-learning.pdf
|
66993e8c01103d79c556ea84
|
10.26434/chemrxiv-2024-tmcxk-v2
|
The photo-isomerization of the cyclononatetraenyl ligand and related rare earth complexes
|
The cyclononatetraenyl (Cnt) ligand is a large monoanionic ligand. It is easily synthesized by ring expansion after cyclopropanation of the cyclooctatetraenyl (Cot) ligand. The Cnt ligand can be reported as the cis-cis-cis-cis (cis) isomer, where the aromatic ring is flat, and all carbon atoms form a homogenous ring, and as the cis-cis-cis-trans (trans) isomer, where one carbon places itself inside the ring. The isomerization from the trans to the cis form has been reported numerous times in previous articles, but no quantitative analysis has been proposed due to contradictory data. This article proposes a detailed analysis involving light in order to rationalize this intrigue concerning isomerization. A careful synthesis at low temperatures and with light protection yields the ligand in its trans form (Cnt-trans). The controlled photo-isomerization of the Cnt-trans ligand is reported herein. A series of divalent or trivalent rare earth complexes, (Cnt)2Sm, and (Cot)(Cnt)Ln (Ln= Y, La, Ce, Pr, Nd, Sm, Gd, Tb, Er, Ho), which synthesis, solid-state X-ray diffraction and solution 1H NMR and UV-Visible measurements, have been revised according to the synthesis using the Cnt-trans ligand. The photo-isomerization of the (Cnt-trans)2Sm evolves to the intermediate (Cnt-cis)(Cnt-trans)Sm and the (Cnt-cis)2Sm complex as the thermodynamical product. The photoisomerization of the trivalent (Cot)(Cnt)Ln complexes highlights the formation of a photostationary state (PSS) after several minutes of irradiation, in which both Cnt-trans and Cnt-cis ligands are present. The ratio of these two forms varies according to metal and irradiation wavelength: while low-energy wavelengths favor the cis isomer, high-energy wavelengths favor the trans isomer. DFT and TD-DFT were performed to provide a tentative orbital explanation.
|
Lucie Pedussaut; Nolwenn Mahieu; Camille Chartier; Thayalan Rajeshkumar; Maxime Tricoire; Iskander Douair; Nicolas Casaretto; Laurent Maron; Gregory Danoun; Gregory Nocton
|
Inorganic Chemistry; Organometallic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66993e8c01103d79c556ea84/original/the-photo-isomerization-of-the-cyclononatetraenyl-ligand-and-related-rare-earth-complexes.pdf
|
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