id
stringlengths 24
24
| doi
stringlengths 28
32
| title
stringlengths 8
495
| abstract
stringlengths 17
5.7k
| authors
stringlengths 5
2.65k
| categories
stringlengths 4
700
| license
stringclasses 3
values | origin
stringclasses 1
value | date
stringdate 1970-01-01 00:00:00
2025-03-24 00:00:00
| url
stringlengths 119
367
⌀ |
|---|---|---|---|---|---|---|---|---|---|
60f8799e40c8bd67f1979f67
|
10.26434/chemrxiv-2021-zm828
|
Dynamic Amide Formation by Reversible Nitrone Exchange of Potassium Acyltrifluoroborates (KATs) and Hydroxylamines in Aqueous Conditions
|
The condensation of potassium acyltrifluoroborates (KATs) and hydroxylamines occurs under ambient, aqueous conditions to form KAT nitrones in a reversible manner. The KAT nitrones exchange rapidly under aqueous acidic conditions, resulting in a dynamic covalent library that can be converted to the corresponding static amides by treatment with strong acid. Extensive studies on the conditions and kinetics show that – counterintuitively – KAT nitrone formation is accelerated by water. The overall process serves as a dynamic system operating at room temperature under aqueous conditions with the rare ability of trapping the mixture into stable secondary amides.
|
Yi-Chung Dzeng; Jeffrey Bode
|
Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-07-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f8799e40c8bd67f1979f67/original/dynamic-amide-formation-by-reversible-nitrone-exchange-of-potassium-acyltrifluoroborates-ka-ts-and-hydroxylamines-in-aqueous-conditions.pdf
|
60c73cc9ee301cb1a2c78491
|
10.26434/chemrxiv.14751660.v1
|
Simplified Tuning of Long-Range Corrected Density Functionals for Use in Symmetry-Adapted Perturbation Theory
|
Long considered a failure, second-order symmetry-adapted perturbation theory (SAPT) based on Kohn-Sham orbitals, or SAPT(KS), can been resurrected for semiquantitative purposes using long-range corrected (LRC) density functionals whose asymptotic behavior is adjusted separately for each monomer. As in other contexts, correct asymptotic behavior can be enforced via "optimal tuning" of LRC functionals, based on the ionization energy theorem, but the tuning procedure is tedious, expensive for large systems, and comes with a troubling dependence on system size. Here, we show that essentially identical results are obtained using an automated tuning procedure based on the size of the exchange hole, making tuned "SAPT(wKS)" fast and convenient. In conjunction with SAPT-based methods that sidestep second-order dispersion, this procedure achieves benchmark-quality interaction energies, along with the usual SAPT energy decomposition, without the hassle of system-specific tuning.
|
Montgomery Gray; John Herbert
|
Theory - Computational; Quantum Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-06-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc9ee301cb1a2c78491/original/simplified-tuning-of-long-range-corrected-density-functionals-for-use-in-symmetry-adapted-perturbation-theory.pdf
|
60c74168702a9b409d18a262
|
10.26434/chemrxiv.8044235.v1
|
Structure and Dynamics of Spherical and Rodlike Alkyl Ethoxylate Surfactant Micelles Investigated Using NMR Relaxation and Atomistic Molecular Dynamics Simulations
|
We study molecular arrangements and dynamics in alkyl ethoxylate nonionic surfactant micelles by combining high field (600 and 700 MHz) NMR relaxation measurements with large-scale atomistic molecular dynamics simulations. For spherical micelles, but not for cylindrical micelles, cross relaxation rates are positive only for surfactant alkyl tail atoms connected to the hydrophilic head group. All cross relaxation rates are negative for cylindrical micelles. This effect is reproducible either by changing composition (ratios of the nonionic surfactants) or changing temperature of a single surfactant in order to change the micelle shape. We validate the micelle shape by SANS and use the results as a guide for our simulations. We calculate parameters that determine relaxation rates directly from simulated trajectories, without introducing specific functional forms. Results indicate that relative motions of nearby atoms are liquid-like, in agreement with 13C T1 measurements, though constrained by micelle morphology. Relative motions of distant atoms have slower components because the relative changes in distances and angles are smaller when the moving atoms are further apart. The slow, long-range motions appear to be responsible for the predominantly negative cross relaxation rates observed in NOESY spectra. The densities of atoms from positions 1 and 2 in the boundary region are lower in spherical micelles compared to cylindrical micelles. Correspondingly, motions in this region are less constrained by micelle morphology in the spherical compared to the cylindrical cases. The two effects of morphology lead to the unusual occurrence of positive cross relaxation involving positions 1 and 2 for spheres.
|
Allison Edwards; Abdolreza Javidialesaadi; Katie Weigandt; George Stan; Charles Eads
|
Computational Chemistry and Modeling; Interfaces; Physical and Chemical Properties; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-04-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74168702a9b409d18a262/original/structure-and-dynamics-of-spherical-and-rodlike-alkyl-ethoxylate-surfactant-micelles-investigated-using-nmr-relaxation-and-atomistic-molecular-dynamics-simulations.pdf
|
653b7313c573f893f134df7e
|
10.26434/chemrxiv-2023-d5lcg
|
C-4 analogs of podophyllotoxin as tubulin inhibitors: Synthesis, biological evaluation, and structure-activity relationship
|
The rich diversity of lignin small molecules derived from podophyllotoxin, a non-covalent tubulin inhibitor isolated from the Podophyllum family, has led to the discovery and clinical development of several anticancer agents including etoposide and teniposide, which received FDA approval for the treatment of various cancers through DNA topoisomerase inhibition. While these compounds share the same tetracyclic core, two subtle structural changes that differentiate 1 from its DNA topoisomerase-binding analogs—the presence of 4’ methylation on the aromatic ring and stereospecific glycosylation at the C-4 hydroxyl—yield two independent mechanisms. Given the immense pharmacological importance of these two features, we sought to establish a structure-activity relationship regarding modification at C-4 on the potency, specificity, and chemical properties of podophyllotoxin. Here, we synthesized and evaluated a systematic library of close-in diversified esters at the C-4 position of podophyllotoxin to evaluate the effect of alkyl bulk at C-4 on the potency of 4-acyl podophyllotoxin analogs as tubulin inhibitors. Additionally, we evaluate their biological target and activity through cell viability assays, tubulin polymerization assays, and cell cycle analysis. Furthermore, we rationalize our results by analyzing the interactions between each ester and the binding site of tubulin through computer docking models. Altogether, we show that increasing steric hindrance at C-4 leads to a loss in potency against human cancer cells but has an insignificant impact on the ex-vitro kinetics of tubulin inhibition. This suggests that the biological activity of our compounds may be attributed to cytosolic and membrane distribution rather than binding interactions within the colchicine site.
|
Breanna Lu; Lexi Xu; Harriet Chen; Grace Yu; Kimberly Khow; Stella Yang; Arushi Dinker; Edward Njoo
|
Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Organic Synthesis and Reactions; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653b7313c573f893f134df7e/original/c-4-analogs-of-podophyllotoxin-as-tubulin-inhibitors-synthesis-biological-evaluation-and-structure-activity-relationship.pdf
|
648cca46e64f843f41e3b2c8
|
10.26434/chemrxiv-2023-llt95
|
MultiBinding Sites United in Covalent-Organic Frameworks (MSUCOF) for H2 Storage and Delivery at Room Temperature
|
The storage of hydrogen gas (\ce{H2}) has presented a significant challenge that has hindered its use as a fuel source for transportation. To meet the Department of Energy's ambitious goals of achieving 50 g L$^{-1}$ volumetric and 6.5 wt \% gravimetric uptake targets, materials-based approaches are essential. Designing materials that can efficiently store hydrogen gas requires careful tuning of the interactions between the gaseous \ce{H2} and the surface of the material. Metal-Organic Frameworks (MOFs) and Covalent-Organic Frameworks (COFs) have emerged as promising materials due to their exceptionally high surface areas and tunable structures that can improve gas-framework interactions. However, weak binding enthalpies have limited the success of many current candidates, which fail to achieve even 10 g L$^{-1}$ volumetric uptake at ambient temperatures. To overcome this challenge, We utilized quantum mechanical (QM) based force fields (FF) to investigate the uptake and binding enthalpies of 3 linkers chelated with 7 different transition metals (TM), including both precious metals (Pd and Pt) and first row TM (Co, Cu, Fe, Ni, Mn), to design 24 different COFs in-silico. By applying QM-based FF with grand canonical Monte Carlo (GCMC) from 0-700 bar and 298 K, We demonstrated that Co-, Ni-, Mn-, Fe-, Pd-, and Pt-based MSUCOFs can already achieve the Department of Energy's hydrogen storage targets for 2025. Surprisingly, the COFs that incorporated the more affordable and abundant first-row TM often outperformed the precious metals. This promising development brings us one step closer to realizing a hydrogen-based energy economy.
|
Marcus Djokic; Jose Mendoza-Cortes
|
Materials Science; Energy; Chemical Engineering and Industrial Chemistry; Hydrogen Storage Materials; Energy Storage
|
CC BY 4.0
|
CHEMRXIV
|
2023-06-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648cca46e64f843f41e3b2c8/original/multi-binding-sites-united-in-covalent-organic-frameworks-msucof-for-h2-storage-and-delivery-at-room-temperature.pdf
|
60c743730f50db0d6e395f16
|
10.26434/chemrxiv.9178136.v1
|
Evaluation of Binding Site Comparison Algorithms and Proteometric Machine Learning Models in the Detection of Protein Pockets Capable of Binding the Same Ligand
|
<div>
<div>
<div>
<p>Non linearities of biological networks present ample opportunity for synergistic protein targeting
combinations. Yet, to date, our ability to design multi-target inhibitors and predict
polypharmacology binding profiles remains limited. Herein, we present a systematic
benchmarking of protein pocket comparison algorithms from the literature, as well as novel
machine learning models developed to predict whether two proteins will bind the same ligand.
The results demonstrate that previously reported performance metrics from the literature could
be inflated due to a bias towards proteins of similar folds when identifying protein capable of
binding the same ligand. This observation motivated a more in-depth evaluation of the methods
against two subsets of same and cross protein fold comparisons. In a head to head comparison
using the cross protein fold subset, we found that the proteometric machine learning models
were the best performing models overall.
</p>
</div>
</div>
</div>
|
Zied Gaieb; conor parks; Rommie Amaro
|
Bioinformatics and Computational Biology; Biophysics; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-07-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743730f50db0d6e395f16/original/evaluation-of-binding-site-comparison-algorithms-and-proteometric-machine-learning-models-in-the-detection-of-protein-pockets-capable-of-binding-the-same-ligand.pdf
|
61eef0fac18d6703c383506d
|
10.26434/chemrxiv-2022-k2j3h
|
Effects of enzyme-ligand interactions on the photoisomerization of a light-regulated chemotherapeutic drug
|
Molecular photoswitches permit using light to control protein activity with high spatiotemporal resolutions, thereby alleviating the side effects of conventional chemotherapy. However, due to the challenges in probing ultrafast photoisomerization reactions in biological environments, it remains elusive how the protein influences the photochemistry of the photoswitches, which hampers the rational design of light-regulated therapeutics. To overcome this challenge, we employed first-principles non-adiabatic dynamics simulations to characterize the photodynamics of the phototrexate (PTX), a recently developed photoswitchable anticancer chemotherapeutic that reversibly inhibits its target enzyme dihydrofolate reductase (DHFR). Our simulations show that the protein environment impedes the trans to cis photoisomerization of the PTX. The confinement in the ligand-binding cavity slows down the isomerization kinetics and quantum yield of the photoswitch by reshaping its conical intersection, increasing its excited-state free energy barrier, and quenching its local density fluctuations. Therefore, we predict that the PTX’s trans to cis photoisomerization in solution precedes its binding with the protein, despite the favorable binding energy of the trans isomer. Our findings highlight the importance of the protein environment on the photochemical reactions of the molecular photoswitches. As such, our work represents an important step towards the rational design of light-regulated drugs in photopharmacology.
|
Ruibin Liang; Amirhossein Bakhtiiari
|
Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Quantum Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-01-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61eef0fac18d6703c383506d/original/effects-of-enzyme-ligand-interactions-on-the-photoisomerization-of-a-light-regulated-chemotherapeutic-drug.pdf
|
663a1dcd21291e5d1da7ab1a
|
10.26434/chemrxiv-2024-m6z57
|
Ice templating water-stable macroporous polysaccharide hydrogels to mimic plant stems
|
Water-stable macroporous hydrogels, inspired by the structural and chemical characteristics of plant stems are expected to open a wide range of possibilities in soft materials for passive liquid transport. However, obtaining efficient materials for these applications still poses a major challenge due to the complexity of shaping hydrogels at the relevant scale-length. Here, water-stable macroporous hydrogels were fabricated using alginate and TEMPO-oxidized cellulose via a new approach involving ice templating and topotactic ion-crosslinking with Ca2+. This approach allows to fully avoid the energy-intensive lyophilization process and results in composite hydrogels with pore sizes akin to those found in celery xylem, a model we chose for plant stems. Importantly, the pore size could be tailored by adjusting both the ice-growth velocities and the ratios of alginate to oxidized cellulose. The resulting hydrogels displayed remarkable water stability along with viscoelastic properties and wettability that depend on the alginate and oxidized cellulose ratios. Mechanical properties, such as compression stress and toughness, consistently increased with higher alginate contents. In addition, liquid transport measurements on crosslinked hydrogels with varying compositions and ice growth velocities revealed comparable rising speeds to those observed in celery, confirming the ability of polysaccharide-based hydrogels obtained by ice templating and topotactic crosslinking as relevant materials to mimic the function of plant stems.
|
Katsuya Komiyama; Maya Allard; Corentin Eschenbrenner; Clémence Sicard; Ahmed Hamraoui; Francisco Fernandes
|
Materials Science; Chemical Engineering and Industrial Chemistry; Biodegradable Materials; Materials Processing; Transport Phenomena (Chem. Eng.); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663a1dcd21291e5d1da7ab1a/original/ice-templating-water-stable-macroporous-polysaccharide-hydrogels-to-mimic-plant-stems.pdf
|
62c8ab40e1aaae368320cb17
|
10.26434/chemrxiv-2022-krs1t
|
Active learning guided drug design lead optimization based on relative binding free energy modeling
|
In silico identification of potent protein inhibitors commonly requires prediction of a ligand binding free energy (BFE). Thermodynamics integration (TI) based on molecular dynamics (MD) simulations is a BFE calculation method capable of predicting accurate BFE, but it is computationally expensive and time-consuming. In this work, we developed an efficient automated workflow for identifying compounds with the lowest BFE among thousands of congeneric ligands which requires only hundreds of TI calculations. Automated Machine Learning (AutoML) orchestrated by Active Learning (AL) in AL-AutoML workflow allows unbiased and efficient search for a small set of best performing molecules. We applied this workflow to select inhibitors of the SARS-CoV-2 papain-like protease. Our work resulted in predicting 133 compounds with improved binding affinity among which 16 compounds with better than 100-fold binding affinity improvement. The hit rate obtained here is better than that of traditional projects where molecule selection is guided by an expert medicinal chemist. We demonstrated that a combination of an AL protocol provides at least 20x the common brute force approaches.
|
Filipp Gusev; Evgeny Gutkin; Maria G. Kurnikova; Olexandr Isayev
|
Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-07-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c8ab40e1aaae368320cb17/original/active-learning-guided-drug-design-lead-optimization-based-on-relative-binding-free-energy-modeling.pdf
|
60c73d4f0f50db8ee8395450
|
10.26434/chemrxiv.12687416.v3
|
Pyrrolinium-substituted Persistent Zwitterionic Ferrocenate Derivative Enabling the Application of Ferrocene Anolyte
|
Here, we report the imidazolium-/pyrrolinium-substituted
persistent zwitterionic ferrocenate derivatives, which were characterized by
electron paramagnetic resonance (EPR) and <sup>57</sup>Fe Mössbauer
spectroscopy. Additional theoretical studies on these zwitterionic ferrocenate
derivatives clearly explain the origin of their thermal stability and the
orbital interactions between iron and imidazolium-/pyrrolinium-substituted zwitterionic
cyclopentadienyl ligand. Exploiting the facile Fe(II/I) redox chemistry, we
successfully demonstrated that the ferrocene derivative can be applied as an
example of derivatized ferrocene anolyte for redox-flow batteries. These zwitterionic
ferrocenate derivatives will not only deepen our understanding of the intrinsic
chemistry of ferrocenate but have the potential to open the way for the
rational design of metallocenate derivatives for various applications.
|
Hayoung Song; Giyun Kwon; Cooper Citek; Seungwon Jeon; Kisuk Kang; Eunsung Lee
|
Coordination Chemistry (Inorg.); Electrochemistry; Ligands (Inorg.); Organometallic Compounds; Transition Metal Complexes (Inorg.); Coordination Chemistry (Organomet.); Electrochemistry - Organometallic; Kinetics and Mechanism - Organometallic Reactions; Ligand Design; Ligands (Organomet.); Transition Metal Complexes (Organomet.); Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-06-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d4f0f50db8ee8395450/original/pyrrolinium-substituted-persistent-zwitterionic-ferrocenate-derivative-enabling-the-application-of-ferrocene-anolyte.pdf
|
60c742f1842e6514fcdb21a6
|
10.26434/chemrxiv.8863823.v1
|
Computational Study of the Ro-Vibrational Spectrum of CO-CO2
|
<p>We report an accurate intermolecular potential energy surface for CO-CO2. We compute and assign many ro-vibrational energies and wavefunctions For both isomers, the fundamental transition frequencies agree well with previous experimental results. The rotational constants also agree well with their experimental counterparts. Vibration along the out-of-plane coordinates is very floppy.<br /></p>
|
Eduardo Castro-Juárez,; Xiaogang Wang; Tucker Carrington; Ernesto Quintas Sanchez; Dawes, Richard
|
Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-07-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742f1842e6514fcdb21a6/original/computational-study-of-the-ro-vibrational-spectrum-of-co-co2.pdf
|
60c743f4702a9b2ad818a6f7
|
10.26434/chemrxiv.9702389.v1
|
Accelerating AutoDock4 with GPUs and Gradient-Based Local Search
|
<div>AutoDock4 is a widely used program for docking small molecules to macromolecular targets. It describes ligand- receptor interactions using a physics-inspired scoring function that has been proven useful in a variety of drug discovery projects. However, compared to more modern and recent software, AutoDock4 has longer execution times, limiting its applicability to large scale dockings. To address this problem, we describe an OpenCL implementation of AutoDock4, called AutoDock-GPU, that leverages the highly parallel architecture of GPU hardware to improve the docking throughput up to 170-fold. Moreover, we introduce the gradient-based local search method ADADELTA, which is more efficient than the original Solis-Wets method, especially for conformationally complex ligands. We estimate a 1300x reduction in the number of scoring function calls for ligands with 20 rotatable bonds, and even higher reductions likely for more complex ligands. The improvements reported here, both in terms of docking throughput and search efficiency, expand the domain of applicability of the AutoDock4 scoring function considerably.</div>
|
Diogo Santos-Martins; Leonardo Solis-Vasquez; Andreas Koch; Stefano Forli
|
Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-08-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743f4702a9b2ad818a6f7/original/accelerating-auto-dock4-with-gp-us-and-gradient-based-local-search.pdf
|
63ca82573e86561e8589f4c7
|
10.26434/chemrxiv-2023-4lsvh
|
Reductive Asymmetric Aza-Mislow-Evans Rearrangement by 1,3,2-Diazaphospholene Catalysis
|
1,3,2-diazaphospholene hydrides (DAP-H) emerged as a nucleophilic main-group hydride able to promote smooth conjugate reduction of polarized double bonds. The transiently formed phosphorus-bound enolate provides a potential platform for reductive α-functionalizations. In this respect, asymmetric C-heteroatom bond forming processes are synthetically appealing but remain so far elusive. We report a 1,3,2-diazaphospholene-catalyzed three-step cascade transformation of α,β-unsaturated N-sulfinyl acrylamides comprised of a conjugate reduction, [2,3]-sigmatropic aza-Mislow-Evans rearrangement and subsequent S-O bond reductive cleavage. The obtained enantio-enriched α-hydroxyl amides are synthetically highly valuable and formed in good yields and excellent enantiospecificity. The stereo-defined P-bound N,O-ketene aminal ensures an excellent transfer of chirality from the sulfur stereocenter to α-carbon atom. The transformation operates under mild conditions at ambient temperature. Moreover, DAP hydrides are found to be competent reductants for the cleavage of the formed sulfenate ester, thus eliminating the required additional step like in traditional Mislow-Evans processes.
|
Nicolai Cramer; Guoting Zhang
|
Organic Chemistry; Catalysis; Stereochemistry; Homogeneous Catalysis; Organocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2023-01-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ca82573e86561e8589f4c7/original/reductive-asymmetric-aza-mislow-evans-rearrangement-by-1-3-2-diazaphospholene-catalysis.pdf
|
60c74db84c8919ae53ad386f
|
10.26434/chemrxiv.12644102.v1
|
In Silico Screening of Potent Bioactive Compounds from Honey Bee Products Against COVID-19 Target Enzymes
|
From the early days of the COVID-19 pandemic, side by side to immense investigates to design specific drugs
or to develop a potential vaccine for the novel coronavirus. Myriads of FDA
approved drugs are massively repurposed for COVID-19 treatment based on
molecular docking of selected protein targets that play vital for the
replication cycle of the virus. Honey bee products are well known of their
nutritional values and medicinal effects. Antimicrobial activity of bee
products and natural honey have been documented in several clinical studies and
was considered a good alternative for antiviral medications to treat some viral
infections. Bee products contain bioactive compounds in the form of a
collection of phenolic acids, flavonoids and terpenes of natural origin. We revealed
by molecular docking the profound binding affinity of 14 selected phenolics and
terpenes present in honey and propolis (bees glue) against the main protease (M<sup>pro</sup>) and RNA dependent RNA polymerase (RdRp) enzymes
of the novel 2019-nCoV coronavirus. Of these compounds, <i>p</i>-coumaric acid, ellagic acid, kaemferol and
quercetin has
the strongest interaction with the 2019-nCoV target enzymes, and they may be
considered as an effective 2019-nCoV inhibitors.
|
Moataz A. Shaldam; Galal Yahya; Nashwa H. Mohamed; Mohamed M. Abdel-Daim; Yahya Al Naggar
|
Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74db84c8919ae53ad386f/original/in-silico-screening-of-potent-bioactive-compounds-from-honey-bee-products-against-covid-19-target-enzymes.pdf
|
661f8af521291e5d1d032cbe
|
10.26434/chemrxiv-2024-hlhr5
|
Boosting hydrogen production at room temperature by synergizing theory and experimentation
|
Methane is a major constituent of natural gas and is widely used in hydrogen production. However, its high symmetry poses a challenge, as breaking the strong C-H bond requires substantial energy input. Hence, there is a pressing need to develop efficient catalysts for methane conversion. By synergizing theory and experimentation, the search for a better catalyst can be accelerated, potentially boosting methane con- version processes. In the present work, theoretical findings prompted the experiments, which revealed the spontaneous dissociation of CH4 on selected facets of β-Ga2O3. Additionally, the activation barrier for ethane formation was merely 0.1 eV. NTP-assisted conversion of methane in the presence of β-Ga2O3 confirmed these findings. The formation rate of hydrogen and ethane rises to 366 µmolg−1h−1 and 86.62 µmolg−1h−1, respectively, in the presence of β-Ga2O3 , in contrast to 281.4 µmolg−1h−1 and 66 µmolg−1h−1 without catalysts. For the CH4-H2O reaction in the presence of β-Ga2O3 , there is an increase of 74.42% in the CO formation rate compared to the reaction without the catalyst. An electronic structure analysis revealed that electrophilic oxygen species on the β-Ga2O3 (-202) surface play a vital role in the decomposition of methane, facilitating C-H bond cleavage.
|
Kavita Thakkar; Abhinav Bajpai; Sushant Kumar; Kavita Joshi
|
Theoretical and Computational Chemistry; Materials Science; Catalysis; Catalysts; Computational Chemistry and Modeling; Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-04-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661f8af521291e5d1d032cbe/original/boosting-hydrogen-production-at-room-temperature-by-synergizing-theory-and-experimentation.pdf
|
65c4bbd966c138172935dc8c
|
10.26434/chemrxiv-2024-c0xc0
|
Consistent Construction of Density Matrix from Surface Hopping Trajectories
|
Proper construction of density matrix based on surface hopping trajectories remains a difficult problem. Due to the well-known overcoherence in traditional surface hopping simulations, the electronic wavefunction cannot be used directly. In this work, we propose a consistent density matrix construction method, which takes the advantage of occupation of active states to rescale the coherence calculated by wavefunctions and ensures the intrinsic consistency of density matrix. This new trajectory analysis method can be used for both Tully’s fewest switches surface hopping (FSSH) and our recently proposed branching corrected surface hopping (BCSH). As benchmarked in both one- and two-dimensional standard scattering models, the new approach combined with BCSH trajectories achieves highly accurate time-dependent spatial distributions of adiabatic populations and coherence compared with exact quantum results.
|
Jiabo Xu; Zhecun Shi; Linjun Wang
|
Theoretical and Computational Chemistry; Theory - Computational
|
CC BY 4.0
|
CHEMRXIV
|
2024-02-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c4bbd966c138172935dc8c/original/consistent-construction-of-density-matrix-from-surface-hopping-trajectories.pdf
|
60c73cc9bb8c1a1eed3d961b
|
10.26434/chemrxiv.14738259.v1
|
Concise and Stereoselective Total Syntheses of Annotinolides C, D, and E
|
The annotinolides are one of the most recent additions
to the <i>Lycopodium</i> family of
alkaloids, with its members possessing challenging, caged structures that
include a [3.2.1]-bicyclic core bearing six contiguous stereocenters, including
oxa-, aza-, and all-carbon quaternary centers.
Herein, we document a concise and stereoselective route that achieves the
first total syntheses of three of its members: annotinolides C, D, and E. Key operations include a gold(I)-catalyzed
Conia-ene reaction that fashions much of the main core in a single operation, as
well as a number of other challenging and chemoselective transformations to generate
the remaining elements. Moreover,
efforts utilizing the natural products themselves, seeking adjustments in their
oxidation states and the rearrangement of individual ring systems, sheds light
on their potential biogenesis with some outcomes counter to those originally
proposed. Finally, formal
enantioenriched syntheses of the target molecules are also presented.
|
Pei Qu; Scott Snyder
|
Natural Products; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-06-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc9bb8c1a1eed3d961b/original/concise-and-stereoselective-total-syntheses-of-annotinolides-c-d-and-e.pdf
|
60c74f0b9abda2d3e4f8d78c
|
10.26434/chemrxiv.12799979.v2
|
Photodissociation Dynamics of Ortho and Meta Fluorophenols: The Origin of Fast Protons
|
A recent
experimental study with time-resolved velocity map imaging demonstrated that the total kinetic energy release
spectra obtained from photodissociation of <i>ortho</i>
and <i>meta</i> fluorophenols have distinct features
after excitation into the origin of the S<sub>1</sub>
state. A peak at 6000 cm<sup>-1</sup>
was observed for both molecules, while another at 13000 cm<sup>-1 </sup>dominates
the spectrum of <i>ortho</i>-fluorophenol.
The peak at 6000 cm<sup>‑1</sup> was assigned to H tunneling. Nevertheless, the
13000 cm<sup>-1</sup> feature remains unassigned. In this work, we performed a
theoretical analysis, investigating two hypotheses for explaining the 13000 cm<sup>‑1</sup>
signal. The first hypothesis is that it is due to one-photon absorption followed by ionization through resonant multiphoton dissociation. The second hypothesis is that the
signal is due to two-photon absorption into a superexcited state, which
dissociates yielding an H atom. We discuss the pros and cons of each hypothesis,
laying the groundwork for future experiments.
|
xinli song; Josene Toldo; Carlos E. V. de Moura; Ying Tang; Bing Zhang; Mario Barbatti
|
Photochemistry (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f0b9abda2d3e4f8d78c/original/photodissociation-dynamics-of-ortho-and-meta-fluorophenols-the-origin-of-fast-protons.pdf
|
66963b4e5101a2ffa885a9de
|
10.26434/chemrxiv-2024-6mr3t
|
Serinophospholipids: A third type of natural phospholipid discovered in a thermophilic bacterium
|
Phospholipids are an essential constituent of cells with all life thought to produce phospholipids with either a glycerol or sphingoid moiety at their core. For the first time, we demonstrate that a thermophilic bacterium, Limisphaera ngatamarikiensis NGM72.4T, produces a third type of phospholipid – serinophospholipids – which are distinct from glycero- and sphingophospholipids by featuring a serinol backbone instead. We show that the major serinophospholipid metabolites are N,O-diacylserinophospho-N-methylethanolamine and N,O-diacylserinophosphoethanolamine, and that serinophospholipids constitute up to 38% of the phospholipid mass. Furthermore, we demonstrate that these metabolites are further differentiated from ‘traditional’ bacterial glycerophospholipids by their backbone stereochemistry. In contrast to bacterial glycerophospholipids, which have an sn-glycerol-3-phosphate (G3P) architecture, the newly discovered serinophospholipids have an (S)-configured serinol core that is equivalent to the sn-glycerol-1-phosphate (G1P) arrangement characteristic of Archaea. This research expands the known diversity of phospholipids beyond the current two backbone paradigm and challenges our understanding of lipid evolution.
|
Mikhail Vyssotski; Kirill Lagutin; Andrew MacKenzie; Kevin Mitchell; Arran Stewart; Dawn Scott; Matthew Stott; Benji Compton
|
Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Microbiology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66963b4e5101a2ffa885a9de/original/serinophospholipids-a-third-type-of-natural-phospholipid-discovered-in-a-thermophilic-bacterium.pdf
|
656b8ef9cf8b3c3cd7a639b1
|
10.26434/chemrxiv-2023-9xsq2
|
Bioorthogonal Chemistry of Polyoxometalates – Challenges and Prospects
|
Bioorthogonal chemistry enabled scientists to carry out controlled chemical processes in high yields in vivo while minimizing hazardous effects. Its extension to the field of polyoxometalates (POMs) could open up new possibilities and new applications in molecular electronics, sensing and catalysis, including inside living cells. However, this comes with many challenges that need to be addressed to effectively implement and exploit bioorthogonal reactions in the chemistry of POMs. In particular, how to protect POMs from the biological environment but make their reactivity selective towards specific bioorthogonal tags (and thereby reduce their toxicity), as well as which bioorthogonal chemistry protocols are suitable for POMs and how reactions can be carried out are questions that we are exploring herein. This Perspective conceptualizes and discusses advances in the supramolecular chemistry of POMs, their click chemistry, and POM-based surface engineering to develop innovative bioorthogonal approaches tailored to POMs and improve POM biological tolerance.
|
Stanislav K. Petrovskii; Elena V. Grachova; Kirill Yu. Monakhov
|
Biological and Medicinal Chemistry; Inorganic Chemistry; Bioinorganic Chemistry; Supramolecular Chemistry (Inorg.); Cell and Molecular Biology; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656b8ef9cf8b3c3cd7a639b1/original/bioorthogonal-chemistry-of-polyoxometalates-challenges-and-prospects.pdf
|
60c7502a469df4d770f44803
|
10.26434/chemrxiv.12981857.v1
|
Surprisal of a Quantum State: Dynamics, Compact Representation and Coherence Effects
|
<p>Partially averaged or resolved distributions of quantum states are measured (or simulated) in diverse branches of Physics, in Chemical Physics and more recently in Biological Physics. Lately they are an output of quantum computations. Surprisal analysis, a blending of information theory and thermodynamics has been extensively used to characterize and compact such distributions. Currently, when coherence between quantum states is of central interest, the algebraic awkwardness of implementing a quantum mechanical procedure of maximal entropy is becoming an issue. We present a novel theoretical approach and its practical computational implementation with special reference to dynamical processes.</p>
|
Ksenia Komarova; Francoise Remacle; Raphael D. Levine
|
Photochemistry (Physical Chem.); Physical and Chemical Processes; Physical and Chemical Properties; Quantum Mechanics; Spectroscopy (Physical Chem.); Statistical Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-09-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7502a469df4d770f44803/original/surprisal-of-a-quantum-state-dynamics-compact-representation-and-coherence-effects.pdf
|
60c75267f96a0082a52881db
|
10.26434/chemrxiv.13289525.v1
|
Graphene Reinforced Polyether Ether Ketone Nanocomposites for Bone Repair Applications
|
To improve the performance of polyether ether ketone matrix (PEEK) in hard tissue repair and replacement applications, we fabricated graphene (G) reinforced PEEK with graded G concentrations (0.1%-5%) through injection molding. The mechanical properties, surface morphology, chemical composition and thermal stability of the composites have been characterized through universal mechanical testing, scanning electron microscopy, contact-angle measurement, transmission electron microscope, X-ray photoelectron spectroscopy, X-ray diffraction and thermal analysis system. The biocompatibility has been assessed in vitro and the bone repair function of the composite implant have been assessed in vivo using a rabbit mandibular bone defect model. Mechanical testing results suggest that the composite samples have compressive moduli similar to that of the natural bone. Although addition of G into PEEK does not significantly influence the composite tensile, flexural or compressive moduli, it can significantly enhance the ductility and toughness of the material. On the other hand, all G-reinforced PEEK implants demonstrated enhanced adhesion and differentiation of rat bone marrow stromal cells (BMSCs), with 5% G-PEEK showing the highest bioactivity among all samples. The in vivo osseointegration data further revealed that 5% G-PEEK has the best effect in promoting osseointegration and bone regeneration, in both early stage and late stage bone re-growth. Study shows that our G-reinforced PEEK-based implants provides a promising strategy for enhancing the performance of future regenerative bone implants.<br />
|
Nan Jiang; Peijie Tan; Miaomiao He; dan Sun; Li Zhang; Songsong Zhu
|
Biocompatible Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-11-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75267f96a0082a52881db/original/graphene-reinforced-polyether-ether-ketone-nanocomposites-for-bone-repair-applications.pdf
|
60c75769567dfe6e02ec6693
|
10.26434/chemrxiv.14400989.v1
|
Rhenium Carbonyl Complexes Conjugated with Methylated Triphenylphosphonium Cations as Sensitive Mitochondria Trackers for X-Ray Fluorescence Imaging
|
<div>Synchrotron
Radiation X-ray Fluorescence (SXRF) imaging is a powerful technique for the
visualization of metal complexes in biological systems. However, due to the
lack of an endogenous elemental signature for mitochondria, probes for the
localization of this organelle are required for colocalization studies. In this
work, we designed and synthesized rhenium pyta tricarbonyl complexes conjugated
to methylated triphenylphosphonium TP*P+ cations as multimodal probes for the
visualization of mitochondria, suitable for fluorescence and SXRF imaging and
quantification. Accumulation of the methylated triphenylphosphonium TP*P+-based
conjugates in cells was observed in fixed A549 cells, and the amount of
mitochondrial uptake was linked to the lipophilicity of the TPP+ vector. Our
work highlights a convenient rhenium-based multimodal mitochondrial-targeted
probe compatible with SXRF nano-imaging.</div>
|
Gabrielle Schanne; Lucas Henry; How Chee Ong; Andrea Somogyi; Kadda Medjoubi; Nicolas DELSUC; Clotilde Policar; Felipe Garcia; Hélène C. Bertrand
|
Bioinorganic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75769567dfe6e02ec6693/original/rhenium-carbonyl-complexes-conjugated-with-methylated-triphenylphosphonium-cations-as-sensitive-mitochondria-trackers-for-x-ray-fluorescence-imaging.pdf
|
6799017b6dde43c908b9fe46
|
10.26434/chemrxiv-2025-q762k
|
Vapor Phase Installation of CpCo(CO)2 in MOF-808
|
Metal-organic frameworks (MOFs) including MOF-808 present an opportunity for vapor phase installation of reactive centers that may serve as uniform sites for precision catalysis. The mechanism of cobalt installation in MOF-808 through atomic layer deposition (ALD) upon CpCo(CO)2 exposure is investigated through in situ FTIR spectroscopy complemented by density functional theory modeling. The role of subsequent H2O exposure in the hydrolysis of carbonyl and cyclopentadienyl ligands to complete the installation is also investigated. In situ FTIR study reveals that upon exposure of CpCo(CO)2 to MOF-808 at 115 °C, a long-lived, stable intermediate is formed that presents carbonyl stretching vibrations similar to the undissociated precursor that are attributed to chemisorbed carbonyl complexes. In MOF-808, the cobalt precursor is initially absorbed near the BTC linker, revealing the importance of non-covalent interactions in the installation process. DFT suggests that subsequent H2O exposure promotes carbonyl elimination but leaves a cyclopentadienyl-capped cobalt that is more stable than the complete hydrolysis product. The calculations are consistent with cobalt installation in MOF-808 using CpCo(CO)2 and H2O at 115 °C and further consistent with a lack of cobalt oxide ALD thin film deposition on planar supports.
|
Thabiso Kunene; Juan Pablo Vizuet; Matthew Klenk; Peter Zapol; Ksenija Glusac; Alex Martinson
|
Materials Science; Catalysis; Energy
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6799017b6dde43c908b9fe46/original/vapor-phase-installation-of-cp-co-co-2-in-mof-808.pdf
|
60c75a2f702a9bf7f218cfac
|
10.26434/chemrxiv.12228362.v7
|
New Potential Drug Candidates Against SARS-CoV-2 Using Generative Model
|
<div>Since known approved drugs like liponavir and ritonavir failed to cure SARS-CoV-2 </div><div>infected patients, it is high time to generate new chemical entities against this virus. </div><div>3CL main protease acts as key enzyme for the growth of a virus which acts as </div><div>biocatalyst and helps to break protein and ultimately in the growth of coronavirus. </div><div>Based on a recently solved structure (PDB ID: 6LU7), we developed a novel </div><div>advanced deep Q-learning network with the fragment-based drug design </div><div>(ADQN-FBDD) along with variational autoencoder with KL annealing and circular </div><div>annealing for generating potential lead compounds targeting SARS-CoV-2 3CLpro. </div><div>Structure-based optimization policy (SBOP) is used in reinforcement learning. The </div><div>reason for using variational autoencoders is that it does not deviate much from actual </div><div>inhibitors, but since VAE suffers from KL diminishing we have used KL annealing </div><div>and circular annealing to address this issue. Researchers can use this compound as </div><div>potential drugs against SARS-CoV-2</div>
|
Madhusudan Verma
|
Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75a2f702a9bf7f218cfac/original/new-potential-drug-candidates-against-sars-co-v-2-using-generative-model.pdf
|
655138fb6e0ec7777fd1be9e
|
10.26434/chemrxiv-2023-n0mf2
|
Carbon-coated Cu nanoparticles as heterogeneous catalysts for cycloaddition of propargylamine to cyclic ketones
|
A set of 22 composites was prepared by pyrolysis of Cu2+ complexes with phenanthroline and 1,2-diaminobenzene, deposited on SiO2 (Aerosil). All composites contained Cu and carboneous components, while some of them additionally contained Cu2O or CuCl. According to the data of powder X-ray diffraction, the size of Cu nanoparticles was 20-37 nm. The presence of Cu nanoparticles was confirmed by TEM, while some aggregates were found by SEM. The composites were tested as the heterogeneous catalysts in the process of cycloaddition of propargylamine with 4-oxocyclohexanecarboxylate leading to ethyl 5,6,7,8-tetrahydroquinoline-6-carboxylate. It was found that the product yield did not correlate with Cu content in the reaction mixture or other single parameters, but reached maximal values at certain values of parameters, proportional to the surface of Cu and surface of C, exposed to the reagents. It was found that the leaching of Cu takes place upon repeated use of the composites.
|
Dmytro Yehorov; Svitlana Sotnik; Vitalii Asaula; Olena Pariiska; Evgenia Senchylo; Illia Pavliei; Igor Kotenko; Anastasiya Terebilenko; Alexander Rozhenko; Konstantin Gavrilenko; Serhiy Ryabukhin; Dmytro Volochnyuk; Sergey Kolotilov
|
Organic Chemistry; Catalysis; Heterogeneous Catalysis
|
CC BY 4.0
|
CHEMRXIV
|
2023-11-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655138fb6e0ec7777fd1be9e/original/carbon-coated-cu-nanoparticles-as-heterogeneous-catalysts-for-cycloaddition-of-propargylamine-to-cyclic-ketones.pdf
|
67c1b575fa469535b9501d48
|
10.26434/chemrxiv-2025-gklc3
|
Reaction between the Ionic Liquid BMP-TFSI and Li: Comparison between Monolayer Films and Thick Multilayer Films on Graphite (0001
|
Aiming at a molecular-scale understanding of the initial stages of the solid-electrolyte interphase (SEI) formation in Li ion batteries, we have investigated the chemical reaction of a monolayer of the ionic liquid 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide (BMP-TFSI) adsorbed on a graphite (0001) substrate during post-deposition of Li and subsequent annealing in a combined experimental and theoretical approach. For comparison, also the reaction between a bulk-like multilayer BMP-TFSI film and post-deposited Li was investigated. Employing x-ray photoelectron spectroscopy (XPS) and density functional theory (DFT) based calculations, we find that already post-deposition of Li at room temperature leads to a significant modification of both monolayer film and bulk BMP-TFSI, including the formation of (adsorbed) molecular fragments, binary Li compounds and desorption of volatile, C- and F-containing species. The initial reaction with Li is highly exothermic and non- or little activated, products are identified by comparison of experimental XP spectra and calculated core level binding energies. Further reaction steps, leaving only binary Li compounds or comparable adsorbed species, are considerably activated and require annealing to >500 K – 650 K, depending on the anion. Consequences of these results for the molecular-scale understanding of the initial stages of SEI formation in an electrochemical environment are discussed.
|
Katrin Forster-Tonigold; Florian Buchner; Axel Groß; R. Juergen Behm
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Processes
|
CC BY 4.0
|
CHEMRXIV
|
2025-03-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c1b575fa469535b9501d48/original/reaction-between-the-ionic-liquid-bmp-tfsi-and-li-comparison-between-monolayer-films-and-thick-multilayer-films-on-graphite-0001.pdf
|
60c756f3567dfeed4eec65ba
|
10.26434/chemrxiv.14347277.v1
|
Rh(III)-Catalyzed Three-Component Syn-Carboamination of Alkenes Using Arylboronic Acids and Dioxazolones
|
<p>Herein we report a Rh(III)-catalyzed three-component carboamination of alkenes from readily available aryl boronic acids as a carbon source and dioxazolones as nitrogen electrophiles. This protocol provides facile access to valuable amine products including <i>a</i>-amino acid derivatives in good yield and excellent regioselectivity without the need for a directing functionality. A series of experiments suggest a mechanism in which the Rh(III) catalyst undergoes transmetalation with the aryl boronic acid followed by turnover limiting, alkene migratory insertion into the Rh(III)-aryl bond. Subsequently, fast Rh-nitrene formation provides the <i>syn</i>-carboamination product selectively after reductive elimination and proto-demetalation. Importantly, the protocol provides 3-component coupling products in preference to a variety of 2-component undesired by-products.</p>
|
Sumin Lee; Tomislav Rovis
|
Organic Synthesis and Reactions; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756f3567dfeed4eec65ba/original/rh-iii-catalyzed-three-component-syn-carboamination-of-alkenes-using-arylboronic-acids-and-dioxazolones.pdf
|
66d57e7c20ac769e5f980b0b
|
10.26434/chemrxiv-2024-tj3p3
|
An analysis of published synthetic routes, route targets and reaction types (2000 – 2020)
|
Using a large dataset (640k synthetic routes and 2.4m reactions) compiled from six popular journals between 2000 – 2020, trends are identified and discussed for topics including journal publishing rates, availability of machine-readable data, characteristics of synthetic route targets and starting materials (molecular weight, complexity, elemental composition, chirality and ring-systems) and the reaction classes utilised in these synthetic routes. We provide evidence of an ongoing shift away from large natural product or “total” syntheses amongst the academic data and a gradual increase in the size and complexity of industrial/medicinal target molecules. The reaction class analyses show key differences between the academic and industrial sectors and how a small number of reaction types have proliferated in the latter, giving rise to a possible lack of target diversity. Overall, there is evidence to support an ongoing increase in synthetic efficiency whereby, as a community, we are synthesizing larger, more-complex molecules from smaller, simpler starting materials, in fewer steps and with diminished reliance on non-productive reaction types such as protecting group manipulations, redox reactions and functional group interconversions.
|
Gareth Howell; Samuel Genheden
|
Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Process Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-09-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d57e7c20ac769e5f980b0b/original/an-analysis-of-published-synthetic-routes-route-targets-and-reaction-types-2000-2020.pdf
|
66e80b54cec5d6c1423826d7
|
10.26434/chemrxiv-2024-h6mw9
|
Low-Temperature Borylation of C(sp3)–O Bonds of Alkyl Ethers by Gold-Metal Oxide Cooperative Catalysis
|
Since ether moieties are often found not only in petrochemical products but also in natural organic molecules, the development of methods for manipulating C–O bonds of ethers is important for expanding the range of compound libraries synthesized from biomass resources, which should contribute to the goal of carbon neutrality. We report herein that gold nanoparticles supported on Lewis acidic metal oxides, namely α-Fe2O3, showed excellent catalytic activity for the reaction of dialkyl ethers and diborons, which enables the conversion of unactivated C(sp3)–O bonds to C(sp3)–B bonds at around room temperature. Various acyclic and cyclic ethers as well as a series of diborons participated in the heterogeneous gold-catalyzed borylation of unactivated C(sp3)–O bonds, to give a series of alkylboronates in high yields. Mechanistic studies corroborated that the present borylation of C(sp3)–O bonds of dialkyl ethers proceeded at the interface between gold nanoparticles and Lewis acidic metal oxides. Furthermore, adsorption IR measurements supported the notion that strong Lewis acid sites were generated at the boron atom of diborons adsorbed at the interface between Lewis acidic metal oxides and gold nanoparticles, which enabled us to ensure that the cooperation of gold nanoparticles and Lewis acidic metal oxides was responsible for the efficient transformation of unactivated C(sp3)–O bonds in ethers under mild conditions. This novel reaction technology which is specific to heterogeneous catalysts enables the activation of stable C(sp3)–O bonds of oxygenated chemical feedstock, which is beneficial for the sustainable synthesis of value-added organoboron compounds.
|
Hidenori Nishio; Hiroki Miura; Tetsuya Shishido
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-09-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e80b54cec5d6c1423826d7/original/low-temperature-borylation-of-c-sp3-o-bonds-of-alkyl-ethers-by-gold-metal-oxide-cooperative-catalysis.pdf
|
648b105fe64f843f41d2588b
|
10.26434/chemrxiv-2023-kl7x8
|
Direct valorization of biomass waste to gamma-valerolactone
|
Biomass is the only renewable hydrocarbon resource on Earth and therefore plays an essential role in a future sustainable society. Nevertheless, biomass is underutilized for production of chemicals, and is instead burned for energy or left for compost. Derived from biogenic carbohydrates, gamma-valerolactone (GVL) holds pivotal potential as a green fuel, solvent, and platform compound. Converting carbohydrate-rich biomass waste directly to GVL is therefore highly attractive but also very challenging owing to the inert nature and high complexity of biomass, necessitating a versatile and selective catalytic system.
Developing benign and complexity-preserving biomass valorization processes would not only allow for sustainable methods to synthesize valuable commodity chemicals, but also provide access to highly attractive carbon-negative procedures. Therefore, producing GVL, that preserves five out of six C–C bonds in hexoses and all the C–C bonds in pentoses, has a high potential.
We describe the first direct conversion of raw lignocellulose, starch, and chitin biomass to GVL. Using 1.8 wt% of the homogeneous catalyst Ru-MACHO-BH in 10.9 M H3PO4(aq) with 30 bar of H2 at 140 °C for 24-120 hours provides GVL in excellent yields (10-26 wt%) from twelve different biogenic or industrially processed biowaste sources, either as individual substrates or a combined pool. This corresponds to 26-48mol% yields, or an average of approximately 80-90 mol% yield in each reaction step.
|
Sakhitha Koranchalil; Martin Nielsen
|
Organic Chemistry; Catalysis; Organometallic Chemistry; Acid Catalysis; Homogeneous Catalysis; Transition Metal Complexes (Organomet.)
|
CC BY 4.0
|
CHEMRXIV
|
2023-06-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648b105fe64f843f41d2588b/original/direct-valorization-of-biomass-waste-to-gamma-valerolactone.pdf
|
66c617eea4e53c48762295f8
|
10.26434/chemrxiv-2024-rk909
|
Basis-set limit CCSD(T) energies for large molecules with local natural orbitals and reduced-scaling basis-set corrections
|
The calculation of density-based basis-set correction (DBBSC), which remedies the basis-set incompleteness (BSI) error of the correlation energy, is combined with local approximations. Aiming at large-scale applications, the procedure is implemented in our efficient local natural orbital-based coupled-cluster singles and doubles with per- turbative triples [LNO-CCSD(T)] scheme. To this end, the range-separation function, which characterizes the one-electron BSI in space, is decomposed into the sum of con- tributions from individual localized molecular orbitals (LMOs). A compact domain is constructed around each LMO, and the corresponding contributions are evaluated only within these restricted domains. Furthermore, for the calculation of the com- plementary auxiliary basis set (CABS) correction, which significantly improves the Hartree–Fock (HF) energy, the local density fitting approximation is utilized. The er- rors arising from the local approximations are examined in detail, efficient prescreening techniques are introduced to compress the numerical quadrature used for DBBSC, and conservative default thresholds are selected for the truncation parameters. The effi- ciency of the DBBSC-LNO-CCSD(T) method is demonstrated through representative examples of up to 1000 atoms. Based on the numerical results, we conclude that the corrections drastically reduce the BSI error using double-ζ basis sets, often to below 1 kcal/mol compared to the reliable LNO-CCSD(T) complete basis set references, while significant improvements are also achieved with triple-ζ basis sets. Considering that the calculation of the DBBSC and CABS corrections only moderately increases the wall-clock time required for the post-HF steps in practical applications, the proposed DBBSC-LNO-CCSD(T) method offers a highly efficient and robust tool for large-scale calculations.
|
David Mester; Peter Nagy; Mihaly Kallay
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c617eea4e53c48762295f8/original/basis-set-limit-ccsd-t-energies-for-large-molecules-with-local-natural-orbitals-and-reduced-scaling-basis-set-corrections.pdf
|
6256d7cc11b14627be20776a
|
10.26434/chemrxiv-2022-9z6j7
|
Insights on the Lewis Superacid Al(OTeF5)3: Solvent Adducts, Characterization and Properties
|
The improved preparation of the Lewis superacid Al(OTeF5)3 and several solvent adducts is presented. These range from thermally stable adducts to highly reactive, weakly bound species. DFT calculations on the ligand affinity of this Lewis acids were performed in order to rank their remaining Lewis acidity. An experimental proof of the Lewis acidity is provided by the reaction of Al(OTeF5)3 with [PPh4][SbF6] and OPPh3. Furthermore, reactivities towards chloride salts as well as CH3SiCl and CH3SiF are shown.
|
Kurt F. Hoffmann; Anja Wiesner; Simon Steinhauer; Sebastian Riedel
|
Inorganic Chemistry; Inorganic Acid/Base Chemistry; Main Group Chemistry (Inorg.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-04-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6256d7cc11b14627be20776a/original/insights-on-the-lewis-superacid-al-o-te-f5-3-solvent-adducts-characterization-and-properties.pdf
|
640897c96642bf8c8f2d4577
|
10.26434/chemrxiv-2023-wc46q
|
Cytochrome P450-Mediated Cyclization in Eunicellane-Derived Diterpenoid Biosynthesis
|
Terpene cyclization, one of the most complex chemical reactions in nature, is generally catalyzed by two classes of terpene cyclases (TCs). Cytochrome P450s that act as unexpected TC-like enzymes are known but are very rare. Here, we genome-mined a cryptic bacterial terpenoid gene cluster, named ari, from the thermophilic actinomycete strain Amycolatopsis arida. By employing a heterologous production system, we isolated and characterized three highly oxidized eunicellane-derived diterpenoids, aridacins AC (13), that possess a rare 6/7/5-fused tricyclic scaffold. In vivo and in vitro experiments systematically established a non-canonical two-step biosynthetic pathway for diterpene skeleton formation. First, a class I TC (AriE) cyclizes geranylgeranyl diphosphate (GGPP) into a 6/10-fused bicyclic cis-eunicellane skeleton. Next, a cytochrome P450 (AriF) catalyzes cyclization of the eunicellane skeleton into the 6/7/5-fused tricyclic scaffold via C2-C6 bond formation. Quantum chemical computations support a hydrogen abstraction and subsequent oxidation mechanism for AriF catalyzed carbocation cyclization. The biosynthetic logic of skeleton construction in the aridacin diterpenoids is unprecedented, expanding the catalytic capacity and diversity of P450s and setting the stage to investigate the inherent principles of carbocation generation by P450s in the biosynthesis of terpenoids.
|
Zengyuan Wang; Qian Yang; Jingyi He; Haixin Li; Xingming Pan; Zining Li; Hui-Min Xu; Jeffrey D. Rudolf; Dean J. Tantillo; Liao-Bin Dong
|
Biological and Medicinal Chemistry; Catalysis; Biochemistry; Chemical Biology; Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640897c96642bf8c8f2d4577/original/cytochrome-p450-mediated-cyclization-in-eunicellane-derived-diterpenoid-biosynthesis.pdf
|
65704ce429a13c4d47c56e0e
|
10.26434/chemrxiv-2023-f32t3
|
Investigating Polypharmacology Through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3
|
Using a combination of state-of-the-art free energy computational approaches together with in vitro IC50 assays, we evaluated the polypharmacological potential of a scaffold currently in clinical trials for inhibition of human neutrophil elastase (HNE), targeting cardiopulmonary disease, for efficacious inhibition of Proteinase 3 (PR3), a related neutrophil serine proteinase. Based on benchmarking of a series of ligands with known inhibitory activity against HNE using multisite λ-dynamics (MSλD) and multiple force field models, we demonstrated the best agreement between measured IC50 values and computed binding free energies using a hybrid force field of CHARMM c36m for the protein and ligand parameters from OPLS LigParGen that utilizes a CM1A-LBCC charge model. Using this computational model, the ligands were assessed as potential inhibitors of PR3 by anchoring the computed relative binding affinities to a single measured IC50. This led to suggested potential additional inhibitors for PR3 from those tested and characterized to be good binders to HNE. We synthesized and assayed a number of these compounds to further test our predicted binding affinities and discovered that both prediction and experiment demonstrated that the compounds bound less well to PR3, we observed a range of IC50s from 7.7-190 nM in PR3 to 0.5-1.3 nM for the same inhibitors for HNE. However, the affinities we observe suggest that the scaffold can serve as a suitable starting point for the establishment of polypharmacologically targeting both enzymes and enhancing the potential for treatments addressing diseases like chronic obstructive pulmonary disease.
|
Parveen Gartan; Fahimeh Khorsand; Pushpak Mizar; Juha Ilmari Vahokovski; Luis F Cervantes; Bengt Erik Haug; Ruth Brenk; Charles L. Brooks; Nathalie Reuter
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-12-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65704ce429a13c4d47c56e0e/original/investigating-polypharmacology-through-targeting-known-human-neutrophil-elastase-inhibitors-to-proteinase-3.pdf
|
630ca0ae58843b37d2a17446
|
10.26434/chemrxiv-2022-xrthv
|
Pauling Number as Efficient Descriptors for Screening the Structures with Negative Thermal Expansion Characteristics
|
In this study, the analysis of the known structure types demonstrating NTE was performed. Describing these structure types by the recently introduced and manifested parameter, Pauling Number (PN), showed that it is possible to circumscribe the candidate compounds with these characteristics by using this structure parameter since the flexibility of the compounds framework and the lattice topology are highly associated with the possibility of materials do not expand the lattice parameters while heating and to limit the changes of the structure during the possible phase transitions by, e.g., polyhedral tilting. We suggest that compounds with PN value close to those of the NTE materials can be considered as the targets for further investigation.
|
Natalia Kireeva; Aslan Yu. Tsivadze
|
Materials Science; Ceramics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630ca0ae58843b37d2a17446/original/pauling-number-as-efficient-descriptors-for-screening-the-structures-with-negative-thermal-expansion-characteristics.pdf
|
61fae635e0f5296976a52906
|
10.26434/chemrxiv-2022-5hgz9
|
Emission and Absorption Tuning in MR-TADF B,N-Doped Hep-tacenes: Towards Ideal-Blue Hyperfluorescent OLEDs
|
Developing high-efficiency purely organic blue organic light-emitting diodes (OLEDs) that meet the stringent industry standards is a major current research challenge. Hyperfluorescent device approaches achieve in large measure the desired high performance by combining the advantages of a high-efficiency thermally activated delayed fluorescence (TADF) assistant dopant with a narrowband deep-blue multi-resonant TADF (MR-TADF) terminal emitter. However, this ap-proach requires suitable spectral overlap to support Förster resonance energy transfer (FRET) between the two.
Here we demonstrate colour tuning of a recently reported MR-TADF B,N-heptacene core through control of the boron substituents. While there is little impact on the intrinsic TADF properties - as both singlet and triplet energies decrease in tandem - this approach improves the emission colour coordinate as well as the spectral overlap for blue hyperfluorescence OLEDs (HF OLEDs). Crucially, the red-shifted and more intense absorption allows us to pair this MR-TADF emitter with a high-performance TADF assistant dopant and achieve maximum external quantum efficiency (EQEmax) of 15% at colour coordinates of (0.15, 0.10). The efficiency values recorded for our device at a practical luminance of 100 cd m-2 are among the highest reported for HF TADF OLEDs with CIEy ≤ 0.1.
|
Kleitos Stavrou; Subeesh Suresh; David Hall; Andrew Danos; Nadzeya Kukhta; Alexandra Slawin; Stuart Warriner; David Beljonne; Yoann Olivier; Andrew Monkman; Eli Zysman-Colman
|
Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Spectroscopy (Physical Chem.); Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-02-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61fae635e0f5296976a52906/original/emission-and-absorption-tuning-in-mr-tadf-b-n-doped-hep-tacenes-towards-ideal-blue-hyperfluorescent-ole-ds.pdf
|
62fcfcd2ceed6f72bb323de6
|
10.26434/chemrxiv-2022-qzvh2
|
Photochemically-Mediated Polymerization of Molecular Furan and Pyridine: Synthesis of Nanothreads at Reduced Pressures
|
Nanothreads are an emerging one-dimensional sp3-hybridized material with high predicted tensile strength and a tunable band gap. They can be synthesized by compressing aromatic, or non-aromatic small molecules under 15-30 GPa of pressure. Recently, new avenues are being sought that reduce the pressure required to afford nanothreads; focus has been placed on the polymerization of molecules with reduced aromaticity, favorable stacking, and/or the use of higher reaction temperatures. Herein, we report the photochemically-mediated polymerization of pyridine and furan aromatic precursors, which achieves nanothread formation at reduced pressures. In the case of pyridine, it was found that a combination of slow compression/decompression with broadband UV light exposure yielded a crystalline product featuring a six-fold diffraction pattern with similar interplanar spacings of previously synthesized pyridine-derived nanothreads at a reduced pressure. When furan is compressed to 8 GPa and exposed to broadband UV light, a crystalline solid is recovered that similarly demonstrates X-ray diffraction with an interplanar spacing akin to that of the high-pressure synthesized furan-derived nanothreads. Our method realizes a 1.9-fold reduction in the maximum pressure required to afford furan-derived nanothreads and a 1.4-fold reduction in pressure required pyridine-derived nanothreads. Density functional theory and multiconfigurational wavefunction-based computations were used to understand the photochemical activation of furan and subsequent cascade thermal cycloadditions. The reduction of the onset pressure is caused by an initial [4+4]-cycloaddition followed by increasingly facile thermal [4+2]-cycloadditions during polymerization. Density functional theory and multiconfigurational wavefunction-based computations were used to understand the photochemical activation of furan and subsequent cascade thermal cycloadditions.
|
Shalisa Oburn; Steven Huss; Jordan Cox; Margaret Gerthoffer; Sikai Wu; Arani Biswas; Morgan Murphy; Vincent Crespi; John Badding; Steven Lopez; Elizabeth Elacqua
|
Organic Chemistry; Polymer Science; Photochemistry (Org.); Organic Polymers; Polymerization (Polymers); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-08-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fcfcd2ceed6f72bb323de6/original/photochemically-mediated-polymerization-of-molecular-furan-and-pyridine-synthesis-of-nanothreads-at-reduced-pressures.pdf
|
60c73f1abdbb8947e8a37f11
|
10.26434/chemrxiv.7234058.v1
|
The Protein’s Role in Substrate Positioning and Reactivity for Biosynthetic Enzyme Complexes: the Case of SyrB2/SyrB1
|
Biosynthetic enzyme complexes selectively catalyze challenging chemical transformations, including alkane functionalization (e.g., halogenation of threonine, Thr, by non-heme iron SyrB2). However, the role of complex formation in enabling reactivity and guiding selectivity is poorly understood, owing to the challenges associated with obtaining detailed structural information of the dynamically associating protein complexes. Combining over 10 ms of classical molecular dynamics of SyrB2 and the acyl carrier protein SyrB1 with large-scale QM/MM simulation, we investigate the substrate–protein and protein–protein dynamics that give rise to experimentally observed substrate positioning and reactivity trends. We confirm the presence of a hypothesized substrate-delivery channel in SyrB2 through free energy simulations that show channel opening with a low free energy barrier. We identify stabilizing interactions at the SyrB2/SyrB1 interface that are compatible with phosphopantatheine (PPant) delivery of substrate to SyrB2. By sampling metal–substrate distances observed in experimental spectroscopy of native SyrB2/SyrB1-PPant-<i>S</i>-Thr and non-native substrates, we characterize essential protein–substrate interactions that are responsible for substrate positioning, and thus, reactivity. We observe the hydroxyl sidechain and terminal amine of the native Thr substrate to form cooperative hydrogen bonds with a single N123 residue in SyrB2. In comparison, non-native substrates that lack the hydroxyl interact more flexibly with the protein and therefore can orient closer to the Fe center, explaining their preferential hydroxylation and higher turnover frequencies.
|
Rimsha Mehmood; Helena W. Qi; Adam H. Steeves; Heather Kulik
|
Biochemistry; Bioinformatics and Computational Biology; Biophysics; Computational Chemistry and Modeling; Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-10-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1abdbb8947e8a37f11/original/the-protein-s-role-in-substrate-positioning-and-reactivity-for-biosynthetic-enzyme-complexes-the-case-of-syr-b2-syr-b1.pdf
|
65edd9229138d23161269673
|
10.26434/chemrxiv-2024-rd9wn
|
Friedel-Crafts Reactions for Biomolecular Chemistry
|
Chemical tools and principles have become central to biological and medical research/applications by leveraging a range of
classical organic chemistry reactions. Friedel-Crafts alkylation and acylation are arguably one of the most well-known and
used synthetic methods for preparation of small molecules but its use in biological and medical fields are relatively less
frequent than the other reactions, possibly owing to the notion about its plausible incompatibility with biological systems.
This Review demonstrates advances of Friedel-Crafts alkylation and acylation reactions in a variety of biomolecular
chemistry fields. With the discoveries and applications of numerous biomolecule-catalyzed or –assisted processes, the
reactions have garnered considerable interests in biochemistry, enzymology, and biocatalysis. Despite the challenges of
reactivity and selectivity of biomolecular reactions, the alkylation and acylation reactions demonstrated its utility for
construction and functionalization of all the four major biomolecules (i.e., nucleosides, carbohydrates/saccharides,
lipids/fatty acids, and amino acids/peptides/proteins), and their diverse applications in biological, medical, and material
fields are discussed. As the alkylation and acylation reactions are often fundamental educational components of organic
chemistry courses, the Review is intended for both experts and nonexperts by discussing their basic reaction patterns (with
the depiction of each reaction mechanism in the Electronic Supplementary Information) and relevant real-world impacts in
order to enrich chemical research and education. The significant growth of biomolecular Friedel-Crafts reactions described
here is a testament to its broad importance and utility, and the further development and investigation of the reactions will
surely be the focus in the organic biomolecular chemistry fields.
|
Jun Ohata
|
Organic Chemistry; Bioorganic Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-03-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65edd9229138d23161269673/original/friedel-crafts-reactions-for-biomolecular-chemistry.pdf
|
6733e60f5a82cea2faecff14
|
10.26434/chemrxiv-2024-798dv-v2
|
Quantification of arginine-rich cyclic cell-penetrating peptide-lipid conjugates using trifluoracetic acid-based UPLC-MS/MS analysis
|
Lipid-based drug delivery systems can be surface-modified by lipid conjugates of the substance in question. The most important modifications include arginine-rich cell-penetrating peptides (CPP). A toxicokinetic evaluation of these lipid conjugates is im-portant during preclinical and clinical development of drug delivery formulations. Due to their amphiphilic properties and high number of basic amino acid residues, lipid conjugates of CPP exhibit difficult characteristics in regard to their plasma bioanalysis with LC-MS/MS instruments. These especially include challenging chromatography with extensive carry-over and minimal extrac-tion recovery, and, due to large numbers of basic amino acids and the resulting immobility of protons, resistance against collision-induced dissociation. We developed a surrogate quantification of a CPP-lipid conjugate relying on elimination of the lipid part by phospholipase D digestion. Chromatographic separation was only feasible with trifluoro acetic acid (TFA)-based mobile phases. Ion suppression caused by TFA was reversed by post-column addition of aqueous ammonia. Efficient extraction of the surrogate peptide fragment was achieved by protein precipitation with TFA. This enabled the highly sensitive quantification of the CPP-lipid conjugate in plasma in the low picomolar range (lower limit of quantification of 0.1 ng/mL; 34 pM). The assay was validated ac-cording to the pertinent recommendations of the ICH M10 guideline on bioanalytical method validation and applied to the deter-mination of the intravenous pharmacokinetics of the CPP-lipid conjugate in Beagle dogs. The established strategy can be used as a general approach to the bioanalysis of amphiphilic lipid conjugates and especially the TFA-based UPLC-MS/MS analysis with post-column desolvation of TFA adducts by ammonia is a feasible approach for the highly sensitive quantification of arginine-rich peptides and other related substances with challenging chromatographic characteristics.
|
Cindy Bay; Philipp Uhl; Andreas D. Meid; Jürgen Burhenne; Walter E. Haefeli; Max Sauter
|
Analytical Chemistry; Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6733e60f5a82cea2faecff14/original/quantification-of-arginine-rich-cyclic-cell-penetrating-peptide-lipid-conjugates-using-trifluoracetic-acid-based-uplc-ms-ms-analysis.pdf
|
65fd772a66c13817298c7cb1
|
10.26434/chemrxiv-2023-7zd44-v3
|
Minimal coarse-grained models of polar solvent for electrolytes: Stockmayer versus dumbbell
|
This study explores the potential of the dumbbell solvent as a minimal model for understanding electrolytes solution in polar solvents. Our investigation involves a comparative analysis of the dumbbell model and the Stockmayer model, focusing on ion solvation and ion-ion correlations. We examine electrolytes containing symmetric monovalent salts dissolved in polar solvents while varying ion density and solvent polarity. Both models predict an augmented solvent coordination number around ions as solvent polarity increases, with the dumbbell solvent displaying a more pronounced effect. Notably, radial distribution functions (RDFs) between solvent and ions yield differing trends; Stockmayer models exhibit a non-monotonic relationship due to strong dipole-dipole interactions at higher polarity, while RDFs for ions and dumbbell solvents consistently rise. In response to increased solvent polarity, Stockmayer solvents within the ion's solvation shell undergo continuous dipole orientation shifts, whereas the dumbbell solvent predominantly adopts pointing-away dipole orientations, diminishing pointing-to orientations. This underscores the significance of the interplay between solvent molecular orientation and dipole rotation. Both models qualitatively predict ion pairing and clustering behaviors across varying solvent dipole strengths and salt concentrations. The Stockmayer solvent generally provides stronger electrostatic screening than the dumbbell solvent due to its neglect of the coupling between molecular orientation and dipole rotation. What's more, at a high dipole moment regime, ion-ion correlations in Stockmayer solvent can become stronger with increasing dipole moment due to stronger solvent-solvent correlations. This study underscores the effectiveness of the dumbbell solvent model in systematically elucidating the fundamental principles governing electrolytes, offering potential applications in the rational design of electrolyte systems.
|
Xinqiang Liu; Xian Kong
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Thermodynamics (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fd772a66c13817298c7cb1/original/minimal-coarse-grained-models-of-polar-solvent-for-electrolytes-stockmayer-versus-dumbbell.pdf
|
66f1d099cec5d6c142ff3864
|
10.26434/chemrxiv-2024-r5s7x
|
A Catalytic, Enantioselective Sulfamate Tethered Aza-Michael Cyclization
|
We show the first examples of enantioselective cyclization reactions of tethered sulfamates onto pendant α,β-unsaturated esters, ketones, and thioesters. This reaction is promoted by a new chiral bifunctional guanidine catalyst and is operationally very simple. Product is formed by simply stirring substrate and catalyst in methylene chloride at room temperature without any special precautions to exclude air or ambient moisture. A variety of primary sulfamates and sulfamides were examined, and, in many cases, products were delivered in excellent yields and enantiomeric ratios. With secondary sulfamates, kinetic resolutions were possible. With these kinetic resolutions, rationally varying reaction conditions allowed for either high enantioenrichment of the racemic sulfamate substrates or for cyclizations with good yields, enantiomeric ratios, and diastereoselectivities. The product oxathiazinanes were
very useful chiral intermediates and could be transformed into an array of enantioenriched small molecules.
|
Shyam Sathyamoorthi; Harshit Joshi; Abhijit Manna; Someshwar Nagamalla; Annu Thomas
|
Organic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-09-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f1d099cec5d6c142ff3864/original/a-catalytic-enantioselective-sulfamate-tethered-aza-michael-cyclization.pdf
|
67a3b4affa469535b92d6ce5
|
10.26434/chemrxiv-2025-j3nsp
|
Coordination Number Dependence of Cysteine Binding to Nanostructured Gold
|
The interaction of cysteine and related aminoacids with metal substrates has applications in several fields of science, technology and health. Despite widespread interest in these systems, the relationship between thiol adsorption and surface coarsening, including the effects of sur- face adatoms and other defect sites, has not been systematically addressed. Here, the effect of binding site unsaturation on the adsorption strength of cysteine on gold substrates is examined using density functional theory. Adsorption sites with a full range of in-surface coordination numbers are generated using surface adatoms or pitting structure. The configurational space of the adsorbate on the nanostructured surface is sampled extensively using Born-Oppenheimer molecular dynamics simulation. Our results indicate that binding strength is primarily deter- mined by a combination of surface site reactivity to the mercapto group and the availablity of additional sites for amino group coordination. The study aims to further our understanding of mercapto-aminoacid binding to defect substrates and low-coordinated nanoparticle sites, and to provide a basis for the development of coordination-dependent force fields that may be used in classical simulations of these systems.
|
Aishat Idris; Clayton Smith; Chao-Ming (Elvis) Ting; Irina Paci
|
Nanoscience; Nanostructured Materials - Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-02-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a3b4affa469535b92d6ce5/original/coordination-number-dependence-of-cysteine-binding-to-nanostructured-gold.pdf
|
630a31f758843b25fb9f6efe
|
10.26434/chemrxiv-2022-x5sjj
|
Extraction of flavonoids from Spatholobus suberectus with deep eutectic solvent
|
In this study, deep eutectic solvents were used for the extraction of flavonoids from Spatholobus suberectus. The extraction effect was measured using UV spectrophotometer and found that the deep eutectic solvent consisting of choline chloride and triethylene glycol (1:2) was the best extraction. The solvent water content (%), liquid-to-material ratio (v/m), and extraction temperature (K) were optimized using the central composite bounded design response surface method in a single-factor experiment. The results showed that the extraction yield of chickweed flavonoids reached 96.01 (mg/g) at a liquid-to-material ratio of 39:1, a water content of 43% in DESs and an extraction temperature of 336.6 K for 5 min, which was 2.85 and 4.12 times higher than that of the control group (90 min extraction) using 60% ethanol and water, respectively. The antioxidant activity of the extracts was evaluated using 2,2-Diphenyl-1-(2,4,6-trinitrophenyl)hydrazin-1-yl (DPPH) and it was found that the extracts inhibited DPPH by 89.765%, indicating the high content of flavonoids extracted. This study provides an idea for the extraction of functional components of biological origin.
|
Long Li; Yanying Zheng; Yongqi Wang; Yiyi Wang
|
Theoretical and Computational Chemistry; Agriculture and Food Chemistry; Food
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630a31f758843b25fb9f6efe/original/extraction-of-flavonoids-from-spatholobus-suberectus-with-deep-eutectic-solvent.pdf
|
60c744a0469df42d87f43386
|
10.26434/chemrxiv.9871898.v1
|
Mercury Sorbents Made by Inverse Vulcanization of Sustainable Triglycerides: The Plant Oil Structure Influences the Rate of Mercury Removal from Water
|
<div>
<div>
<div>
<p>High sulfur content polymers were prepared through the copolymerization of sustainable triglycerides and sulfur.
The products of the so-called “inverse vulcanization” contain 50% sulfur by mass and were evaluated in the removal of inorganic
and alkylmercury compounds from water. The structurally distinct triglycerides found in canola oil, castor oil, and rice bran oil
were all examined as co-monomers in the inverse vulcanization reaction to determine how each influences the rate and capacity of
mercury uptake. It was found that the high percentage of hydroxylated ricinoleic acid in castor oil improves both wetting and the
rate of uptake of mercury(II) chloride into the polymer, in comparison to the polymers made from canola oil and rice bran oil. For
the castor oil, the initial rate of uptake of mercury(II) chloride was more than three times the initial rate of uptake of the canola oil
polymer, with a mercury removal efficiency exceeding 99.99%. The affinity of the castor oil polymer for HgCl2 was also excellent,
with a distribution coefficient (Kd) on the order of 106 mL/g. In contrast, the polymer made from the inverse vulcanization of canola
oil and sulfur had an initial rate of uptake more the twice the rate of the castor oil copolymer in experiments involving sorption of
the mercury-based fungicide 2-methoxyethylmercury chloride (MEMC). In addition to kinetics, sorption isotherms were obtained
for all polymer sorbents and fit to both Langmuir and Freundlich isotherm models. In terms of sustainability, this work advances
the use renewable monomers such as triglycerides sourced from plants and inexpensive industrial byproducts such as sulfur to make
affordable mercury-binding materials. </p>
</div>
</div>
</div>
|
Alfrets Tikoalu; Nicholas Lundquist; Justin Chalker
|
Polymerization (Polymers); Hydrology and Water Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-09-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744a0469df42d87f43386/original/mercury-sorbents-made-by-inverse-vulcanization-of-sustainable-triglycerides-the-plant-oil-structure-influences-the-rate-of-mercury-removal-from-water.pdf
|
6421b3c462fecd2a83857088
|
10.26434/chemrxiv-2023-88slr
|
The Protein Environment Restricts the Intramolecular Charge Transfer Character of the Luciferine/Luciferase Complex
|
The elecronic characterization of the luciferine/luciferase complex is fundamental to tune its photophysical properties and develop more efficient devices based on this luminiscent system. Here, we apply molecular dynamics simulations, hybrid quantum mechanics/molecular mechanics (QM/MM) calculations and transition density analysis to compute the absorption and emission spectra of luciferine/luciferase and analyze the nature of the relevant electronic state and its behaviour with the intramolecular and intermolecular degrees of freedom. It is found that the torsional motion of the chromophore is hampered by the presence of enzyme, reducing the intramolecular charge transfer nature of the absorbing and emitting state. In addition, such a reduced charge transfer character does not correlate in a strong way with any individual intramolecular or intermolecular degree of freedom because it is likely influenced by a combination of them.
|
Henar Mateo-delaFuente; Davide Avagliano; Marco Garavelli; Juan Jose Nogueira
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6421b3c462fecd2a83857088/original/the-protein-environment-restricts-the-intramolecular-charge-transfer-character-of-the-luciferine-luciferase-complex.pdf
|
60c7480f567dfeffc0ec4956
|
10.26434/chemrxiv.11855469.v1
|
How to Control the Rate of Heterogeneous Electron Transfer Across the Rim of M6L12 and M12L24 Nanospheres
|
Catalysis in confined spaces, such as provided by supramolecular cages, is quickly gaining momentum. It allows for second coordination sphere strategies to control the selectivity and activity of transition metal catalysts, beyond the classical methods like fine-tuning the steric and electronic properties of the coordinating ligands. Only a few electrocatalytic reactions within cages have been reported, and there is no information regarding the electron transfer kinetics and thermodynamics of redox-active species encapsulated into supramolecular assemblies. This contribution revolves around the preparation of M<sub>6</sub>L<sub>12 </sub>and larger M<sub>12</sub>L<sub>24</sub> (M= Pd or Pt) nanospheres functionalized with different numbers of redox-active probes encapsulated within their cavity, either in a covalent fashion via different types of linkers (flexible, rigid and conjugated or rigid and non-conjugated) or by supramolecular hydrogen bonding interactions. The redox-probes can be addressed by electrochemical electron transfer across the rim of nanospheres and the thermodynamics and kinetics of this process are described. Our study identifies that the linker type and the number of redox probes within the cage are useful handles to fine-tune the electron transfer rates, paving the way for the encapsulation of electro-active catalysts and electrocatalytic applications of such supramolecular assemblies.
|
Riccardo Zaffaroni; Eduard.O. Bobylev; Plessius, Raoul; Jarl Ivar van der Vlugt; Joost reek
|
Electrochemistry; Kinetics and Mechanism - Inorganic Reactions; Supramolecular Chemistry (Inorg.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-02-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7480f567dfeffc0ec4956/original/how-to-control-the-rate-of-heterogeneous-electron-transfer-across-the-rim-of-m6l12-and-m12l24-nanospheres.pdf
|
60c752e0469df41362f44c59
|
10.26434/chemrxiv.13168883.v2
|
Screening of World Approved Drugs against Highly Dynamical Spike Glycoprotein SARS-CoV-2 using CaverDock and Machine Learning
|
The
new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes pathological
pulmonary symptoms. Most efforts to develop vaccines and drugs against this
virus target the spike glycoprotein, particularly its S1 subunit, which is
recognised by angiotensin-converting enzyme 2. Here we use the <i>in-house</i> developed tool CaverDock to
perform virtual screening against spike glycoprotein using a cryogenic electron
microscopy structure (PDB-ID: 6VXX) and the representative structures of five
most populated clusters from a previously published molecular dynamics
simulations. The dataset of ligands was obtained from the ZINC database and
consists of drugs approved for clinical use worldwide. Trajectories for the passage
of individual drugs through the tunnel of the spike glycoprotein homotrimer,
their binding energies within the tunnel, and the duration of their contacts
with the trimer’s three subunits were computed for the full dataset.
Multivariate statistical methods were then used to establish structure-activity
relationships and select top candidate molecules. This new protocol for rapid screening
of globally approved drugs (4359 ligands) in a multi-state protein structure (6
states) required a total of 26,148 calculations and showed high robustness. The
protocol is universal and can be applied to any target protein with an experimental
tertiary structure containing protein tunnels or channels. The protocol will be
implemented in the next version of CaverWeb (<a href="https://loschmidt.chemi.muni.cz/caverweb/">https://loschmidt.chemi.muni.cz/caverweb/</a>)
to make it accessible to the wider scientific community
|
Gaspar Pinto; Ondrej Vavra; Sérgio M. Marques; Jiri Filipovic; David Bednar; Jiri Damborsky
|
Biochemistry; Bioinformatics and Computational Biology; Chemical Biology
|
CC BY 4.0
|
CHEMRXIV
|
2020-12-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752e0469df41362f44c59/original/screening-of-world-approved-drugs-against-highly-dynamical-spike-glycoprotein-sars-co-v-2-using-caver-dock-and-machine-learning.pdf
|
6761b1e46dde43c90872a56d
|
10.26434/chemrxiv-2024-8tw83
|
A NEW AROMATICITY DESCRIPTOR BASED ON ELECTRON DELOCALIZATION EMPLOYING THE DISTRIBUTED MULTIPOLE ANALYSIS (DMA)
|
Aromatic compounds are energetically stable and have low reactivity, but an aromaticity concept is difficult to establish because it cannot be measured. For this reason, different descriptors have been developed to rationalize and quantify this phenomenon. Given that cyclic electron delocalization is an essential property of aromatic compounds, in this work, we propose six new aromatic descriptors based on Stone's distributed multipole analysis (DMA) to partition the molecular electron density on electric multipoles localized on different sites of a molecule. The new aromatic descriptors are based on different components of DMA quadrupole electric moment tensor Q_2, the first term of the DMA multipole expansion having contributions from the out-of-plane electron density. The proposed descriptors are straightforward to obtain because the DMA method is implemented on different popular electronic structure packages. For users of Gaussian, the formatted checkpoint with the calculated molecular electron density is used as input for the GDMA2 program of Stone to compute the necessary Q_2 components. The computer protocol for computing the Q_2-based descriptors in either way is presented. To assess the performance of the aromaticity descriptors, we used 12 tests of the Girona benchmark developed by the Solà group involving different distortions of benzene, substitutions, complexation, ring size dependence, atom size dependence, heteroatomic species, Clar systems, and fulvenes. The correct aromaticity trends of the six new indices were predicted entirely in 78% of the cases; for 16%, most trends were predicted and only failed utterly in 6%. The failed cases were related to the appreciable contribution of in-plane sigma electrons. Our proposal joins others to contribute to understanding the important and complex chemical concept of aromaticity.
|
Roberta Siqueira Soldaini Oliveira; Marco Aurélio Souza Oliveira; Itamar Borges Jr
|
Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-12-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6761b1e46dde43c90872a56d/original/a-new-aromaticity-descriptor-based-on-electron-delocalization-employing-the-distributed-multipole-analysis-dma.pdf
|
60c7493b469df4a3d2f43b81
|
10.26434/chemrxiv.12000132.v2
|
Polypeptides Folding: Rules for the Calculation of the Backbone Dihedral Angles φ starting from the Amino Acid Sequence
|
<p>Protein folding is strictly related
to the determination of the backbone dihedral angles and depends on the
information contained in the amino acid sequence as well as on the hydrophobic
effect. To date, the type of information embedded in the amino acid sequence
has not yet been revealed. The present study deals with these problematics and
aims to furnish a possible explanation of the information contained in the
amino acid sequence, showing and reporting rules to calculate the backbone
dihedral angles φ. The study is based on the development of mechanical forces
once specific chemical interactions are established among the side chain of the
residues in a polypeptide chain. It aims to furnish a theoretical approach to
predict backbone dihedral angles which, in the future, may be applied to
computational developments focused on the prediction of polypeptide structures.</p>
|
Michele Larocca
|
Theory - Computational; Biophysical Chemistry; Physical and Chemical Properties
|
CC BY 4.0
|
CHEMRXIV
|
2020-03-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7493b469df4a3d2f43b81/original/polypeptides-folding-rules-for-the-calculation-of-the-backbone-dihedral-angles-starting-from-the-amino-acid-sequence.pdf
|
629a4fb8dd1809386af49d9f
|
10.26434/chemrxiv-2022-m0q59
|
The role of polaronic states in the enhancement of CO oxidation by single-atom Pt/CeO2
|
Single Atom Catalysts (SACs) have shown that the miniaturization of the active site implies new phenomena like dynamic charge transfer between isolated metal atoms and the oxide. To obtain direct proof of this phenomenon is challenging, as many experimental techniques provide averaged properties or have limitations with poorly conductive materials, leaving kinetic measurements from catalytic testing as the only reliable reference.
Here we present an integrated Density Functional Theory-Microkinetic model including ground and high-energy metastable states to address the reactivity of Pt1CeO2 for CO oxidation. Our model agrees with experimentally available kinetic data showing that CO oxidation activity of Pt1/CeO2 is tunable via the electronic properties of the support.
Particularly, samples with higher n-doping via oxygen depletion should be better in CO oxidation, as they help maintain the active state Pt^0 of the catalyst. This provides a general route to improve low-temperature oxidations at metal/oxides interfaces via charge transfer control.
|
Minttu Kauppinen; Nathan Daelman; Nuria Lopez; Karoliina Honkala
|
Theoretical and Computational Chemistry; Catalysis; Theory - Computational; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-06-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629a4fb8dd1809386af49d9f/original/the-role-of-polaronic-states-in-the-enhancement-of-co-oxidation-by-single-atom-pt-ce-o2.pdf
|
67531dc0085116a13394f7f7
|
10.26434/chemrxiv-2024-ltphc-v2
|
Robust Automated Truncation Point Selection for Molecular Simulations
|
Quantities calculated from molecular simulations are often subject to an initial bias due to unrepresentative starting configurations. Initial data are usually discarded to reduce bias. Chodera's method for automated truncation point selection [J. Chem. Theory Comput. 2016, 12, 4, 1799–1805] is popular but has not been thoroughly assessed. We reformulate White’s marginal standard error rule to provide a spectrum of truncation point selection heuristics that differ in their treatment of autocorrelation. These include a method effectively equivalent to Chodera's. We test these methods on ensembles of synthetic time series modelled on free energy change estimates from long absolute binding free energy calculations. Methods that more thoroughly account for autocorrelation often show late and variable truncation times, while methods that less thoroughly account for autocorrelation often show early truncation, relative to the optimal truncation point. This increases variance and bias, respectively. We recommend a method that achieves robust performance across our test sets by balancing these two extremes. None of the methods reliably detected insufficient sampling. All heuristics tested are implemented in the open-source Python package RED (https://github.com/fjclark/red).
|
Finlay Clark; Daniel Cole; Julien Michel
|
Theoretical and Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-12-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67531dc0085116a13394f7f7/original/robust-automated-truncation-point-selection-for-molecular-simulations.pdf
|
6650864891aefa6ce1e1c238
|
10.26434/chemrxiv-2024-22tsj
|
Tracing Ultrafast Photo-Dissociation Pathways in Phenol: Transient X-ray Absorption Signatures
|
The photo-induced dissociation dynamics of phenol have attracted long interest of researchers, as this is fundamental for understanding the non-radiative decay mechanisms of bio-molecules with more complex substitutions at the aromatic ring. There is a controversy in the photochemical mechanisms that give rise to the fast and slow components in the photofragment translational kinetic energy distributions. Herein, we demonstrate that the transient X-ray absorption spectroscopy (TXAS) at the O K-edge is effective for tracking the ultrafast electronic and nuclear dynamics in photochemical processes, by multi-configurational simulations along different reaction pathways in the potential energy surfaces (PESs) along the O-H distance $R_\text{OH}$. PESs were generated for the lowest 3 singlet valence states (S$_0$--S$_2$) and 30 O1s core-excited states (e$_1$--e$_{30}$), and TXAS spectra in three nonradiative reaction pathways were simulated showing distinct spectral signatures. The direct dissociation into the H atom and the first excited-state ($~{A}$) of phenoxyl (PhO$\cdot$) residue (path 1) associates with a strong peak observed at 527-528 eV and a weak peak at 540-541 eV which vanishes rapidly along the dissociation coordinate. In comparison, the channel of dissociation into the ground state of PhO$\cdot$ (path 2) leads to a medium peak at 528-529 eV, and two weak peaks at 531-534 and 535-536 eV, respectively. Concerning the recrossing pathway (path 3), all peaks show obvious shifts when the photo-excited phenol decays along the S$_0$-state PES. The mechanisms underlying the photodissociation of phenol thus can be sensitively encoded in the O1s TXAS signals. The early-stage dynamics of photo-excited phenol were also investigated to explore the reaction pathways in S$_1$ and direct internal conversion into the high internal energy S$_0$ state, followed by decay with the increase of $R_\text{OH}$.
|
Guoyan Ge; Sheng-Yu Wang; Weijie Hua
|
Theoretical and Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6650864891aefa6ce1e1c238/original/tracing-ultrafast-photo-dissociation-pathways-in-phenol-transient-x-ray-absorption-signatures.pdf
|
64b547b0b605c6803be088fb
|
10.26434/chemrxiv-2023-x8pjt
|
Unveiling the chemical underpinnings behind the enhanced adsorption interaction of NO2 on MoS2, MoSe2, and MoTe2 transition metal dichalcogenides
|
The demand for efficient gas sensors has fueled research into novel materials like transition-metal chalcogenide (TMD) compounds. TMDs such as MoS2, MoSe2, and MoTe2 have shown promise in detecting NO2. However, it remains uncertain which one is best suited for this purpose. Consequently, this study employs computational methods to investigate NO2 adsorption on monolayers of MoS2, MoSe2, and MoTe2. The results show that MoTe2 exhibits the strongest interaction with the highest charge transfer, suggesting its potential for superior NO2 detection compared to MoSe2 and MoS2. The sheets share the same type of outward projecting orbitals and thus the principle model for charge projections. However, the bonding within the sheet influences the accumulation of charge within it, which in turn impacts the availability of electrons on its surface. Subsequently, the mechanism of charge transfer between the TMDs and NO2 remains the same, but more available charge results in an enhanced adsorption interaction. The described mechanism is likely to affect the adsorption of other acceptor-type molecules (e.g., CO2, SO2, H2S, or BF3) and also be behind differences in charge transfer observed among group VI compounds (e.g., MoS2 and WS2).
|
Maciej Jan Szary; Piotr Radomski
|
Theoretical and Computational Chemistry; Physical Chemistry; Materials Science
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-07-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b547b0b605c6803be088fb/original/unveiling-the-chemical-underpinnings-behind-the-enhanced-adsorption-interaction-of-no2-on-mo-s2-mo-se2-and-mo-te2-transition-metal-dichalcogenides.pdf
|
667d7f34c9c6a5c07a9b346c
|
10.26434/chemrxiv-2024-gq4gf
|
Arylthianthrenium salts for triplet energy transfer catalysis
|
Sigma bond cleavage through electronically excited states allows synthetically useful transformations with two radical species. Direct excitation of simple aryl halides to form both aryl and halogen radicals necessitates UV-C light, so undesired side reactions are often observed, and specific equipment is required. Moreover, only aryl halides with extended pi systems and comparatively low triplet energy are applicable to synthetically useful energy transfer catalysis with visible light. Here we show the conceptual advantages of arylthianthrenium salts (ArTTs) for energy transfer catalysis with visible light in high quantum yield as compared to conventional aryl(pseudo)halides, and their utility in arylation reactions of ethylene. The fundamental advance is enabled by the low triplet energy of ArTTs that may originate in large part from the electronic interplay between the distinct sulfur atoms in the tricyclic thianthrene scaffold, which is neither accessible in simple (pseudo)halides nor other conventional sulfonium salts.
|
Yuan Cai; Triptesh Kumar Roy; Till J. B. Zähringer; Beatrice Lansbergen ; Christoph Kerzig ; Tobias Ritter
|
Organic Chemistry; Catalysis; Photochemistry (Org.); Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667d7f34c9c6a5c07a9b346c/original/arylthianthrenium-salts-for-triplet-energy-transfer-catalysis.pdf
|
60d9ed4367d4915e779656cb
|
10.26434/chemrxiv-2021-8wsz9
|
Mechanism of the Photodegradation of A-D-A Acceptors for Organic Photovoltaics
|
In this work, we elucidate the photodegradation pathway of IT-4F, a benchmark A-D-A type semiconductor for organic photovoltaics. The photoproducts were isolated and shown to be isomers of IT-4F formed via a 6-e electrocyclic reaction between the dicyanomethylene unit and the thiophene ring, followed by a 1,5-sigmatropic hydride shift. Importantly, this photoisomerization is accelerated under inert conditions which is explained by DFT calculations that predict the reaction to occur via the excited triplet state (quenchable by oxygen). Adding controlled amounts of the photocyclized product P1 to PM6:IT-4F bulk heterojunction cells shows a progressive decrease of photocurrent and fill factor attributed to its poorer absorption and charge transport properties. The power conversion efficiency drops from 12% for pure IT-4F to 3% for pure P1 acceptor. This cyclization is a general photodegradation pathway for a series of analogous A-D-A molecules with 1,1-dicyanomethylene-3-indanone termini. However, the rate of the reaction varies widely with the nature of the donor moiety.
|
Yuxuan Che; Rizwan Niazi; Ricardo Izquierdo; Dmitrii Perepichka
|
Organic Chemistry; Energy; Photochemistry (Org.); Photovoltaics; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-06-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d9ed4367d4915e779656cb/original/mechanism-of-the-photodegradation-of-a-d-a-acceptors-for-organic-photovoltaics.pdf
|
62ce5e37a7d17e44da57a162
|
10.26434/chemrxiv-2022-dcn3z
|
Catalytic nitrogen fixation using visible light energy
|
Herein, we established an iridium- and molybdenum-catalysed process for the synthesis of ammonia from dinitrogen that takes place under ambient reaction conditions and under visible light irradiation. In this reaction system, cationic iridium complexes bearing 2-(2-pyridyl)phenyl and 2,2’-bipyridine-type ligands and molybdenum triiodide complexes bearing N-heterocyclic carbene-based PCP-type pincer ligands acted as cooperative catalysts to activate 9,10-dihydroacridine and dinitrogen, respectively. Interestingly, under visible light irradiation, 9,10-dihydroacridine acted as a one-electron and one-proton source. The findings of this study provide a novel approach to catalytic nitrogen fixation that is driven by visible light energy. The reaction of dinitrogen with 9,10-dihydroacridine was not thermodynamically favoured, and it only took place under visible light irradiation. Therefore, the described reaction system is one that affords visible light energy–driven ammonia formation from dinitrogen. The findings reported herein can contribute to the development of novel next-generation nitrogen fixation systems powered by renewable energy.
|
Yuya Ashida; Yuto Onozuka; Kazuya Arashiba; Asuka Konomi; Hiromasa Tanaka; Shogo Kuriyama; Yasuomi Yamazaki; Kazunari Yoshizawa; Yoshiaki Nishibayashi
|
Organometallic Chemistry; Coordination Chemistry (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-07-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ce5e37a7d17e44da57a162/original/catalytic-nitrogen-fixation-using-visible-light-energy.pdf
|
62608592d048ed03304b657d
|
10.26434/chemrxiv-2022-t2zb4
|
A Sterically Tuned Directing Auxiliary Promotes Catalytic 1,2-Carbofluorination of Alkenyl Carbonyl Compounds
|
The site-selective palladium-catalyzed three-component coupling of unactivated alkenyl carbonyl compounds, aryl- or alkenylboronic acids, and N-fluorobenzenesulfonimide is described herein. Tuning of the steric environment on the bidentate directing auxiliary is proposed to facilitate challenging C(sp3)–F reductive elimination from a Pd(IV) intermediate to afford 1,2-carbofluorination products in good yields and with high regioselectivity.
|
Zhonglin Liu; Lucas Oxtoby; Zi-Qi Li; Nana Kim; Geraint Davies; Keary Engle
|
Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-04-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62608592d048ed03304b657d/original/a-sterically-tuned-directing-auxiliary-promotes-catalytic-1-2-carbofluorination-of-alkenyl-carbonyl-compounds.pdf
|
657884ac7acf130c3211f866
|
10.26434/chemrxiv-2023-rb0r2-v2
|
Mixed-potential-driven catalysis
|
Mixed-potential-driven catalysis is expected to be a new heterogeneous catalytic mechanism that produces products different from those produced by thermal catalytic reactions without the application of external energy. Electrochemically, the mechanism is similar to that of corrosion. However, a theory that incorporates catalytic activity as a parameter has not been established. Herein, we report the theoretical framework of mixed-potential-driven catalysis, including exchange currents, as a parameter of catalytic activity. The mixed potential and partitioning of the overpotential were determined from the exchange current by applying the Butler–Volmer equation at a steady state far from equilibrium. Mixed-potential-driven catalysis is expected to open new areas not only in the concept of catalyst development but also in the field of energetics of biological enzyme reactions.
|
Mo Yan; Nuning Namari; Junji Nakamura; Kotaro Takeyasu
|
Physical Chemistry; Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657884ac7acf130c3211f866/original/mixed-potential-driven-catalysis.pdf
|
6667a70d12188379d8cf2e40
|
10.26434/chemrxiv-2024-33v24-v2
|
A High-Performance Workflow for Identifying Site-Specific Crosslinks Originating from a Genetically Incorporated, Photoreactive Amino Acid
|
In conventional crosslinking mass spectrometry, proteins are crosslinked using a highly selective, bifunctional chemical reagent, which limits crosslinks to residues that are accessible and reactive to the reagent. Genetically incorporating a photoreactive amino acid offers two key advantages: any site can be targeted, including those that are inaccessible to conventional crosslinking reagents, and photoreactive amino acids can potentially react with a broad range of interaction partners. However, broad reactivity imposes additional challenges for crosslink identification. In this study, we incorporate benzoylphenylalanine (BPA), a photoreactive amino acid, at selected sites in an intrinsically disordered region of the human protein HSPB5. We report and characterize a workflow for identifying and visualizing residue-level interactions originating from BPA. We routinely identify 30 to 300 crosslinked peptide spectral matches with this workflow, which is up to ten times more than existing tools for residue-level BPA crosslink identification. Most identified crosslinks are assigned to a precision of one or two residues, which is supported by a high degree of overlap between replicate analyses. Based on these results, we anticipate that this workflow will support the more general use of genetically incorporated, photoreactive amino acids for characterizing the structures of proteins that have resisted high-resolution characterization.
|
Lindsey D. Ulmer; Daniele Canzani; Christopher N. Woods; Natalie L. Stone; Maria K. Janowska; Rachel E. Klevit; Matthew F. Bush
|
Biological and Medicinal Chemistry; Analytical Chemistry; Biochemistry; Bioinformatics and Computational Biology; Biophysics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6667a70d12188379d8cf2e40/original/a-high-performance-workflow-for-identifying-site-specific-crosslinks-originating-from-a-genetically-incorporated-photoreactive-amino-acid.pdf
|
60c748f2702a9b688818b08f
|
10.26434/chemrxiv.12003321.v1
|
Semiconductive Microporous Hydrogen-Bonded Organophosphonic Acid Frameworks
|
<p>We report the first semiconductive, proton-conductive, microporous hydrogen-bonded organic framework (HOF) derived from phenylphosphonic acid and 5,10,15,20‐tetrakis[<i>p</i>‐phenylphosphonic acid] porphyrin (known as GTUB5). The structure of GTUB5 was characterized using single crystal X-ray diffraction (XRD). A narrow band gap of 1.56 eV was extracted from a UV-Vis spectrum of pure GTUB5 crystals, in excellent agreement with the 1.65 eV band gap obtained from density functional theory calculations. The same band gap was also measured for GTUB5 in DMSO. The proton conductivity of GTUB5 was measured to be 3.00 ´ 10<sup>-6 </sup>S cm<sup>-1</sup> at 75 °C and 75 % relative humidity. The surface area of GTUB5’s hexagonal voids were estimated to be 422 m<sup>2</sup> g<sup>-1</sup> from grand canonical Monte Carlo simulations. XRD showed that GTUB5 is thermally stable under relative humidities of up to 90 % at 90 °C. These findings pave the way for a new family of microporous, organic, semiconducting materials with high surface areas and high thermal stabilities. Such materials could find applications in printed electronics, optoelectronics, and electrodes in supercapacitors.<br /></p>
|
Patrik Tholen; Craig A. Peeples; Raoul Schaper; Ceyda Bayraktar; Turan Erkal; Mehmet Menaf Ayhan; Bünyemin Çoşut; Jens Beckmann; A. Ozgur Yazaydin; Michael Wark; Gabriel Hanna; Yunus Zorlu; Gündoğ Yücesan
|
Supramolecular Chemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-03-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748f2702a9b688818b08f/original/semiconductive-microporous-hydrogen-bonded-organophosphonic-acid-frameworks.pdf
|
6706921f12ff75c3a1f742a4
|
10.26434/chemrxiv-2024-nbqqp
|
Degradation of a water-in-salt electrolyte at graphite and Na metal electrodes from first principles
|
By preventing water decomposition on the electrode surface, the solid-electrolyte interphase (SEI) plays a crucial role in enhancing the electrochemical stability of water-in-salt electrolytes, thereby facilitating their commercialization. In this study, we employ density functional theory calculations to explore the initial stages of SEI formation within a sodium triflate water-in-salt electrolyte on two types of electrodes: graphite, known for its inert characteristics, and a highly reactive sodium metal surface, both commonly used in sodium-ion batteries. The insights gained from our calculations offer predictive information on the potential composition of the interfacial layer forming on these surface models, shedding light on the electrochemical performance of the system as a battery feature.
|
Majid Rezaei; Axel Groß
|
Theoretical and Computational Chemistry; Physical Chemistry; Energy; Computational Chemistry and Modeling; Energy Storage; Interfaces
|
CC BY 4.0
|
CHEMRXIV
|
2024-10-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6706921f12ff75c3a1f742a4/original/degradation-of-a-water-in-salt-electrolyte-at-graphite-and-na-metal-electrodes-from-first-principles.pdf
|
60c74f83567dfeca47ec56e7
|
10.26434/chemrxiv.12917762.v1
|
Correlation Between Optical Activity and the Helical Molecular Orbitals of Allene and Cumulenes
|
<div><div><div><p>Helical frontier molecular orbitals (MOs) appear in disubstituted allenes and even-n cumulenes. Chiral molecules are optically active, but while these molecules are single-handed chiral, π-orbitals of both helicities are present. Here we computationally examine whether the optical activity of chiral cumulenes is controlled by the axial chirality or the helicity of the electronic structure. We exploit hyperconjugation with alkyl, silaalkyl, and germaalkyl substituents to adjust the MO helicity without altering the axial chirality. For the same axial chirality, we observe an inversion of the helical MOs contribution to the electronic transitions and a change of sign in the electronic circular dichroism and optical rotation dispersion spectra. While the magnitude of the chiroptical response also increases, it is similar to that of chiral cumulenes without helical π-orbitals. Overall, Helical π-orbitals correlate with the big chiroptical response in cumulenes, but are not a prerequisite for it.</p></div></div></div>
|
Marc Hamilton Garner; Clemence Corminboeuf
|
Photochemistry (Org.); Physical Organic Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-09-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f83567dfeca47ec56e7/original/correlation-between-optical-activity-and-the-helical-molecular-orbitals-of-allene-and-cumulenes.pdf
|
663a37a721291e5d1da96322
|
10.26434/chemrxiv-2024-mg64g
|
Photochemical Phosphorus-Enabled Scaffold Remodeling of Carboxylic Acids
|
The excitation of carbonyl compounds by light to generate radical intermediates is a distinctive mode of molecular activation. These processes play important roles in organic synthesis, especially for the challenging formation of carbon-carbon bonds that conventional two-electron chemical processes are unable to achieve. This approach has historically been restricted to ketones and aldehydes, and carboxylic acids have been overlooked due to high energy requirements and their low quantum efficiency. The development of a robust and general method for the direct excitation of carboxylic acid derivatives holds significant promise for advancing the field of chemistry. A successful activation method strategy necessitates a bathochromic shift in the absorbance profile, an increase in triplet diradical lifetime, and ease of further functionalization. We present a phosphorus-based strategy through a single-flask transformation of carboxylic acids into acyl phosphonates that access synthetically useful triplet diradicals under visible light or near-ultraviolet irradiation. The use of phosphorus circumvents unproductive Norrish type I processes, promoting selectivity that enables new hydrogen atom transfer (HAT) logic and facilitates diverse reactivity. Employing this strategy promotes the efficient scaffold remodeling of carboxylic acids through various annulation, contraction, and expansion manifolds. This expansion of HAT logic enabled by easily accessed acyl phosphonates represents significant potential for pharmaceuticals, materials science, and environmental applications.
|
Karl Scheidt; Qiupeng Peng; Meemie Hwang; Ángel Rentería-Gómez; Poulami Mukherjee; Ryan Young; Yunfan Qiu; Michael Wasielewski; Osvaldo Gutierrez
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photochemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663a37a721291e5d1da96322/original/photochemical-phosphorus-enabled-scaffold-remodeling-of-carboxylic-acids.pdf
|
62449ad53b5f991949ca05e8
|
10.26434/chemrxiv-2022-2dbzj-v3
|
Effects of Ion Adsorption on Graphene Oxide Films and Interfacial Water Structure: A Molecular-Scale Description
|
Graphene oxide is a promising, emerging separation material, as it is durable, dispersible in water, and has naturally forming functional groups. Bulk studies using graphene oxide flakes have demonstrated impressive metal adsorption. However, little interfacial information about water and metal organization near graphene oxide is available. A mechanistic understanding of water and ions interactions with graphene oxide films is critical toward advanced separations, including improved sorption efficiency and membrane regeneration. We study metal ion and local water organization near graphene oxide thin films formed at the air/water interface. These films are not typical membranes and allow us to determine nanoscale information about the graphene oxide-water interface. We accomplish this with x-ray reflectivity (XR), x-ray fluorescence near total reflection (XFNTR), and vibrational sum frequency generation spectroscopy (SFG). These interface-specific techniques provide the electron density profile normal to the interface, number of adsorbed ions, and information about the orientational ordering and hydrogen-bonding network of interfacial water, respectively. Via XFNTR and SFG, we find that trivalent yttrium ions preferentially adsorb to graphene oxide and affect its structure, compared to divalent strontium and monovalent cesium ions. Two different interfacial water populations can be described, based on their hydrogen bonding strength, and the adsorbed ions affect these populations differently. These results provide fundamental information about ion and water organization at the interface and help address the large computational-experimental agreement gap for graphene oxide systems. Additionally, they are relevant for improved soft-scaffold graphene oxide membranes and downstream applications.
|
Amanda Carr; Raju Kumal; Wei Bu; Ahmet Uysal
|
Physical Chemistry; Interfaces; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-03-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62449ad53b5f991949ca05e8/original/effects-of-ion-adsorption-on-graphene-oxide-films-and-interfacial-water-structure-a-molecular-scale-description.pdf
|
65ef18ef66c1381729bf1cbc
|
10.26434/chemrxiv-2024-lcm83
|
Augmenting Genetic Algorithms with Machine Learning for Inverse Molecular Design
|
Evolutionary and machine learning methods have been successfully applied to the generation of molecules and materials exhibiting desired properties. The combination of these two paradigms in inverse design tasks can yield powerful methods that explore massive chemical spaces more efficiently, improving the quality of the generated compounds. However, such synergistic approaches are still an incipient area of research and appear underexplored in the literature. This review covers different ways of incorporating machine learning approaches into evolutionary learning frameworks, with the overall goal of increasing the optimization efficiency of genetic algorithms. In particular, machine learning surrogate models for faster fitness function evaluation, discriminator models to control population diversity on-the-fly, machine learning based crossover operations, and evolution in latent space are discussed. The further potential of these synergistic approaches in generative tasks is also assessed, outlining promising directions for future developments.
|
Hannes Kneiding; David Balcells
|
Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ef18ef66c1381729bf1cbc/original/augmenting-genetic-algorithms-with-machine-learning-for-inverse-molecular-design.pdf
|
631de15349042a6922d37731
|
10.26434/chemrxiv-2022-7mzsj
|
Room Temperature Pseudo-Solid State Iron Fluoride Conversion Battery with High Ionic Conductivity and Low Interfacial Resistance
|
Li metal batteries (LMBs) employing conversion cathode materials (e.g., FeF3) are a promising way to prepare inexpensive, environmentally friendly batteries with high energy density. Pseudo-solid state ionogel separators harness the energy density and safety advantages of solid state LMBs, while alleviating key drawbacks (e.g., poor ionic conductivity and high interfacial resistance). In this work, a pseudo-solid state conversion battery (Li-FeF3) is presented that achieves stable, high rate (1.0 mA cm-2) cycling at room temperature. The batteries described herein contain gel-infiltrated FeF3 cathodes prepared by exchanging the ionic liquid in a polymer ionogel with a localized high concentration electrolyte (LHCE). The LHCE gel merges the benefits of a flexible separator (e.g., adaptation to conversion-related volume changes) with the excellent chemical stability and high ionic conductivity (~2 mS cm-1 at 25°C) of an LHCE. The latter property is in contrast to previous solid state iron fluoride batteries, where poor ionic conductivities necessitated elevated temperatures to realize practical power levels. The stable, room temperature Li-FeF3 cycling performance obtained with the LHCE gel at high current densities paves the way for exploring a range of architectures including flexible, three-dimensional, and custom shape batteries.
|
Aliya Lapp; Laura Merrill; Bryan Wygant; David Ashby; Austin Bhandarkar; Alan Zhang; Elliot Fuller; Katharine Harrison; Timothy Lambert; Albert Alec Talin
|
Energy; Energy Storage
|
CC BY 4.0
|
CHEMRXIV
|
2022-09-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631de15349042a6922d37731/original/room-temperature-pseudo-solid-state-iron-fluoride-conversion-battery-with-high-ionic-conductivity-and-low-interfacial-resistance.pdf
|
60c742529abda2f153f8bfbd
|
10.26434/chemrxiv.8026475.v2
|
Sulfur Mediated Allylic C-H Arylation, Epoxidation and Aziridination
|
Transition-metal-free, sulfur mediated allylic C-H arylation, epoxidation and aziridination were realized through one-pot procedures. The reaction design involved initial addition between olefins and triflic anhydride activated sulfoxides, followed by subsequent reactions of the allylic sulfur ylides generated under basic conditions with arylboronic acids, aldehydes, or aldimines, to give allylic arylation, epoxidation or aziridination products, respectively.<br />
|
Hang Luo; Gang Hu; Pingfan Li
|
Organic Compounds and Functional Groups; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-05-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742529abda2f153f8bfbd/original/sulfur-mediated-allylic-c-h-arylation-epoxidation-and-aziridination.pdf
|
6735933af9980725cf2331c8
|
10.26434/chemrxiv-2024-xjg2k
|
Synthesis, Characterization, and Potential Applications of Novel Schiff Base Metal(II) Complexes Derived from 3-Hydroxy-2-Naphthoic Hydrazide and 3-Acetyl-2-Hydroxy-6-Methyl-4H-Pyran-4-One
|
Schiff base metal complexes presents a broad range of opportunities in the industry and pharmaceuticals alike. Here, we present the synthesis and characterization of novel Schiff base metal complexes. The Synthesis of metal(II) complexes of (E)-3-hydroxy-N’-(1-(6-methyl-2,4-dioxo-3,4-dihydro-2H-pyran-3-yl)ethylidene)-2-naphthohydrazide was conducted through a two-pot synthesis method. The mechanism of reaction of the ligand involved the nucleophilic attack of the primary amine (3-hydroxy-2-naphthoic hydrazide) on one of the carbonyl carbon atoms of 3-acetyl-2-hydroxy-6-methyl-4H-pyran-4-one in an alcohol medium to give the ligand. The reaction of the ligand with metal chlorides of Co(II) and Ni(II) afforded two metal complexes. The mass spectrometry and the color and melting point of the sample was analyzed, the Mass Spectra, Percentage Metal and Elemental properties were analyzed as well H1 NMR, C13NMR to confirm the formation of the novel Schiff base metal complexes. While the color and elemental properties gave a satisfactory result, the ligand spectrum gave a molecular ion of 353.087. The M+ ions of 482.0478 and 483.0428 was obtained from the spectra of the complexes respectively. The protons of the methyl groups were seen as singlet peaks at 2.66 and 2.16 ppm. Aromatic C-H of the naphthene ring gave peaks within the range 8.49-7.34 ppm in the spectrum of the ligand. The 13C NMR spectrum of the ligand was used to corroborate inferences drawn from the proton NMR spectrum. The carbon atoms of the carbonyl groups were seen at 181.51 and 168.53, 162.68 ppm. The carbon atom of the azomethine group presented a peak at 162.84 ppm which is indicative of the formation of the Schiff base ligand. The carbon atoms of the naphthene ring were observed at 105.98-129.29 ppm. Carbon atoms of the methyl groups were assigned to the peaks at 17.16 and 19.77ppm confirming the formation of the metal complex. While other characterization attempts proved a successful synthesis of the target Schiff metal complexes, it is recommended for application in the industry and pharmaceuticals.
|
Chidi Daniel Chukwu
|
Inorganic Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-11-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6735933af9980725cf2331c8/original/synthesis-characterization-and-potential-applications-of-novel-schiff-base-metal-ii-complexes-derived-from-3-hydroxy-2-naphthoic-hydrazide-and-3-acetyl-2-hydroxy-6-methyl-4h-pyran-4-one.pdf
|
64bd0abcb605c6803b378186
|
10.26434/chemrxiv-2023-2vd0n
|
On the synthesis of WS2 nanotubes: reaction mechanism revelation by in-situ scanning and ex-situ transmission electron microscopy
|
This study provides a comprehensive understanding of the WS2 nanotube synthesis mechanism by conducting in-situ SEM and ex-situ TEM analyses of the sulfidation reaction of W18O49 nanowhiskers. The formation of WS2 nanotubes initiates with the rapid passivation of the reactive tungsten suboxide surface, followed by the evaporation of the oxide core and pressure buildup inside the nascent nanotube. The compactness and defectiveness of the initial passivation layer, gas pressure differences, and the structure of the W18O49 nanowhisker play crucial roles in determining the morphology of the final WS2 nanotubes. Additionally, this work elucidates the cause of open or closed nanotube tips based on gas pressure conditions. The combination of in-situ SEM technology and ex-situ sequential TEM analysis emerges as a robust and reliable methodology for investigating high-temperature heterogeneous reactions.
|
Vojtech Kundrat; Libor Novak; Jakub Zalesak; Kristyna Bukvisova; Miroslav Kolibal; Reshef Tenne
|
Inorganic Chemistry; Nanoscience; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-07-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64bd0abcb605c6803b378186/original/on-the-synthesis-of-ws2-nanotubes-reaction-mechanism-revelation-by-in-situ-scanning-and-ex-situ-transmission-electron-microscopy.pdf
|
61e1ae164a603dc4003030fc
|
10.26434/chemrxiv-2022-2mhdr
|
Enzyme-Independent Interaction of Pyridoxal-5’-Phosphate with Cysteine
|
Pyridoxal-5′-phosphate (PLP), commonly known as Vitamin B6, is a versatile co-factor that assists in different types of enzymatic reactions. PLP has also been reported to react with substrates and catalyze some of these reactions independent of enzymes. One such catalytic reaction is the breakdown of cysteine to produce hydrogen sulfide (H2S) in the presence of multivalent metal ions. However, the catalytic activity of PLP in catabolizing cysteine in the absence of multivalent ions is unknown. In this study, we show that, under physiological conditions and in the absence of enzymes and multivalent metal ions, PLP reacts with cysteine to form a thiazolidine product. The formation of a thiazolidine product is supported by quantum chemical simulation of the absorption spectrum. The reaction of PLP with cysteine is dependent on ionic strength and pH. The thiazolidine product slowly decomposes to produce H2S and the PLP regenerates to its active form with longer reaction times (>24 hours), suggesting that PLP can act as a catalyst. We have proposed an enzyme-independent plausible reaction mechanism for PLP-cysteine catalysis which proceeds through the formation of thiazolidine ring intermediates that later hydrolyzes slowly to regenerate the PLP. This work demonstrates that PLP catalyzes cysteine in the absence of (i) enzymes, (ii) base, and (iii) multivalent metal ions to produce H2S.
|
Prajakatta Mulay; Cindy Chen; Vijay Krishna
|
Catalysis; Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-01-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e1ae164a603dc4003030fc/original/enzyme-independent-interaction-of-pyridoxal-5-phosphate-with-cysteine.pdf
|
649aeaad9ea64cc1670d5206
|
10.26434/chemrxiv-2023-1jrcq-v2
|
Origins of Life: Chemistry and Evolution
|
Our understanding of the origins of life will be enhanced if models and their predictions are clearly understood and explicitly articulated. Here we outline two distinct models that are currently used to explain the origins of life. In one model, which has been pursued for a half century, inherent chemical reactivities of prebiotic chemical species produced RNA, which then invented evolution. This direct synthesis model enables the prediction that if the conditions of the ancient earth are sufficiently constrained, chemists will discover the synthetic pathways that produced RNA. In a fundamentally different model, which is more recent and less mature, RNA in concert with other biopolymers arose from prolonged, selection-based changes that occurred during chemical evolution, which transitioned smoothly into biological evolution. This evolutionary model predicts common chemistry of linkage and amazing structures, assemblies and co-assemblies, as represented by double stranded DNA, tRNA, cellulose, collagen, globular proteins, ATP synthase, and the ribosome. This evolutionary model predicts profound integration of biological subsystems as represented by ATP, which is central to and inextricable from biopolymer structure and biosynthesis and metabolic systems. In the evolutionary model, inherent chemical reactivities of biological building blocks are not necessarily relevant to the origins of life and do not predict biosynthesis. The two models of the origins of life are fundamentally different from one another and guide design of very different experimental approaches to test their underlying assumptions. It is currently undetermined which model, or a hybrid of them, is closer to reality.
|
Kavita Matange; Vahab Rajaei; Gary Schuster; Nicholas Hud; Cesar Menor-Salvan; Pau Capera-Aragonès; Moran Frenkel-Pinter; Loren Williams
|
Biological and Medicinal Chemistry; Earth, Space, and Environmental Chemistry; Space Chemistry; Biochemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-06-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649aeaad9ea64cc1670d5206/original/origins-of-life-chemistry-and-evolution.pdf
|
60c73db8ee301c0690c785fe
|
10.26434/chemrxiv.6030563.v1
|
Statistical Force-Field for Structural Modeling Using Chemical Cross-Linking/mass Spectrometry Distance Constraints
|
<div><p>Chemical cross-linking/Mass Spectrometry (XLMS) is an experimental method to obtain distance constraints between amino acid residues, which can be applied to structural modeling of tertiary and quaternary biomolecular structures. These constraints provide, in principle, only upper limits to the distance between amino acid residues along the surface of the biomolecule. In practice, attempts to use of XLMS constraints for tertiary protein structure determination have not been widely successful. This indicates the need of specifically designed strategies for the representation of these constraints within modeling algorithms. Here, a force-field designed to represent XLMS-derived constraints is proposed. The potential energy functions are obtained by computing, in the database of known protein structures, the probability of satisfaction of a topological cross-linking distance as a function of the Euclidean distance between amino acid residues. The force-field can be easily incorporated into current modeling methods and software. In this work, the force-field was implemented within the Rosetta ab initio relax protocol. We show a significant improvement in the quality of the models obtained relative to current strategies for constraint representation. This force-field contributes to the long-desired goal of obtaining the tertiary structures of proteins using XLMS data. Force-field parameters and usage instructions are freely available at http://m3g.iqm.unicamp.br/topolink/xlff <br /></p></div><p></p><p></p>
|
Allan J. R. Ferrari; Fabio C. Gozzo; Leandro Martinez
|
Bioinformatics and Computational Biology; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-03-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73db8ee301c0690c785fe/original/statistical-force-field-for-structural-modeling-using-chemical-cross-linking-mass-spectrometry-distance-constraints.pdf
|
665030f191aefa6ce1dc453d
|
10.26434/chemrxiv-2024-3vwf1
|
Crystals of Organic Acid-Bases Complexes Defy the pKa Rule Under Compression
|
Crystals of organic acid-base adducts are major components in the active pharmaceutical ingredients (API). These 1:1 adducts either form a co-crystal with a hydrogen-bonded motif or a salt by transfer of proton from the acid to the base. As a rule of thumb if the difference in pKa between the protonated base and the acid (ΔpKa) is ≤ 1, a co-crystal is expected while ΔpKa > 3 leads to a salt. The preferred crystalline form for 1:1 adducts of pyridine, pyridazine, pyrazine and furan with formic acid are elucidated using genetic algorithm assisted first-principles crystal structure predictions (CSP). In agreement with the ΔpKa rule, all the adducts stabilize as H-bonded co-crystals under ambient pressure. However, under isotropic pressure formic acid transfers the protons to the three nitrogenous bases forming salts of pyridinium formate, pyridazinium formate and pyrazinium formate. External pressure is found to dictate the co-crystal – salt equilibrium. The critical pressure (Pc) required to induce co-crystal → salt conversion for formic acid… pyridine/pyridazine/pyrazine is 3 GPa, 5 GPa and 15 GPa respectively. Compression is shown to enhance the electrostatic interactions between the molecules leading to additional stabilization of the ionic configurations namely, N+-H…O- in salts vis-à-vis the neutral N-H…O motifs in the co-crystals. Violating the ΔpKa rule, Pc overcomes the free-energy required for the proton-transfer (ΔGPT) to stabilize the salts. The very high ΔGPT = 177.9 kcal/mol for the furan…formic acid adduct prevents salt formation even at 30 GPa. Apart from the thermodynamic and kinetic control during crystallization, pressure acts as a key control for organic acid-base adducts.
|
Shovan Das; Saied Pratik; Ayan Datta
|
Theoretical and Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-05-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665030f191aefa6ce1dc453d/original/crystals-of-organic-acid-bases-complexes-defy-the-p-ka-rule-under-compression.pdf
|
62f4d8af5f6870086eb46238
|
10.26434/chemrxiv-2022-rlw12
|
Synthesis of Some Heterocyclic Compounds Using Cyanoacetohydrazide as Versatile Precursor
|
This study reviewed the use of cyanoacetohydrazide as versatile precursor for synthesis of some heterocyclic compounds, as it contains five different functional groups ( cyano group, No. 1, active methylene group, No. 2, carbonyl group, No. 3, amido group, No. 4 and hydrazine group, No.5 ) The reviewed reactions were classified according to the active centers of cyanoacetohydrazide involved. Accordingly, they are divided into 12 classes in which heterocycles was obtained via the utility of the following functional groups: a - groups No. 1, 2, b - groups No. 1,5, c - groups No. 2, 3 , d - groups No. 2,4 , e - groups No. 2,5 , f- groups No. 3,5 , g- groups No. 4,5 , h- groups No. 1,2,5, i- groups No. 1,4,5, j- groups No. 2,4,5, k- groups No. 1,2,4,5, l-groups No. 2,3,4,5 .This review covers literature up to 2021.
|
Marwa Fouad; Yehia Allam
|
Organic Chemistry; Organic Compounds and Functional Groups
|
CC BY 4.0
|
CHEMRXIV
|
2022-08-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f4d8af5f6870086eb46238/original/synthesis-of-some-heterocyclic-compounds-using-cyanoacetohydrazide-as-versatile-precursor.pdf
|
60c74f43ee301c446fc7a68e
|
10.26434/chemrxiv.12877685.v1
|
Investigation of Co3Mo and Co6Mo7 Binary Alloys as Electrocatalysts for Hydrogen Evolution Reaction in Acidic Media
|
Metal alloys have become ubiquitous choice as catalysts for electrochemical hydrogen evolution in alkaline media. However, scarce and expensive Pt remains the key electrocatalyst in acidic electrolytes making the search for earth-abundant and cheaper alternatives appealing. Herein, we present a facile and efficient synthetic route towards polycrystalline Co<sub>3</sub>Mo and Co<sub>6</sub>Mo<sub>7</sub> metal alloys that achieve competitively low overpotentials of 115 mV and 160 mV at 10 mA cm<sup>–2</sup> in 0.5 M H<sub>2</sub>SO<sub>4</sub>. Both alloys outperform Co and Mo metals which showed significantly higher overpotentials and lower current densities when tested under identical conditions. However, the low overpotential in Co<sub>3</sub>Mo comes at the price of stability. It rapidly becomes inactive when tested under applied potential bias. On the other hand, Co<sub>7</sub>Mo<sub>6</sub> retains the current density over time without the evidence of current decay. The findings demonstrate that even in free-standing form and without nanostructuring polycrystalline bimetallic electrocatalysts could challenge the dominance of Pt in the acidic media if the ways for improving their stability were found.
|
youyi sun; Alexey Ganin
|
Alloys; Catalysts; Nanostructured Materials - Materials; Electrocatalysis; Heterogeneous Catalysis; Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f43ee301c446fc7a68e/original/investigation-of-co3mo-and-co6mo7-binary-alloys-as-electrocatalysts-for-hydrogen-evolution-reaction-in-acidic-media.pdf
|
60c749df469df44878f43c53
|
10.26434/chemrxiv.12111552.v1
|
A Transfer Learning Study of Gas Adsorption in Metal-Organic Frameworks
|
<p>Metal-organic frameworks (MOFs) are a class of materials promising for gas adsorption due to their highly tunable nano-porous structures and host-guest interactions. While machine learning (ML) has been leveraged to aid the design or screen of MOFs for different purposes, the needs of big data are not always met, limiting the applicability of ML models trained against small data sets. In this work, we introduce a transfer learning technique to improve the accuracy and applicability of ML models trained with small amount of MOF adsorption data. This technique leverages potentially shareable knowledge from a source task to improve the models on the target tasks. As demonstrations, a deep neural network (DNN) trained on H<sub>2</sub> adsorption data with 13,506 MOF structures at 100 bar and 243 K is used as the source task. When transferring knowledge from the source task to H<sub>2</sub> adsorption at 100 bar and 130 K (one target task), the predictive accuracy on target task was improved from 0.960 (direct training) to 0.991 (transfer learning). We also tested transfer learning across different gas species (i.e. from H<sub>2</sub> to CH<sub>4</sub>), with predictive accuracy of CH<sub>4</sub> adsorption being improved from 0.935 (direct training) to 0.980 (transfer learning). Based on further analysis, transfer learning will always work on the target tasks with low generalizability. However, when transferring the knowledge from the source task to Xe/Kr adsorption, the transfer learning does not improve the predictive accuracy, which is attributed to the lack of common descriptors that is key to the underlying knowledge. <b></b></p>
|
RUIMIN MA; Yamil J. Colon; Tengfei Luo
|
Machine Learning
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749df469df44878f43c53/original/a-transfer-learning-study-of-gas-adsorption-in-metal-organic-frameworks.pdf
|
60c73d0fee301cf618c784f7
|
10.26434/chemrxiv.5446564.v1
|
Combining First-Principles and Data Modeling for the Accurate Prediction of the Refractive Index of Organic Polymers
|
Organic materials with a high index of refraction (RI) are attracting considerable interest due to their potential application in optic and optoelectronic devices. However, most of these applications require an RI value of 1.7 or larger, while typical carbon-based polymers only exhibit values in the range of 1.3–1.5. This paper introduces an efficient computational protocol for the accurate prediction of RI values in polymers to facilitate in silico studies that an guide the discovery and design of next-generation high-RI materials. Our protocol is based on the Lorentz-Lorenz equation and is parametrized by the polarizability and number density values of a given candidate compound. In the proposed scheme, we compute the former using first-principles electronic structure theory and the latter using an approximation based on van der Waals volumes. The critical parameter in the number density approximation is the packing fraction of the bulk polymer, for which we have devised a machine learning model. We demonstrate the performance of the proposed RI protocol by testing its predictions against the experimentally known RI values of 112 optical polymers. Our approach to combine first-principles and data modeling emerges as both a successful and highly economical path to determining the RI values for a wide range of organic polymers.
|
Mohammad Atif Faiz Afzal; Chong Cheng; Johannes Hachmann
|
Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0fee301cf618c784f7/original/combining-first-principles-and-data-modeling-for-the-accurate-prediction-of-the-refractive-index-of-organic-polymers.pdf
|
6377bad6207981ee472c3bfc
|
10.26434/chemrxiv-2022-xt6vf
|
Comparison of Detailed Capital Expense Estimates for Two NGCC Retrofits with Capture by Amine Scrubbing
|
Two front-end engineering designs (FEED) for commercial-scale carbon capture from natural gas combined-cycle (NGCC) power plants have been published in full, including detailed capital cost estimates . The two studies are the Piperazine with the Advanced Stripper (PZAS) FEED at Mustang Station in Denver City, TX, USA (“Mustang FEED”) and the FEED at Panda Sherman Power Station in Sherman, TX, USA (“Panda FEED”). This work compares both designs with the aim of gaining insight about the cost of carbon capture processes. Direct field costs for each process are adjusted to account for differences in the estimating methodology in each FEED. This adjustment results in estimated direct field costs of $574MM for Mustang and $411MM for Panda. The breakdowns of capital costs for each process area are compared, to highlight differences in costs due to the respective processes or particular requirements of each host power plant. A key finding is that site-specific factors not typically represented in less rigorous cost estimates are observed to have a significant impact on cost. To compare both estimates on a similar design basis, the Mustang unit was scaled to the Panda FEED design capacity, resulting in direct field costs of $489MM for Mustang and $411MM for Panda. Additionally,
the cost estimates of the CO2 absorbers are analyzed in greater detail to directly compare three equivalent designs that include rectangular and cylindrical absorber columns. Adjusting the absorber estimates to the same scope and scaling to the same size results in estimated costs of
$19.7MM, $18.2MM, and $14.9MM, with the rectangular absorber approximately 10% to 30% more expensive than the cylindrical designs.
|
Jorge Martorell; Gary Rochelle; Michael Baldea; William Elliott; Camila Bauer
|
Chemical Engineering and Industrial Chemistry; Industrial Manufacturing
|
CC BY 4.0
|
CHEMRXIV
|
2022-11-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6377bad6207981ee472c3bfc/original/comparison-of-detailed-capital-expense-estimates-for-two-ngcc-retrofits-with-capture-by-amine-scrubbing.pdf
|
60c74effbb8c1a13193db84f
|
10.26434/chemrxiv.12445394.v3
|
A Steady-State Algebraic Model for the Time Course of Covalent Enzyme Inhibition
|
This report describes an algebraic equation for the
time course of irreversible enzyme inhibition following a two-step mechanism. In the first step, the enzyme and the
inhibitor associate reversibly to form a non-covalent complex. In the second step, the noncovalent complex
is irreversibly converted to the final covalent conjugate. Importantly, the algebraic derivation was
performed under the<i> steady-state approximation</i>. Under the previously
invoked <i>rapid-equilibrium approximation</i> [Kitz & Wilson (1962) <i>J.
Biol. Chem.</i> <b>237</b>, 3245] it is by definition assumed that the rate
constant for the reversible dissociation of the initial noncovalent complex is
very much faster than the rate constant for the irreversible inactivation step.
In contrast, the steady-state algebraic
equation reported here removes any restrictions on the relative magnitude of
microscopic rate constants. The resulting formula was used in heuristic
simulations designed to test the performance of the standard rapid-equilibrium
kinetic model. The results show that if the inactivation rate constant is
significantly higher than the dissociation rate constant, the conventional
“kobs” method for evaluating the potency of covalent inhibitors in drug
discovery is incapable of correctly distinguishing between the two-step
inhibition mechanism and a simpler one-step variant, even for inhibitors that
have very high binding affinity in the reversible noncovalent step.
|
Petr Kuzmic
|
Biochemistry; Biophysics; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74effbb8c1a13193db84f/original/a-steady-state-algebraic-model-for-the-time-course-of-covalent-enzyme-inhibition.pdf
|
6772fbecfa469535b948c94f
|
10.26434/chemrxiv-2024-9gt3g
|
On-line OCHEM Multi Task Model for Solubility and Lipophilicity Prediction of Platinum Complexes
|
Predicting the solubility of platinum(II, IV) complexes is essential to the process of prioritizing potential anticancer candidates in drug discovery. This study presents the first publicly available on-line model for predicting the solubility of platinum complexes, addressing the current scarcity of literature and absence of models in this regard. Using a time-split dataset, the consensus model that we developed had a Root Mean Squared Error (RMSE) of 0.62 through 5-cross-validation on a training set of 284 historical compounds (solubility data reported prior to 2017). However, the RMSE increased to 0.86 when applied to a prospective test set of 108 compounds measured after 2017. Further analysis of the high prediction errors revealed that these inaccuracies are primarily attributed to the underrepresentation of novel chemical scaffolds–mainly Pt(IV) derivatives, in the training sets. For instance, a series of eight phenanthroline-containing compounds, not covered by the training set’s chemical space, had an RMSE of 1.3. When the model was redeveloped using a combined dataset, the RMSE of this series significantly decreased to 0.34 under the same validation protocol. Additionally, we developed an interpretable linear model to identify structural features and functional groups that influence the solubility of platinum complexes. We further validated the correlation between solubility and lipophilicity, consistent with the Yalkowsky General Solubility Equation. Building on these insights, we developed a final multitask model that simultaneously predicts solubility and lipophilicity as two endpoints with RMSE = 0.62 and 0.44, respectively. The data and final developed model is available at https://ochem.eu/article/31.
|
Nesma Mousa; Hristo P. Varbanov; Vidya Kaipanchery; Elisabetta Gabano; Mauro Ravera; Andrey A. Toropov; Larisa Charochkina; Filipe Menezes; Guillaume Godin; Igor V. Tetko
|
Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Artificial Intelligence; Chemoinformatics - Computational Chemistry; Coordination Chemistry (Organomet.)
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-12-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6772fbecfa469535b948c94f/original/on-line-ochem-multi-task-model-for-solubility-and-lipophilicity-prediction-of-platinum-complexes.pdf
|
6683f89bc9c6a5c07a0b82d4
|
10.26434/chemrxiv-2024-9rgf6
|
A novel G-Quadruplex structure within Apolipoprotein E promoter: a new promising target in cancer and dementia fight?
|
Human Apolipoprotein E (APOE) is a crucial lipid transport glycoprotein involved in various biological processes, including lipid metabolism, immune response, and neurodegeneration. Elevated APOE levels are linked to poor prognosis in several cancers and increased risk of Alzheimer's disease (AD). Therefore, modulating APOE expression presents a promising therapeutic strategy for both cancer and AD.
Considering the pivotal role of G-quadruplex (G4) structures in medicinal chemistry as modulators of gene expression, here we present a newly discovered G-quadruplex (G4) structure within the ApoE gene promoter. Bioinformatic analysis identified 21 potential G4-forming sequences in the ApoE promoter, with the more proximal to the transcription start site, pApoE, showing the highest G-score. Biophysical studies confirmed the folding of pApoE into a stable parallel G4 under physiological conditions, supported by circular dichroism, NMR spectroscopy, UV-melting, and quantitative PCR stop assay. Moreover, the ability to modulate pApoE-G4 folding was demonstrated using G4-stabilizing ligands (HPHAM, Braco19, and PDS), which increased the thermal stability of pApoE-G4. In contrast, peptide nucleic acid conjugates synthesized to disrupt G4 formation, effectively hybridizing with pApoE sequences, confirming the potential to unfold G4 structures. Overall, our findings provide a mainstay for future therapeutic approaches targeting ApoE-G4s to regulate APOE expression, offering potential advancements in cancer and AD treatment.
|
Valentina Pirota; Angela Dello Stritto; Lisa Rita Magnaghi; Raffaela Biesuz; Filippo Doria; Mariella Mella; Mauro Freccero; Emmanuele Crespan
|
Biological and Medicinal Chemistry; Biochemistry; Biophysics; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6683f89bc9c6a5c07a0b82d4/original/a-novel-g-quadruplex-structure-within-apolipoprotein-e-promoter-a-new-promising-target-in-cancer-and-dementia-fight.pdf
|
60c7543e469df4be7af44eed
|
10.26434/chemrxiv.13634021.v1
|
Computational Protein Stabilization Can Affect Folding Energy Landscapes and Lead to Domain-Swapped Dimers
|
<p>The functionality of a protein depends on its unique three-dimensional structure,
which is a result of the folding process when the nascent polypeptide follows a
funnel-like energy landscape to reach a global energy minimum. Computer-encoded
algorithms are increasingly employed to
stabilize native proteins
for use in research and biotechnology applications. Here, we reveal a unique example where
the computational stabilization of a monomeric α/β-hydrolase enzyme (<i>T</i><sub>m</sub> = 73.5°C;
Δ<i>T</i><sub>m</sub> > 23°C) affected the protein
folding energy landscape. Introduction of eleven single-point stabilizing
mutations based on force field
calculations and evolutionary analysis yielded catalytically active domain-swapped
intermediates trapped in local energy minima. Crystallographic
structures revealed that these stabilizing mutations target cryptic hinge regions and newly introduced secondary
interfaces, where they make extensive non-covalent interactions between the
intertwined misfolded protomers. The existence of domain-swapped dimers in a solution is further confirmed
experimentally by data obtained from SAXS and crosslinking mass spectrometry. Unfolding experiments showed that
the domain-swapped dimers can be
irreversibly converted into native-like monomers, suggesting that the domain-swapping
occurs exclusively <i>in vivo</i>. Our findings uncovered hidden protein-folding consequences
of computational protein design, which need to be taken into account when
applying a rational stabilization to proteins of biological and pharmaceutical
interest.</p>
|
Klara Markova; Antonin Kunka; Klaudia Chmelova; Martin Havlasek; Petra Babkova; Sérgio M. Marques; Michal Vasina; Joan Planas-Iglesias; Radka Chaloupková; David Bednar; Zbynek Prokop; Jiri Damborsky; Martin Marek
|
Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-01-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7543e469df4be7af44eed/original/computational-protein-stabilization-can-affect-folding-energy-landscapes-and-lead-to-domain-swapped-dimers.pdf
|
6792a508fa469535b98fa6eb
|
10.26434/chemrxiv-2025-wmsfc
|
Is there a future for 43Ca nuclear magnetic resonance in cement science?
|
Calcium and silicon are critical components of cement. While 29Si nuclear magnetic resonance (NMR) is widely used in cement science, 43Ca NMR has received comparatively less attention given the experimental challenges associated with it. To investigate the potential of 43Ca NMR in cement research, a density functional theory study was carried out. The study focused on distinct calcium sites within the calcium silicate hydrate (C-S-H) structure. Four unique calcium sites were identified, each predicted to display distinct 43Ca chemical shifts due to differences in their local environments. These findings were used to generate theoretical 43Ca NMR spectra for C-S-H. Furthermore, theoretical 43Ca NMR spectra for the hydration reaction of triclinic tricalcium silicate were developed, illustrating the potential of 43Ca NMR for tracking the hydration process in multiphase systems.
|
Ziga Casar; Davide Tisi; Samuel J. Page; H. Chris Greenwell; Franco Zunino
|
Theoretical and Computational Chemistry; Materials Science
|
CC BY 4.0
|
CHEMRXIV
|
2025-01-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6792a508fa469535b98fa6eb/original/is-there-a-future-for-43ca-nuclear-magnetic-resonance-in-cement-science.pdf
|
6202818f49bd320c97494183
|
10.26434/chemrxiv-2022-4b7hv
|
One-Pot Synthesis of Heteroatom-Bridged Cyclic Diaryliodonium Salts
|
Two one-pot procedures for the construction of O- and N-bridged diaryliodonium triflates are described. An effective aryne-mediated arylation of o-iodophenols and sulfonamides provides diarylether and diarylamine intermediates, which are subsequently oxidized and cyclized to the corresponding diaryliodaoxinium and iodazinium salts. Different derivatizations were applied to demonstrate their capacity as useful building blocks and gain a deeper understanding towards the general reactivity of these underdeveloped but potentially highly useful compounds.
|
Mattis Damrath; Lucien Caspers; Daniel Duvinage; Boris Johannes Nachtsheim
|
Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2022-02-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6202818f49bd320c97494183/original/one-pot-synthesis-of-heteroatom-bridged-cyclic-diaryliodonium-salts.pdf
|
630e2eaeeadd9a29de875b48
|
10.26434/chemrxiv-2022-3dnw8
|
Enantioselective Synthesis of Skipped Dienes via Iridium-Catalyzed Allylic Alkylation of Phosphonate Carbanions
|
An enantioselective synthesis of skipped diene has been developed based on an iridium-catalyzed allylic alkylation of phosphonate carbanions and Horner-Wadsworth-Emmons olefination. This two-step protocol benefits from the ease of accessibility of the starting materials and delivers C2-substituted skipped dienes, bearing a C3 stereogenic center, in moderate to excellent yields and generally with outstanding enantioselectivities. This is the first catalytic enantioselective allylic alkylation of phosphonate carbanions.
|
Arko Seal; Santanu Mukherjee
|
Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Homogeneous Catalysis; Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630e2eaeeadd9a29de875b48/original/enantioselective-synthesis-of-skipped-dienes-via-iridium-catalyzed-allylic-alkylation-of-phosphonate-carbanions.pdf
|
6656f84991aefa6ce1407d7a
|
10.26434/chemrxiv-2024-zz3m5-v2
|
Adsorption of 5-fluorouracil, an anticancer drug, in faujasite-type zeolites: Understanding storage and release with density functional theory calculations
|
Zeolites have been proposed as carrier materials for the encapsulation and controlled release of the anticancer drug 5-fluorouracil (5-FU). Besides, they could also find use in the adsorption-based removal of 5-FU from water, for example in the treatment of hospital effluents. In the present work, dispersion-corrected density functional theory (DFT) calculations and DFT-based ab initio molecular dynamics (AIMD) simulations are employed to study the interaction of 5-FU with faujasite-type zeolites having different Si/Al ratios. Comparing distinct local arrangements of Al atoms and charge-balancing protons, it is evaluated to what extent “multi-site” interactions, i.e., interactions of 5-FU with more than one proton, affect the adsorption energy. While the most pronounced increase in interaction strength occurs when moving from an all-silica zeolite to a protonic zeolite having a single proton in one twelve-membered ring, a significant additional stabilisation arises if a second framework proton is present in the same ring. Typically, several hydrogen bonds are formed between 5-FU and protonic zeolite frameworks, with 5-FU simultaneously acting as donor and acceptor. AIMD simulations confirm the stability of these hydrogen bonds at room temperature in the absence of water. Additionally, infrared spectra are predicted for selected low-energy configurations in order to facilitate an experimental identification of different bonding environments. AIMD simulations probing the competitive adsorption of 5-FU and water show that the high affinity of water to the framework protons causes a breaking of hydrogen bonds, framework deprotonation, and a displacement of 5-FU from its initial position. Exposure of dehydrated 5-FU@FAU composites to water might thus be a useful approach to trigger 5-FU release in drug delivery applications.
|
Michael Fischer
|
Theoretical and Computational Chemistry; Materials Science; Controlled-Release Systems; Computational Chemistry and Modeling; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-05-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6656f84991aefa6ce1407d7a/original/adsorption-of-5-fluorouracil-an-anticancer-drug-in-faujasite-type-zeolites-understanding-storage-and-release-with-density-functional-theory-calculations.pdf
|
613f432166dedd7fb60c8d2c
|
10.26434/chemrxiv-2021-rrm10
|
(PNSiMe3)4(NMe)6: A robust tetravalent phosphaza-adamantane scaffold for molecular and macromolecular chemistry
|
Tetraarylmethanes and adamantanes are very rare examples of rigid, four-way, anionic connectors that play a scaffolding role in multiple areas of molecular and materials chemistry. We report the synthesis of a tetravalent phosphaza-adamantane cage, (PNSiMe3)4(NMe)6 (2), that shows unusually high ambient, thermal, and redox stability due to its unique geometry. It nevertheless participates in four-fold functionalization reactions on its periphery. The combination of a robust core but a reactive corona makes 2 a convenient inorganic scaffold upon which tetrahedral molecular and macromolecular chemistry can be reliably constructed. This potential is exemplified by the unprecedented synthesis of a tetracationic tetraphosphinimine (3) and the first porous all-P/N polyphosphazene network (5).
|
Joseph Bedard; Nicholas J. Roberts; Karlee L. Bamford; Ulrike Werner-Zwanziger; Katherine M. Marczenko; Saurabh S. Chitnis
|
Materials Science; Inorganic Chemistry; Polymer Science; Inorganic Polymers; Main Group Chemistry (Inorg.)
|
CC BY 4.0
|
CHEMRXIV
|
2021-09-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613f432166dedd7fb60c8d2c/original/pn-si-me3-4-n-me-6-a-robust-tetravalent-phosphaza-adamantane-scaffold-for-molecular-and-macromolecular-chemistry.pdf
|
60c756ee842e653072db45b8
|
10.26434/chemrxiv.14346848.v1
|
Solvated Nickel Complexes as Stoichiometric and Catalytic Perfluoroalkylation Agents
|
<br />The acetonitrile-solvated [(MeCN)Ni(C2F5)3]– was prepared in order to compare and contrast
its reactivity with the known [(MeCN)Ni(CF3)3]– towards organic electrophiles. Both [(MeCN)Ni(CF3)3]– and [(MeCN)Ni(C2F5)3]– successfully react with aryl
iodonium and diazonium salts as well as alkynyl iodonium salts to give
fluoroalkylated organic products.
Electrochemical analysis of [(MeCN)NiII(C2F5)3]– suggests that, upon electro-oxidation to [(MeCN)nNi(C2F5)3],
reductive homolysis of a perfluoroethyl radical occurs, with the concomitant
formation of [(MeCN)Ni(C2F5)2].
Catalytic C-H trifluoromethylations of electron rich arenes were
successfully achieved using either [(MeCN)Ni(CF3)3]– or the related [Ni(CF3)4]2–. Stoichiometric reactions of the solvated
nickel complexes reveal that “ligandless” nickel is exceptionally capable of
serving as reservoir of CF3 anions or radicals under catalytically relevant
conditions. <br />
|
Scott
T. Shreiber; David Vicic
|
Catalysis; Ligands (Organomet.); Reaction (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756ee842e653072db45b8/original/solvated-nickel-complexes-as-stoichiometric-and-catalytic-perfluoroalkylation-agents.pdf
|
60c757d44c8919fd5fad4ab4
|
10.26434/chemrxiv.14459319.v1
|
Chemical Compositions in Modified Salinity Waterflooding of Carbonate Reservoirs -- Experiment
|
<br />Modified or low-salinity waterflooding of carbonate oil reservoirs is of considerable economic interest because of potentially inexpensive incremental oil<br />production. The injected modified brine changes the surface chemistry of the carbonate rock and crude oil interfaces and detaches some adhered crude oil.<br />Composition design of the modified brine to enhance oil recovery is determined by labor-intensive trial-and-error laboratory corefloods. Unfortunately, limestone,<br />which predominantly consists of aqueous-reactive calcium carbonate, alters injected brine composition by mineral dissolution/precipitation. Accordingly, the rock reactivity<br />hinders rational design of the tailored brine to improve oil recovery. <br />Previously, we presented a theoretical analysis of 1D, single-phase brine injection into calcium carbonate-rock that accounts for mineral dissolution, ion<br />exchange, and dispersion (Yutkin et. al 2021). Here we present the results of single-phase waterflood-brine experiments that verify the theoretical framework. We show that concentration histories eluted from Indiana limestone cores possess features characteristic of fast calcium<br />carbonate dissolution, 2:1 ion exchange, and high dispersion. The injected brine reaches chemical equilibrium inside the porous rock even at<br />injection rates higher than 1000 ft/day. Ion exchange results in salinity waves observed experimentally, while high dispersion is responsible for long<br />concentration history tails. <br />Using the verified theoretical framework, we briefly explore how these processes modify aqueous-phase composition during the injection of designer brines into a calcium-carbonate reservoir. Because of high salinity of the initial and injected brines, ion exchange affects injected concentrations only in<br />high surface area carbonates/limestones, such as chalks. Calcium-carbonate dissolution only affects aqueous solution pH. The rock surface composition is affected by all processes.<br /><br />
|
Maxim Yutkin; Clayton J. Radke; Tadeusz Patzek
|
Natural Resource Recovery; Reaction Engineering; Transport Phenomena (Chem. Eng.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757d44c8919fd5fad4ab4/original/chemical-compositions-in-modified-salinity-waterflooding-of-carbonate-reservoirs-experiment.pdf
|
60c74386ee301c0e6ec78ffc
|
10.26434/chemrxiv.8282204.v2
|
Electrophysiological Characterization of Transport Across Outer Membrane Channels from Gram-Negative Bacteria in Their Native Environment
|
Multi-drug-resistance
in Gram-negative bacteria is often associated with low permeability of outer
membrane. To investigate the role of membrane protein channels in the passage of
antibiotics, we extract, purify, reconstitute them into artificial bilayer.
Here we demonstrate that using a fusion of native outer membrane vesicles (OMV)
facilitates channel reconstitution into bilayer and allows to characterize them
in their native environment. Proteins from <i>E.
coli</i> (OmpF, OmpC) were overexpressed from the host, and the corresponding
OMVs were collected. Each OMV fusion revealed surprisingly only a few channel
activities. The asymmetry of the OMV translates after fusion into bilayer with
the LPS dominantly present at OMV addition side. Compared to conventional methods,
channels fused from OMVs have similar conductance but broader distribution. The
further addition of Enrofloxacin yielded higher association but lower
dissociation rates attribute to the presence of LPS. We conclude using OMV is a
robust approach for functional and structural studies of membrane channels in
the native membrane.
|
Jiajun Wang; Rémi Terrasse; Jayesh Arun Bafna; Lorraine Benier; Mathias Winterhalter
|
Cell and Molecular Biology; Microbiology; Biophysical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-07-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74386ee301c0e6ec78ffc/original/electrophysiological-characterization-of-transport-across-outer-membrane-channels-from-gram-negative-bacteria-in-their-native-environment.pdf
|
64d6188369bfb8925ac128f8
|
10.26434/chemrxiv-2023-84f91
|
Understanding the effects of transition metal intercalation on electronic and electrochemical properties of Ti3C2Tx MXene
|
MXenes are 2D transition metal carbides, nitrides, and/or carbonitrides, capable of intercalation by various cations through chemical or electrochemical means. Previous research has primarily focused on intercalating alkaline and alkaline earth cations, such as Li+, K+, Na+, Mg2+ or alkylammonium cations, into Ti3C2Tx MXenes. However, the impact of intercalated transition metal (TM) ions on the electronic and electrochemical properties of MXenes remains largely unexplored. In this study, we investigated the effects of pre-intercalated Cu ions on Ti3C2Tx MXenes and vice versa to gain a comprehensive understanding of how the electronic and electrochemical properties of both intercalated TM ion and MXene host are altered. Using in-situ X-ray absorption spectroscopy (XAS), we reveal changes in the oxidation states of intercalated Cu ions and Ti atoms during charging and their corresponding role in charge storage mechanisms. Our findings show that electronic coupling between Ti3C2Tx and Cu ions results in modified electrochemical and electronic properties compared to pristine Ti3C2Tx. These insights lay the foundation for the rational design and utilization of TM ion intercalants to tailor the properties of MXenes for various electrochemical systems and beyond.
|
Shianlin Wee; Xiliang Lian; Evgeniya Vorobyeva; Akhil Tayal; Vladimir Roddatis; Fabio La Mattina; Dario Gomez Vazquez; Netanel Shpigel; Mathieu Salanne; Maria R. Lukatskaya
|
Materials Science; Nanoscience; Nanostructured Materials - Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d6188369bfb8925ac128f8/original/understanding-the-effects-of-transition-metal-intercalation-on-electronic-and-electrochemical-properties-of-ti3c2tx-m-xene.pdf
|
6285e6d343d1f040ee316af5
|
10.26434/chemrxiv-2022-t2dhm
|
Cyclic(alkyl)(amino)carbene Ruthenium Complexes for Z-Stereoselective (Asymmetric) Olefin Metathesis
|
The first Z-stereoselective catechodithiolate ruthenium complexes containing cyclic(alkyl)(amino)carbene ligands are reported. Isolated in nearly quantitative yields or in-situ generated, these catalysts demonstrated remarkable Z selectivity (Z/E ratio up to >98/2) in ring-opening metathesis polymerization (ROMP), ring-opening-cross metathesis (ROCM) and cross-metathesis (CM). Thanks to the efficient chiral HPLC resolution of racemic CAAC-complex precursors, optically pure dithiolated complexes were also synthesized allowing to produce enantioenriched Z-ROCM products in >99/1 Z/E with good levels of enantioselectivity.
|
Jennifer MORVAN; François VERMERSCH; Jan LORKOWSKI; Jakub TALCIK; Thomas VIVES; Thierry ROISNEL; Christophe CREVISY; Nicolas VANTHUYNE; Guy BERTRAND; Rodolphe JAZZAR; Marc MAUDUIT
|
Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Ligand Design; Transition Metal Complexes (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-05-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6285e6d343d1f040ee316af5/original/cyclic-alkyl-amino-carbene-ruthenium-complexes-for-z-stereoselective-asymmetric-olefin-metathesis.pdf
|
648324d7be16ad5c57b1b6f7
|
10.26434/chemrxiv-2023-bw143
|
DFT Studies of Rotational Conformers of 4-Azido-N-Phenylmalemide
|
DFT calculations were performed to study the rotational conformers of 4-Azido-N-Phenylmalemide using B3LYP with 7 basis sets, 6-31G(d,p), 6-31+G(d,p), 6-31++G(d,p), 6-311G(d,p), 6-311+G(d,p), 6-311++G(d,p), and 6-311++G(df,pd). DFT studies show that the two isomers of 4-Azido-N-Phenylmalemide have the same energetics. Furthermore, the rotational barrier between the isomers is 0.17 eV in N, N-dimethylacetamide (NNDMA) and 0.15 eV in tetrahydrofuran (THF). These indicate that the isomers are present in the solvents and can be easily converted between them. The azido asymmetric stretch differs by about 1 cm-1 between the isomers in NNDMA and less than 1 cm-1 in THF. The most significant effect of rotational conformers is in the coupling strength of fermi resonances with the most impact in THF environment. Therefore, the current DFT results show that isomers of 4-Azido-N-Phenylmalemide can be mostly detected in THF by 2D IR technique. Furthermore, the results from seven basis set provide consistent conclusion on the isomers, dependence of the basis sets may be useful information to the development of functionals in DFT method and may be served as a useful tool to understand coupling of vibrational modes of complex molecules and their isomers.
|
Sathya Perera; Lichang Wang
|
Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry; Computational Chemistry and Modeling; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-06-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648324d7be16ad5c57b1b6f7/original/dft-studies-of-rotational-conformers-of-4-azido-n-phenylmalemide.pdf
|
6147f8d018be85898b2860b6
|
10.26434/chemrxiv-2021-46cg5
|
Investigation of the structure and properties of ceramic materials with a rigid system of microfiltration transport pores based on basalt fibers
|
The report provides information on the formation of the structure of porous ceramic materials made of basalt fiber obtained by pressing with subsequent sintering. The phase composition, structure, and properties of ceramics are studied. The relationship between the structure, phase composition, and properties of the ceramic material is established.
|
Siarhei Besarab; Sergey Azarov; Justyna Sauka; Evgeny Petyushik; Tatyana Azarova; Alexey Drobysh
|
Materials Science; Inorganic Chemistry; Ceramics; Fibers; Nanostructured Materials - Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-09-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6147f8d018be85898b2860b6/original/investigation-of-the-structure-and-properties-of-ceramic-materials-with-a-rigid-system-of-microfiltration-transport-pores-based-on-basalt-fibers.pdf
|
64e7cb6ddd1a73847f716344
|
10.26434/chemrxiv-2023-rrs7z
|
Unsymmetrical Imidazopyrimidine-based Bimetallic Ligand and Complexes
|
With bimetallic catalysts becoming increasingly important, the development of electronically and structurally diverse binucleating ligands is desired. This work describes the synthesis of unsymmetric ligand 2,7-di(pyridin-2-yl)imidazo[1,2-a]pyrimi-dine (dpip) that is achieved in four steps on a multi-gram scale in an overall 54% yield. The ability of dpip to act as a scaffold for the formation of bimetallic complexes is demonstrated with the one-step syntheses of the dicopper complex Cu2(dpip)(µ-OH)(CF3COO)3 (4), the dipalladium complex [Pd2(dpip)(µ-OH)(CF3COO)2][(CF3COO)2H] (5), and the dinickel complex [{Ni2(dpip)(µ-Cl)Cl2(MeOH)3}2][2Cl] (6) in good yields (79-92%). All bimetallic complexes were characterized by spectroscopic methods and x-ray crystallography which revealed metal-metal distances between 3.4821(9)−4.106(2) Å. Additionally, quantum-chemical calculations were conducted on complex 4 and an analogous 1,8-naphthyridine-based dicopper complex to investigate the differences between the imidazopyrimidine motif reported here and the widely used 1,8-naphthyridine motif. Natural bonding orbital (NBO) and Mayer Bond order (MBO) analyses validated the ability of dpip to coordinate metals more strongly. Finally, NBO cal-culations quantified the differences in the binding energy between the two pockets of the unsymmetrical dpip ligand.
|
Mila Abaeva; Christian Ieritano; Scott Hopkins; Derek Schipper
|
Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Inorg.); Transition Metal Complexes (Inorg.); Coordination Chemistry (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e7cb6ddd1a73847f716344/original/unsymmetrical-imidazopyrimidine-based-bimetallic-ligand-and-complexes.pdf
|
659e52799138d2316198126c
|
10.26434/chemrxiv-2024-hdr0w
|
Porous and Meltable Metal-Organic Polyhedra for the Generation and Shaping of Porous Mixed-Matrix Composites
|
Here, we report the synthesis of BCN-93, a meltable, functionalized and permanently porous metal-organic polyhedron (MOP), and its subsequent transformation into amorphous or crystalline, shaped, self-standing, transparent porous films via melting and subsequent cooling. The synthesis entails the outer functionalization of a MOP with meltable polymer chains: in our model case, we functionalized a Rh(II)-based cuboctahedral MOP with polyethylene glycol (PEG). Finally, we demonstrate that once melted, BCN-93 can serve as a porous matrix into which other materials or molecules can be dispersed to form mixed-matrix composites. To illustrate this, we combined BCN-93 with one of various additives (either two MOF crystals, a porous cage, or a linear polymer) to generate a series of mixed-matrix films, each of which exhibited greater CO2 uptake relative to the parent film.
|
Cornelia von Baeckmann; Jordi Martínez-Esaín; José Suárez; Lingxin Meng; Joan Garcia-Masferrer; Jordi Faraudo; Jordi Sort; Arnau Carné-Sánchez; Daniel Maspoch
|
Materials Science; Inorganic Chemistry; Materials Processing; Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659e52799138d2316198126c/original/porous-and-meltable-metal-organic-polyhedra-for-the-generation-and-shaping-of-porous-mixed-matrix-composites.pdf
|
60f2693e78578734b56a5064
|
10.26434/chemrxiv-2021-b43s1
|
Predicting the stability and electronic structure of alkali metal aurides
|
Density functional theory calculations of phonon modes predict that some compounds of the alkali metal aurides family, general formula A2MAu6 (A = K+, Rb+ or Cs+; M = Ti, Zr, Hf, Sn or Pb), have stable three-dimensional phase with a double perovskite-type structure and cubic Fm3m space group (K2PtCl6-type). Bader’s charge analysis shows that most electron density is located within the six atoms at the octahedra vertices like double perovskite halides. However, the short spacing between Au anions enables d-orbital interactions between them. Compounds of this family, with group 4 metals only, carry conduction states around the Gamma point (k = 0). On the other hand, compounds with group 14 metals possess more conduction states around all the Brillouin zone and have electron pockets in their bandstructure. These compounds provide further insights into the unusual anionic behavior of gold and present other alternatives for the construction of divergent nanodevices.
|
Axel Melchor Gaona Carranza; Jesús María Siqueiros; Reyes García Díaz; Jonathan Guerrero Sánchez
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-07-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f2693e78578734b56a5064/original/predicting-the-stability-and-electronic-structure-of-alkali-metal-aurides.pdf
|
642bd55016782ec9e6527102
|
10.26434/chemrxiv-2023-rfvnk
|
Gram-Scale Synthesis of Site-Specific Antibody-Drug Conjugates Using AJICAP Second-Generation Technology
|
Chemical site-specific conjugation technology utilizing immunoglobulin-G (IgG) Fc-affinity reagents is a versatile and promising tool for producing next-generation antibody-drug conjugates (ADCs). Our research group recently reported a novel Fc-affinity peptide-mediated conjugation method, termed AJICAP second-generation. This technology, based on thioester chemistry, produces site-specific ADCs without aggregation. Herein, we report further investigations into the AJICAP second-generation technology. By varying the parameters of the peptide conjugation step, it was found that this reaction is feasible under a wide range of reaction conditions. All synthetic intermediates of the AJICAP-ADCs were sufficiently stable, indicating that each synthetic step is a possible holding point in ADC manufacturing. The Lys248- and Lys288-conjugated ADCs were prepared on a gram-scale using two different Fc-affinity peptide reagents, employing a scale-down manufacturing approach involving tangential flow filtration (TFF). The total product yield was > 80%, and ultimately, 13.2 g of trastuzumab-Lys248-MMAE and 1.26 g of trastuzumab-Lys288-MMAE were obtained with high drug to antibody ratios (DARs). The results strongly indicate that the AJICAP second-generation method is a robust and practical approach for the manufacture of ADCs.
|
Tomohiro Watanabe; Tomohiro Fujii; Jason Stofleth; Rika Takasugi; Kazutoshi Takahashi; Yutaka Matsuda
|
Organic Chemistry; Bioorganic Chemistry; Process Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642bd55016782ec9e6527102/original/gram-scale-synthesis-of-site-specific-antibody-drug-conjugates-using-ajicap-second-generation-technology.pdf
|
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.