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63eb897e9da0bc6b33eb55c0
|
10.26434/chemrxiv-2023-p7hdw-v2
|
State of the Art and of Outlook of Data Science and Machine Learning in Organic Chemistry
|
The use of data science, artificial intelligence, and big data in the field of chemistry has recently grown to speed up the discovery of new materials, drugs, and synthetic substances and the identification of automated compounds. Machine learning and data science are commonly used in organic chemistry to predict biological and physicochemical properties of molecules and are referred to as quantitative structure active relationship (QSAR, for biological properties) and quantitative structure property relationship (QSPR, for nonbiological properties). In addition, data science and machine learning have advanced the optimization of molecular properties, synthetic pathways, and even the design of novel compounds. These models can learn the underlying patterns of molecular structures to generate new compounds with desirable properties. Hence, machine learning (ML) is extensively used in chemistry, and the field is rapidly adopting state-of-the-art ML algorithms and tools such as deep learning, tensors, and transformers to solve and model chemical problems. The application of data science and ML, particularly deep learning, plays a significant role in advancing research in organic chemistry.
|
Ricardo Stefani
|
Theoretical and Computational Chemistry; Organic Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-02-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63eb897e9da0bc6b33eb55c0/original/state-of-the-art-and-of-outlook-of-data-science-and-machine-learning-in-organic-chemistry.pdf
|
60c7564a337d6cec6ce28de0
|
10.26434/chemrxiv.14226836.v1
|
Photodissociation Dynamics of the Cyclohexyl Radical from the 3p Rydberg State at 248 nm
|
The photodissociation of jet-cooled cyclohexyl was studied by exciting
the radicals to their 3p Rydberg state using 248 nm laser light and detecting
photoproducts by photofragment translational spectroscopy. Both H-atom loss and
dissociation to heavy fragment pairs are observed. The H-atom loss channel exhibits
a two-component translational energy distribution. The fast photoproduct
component is attributed to impulsive cleavage directly from an excited state,
likely the Rydberg 3s state, forming cyclohexene. The slow component is due to
statistical decomposition of hot cyclohexyl radicals that internally convert to
the ground electronic state prior to H-atom loss. The fast and slow components
are present in a ~0.7:1 ratio, similar to findings in other alkyl radicals. Internal
conversion to the ground state also leads to ring-opening followed by
dissociation to 1-buten-4-yl + ethene in comparable yield to H-loss, with the C<sub>4</sub>H<sub>7</sub>
fragment containing enough internal energy to dissociate further to butadiene
via H-atom loss. A very minor ground-state C<sub>5</sub>H<sub>8</sub> + CH<sub>3</sub>
channel is observed, attributed predominantly to 1,3-pentadiene formation. The
ground-state branching ratios agree well with RRKM calculations, which also
predict C<sub>4</sub>H<sub>6</sub> + C<sub>2</sub>H<sub>5</sub> and C<sub>3</sub>H<sub>6</sub>
+ C<sub>3</sub>H<sub>5</sub> channels with similar yield to C<sub>5</sub>H<sub>8</sub>
+ CH<sub>3</sub>. If these channels were active it was at levels too low to be observed.
|
Isaac Ramphal; Mark Shapero; Daniel Neumark
|
Chemical Kinetics; Photochemistry (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7564a337d6cec6ce28de0/original/photodissociation-dynamics-of-the-cyclohexyl-radical-from-the-3p-rydberg-state-at-248-nm.pdf
|
668af8db01103d79c5519a3b
|
10.26434/chemrxiv-2024-7859s
|
Diffusion power spectra as a window into dynamic materials architecture
|
Understanding molecular dynamics in heterogeneous environments is a foundational step in tuning macromolecular reactivity. This is especially important in the chemical recycling of commodity and specialty polymers, which is often undertaken in aqueous media using molecular or enzymatic catalysts. Yet, it remains a challenge study dynamic materials architectures without accurate discernment of the behavior of water in confining media to capture the complexity of the operative transport processes. Here, we develop experimental and analytical methodologies describing the complete set of diffusive eigenmodes that exist within time-varying, non-Euclidean boundary conditions—a situation commonly found in the reactive deconstruction of polymers. Diffusion power spectra, as discerned by an NMR-based method, yield frequency-domain velocity autocorrelation functions that are analyzed in the context of physical models parameterized with fractal mathematics. The results connect time-evolving local motion in polymers to chemical reactivity during acid-catalyzed deconstruction of elastomers. The fundamental understanding provided herein offers practical tools for engineering materials with tailored properties and behaviors, with particular attention to the design of reactive polymers that advance circular materials economies and sustainable chemistry practices.
|
Sophia Fricke; Mia Salgado; Shira Haber; Mutian Hua; Jeremy Demarteau; Ah-Young Song; Brett Helms; Jeffrey Reimer
|
Physical Chemistry; Polymer Science; Chemical Engineering and Industrial Chemistry; Polymerization kinetics; Physical and Chemical Processes; Transport phenomena (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668af8db01103d79c5519a3b/original/diffusion-power-spectra-as-a-window-into-dynamic-materials-architecture.pdf
|
656bf19dcf8b3c3cd7a95cdb
|
10.26434/chemrxiv-2023-g8x1b
|
Ultrafast Charge Transfer Cascade in a Mixed-Dimensionality Nanoscale Trilayer
|
Innovation in optoelectronic semiconductor devices is driven by a fundamental understanding of how to move charges and/or excitons (electron-hole pairs) in specified directions for doing useful work, e.g. for making fuels or electricity. The diverse and tunable electronic and optical properties of two-dimensional (2D) transition metal dichalcogenides (TMDCs) and one-dimensional (1D) semiconducting single-walled carbon nanotubes (s-SWCNTs) make them good quantum confined model systems for fundamental studies on charge and exciton transfer across heterointerfaces. Here we demonstrate a mixed-dimensionality 2D/1D/2D MoS2/SWCNT/WSe2 hetero-trilayer that enables ultrafast photoinduced exciton dissociation, followed by charge diffusion and slow recombination. Importantly, the hetero-trilayer serves to double charge carrier yield relative to a MoS2/SWCNT hetero-bilayer, and also demonstrates the ability of the separated charges to overcome inter-layer exciton binding energies to diffuse from one TMDC/SWCNT interface to the other 2D/1D interface, resulting in coulombically unbound charges. Interestingly, the hetero-trilayer also appears to enable ef- ficient hole transfer from SWCNTs to WSe2, which is not observed in the identically prepared WSe2/SWCNT heterobilayer, suggesting that new dynamic pathways may be opened up by increasing the complexity of nanoscale heterostructures. Our work suggests "mixed-dimensionality" TMDC/SWCNT based hetero-trilayers as both inter- esting model systems for mechanistic studies of carrier dynamics at nanoscale heteroin- terfaces, and for potential applications in advanced optoelectronic systems.
|
Alexis R. Myers; Zhaodong Li; Melissa Gish; Justin Earley; Justin Johnson; M. Alejandra Hermosilla-Palacios; Jeffrey Blackburn
|
Materials Science; Nanoscience; Energy; Multilayers; Optical Materials; Nanostructured Materials - Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656bf19dcf8b3c3cd7a95cdb/original/ultrafast-charge-transfer-cascade-in-a-mixed-dimensionality-nanoscale-trilayer.pdf
|
67b27bb46dde43c908325a85
|
10.26434/chemrxiv-2025-k55xd
|
Structural basis of Bis-quinolinium scaffolds binding to Quadruplex-duplex hybrids from PIM1 oncogene
|
This study investigates the interactions of two bis-quinolinium ligands, Phen-DC3, and 360A, with G-quadruplex-duplex hybrids (QDHs), focusing on the different QDH constructs from the PIM1 oncogene. Using solution NMR spectroscopy and molecular dynamics simulations, we show that both ligands selectively bind the hybrid QDH conformation while exhibiting negligible affinity for the antiparallel topology. High-resolution NMR structures reveal that both ligands localize at the G-quadruplex-duplex (Q-D) junction but with distinct binding dynamics. Our results indicate that ligand binding specificity depends on factors such as ligand structure and the Q-D interface's integrity rather than the base pair's nature or the length of the lateral duplex domain. Stable capping structures, such as the G-C-G-C quartet in antiparallel PIM1 QDH, hinder specific binding with high affinity. Notably, a single Watson-Crick base pair in the lateral loop, stacked with the G-tetrad, suffices for accommodating bis-quinolinium ligands. The strong binding affinity and specificity of Phen-DC3 and 360A for hybrid QDHs in the Xenopus laevis oocytes suggest their potential for selectively targeting QDH structures under complex cellular environments. Our findings offer valuable insights into conformational fluctuations of G-rich sequences using small molecule-based ligands for therapeutic, biotechnological, and nanotechnology applications.
|
Anirban Ghosh; Jakub Harnoš; Petr Stadlbauer; Jiri Sponer; Martina Lenarcic Zivkovic; Lukáš Trantírek
|
Physical Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Biochemistry; Biophysics; Biophysical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-02-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b27bb46dde43c908325a85/original/structural-basis-of-bis-quinolinium-scaffolds-binding-to-quadruplex-duplex-hybrids-from-pim1-oncogene.pdf
|
60c752269abda28236f8dd5c
|
10.26434/chemrxiv.13259303.v1
|
Synergistic Effect of Hydrogen Bonding and π-π Stacking Enables Long Cycle Life in Organic Electrode Materials
|
Small-molecule organic compounds have emerged as
attractive candidates for energy storage in lithium-ion batteries due to their
sustainability and modularity. To develop generalizable design principles for
organic electrode materials (OEMs), we investigated the correlation between electrochemical
performance and addition of functional groups that promote synergistic hydrogen
bonding and π-π stacking using a series of quinone-fused aza-phenazines (QAPs)
with different hydrogen bonding donor/acceptor arrays. The QAP containing the
most hydrogen bonding groups (<b>3</b>) exhibits the best performance with discharge
capacities of 145 mAh g<sup>-1</sup> at 2C with 82% capacity retention over
1000 cycles. The performance of <b>3</b> is attributed to the strategically
incorporated -OH and -NH<sub>2</sub> groups, which facilitate strong
intermolecular interactions and a tightly packed 2D structure. The intermolecular
interaction strength was evaluated using variable temperature 1D <sup>1</sup>H
NMR and 2D <sup>1</sup>H-<sup>1</sup>H NOESY, offering a new strategy to help understand
and predict the performance of OEMs with hydrogen bonding motifs.
|
Madison R. Tuttle; Shelby Davis; Shiyu Zhang
|
Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-11-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752269abda28236f8dd5c/original/synergistic-effect-of-hydrogen-bonding-and-stacking-enables-long-cycle-life-in-organic-electrode-materials.pdf
|
60c745aeee301c1889c7937e
|
10.26434/chemrxiv.10102289.v1
|
Making Soup: Preparing and Validating Molecular Simulations of the Bacterial Cytoplasm
|
Biomolecular crowding affects the biophysical and biochemical behavior of macro- molecules when compared to the dilute environment present in experiments made with isolated proteins. Computational modeling and simulation are useful tools to study how crowding affects the structural dynamics and biological properties of macromolecules. As computational power increased, modeling and simulating large scale all-atom explicit solvent models of the prokaryote cytoplasm become possible. In this work, we build an atomistic model of the cytoplasm of Escherichia coli composed of 1.5 million atoms and submit it to a total of 3 μs of molecular dynamics simulations. The properties of biomolecules under crowding conditions are compared to those from simulations of the individual compounds under dilute conditions. The simulation model is found to be consistent with experimental data about the diffusion coefficient and stability of macromolecules under crowded conditions. In order to stimulate further work we provide a Python script and a set of files that enables other researchers to build their own E. coli cytoplasm models to address questions related to crowding.<br />
|
Leandro Oliveira Bortot; Zahedeh Bashardanesh; David van der Spoel
|
Biophysical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-11-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745aeee301c1889c7937e/original/making-soup-preparing-and-validating-molecular-simulations-of-the-bacterial-cytoplasm.pdf
|
6720c07ef9980725cf407574
|
10.26434/chemrxiv-2024-4z37h-v2
|
Recent progress in modeling and simulation of
biomolecular crowding and condensation inside
cells
|
Macromolecular crowding in the cellular cytoplasm can potentially impact diffusion
rates of proteins, their intrinsic structural stability, binding of proteins to their corresponding partners as well as biomolecular organization and phase separation. While
such intracellular crowding can have a large impact on biomolecular structure and
function, the molecular mechanisms and driving forces that determine the effect of
crowding on dynamics and conformations of macromolecules are so far not well understood. At a molecular level, computational methods can provide a unique lens to
investigate the effect of macromolecular crowding on biomolecular behavior, providing
us with a resolution that is challenging to reach with experimental techniques alone.
In this review, we focus on the various physics-based and data-driven computational
methods developed in the last few years to investigate macromolecular crowding and intracellular protein condensation. We review recent progress in modeling and simulation of biomolecular systems of varying sizes, ranging from single protein molecules
to the entire cellular cytoplasm. We further discuss the effects of macromolecular
crowding on different phenomena, such as diffusion, protein-ligand binding, and their
mechanical and viscoelastic properties, such as surface tension of condensates. Finally,
we discuss some of the outstanding challenges that we anticipate the community addressing in the next few years in order to investigate biological phenomena in model
cellular environments by reproducing in-vivo conditions as accurately as possible.
|
Apoorva Mathur; Rikhia Ghosh; Ariane Nunes-Alves
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-10-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6720c07ef9980725cf407574/original/recent-progress-in-modeling-and-simulation-of-biomolecular-crowding-and-condensation-inside-cells.pdf
|
60c758f8bdbb893e72a3ae79
|
10.26434/chemrxiv.14556153.v2
|
Direct Amidation of Esters via Ball Milling
|
<p><i>The direct mechanochemical amidation of esters – enabled by ball-milling – is herein described. The operationally simple procedure requires inputs of ester, amine, and sub-stoichiometric KOtBu and is applicable to a preparation of a large and diverse library of 78 amide structures with modest to excellent efficiency. Heteroaromatic and heterocyclic components are specifically shown to be amenable to this mechanochemical protocol. This direct synthesis platform has been applied to the synthesis of API’s, agrochemicals, and its ability to deliver gram-scale synthesis of active pharmaceuticals and building blocks is demonstrated, all in the absence of a reaction solvent.</i></p>
|
William I. Nicholson; Fabien Barreteau; Jamie Leitch; Riley Payne; Ian Priestley; Edouard Godineau; Claudio Battilocchio; Duncan Browne
|
Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758f8bdbb893e72a3ae79/original/direct-amidation-of-esters-via-ball-milling.pdf
|
60c75171ee301c5e15c7aa7d
|
10.26434/chemrxiv.13169627.v1
|
Operando Calorimetry Informs the Origin of Rapid Rate Performance in Microwave-Prepared TiNb2O7 Electrodes
|
<div>The shear-phase compound TiNb<sub>2</sub>O<sub>7</sub> has recently emerged as a safe and high-volumetric density replacement for graphite anodes in lithium ion batteries. An appealing feature of TiNb<sub>2</sub>O<sub>7</sub> is that it retains capacity even at high cycling rates. Here we demonstrate that phase pure and crystalline TiNb<sub>2</sub>O<sub>7</sub> can be rapidly prepared using a high-temperature microwave synthesis method. Studies of the charging and discharging of this material, including through operando calorimetry, permit key thermodynamic parameters to be revealed. The nature of heat generation is dominated by Joule heating, which sensitively changes as the conductivity of the electrode increases with increasing lithiation. The enthalpy of mixing, obtained from operando calorimetry, is found to be small across the different degrees of lithiation pointing to the high rate of lithium ion diffusion at the origin of rapid rate performance.</div>
|
Sun Woong Baek; Kira E. Wyckoff; Danielle M. Butts; Jadon Bienz; AMPOL LIKITCHATCHAWANKUN; Molleigh
B. Preefer; Matevz Frajnkovic; Bruce S. dunn; Ram Seshadri; Laurent Pilon
|
Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-11-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75171ee301c5e15c7aa7d/original/operando-calorimetry-informs-the-origin-of-rapid-rate-performance-in-microwave-prepared-ti-nb2o7-electrodes.pdf
|
647072afbe16ad5c57f2470f
|
10.26434/chemrxiv-2023-q80nz
|
Interplay of Local pH and Cation Hydrolysis During Electrochemical CO2 Reduction Visualized by In Operando Chemical Shift Resolved Magnetic Resonance Imaging
|
The Cu-catalyzed electrochemical CO2 reduction enables the conversion of greenhouse gas emissions to fuels or platform chemicals, with prospects of storing intermittent energy from renewable sources. While current research in tuning catalyst activity and product selectivity is often mired in finding electrode engineering solutions, the importance of electrolyte engineering is mostly overlooked. This study presents a method for measuring local pH profiles in electrode-proximity and correlating them to cation-induced buffering effects. Magnetic Resonance Imaging (MRI) techniques were applied to evaluate the local pH values using spatially resolved 13C resonances of the CO2/HCO3–/CO32– equilibrium. The buffering effect of cation hydrolysis is substantiated by local shifts of the 23Na resonance of Na+ in NaHCO3 electrolytes. Steeper local pH gradients, compared to experiments with KHCO3, account for increased selectivity for acetate formation from solution-based reaction. Proven itself capable of elucidating the effect of cations on local pH values, our presented method supports tailoring the electrode–electrolyte interface to selectively generate value-added products.
|
Michael Schatz; Johannes Kochs; Sven Jovanovic; Rüdiger-A. Eichel; Josef Granwehr
|
Physical Chemistry; Catalysis; Energy; Electrocatalysis; Electrochemistry - Mechanisms, Theory & Study; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647072afbe16ad5c57f2470f/original/interplay-of-local-p-h-and-cation-hydrolysis-during-electrochemical-co2-reduction-visualized-by-in-operando-chemical-shift-resolved-magnetic-resonance-imaging.pdf
|
67b110c9fa469535b985e58c
|
10.26434/chemrxiv-2025-1l111-v2
|
Electronic and Geometric contributors to Hydrogen Binding in Uranium Oxide Grain Boundaries
|
Hydrogen induced corrosion of uranium, which leads to the formation of toxic and pyrophoric UH3, raises significant safety concerns for long-term storage of nuclear materials. Previous work suggests hydrogen diffuses through the top passivating oxide layer to initiate hydriding reactions within the underlying grain boundaries (GB). However, the atomistic mechanisms underlying this phenomenon and the structural factors that control its initiation are not well understood. To address this knowledge gap, here we use a high-throughput density function theory (DFT) workflow to investigate the adsorption of H and H2 in the defective bulk UO2. Specifically, we exhaustively investigated the adsorption of H (107 sites) and H2 (26 sites) in three different coincidence site lattice (CSL) GBs: Σ3, Σ5, and Σ9. Compared to the binding energies in pristine UO2, we observe significantly stronger hydrogen adsorption at these GB sites. Interestingly, we find that the trends in H and H2 adsorption vary considerably across the three GB models. In particular, while a small number of sites in Σ5 and Σ9 show exothermic adsorption of H and H2, respectively, no such sites are found in Σ3. Further statistical analysis of these trends suggests that H adsorption, which is adsorbed as a hydride anion (i.e., H-), is positively correlated with the value of its negative charge and depends on the number of neighboring oxygen and uranium atoms. Together, these results provide fundamental atomistic insights that could guide the development of future corrosion mitigation strategies for the storage of nuclear materials.
|
Rajat Goel; Nir Goldman; Ambarish Kulkarni
|
Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Ceramics; Computational Chemistry and Modeling; Physical and Chemical Processes
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-02-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b110c9fa469535b985e58c/original/electronic-and-geometric-contributors-to-hydrogen-binding-in-uranium-oxide-grain-boundaries.pdf
|
60c74b64842e65488edb3147
|
10.26434/chemrxiv.12324980.v1
|
Drug Repurposing for COVID-19 from FDA Approved and Experiment Stage Drugs by in Silico Methods with SARS CoV-2 Spike Protein
|
E-pharmacophore based virtual screening of DrugBank database is
carried out to identify candidate drugs for repurposing. The dug molecules were
screened based on the pharmacophore generated and filtered through the 6000
drug molecule to obtain better 2000 of them. This filtered drug molecules
further screened via structure based approach, involving molecular docking at
different precisions. From the large database seven drug lead molecules were
selected as hits and their binding energy with the spike protein were
calculated. Cladribine, Clofarabine, Fludarabine from approved category and 7-methyl-guanosine-5'-triphosphate-5'-guanosine,
Adenosine-2'-5'-Diphosphate, 8-Bromo-Adenosine-5'-Monophosphate, Alpha-Methylene
Adenosine Monophosphate in the experimental category were found to be potent
inhibitors of SARS CoV-2 spike protein to repurpose as drugs for COVID-19.
|
Sharanya CS; arun kumar; Abhithaj J; Sabu A; Haridas Madathilkovilakathu
|
Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b64842e65488edb3147/original/drug-repurposing-for-covid-19-from-fda-approved-and-experiment-stage-drugs-by-in-silico-methods-with-sars-co-v-2-spike-protein.pdf
|
670232b412ff75c3a1966628
|
10.26434/chemrxiv-2024-vjmj1
|
A Machine Learned Potential for Investigating Single Crystal to Single Crystal Transformations in Complex Organic Molecular Systems
|
The packing of organic molecular crystals is often dominated by weak non-covalent interactions, making their in-situ rearrangement under external stimuli challenging to understand. We investigate a pressure-induced single-crystal-to-single- crystal (SCSC) transformation between two polymorphs of 2,4,5-triiodo-1H-imidazole using machine learning potentials. This process involves the rearrangement of halogen and hydrogen bonds combined with proton transfer within a complex solid- state system. We developed a strategy to progressively approach the transition state along the phase transition path from both ends by using both the α and β crystal phases as initial structures for active learning. This method allowed us to develop a DFT-based machine learning potential that faithfully describes both of the stable phases and the transition processes. Our results demonstrate that these anisotropic interactions are represented accurately during molecular dynamic simulations. Bond breaking and reforming during proton transfer is observed and analysed in detail. This approach holds promise for simulating SCSC transitions in organic molecular crystals that involving anisotropic interactions and chemical bond changes.
|
Chengxi Zhao; Honglai Liu; Da-Hui Qu; Andrew Cooper; Linjiang Chen
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670232b412ff75c3a1966628/original/a-machine-learned-potential-for-investigating-single-crystal-to-single-crystal-transformations-in-complex-organic-molecular-systems.pdf
|
60c73f1f337d6c6cabe264de
|
10.26434/chemrxiv.7257155.v1
|
Enhancing Electrocatalytic CO2 Reduction Using a System-Integrated Approach to Catalyst Discovery
|
The presented modelling results in this article show that electrochemical CO2 reduction performed at commercially-relevant current densities will ultimately lead to locally alkaline reaction conditions regardless of the electrolyte, configuration and reasonable mass transport scenarios. Discussed in detail are the large implications that this result has for the CO2 reduction reaction itself, and the current way in which catalysts are designed and tested in different electrochemical cell architectures.
|
Thomas Burdyny; Wilson A. Smith
|
Catalysts; Electrocatalysis; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Surface
|
CC BY 4.0
|
CHEMRXIV
|
2018-10-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1f337d6c6cabe264de/original/enhancing-electrocatalytic-co2-reduction-using-a-system-integrated-approach-to-catalyst-discovery.pdf
|
6622d9b721291e5d1d341f1f
|
10.26434/chemrxiv-2024-r3hbl
|
Sub-Picosecond Photodynamics of Small Neutral Copper Oxide Clusters
|
The ultrafast dynamics of neutral copper oxide clusters (CnOx, n < 5) are reported using femtosecond pump probe spectroscopy in the gas phase. The transient spectra recorded for each cluster demonstrates they relax on a 100s of fs timescale followed by a long-lived (>50 ps) response. Density functional theory calculations are performed to determine the lowest energy structures and spin states. Topological descripters for the excited states are calculated (time-dependent density functional theory) to relate the measured excited state dynamics to changes in the cluster’s electronic structure with increasing oxidation. Strong field ionization is demonstrated here to be a soft form of ionization and able to record transient signals for clusters previously determined to be unstable to nanosecond multiphoton ionization. The relative cluster stability is further demonstrated by signal enhancement/depreciation that is recorded through the synergy from the two laser pulses. Once the oxygen atoms exceed the number of copper atoms, a weakly bound superoxide O2 unit forms, exhibiting a higher spin state. All clusters that are not in the lowest spin configuration demonstrate fragmentation.
|
Chase Rotteger; Carter Jarman; Madison Sobol; Shaun Sutton; Scott Sayres
|
Physical Chemistry; Clusters; Photochemistry (Physical Chem.); Physical and Chemical Properties
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6622d9b721291e5d1d341f1f/original/sub-picosecond-photodynamics-of-small-neutral-copper-oxide-clusters.pdf
|
63fcb575937392db3d21d4d2
|
10.26434/chemrxiv-2023-gzxl1
|
Room Temperature Defluorination of Poly(tetrafluoro)ethylene by a Magnesium Reagent
|
Perfluoroalkyl substances (PFAS) are now pervasive in the environment. The largest single use material within the PFAS compound class is poly(tetrafluoro)ethylene) (PTFE), a robust and chemically resistant polymer. Despite their widespread use and serious concerns about their role as pollutants, methods for repurposing PFAS are rare. Here we show that a nucleophilic magnesium reagent reacts with PTFE at room temperature, generating a molecular magnesium fluoride which is easily separated from the surface-modified polymer. The fluoride in turn can be used to transfer the fluorine atoms to a small array of compounds. This proof-of-concept study demonstrates that the atomic fluorine content of PTFE can be harvested and re-used in chemical synthesis.
|
Daniel Sheldon; Joseph Parr; Mark Crimmin
|
Inorganic Chemistry; Organometallic Chemistry; Main Group Chemistry (Inorg.); Bond Activation; Materials Chemistry
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CC BY 4.0
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CHEMRXIV
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2023-02-28
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63fcb575937392db3d21d4d2/original/room-temperature-defluorination-of-poly-tetrafluoro-ethylene-by-a-magnesium-reagent.pdf
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65f11370e9ebbb4db996dc53
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10.26434/chemrxiv-2024-jg998-v2
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Photoelectron Imaging Signature for Selective Formation of Icosahedral Anionic Silver Cages Encapsulating Group 5 Elements: M@Ag12− (M = V, Nb, and Ta)
|
An assembly of thirteen atoms is expected to be a distinctive nanocluster, as they can form highly symmetric architectures like those belonging to D3h, Oh, D5h, and Ih point groups. Among them, icosahedra are the best known as the iconic structures in the finite size regime. Here, using photoelectron imaging spectroscopy in combination with density functional theory (DFT) calculations, we present a simple yet convincing experimental signature for selective formation of icosahedral cages of anionic silver clusters encapsulating a dopant atom of group 5 elements: M@Ag12− (M = V, Nb, and Ta). Their photoelectron images obtained at 4 eV closely resemble one another, indicating that the doped clusters are all in valence iso-electronic systems. Most strikingly, only a single ring is observed, which is assignable to photodetachment signals from a five-fold degenerate superatomic 1D electronic shell in the 1S21P61D10 configuration of valence electrons. The perfect degeneracy of the 1D orbital represents an unambiguous fingerprint of an icosahedral symmetry, which would otherwise be lifted in all the other possible structural isomers. The experimental results are fully supported by DFT calculations, which reveal that icosahedral geometries with the spin multiplicity of singlet are the most stable forms for M@Ag12− (M = V, Nb, and Ta) and that D5h, Oh, and D3h structures are not found even in metastable states.
|
Yuta Suzuki; Kazuaki Matsumoto; Rin Nomi; Masashi Arakawa; Takuya Horio; Akira Terasaki
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Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Clusters; Spectroscopy (Physical Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-03-13
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f11370e9ebbb4db996dc53/original/photoelectron-imaging-signature-for-selective-formation-of-icosahedral-anionic-silver-cages-encapsulating-group-5-elements-m-ag12-m-v-nb-and-ta.pdf
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6580cfede9ebbb4db93b5b73
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10.26434/chemrxiv-2023-cz5kp
|
Effects of Surface Area and Particle Size of Graphite and Graphene Nanoplatelets on Their Oxidation and Subsequent Use in the Modification of Asphalt Binder
|
Graphene oxide (GO) has gained significant attention for its unique physical and chemical properties. GO finds application in a wide range of fields, including biomedicine, electronics, energy, and the environment. It also plays a significant role in the modification of infrastructure materials, such as asphalt and cement, in civil engineering. In this study, we report on the synthesis of GOs from graphite (Gr) powder and graphene nanoplatelets (GNPs) using an improved Hummers’ method. We extensively investigated the effects of particle size and specific surface area of the Gr and GNP precursors on their oxidation, which have not been addressed in literature. The results from Fourier-transform infrared (FTIR) and X-ray photoelectron spectroscopy (XPS) analyses show that the GO made from Gr powder with a large surface area and small size has a higher degree of oxidation with about 9.8% carboxyl functional groups. This provides more opportunities for interactions with different molecules, including asphalt components. In this regard, we investigated the impact of carboxyl-rich GO (higher oxidation percentage) on the high-temperature performance of asphalt binder through rotational viscosity, rheology, multiple stress creep and recovery (MSCR), and anti-aging property measurements. Our experimental results indicate that GO obtained from the Gr powder precursor (designated ox-Gr) can significantly improve the high-temperature performance of asphalt binder. For example, the introduction of only 2 wt.% GO to a performance grade asphalt binder (PG 67-22) can dramatically increase its complex shear modulus (G*), as well as decrease the phase angle (δ), at high temperatures. The MSCR tests showed that the addition of GO to asphalt binder effectively mitigates its permanent deformation and improves its elastic response, as demonstrated by about 39% reduction in the creep compliance (J_nr) and an impressive 297% increase in the percent recovery (εR) of the GO-modified binder. Furthermore, the measured viscosity aging index and G* ratio of the GO-modified asphalt binder confirm the significant effect of GO on the improvement of the anti-aging properties of the binder.
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Dineshkumar Sengottuvelu; Hashem Khaled Almashaqbeh; Mohammed Majdoub ; Avijit Pramanik ; Grace Rushing ; Jesse Doyle ; Sasan Nouranian ; Paresh C. Ray ; Mine G. Ucak-Astarlioglu ; Ahmed Al-Ostaz
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Materials Science; Chemical Engineering and Industrial Chemistry; Carbon-based Materials; Composites; Nanostructured Materials - Materials; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-12-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6580cfede9ebbb4db93b5b73/original/effects-of-surface-area-and-particle-size-of-graphite-and-graphene-nanoplatelets-on-their-oxidation-and-subsequent-use-in-the-modification-of-asphalt-binder.pdf
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65d721e09138d23161b5564e
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10.26434/chemrxiv-2024-ks1v5
|
Cationic Nanoparticle Interactions with Catabolic Cartilage Modify Macrophage Cytokine Production
|
Cationic nanoparticles (NPs) have emerged as promising candidates for intra-articular drug delivery, showcasing their potential as efficient carriers. However, despite their evident utility, many studies neglect to investigate their interactions with the extracellular matrix (ECM). This oversight represents a significant gap in our understanding, particularly in the context of osteoarthritis (OA) treatment, where viable therapeutic options are limited. The clinical translation of functionalize drug carriers for OA has been hindered, in part, by our incomplete comprehension of how these materials interact with and respond to the pathological environment. This study aims to address this gap by examining how cationic NPs interact with ECM components in an ex vivo OA cartilage explant model. By comparing the behavior of smaller (<10nm) and larger (~270 nm) cationic NPs and subjecting them to explants preconditioned with OA-specific catabolic enzymes, we observed multifaceted effects on ECM integrity and biomolecule conformation. All NP-biomolecule complexes induced differential cytokine production from stimulated macrophages. Smaller polyamidoamine (PAMAM) nanocarriers reduced glycosaminoglycan (GAG) release from explants but increased proinflammatory cytokine stimulation under pathological conditions, while larger poly lactic(co-glycolic)acid(PLGA)/polyethylenimine(PEI)-based nanocarriers maintained GAG release but induced a significantly lower proinflammatory cytokine response. Collagenase-induced OA-mimicking preconditioning produced distinct profiles across the NP panel in GAG interactions and cytokine production. The findings from these studies underscore the significance of tailored nanocarrier approaches to achieve optimal therapeutic efficacy for OA and other complex diseases.
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Ula von Mentzer; Fritjof Havemeister; Loise Råberg; Gizem Erensoy; Elin K Esbjörner; Alexandra Stubelius
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Biological and Medicinal Chemistry; Polymer Science; Nanoscience; Biopolymers; Drug delivery systems; Bioengineering and Biotechnology
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CC BY 4.0
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CHEMRXIV
|
2024-02-23
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d721e09138d23161b5564e/original/cationic-nanoparticle-interactions-with-catabolic-cartilage-modify-macrophage-cytokine-production.pdf
|
65bf8042e9ebbb4db9a53e72
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10.26434/chemrxiv-2023-q0vnf-v2
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Breaking down the Barriers between the Digital and the Real: Mixed Reality applied to battery manufacturing R&D and Training
|
In a scenario in which the manufacturing of high-performance, safe batteries on an unprecedented large scale is crucial for the energy transition and fight against climate change, research laboratories and cell production industries are facing challenges due to the lack of efficient data management and training tools. In this context, the use of intelligent devices plays an important role on the path towards the optimization of the manufacturing process and the enhancement of the battery performance while reducing production costs. In this Concept, we show how Mixed Reality technology can be used for data collection and training in real-time in battery research laboratories and pilot lines. We introduce a Mixed Reality application run on Microsoft HoloLens 2 glasses, provide a deep analysis on its ergonomic and usability aspects, and we describe how we solved the problems found during its development. Thanks to this application, users can collect data while keeping their hands free and receive advice in real time to design and build batteries with tailored properties. This optimizes data management in complex and dangerous environments, like the ones found in battery research laboratories or pilot lines. Now, thanks to our Mixed Reality application, users can collect data in the place of work, save this data automatically on a server and exploit it to receive advice and feedback to support their decision-making and learning of the manufacturing process.
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Lucie Denisart; Javier F. Troncoso; Emilie Loup-Escande; Alejandro A. Franco
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Energy; Chemical Engineering and Industrial Chemistry; Chemical Education; Chemical Education - General; Industrial Manufacturing; Energy Storage
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CC BY 4.0
|
CHEMRXIV
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2024-02-06
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bf8042e9ebbb4db9a53e72/original/breaking-down-the-barriers-between-the-digital-and-the-real-mixed-reality-applied-to-battery-manufacturing-r-d-and-training.pdf
|
6333c166114b7e2ca520034b
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10.26434/chemrxiv-2022-1hlv5
|
X-Yne Click Polymerization
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Alkyne-based click polymerizations have been nurtured into a powerful synthetic technique for the synthesis of new polymers with advanced structures and versatile functionalities. Among them, the emerging thiol-yne, hydroxyl-yne and amino-yne click polymerizations have made remarkable progresses from reactions to applications. All three polymerizations avoid the usage of inherently dangerous monomer and are safer to operate than the classical azide-alkyne click polymerization, making them more prospective for widespread applications. To greatly promote the new alkyne-based click polymerizations beyond the azide-alkyne click polymerization, we propose a new concept of “X-yne click polymerization” to unify them. In this Perspective, we mainly give a brief account of the progression of X-yne click polymerization and discuss in detail the challenges and opportunities in this field.
|
Xinyao Fu; Anjun Qin; Ben Zhong Tang
|
Polymer Science
|
CC BY NC ND 4.0
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CHEMRXIV
|
2022-09-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6333c166114b7e2ca520034b/original/x-yne-click-polymerization.pdf
|
651dd59bbda59ceb9ae1140a
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10.26434/chemrxiv-2023-gbzxv
|
Discussion paper: “In situ SR-XRD study of FeCO3 precipitation kinetics onto carbon steel in CO2-containing environments: The influence of brine pH” D. Burkle et al.. Electrochimica Acta 255 (2017) 127–144
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Burkle et al. [1] present an elegant study using a flow cell designed to allow synchrotron X-ray diffraction study of the growth of siderite layers on carbon steel at elevated temperature in the presence of CO2 under rigorously de-oxygenated conditions. However, they state that in earlier work, “the growth of the corrosion product was accelerated by applying excessive currents/voltages (unlike in this research) to the sample under study which were not realistic of the actual corrosion kinetics encountered in the field and consequently prevented the true processes of film formation from being established”. In the present comment, the hydrodynamics of the cell of Burkle et al. are analysed using an approximate model and it is shown that the results of the different studies are in fact completely consistent, further supporting the deductions and model of the earlier work for the effects of hydrodynamics on anodic crystal growth. Further it is shown that fitting of their results to the Avrami model used in the earlier studies illustrates the transition from anodic to cathodic reaction rate control with increase of solution pH. Comparison of the different studies indeed illustrates “the true processes of film formation”. The hydrodynamic model in conjunction with that developed in previous studies implies a significant variation over the surface of the anodic electrocrystallisation rate in the cell used by Burkle et al..
|
David Williams
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Physical Chemistry; Materials Science; Electrochemistry - Mechanisms, Theory & Study
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CC BY NC 4.0
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CHEMRXIV
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2023-10-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651dd59bbda59ceb9ae1140a/original/discussion-paper-in-situ-sr-xrd-study-of-fe-co3-precipitation-kinetics-onto-carbon-steel-in-co2-containing-environments-the-influence-of-brine-p-h-d-burkle-et-al-electrochimica-acta-255-2017-127-144.pdf
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60c74ce04c8919399cad36f4
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10.26434/chemrxiv.12551234.v1
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Simulating the Ghost: Quantum Dynamics of the Solvated Electron
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The nature of bulk hydrated electron has been a challenge for both experiment and theory due to
its short life time and high reactivity, and the need for a high-level of electronic structure theory to
achieve predictive accuracy. The lack of a classical atomistic structural formula makes it exceedingly
difficult to model the solvated electron using conventional empirical force fields, which describe
the system in terms of interactions between point particles associated with atomic nuclei. Here
we overcome this problem using a machine-learning model, that is sufficiently flexible to describe
the effect of the excess electron on the structure of the surrounding water, without including the
electron in the model explicitly. The resulting potential is not only able to reproduce the stable
cavity structure, but also recovers the correct localization dynamics that follows the injection of an
electron in neat water. The machine learning model achieves the accuracy of the state-of-the-art
correlated wave function method it is trained on. It is sufficiently inexpensive to afford a full quantum
statistical and dynamical description, and allows us to achieve a highly accurate determination of
the structure, diffusion mechanisms and vibrational spectroscopy of the solvated electron
|
Jinggang Lan; Venkat Kapil; Piero Gasparotto; Michele Ceriotti; Marcella Iannuzzi; Vladimir V. Rybkin
|
Computational Chemistry and Modeling; Machine Learning; Quantum Mechanics; Quasiparticles and Excitations; Statistical Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ce04c8919399cad36f4/original/simulating-the-ghost-quantum-dynamics-of-the-solvated-electron.pdf
|
62471a3754b5d97a2de7a3c8
|
10.26434/chemrxiv-2022-csmv9
|
Synthesis and styrene copolymerization of novel methyl, methoxy, chloro, and fluorophenoxy ring-substituted 2-methoxyethyl phenylcyanoacrylates
|
Novel phenoxy ring-substituted 2-methoxyethyl phenylcyanoacrylates, RPhCH=C(CN)CO2CH2CH2OCH3 (where R is 3-phenoxy, 3-(4-chlorophenoxy), 4-(4-chlorophenoxy), 2-(4-fluorophenoxy), 4-(4-fluorophenoxy), 2-(3-methoxyphenoxy), 2-(4-methoxyphenoxy), 3-(4-methoxyphenoxy), 4-(4-methoxyphenoxy), 3-(4-methylphenoxy), 4-(4-methylphenoxy), 3-(3,5-dichlorophenoxy), 4-(2,4-dichlorophenoxy), 3-(3-trifluoromethyl)phenoxy) were prepared and copolymerized with styrene. The acrylates were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-substituted benzaldehydes and 2-methoxyethyl cyanoacetate, and characterized by CHN analysis, IR, 1H and 13C NMR. All the ethylenes were copolymerized with styrene in solution with radical initiation (ABCN) at 70C. The compositions of the copolymers were calculated from nitrogen analysis.
|
Kacy S. Bradford; Abeer Fatima; Muhammed M. Ghazal; Ljupka Gjorgjevska; Stephen J. Heimann; Alexis B. Jordan; Erick Ortega; Francis C. Regacho; Anna M. Rohrer; Karla A. Santana; Caitlin Smicklas; Isabel Uribe; Yazmeen I. Villanueva; Jin Ju Yi; Sara M. Rocus; William S. Schjerven; Gregory B. Kharas
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Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organic Polymers
|
CC BY 4.0
|
CHEMRXIV
|
2022-04-05
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62471a3754b5d97a2de7a3c8/original/synthesis-and-styrene-copolymerization-of-novel-methyl-methoxy-chloro-and-fluorophenoxy-ring-substituted-2-methoxyethyl-phenylcyanoacrylates.pdf
|
60c7534e9abda24d81f8df74
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10.26434/chemrxiv.13473642.v1
|
Closing the Yellow Gap with Eu- and Tb-Doped GaN: One Luminescent Host Resulting in Three Colours
|
GaN is a key material when it comes to highly efficient warm white all-nitride phosphor converted light emitting diodes (pc-LED). Here we present the doping of bulk GaN with Europium and Terbium and the combination of both resulting in intriguing luminescence properties, pushing the role of GaN:Eu,Tb as a chief component in future light emitiing diodes. By this colour tuning we prove that one luminescent host can provide three colours (red, green, orange) and even the so called "yellow gap" could be closed with a III-nitride.<br />
|
Cordula Braun; liuda Mereacre; Zheng Chen; Adam Slabon
|
Main Group Chemistry (Inorg.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-12-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7534e9abda24d81f8df74/original/closing-the-yellow-gap-with-eu-and-tb-doped-ga-n-one-luminescent-host-resulting-in-three-colours.pdf
|
60c757bbbb8c1a9fc23dc8ce
|
10.26434/chemrxiv.14454585.v1
|
A Mechanistic Investigation of the Suzuki Polycondensation Reaction Using MS/MS Methods
|
<p>Understanding catalytic
reactions is inherently difficult because not only is the catalyst the least
abundant component in the mixture, but it also takes many different forms as
the reaction proceeds. Precatalyst is converted into active catalyst,
short-lived intermediates, resting states, and decomposition products.
Polymerization catalysis is harder yet to study, because as the polymer grows
the identities of these species change with every turnover as monomers are
added to the chain. Modern mass spectrometric methods have proved to be up to
the challenge, with multiple reaction monitoring (MRM) in conjunction with
pressurized sample infusion (PSI) used to continuously probe all stages of the
Suzuki polycondensation (SPC) reaction. Initiation, propagation, and
termination steps were tracked in real time, and the outstanding sensitivity
and low signal-to-noise of the approach has real promise with respect to the
depth with which this reaction and others like it can be studied.</p>
|
Michelle Ting; Lars Yunker; Ian Chagunda; Katherine Hatlelid; Meghan Vieweg; J Scott McIndoe
|
Physical Organic Chemistry; Homogeneous Catalysis
|
CC BY NC ND 4.0
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CHEMRXIV
|
2021-04-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757bbbb8c1a9fc23dc8ce/original/a-mechanistic-investigation-of-the-suzuki-polycondensation-reaction-using-ms-ms-methods.pdf
|
65d7ee2ae9ebbb4db9008adf
|
10.26434/chemrxiv-2024-9kwg3
|
An exceptional fluorescence turn-on nucleoside: Lighting up single-stranded DNA with constant brightness regardless neighboring bases
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Fluorescent nucleobase analogs (FBAs) have proven valuable for studying nucleic acid structure and dynamics. Regrettably, most FBAs exhibit reduced quantum yields when incorporated into DNA, particularly when neighboring residues are present. In this study, we introduce a turn-on nucleoside (thieno cyclopenta -dU, 3b) that increases the brightness of single-stranded oligonucleotides by approximately 10-fold compared to the free nucleoside, regardless of neighboring bases. Furthermore, an up to 50-fold increase in brightness is observed during duplex formation. To the best of our knowledge, compound 3b is the only turn-on type fluorescent nucleoside known to maintain a stable quantum yield after incorporation, and it can be well-accepted by DNA polymerases. These findings highlight the potential of turn-on FBAs for fluorescence sensing applications in enzymatic DNA synthesis and in vivo strand hybridization.
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Jinsi Li; Lei He; Junlin Wen; Chenghe Xiong; Jingwei Zhou; Chenguang Lou; Xiaoluo Huang; Hui Mei; Xin Ming
|
Biological and Medicinal Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-02-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d7ee2ae9ebbb4db9008adf/original/an-exceptional-fluorescence-turn-on-nucleoside-lighting-up-single-stranded-dna-with-constant-brightness-regardless-neighboring-bases.pdf
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6438bbf073c6563f14d19cba
|
10.26434/chemrxiv-2023-x02qw
|
cis-Selective Acyclic Diene Metathesis Polymerization of α, ω-Dienes
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The cis/trans (Z/E) stereochemistry of repeating alkenes in polymers provides a powerful handle to modulate the thermal and mechanical properties of these soft materials, but synthetic methods to precisely dictate this parameter remain scarce. Herein, a cis-selective ADMET process of readily available α, ω-diene monomers with high functional-group tolerance is disclosed. Identification of a highly sterereoselective cyclometalated Ru catalyst allowed the synthesis of a broad array of polymers with cis-content up to 99%. This platform was leveraged to study the impact of the cis geometry on thermal and mechanical properties including through the synthesis of ABA triblock copolymers via extension of a cis-rich telechelic polyoctenamer with D,L-lactide. These results suggest that cis-selective ADMET affords an efficient strategy to tune the properties of a variety of polymers.
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Samuel J. Kempel; Ting-Wei Hsu; Jake L. Nicholson; Quentin Michaudel
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Catalysis; Polymer Science; Organic Polymers; Polymerization catalysts; Homogeneous Catalysis; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-04-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6438bbf073c6563f14d19cba/original/cis-selective-acyclic-diene-metathesis-polymerization-of-dienes.pdf
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635bc2491db0bd95c13d5dbd
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10.26434/chemrxiv-2022-zghv6
|
Disentangling the effect of pressure on a mechanochemical bromination reaction by solid-state NMR spectroscopy
|
Mechanical forces, including compressive stresses as one of the most important consequences, have a significant impact on chemical reactions. Besides the preparative opportunities, mechanochemical conditions benefit from the absence of any organic solvent, the possibility of a significant synthetic acceleration and unique reaction pathways. Together with an accurate characterization of ball-milling products, the development of a deeper mechanistic understanding of the occurring transformations at a molecular level is critical for fully grasping the potential of organic mechanosynthesis. In this vein, we studied a bromination of a cyclic sulfoximine in a mixer mill and used solid-state nuclear magnetic resonance (NMR) spectroscopy for structural characterization of the reaction products. Magic-angle spinning (MAS) NMR was applied for elucidating the product mixtures taken from the milling jar without introducing any further post-processing on the sample-of-interest. Ex-situ 13C-detected NMR spectra of ball-milling products showed the formation of a rather crystalline solid phase with the regioselective bromination of the S-aryl group of the heterocycle in position 4. Completion is reached in less than 30 minutes as deduced from the NMR spectra. The bromination can also be achieved by magnetic stirring, but then, a longer reaction time is required. Mixing the solid educts in the NMR rotor allows to get in-situ insights into the reaction and enables the detection of a reaction intermediate. The pressure alone induced in the rotor by MAS is not sufficient to lead to full conversion and the reaction occurs on slower time scales than in the ball mill, which is crucial for analysing mixtures taken from the milling jar by solid-state NMR. Our data suggest that on top of centrifugal forces, an efficient mixing of the starting materials is required for reaching a complete reaction.
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Ettore Bartalucci; Christian Schumacher; Leeroy Hendrickx; Francesco Puccetti; Igor d'Anciães Almeida Silva; Rıza Dervişoğlu; Rakesh Puttreddy; Carsten Bolm; Thomas Wiegand
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Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Spectroscopy (Physical Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-10-31
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635bc2491db0bd95c13d5dbd/original/disentangling-the-effect-of-pressure-on-a-mechanochemical-bromination-reaction-by-solid-state-nmr-spectroscopy.pdf
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63285774cf3829f422a9e3cb
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10.26434/chemrxiv-2022-nrb3h
|
Molecular Nanocomposites with Lanthanide- and Counter-Cation-Mediated Interfacial Electron Transfer between Phthalocyanine and Polyoxovanadate
|
A series of {V12}-nuclearity polyoxovanadate cages covalently functionalised with one or sandwiched by two phthalocyaninato (Pc) lanthanide (Ln) moieties via V−O−Ln bonds were prepared and fully characterised for paramagnetic Ln = SmIII–ErIII and diamagnetic Ln = LuIII, including YIII. The LnPc-functionalised {V12O32} cages with fully-oxidised vanadium centres in the ground state were isolated as (nBu4N)3[HV12O32Cl(LnPc)] and (nBu4N)2[HV12O32Cl(LnPc)2] compounds. As corroborated by a combined experimental (EPR, DC and AC SQUID, laser photolysis transient absorption spectroscopy, electrochemistry) and computational methods (DFT, MD, model Hamiltonian approach), the compounds feature intra- and intermolecular electron transfer that is responsible for a partial reduction at V(3d) centres from VV to VIV in the solid state and at high sample concentrations. The effects are generally Ln-dependent and are clearly demonstrated for the (nBu4N)3[HV12O32Cl(LnPc)] representative with Ln= LuIII or DyIII. Intramolecular charge transfer takes place for Ln = LuIII and occurs from a Pc ligand via the Ln centre to the {V12O32} core of the same molecule, whereas for Ln= DyIII only intermolecular charge transfer is allowed, which is realised from Pc in one molecule to {V12O32} core of another molecule usually via the nBu4N+ counter-cation. For all Ln but DyIII two of these phenomena may be present in different proportions. Besides, it is demonstrated that (nBu4N)3[HV12O32Cl(DyPc)] is a field induced single molecule magnet with a maximal relaxation time of order 10–3 s. The obtained results open up the way to further exploration and fine-tuning of these three-modular molecular nanocomposites regarding tailoring and control of their Ln-dependent charge-separated states (induced by intramolecular transfer) and relaxation dynamics as well as of electron hopping between molecules. This should enable to realise ultra-sensitive polyoxometalate powered quasi-superconductors, sensors and data storage/processing materials for quantum technologies.
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Irina Werner; Jan Griebel; Albert Masip-Sánchez; Xavier López; Karol Załęski; Piotr Kozłowski; Axel Kahnt; Martin Börner; Ziyan Warneke; Jonas Warneke; Kirill Monakhov
|
Theoretical and Computational Chemistry; Inorganic Chemistry; Materials Chemistry
|
CC BY NC ND 4.0
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CHEMRXIV
|
2023-12-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63285774cf3829f422a9e3cb/original/molecular-nanocomposites-with-lanthanide-and-counter-cation-mediated-interfacial-electron-transfer-between-phthalocyanine-and-polyoxovanadate.pdf
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60c74466bdbb8950bda387d5
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10.26434/chemrxiv.9786008.v1
|
Multi-Color Emission with Orthogonal Input Triggers from a Diarylethene Pyrene-OTHO Organogelator Cocktail
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<div><div><div><p>Controlling spectral and physicochemical properties with external stimuli is vital for the development of smart materials. Here we demonstrate a supramolecular gelator based on a fluorescent oxotriphenylhexanoate (OTHO) that can switch emission profiles between the solution and gel phase. Furthermore, a cocktail of the gelator and a photochromic diarylethene derivative enables four distinct emissive states to be obtained, which are modulated with light and heat as orthogonal input triggers.</p></div></div></div>
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Mark D. Johnstone; Chin-wei hsu; Nicolas Hochbaum; Joakim Andréasson, Andréasson; Henrik Sundén
|
Supramolecular Chemistry (Org.); Fibers; Nanostructured Materials - Nanoscience
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CC BY NC ND 4.0
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CHEMRXIV
|
2019-09-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74466bdbb8950bda387d5/original/multi-color-emission-with-orthogonal-input-triggers-from-a-diarylethene-pyrene-otho-organogelator-cocktail.pdf
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65de5509e9ebbb4db96b2cff
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10.26434/chemrxiv-2024-b5llr
|
Enantioselective Paternò–Büchi Reactions: Strategic Application of a Triplet Rebound Mechanism for Asymmetric Photocatalysis
|
The Paternò–Büchi reaction is the [2+2] photocycloaddition of a carbonyl with an alkene to afford oxetane products. Enantioselective catalysis of this classical photoreaction, however, has proven to be a long-standing challenge. Many of the best-developed strategies for asymmetric photochemistry are not suitable to address this problem because the interaction of carbonyls with Brønsted or Lewis acidic catalysts can alter the electronic structure of their excited state and divert their reactivity towards alternate photoproducts. We show herein that an alternative triplet rebound strategy enables the stereocontrolled reaction of an excited-state carbonyl compound in its native, unbound state. These studies have resulted in the development of the first highly enantioselective catalytic Paternò–Büchi reaction, catalyzed by a novel hydrogen-bonding chiral Ir photocatalyst.
|
Jesse Kidd; Tahoe Fiala; Wesley Swords; Yerin Park; Kent Meyer; Kyana Sanders; Ilia Guzei; John Wright; Tehshik Yoon
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Photocatalysis
|
CC BY NC ND 4.0
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CHEMRXIV
|
2024-02-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65de5509e9ebbb4db96b2cff/original/enantioselective-paterno-buchi-reactions-strategic-application-of-a-triplet-rebound-mechanism-for-asymmetric-photocatalysis.pdf
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63b56ec9e9d0fd8120354317
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10.26434/chemrxiv-2023-k1l9h
|
Spin-Orbit Coupling corrections for the GFN-xTB method
|
Spin-orbit coupling (SOC) is crucial for correct electronic structure analysis in molecules and materials, for example in large molecular systems as in superatoms, for understanding the role of transition metals in enzymes, and when investigating the energy transfer processes in metal-organic frameworks. We extend the GFN-xTB method, popular to treat extended systems, by including SOC into the hamiltonian operator. We followed the same approach as previously reported for the density-functional tight-binding (DFTB) method and provide and validate the necessary parameters for all elements throughout the periodic table. The parameters have been obtained consistently from atomic SOC calculations using density-functional theory. We tested them for reference structures where SOC is decisive, as in transition metal containing heme moiety, chromophores in metal-organic frameworks, and in superatoms. Our parametrization paves the path for incorporation of SOC in GFN-xTB based electronic structure calculations of computationally expensive molecular systems.
|
Gautam Jha; Thomas Heine
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-01-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b56ec9e9d0fd8120354317/original/spin-orbit-coupling-corrections-for-the-gfn-x-tb-method.pdf
|
676e2d3a6dde43c908797898
|
10.26434/chemrxiv-2024-hxfgm
|
Multi-substrate Screening for Asymmetric Catalysis Enabled by 19F NMR-based Simultaneous Chiral Analysis
|
Exploring a broad chemical space is essential for advancing asymmetric catalysis, but the intricate nature of chiral catalysts demands highly resource-intensive optimization processes. Multi-substrate screening offers a promising solution for high-throughput screening (HTS). However, analyzing complex mixtures remains challenging and typically relies on chromatography-based methods. This study introduces ¹⁹F NMR spectroscopy for simultaneous chiral analysis, enabling accurate determination of yield and enantiomeric excess in multi-substrate screening. Applied to the ruthenium-catalyzed asymmetric reductive amination of ammonia with twenty-one distinct ketones, this method enables precise simultaneous chiral analysis through NMR shift reagent-induced dynamic peak shifts and splitting in ¹⁹F NMR spectra. This approach enhances HTS by simplifying the analysis of complex mixtures, providing a powerful tool to accelerate the discovery of chiral catalysts and optimize asymmetric reactions.
|
Donghun Kim; Gyeongseon Choi; Hyunwoo Kim
|
Organic Chemistry; Catalysis; Analytical Chemistry
|
CC BY NC ND 4.0
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CHEMRXIV
|
2024-12-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676e2d3a6dde43c908797898/original/multi-substrate-screening-for-asymmetric-catalysis-enabled-by-19f-nmr-based-simultaneous-chiral-analysis.pdf
|
66754a4b5101a2ffa822ba1a
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10.26434/chemrxiv-2024-knpvw
|
SpaiNN: Equivariant Message Passing for Excited-State Nonadiabatic Molecular Dynamics
|
Excited-state molecular dynamics simulations are crucial for understanding processes like photosynthesis, vision, and radiation damage. However, the computational complexity of quantum chemical calculations restricts their scope. Machine learning (ML) offers a solution by delivering high accuracy properties at lower computational costs. We present SpaiNN, an open-source Python software for ML-driven surface hopping nonadiabatic molecular dynamics simulations. SpaiNN combines the invariant and equivariant neural network architectures of SchNetPack with SHARC for surface hopping dynamics. Its modular design allows users to implement and adapt modules easily. We compare rotationally-invariant and equivariant representations in fitting potential energy surfaces of multiple electronic states and properties arising from the interaction of two electronic states. Simulations of the methylenimmonium cation and various alkenes demonstrate the superior performance of equivariant SpaiNN models, improving accuracy, generalization, and efficiency in both training and inference.
|
Sascha Mausenberger; Carolin Müller; Alexandre Tkatchenko; Philipp Marquetand; Leticia González; Julia Westermayr
|
Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
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CHEMRXIV
|
2024-06-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66754a4b5101a2ffa822ba1a/original/spai-nn-equivariant-message-passing-for-excited-state-nonadiabatic-molecular-dynamics.pdf
|
620f6a30cbb4f4c804c52c8e
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10.26434/chemrxiv-2022-6x1v6
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Beyond Copper: Novel Ni Foam Catalysts for Sustainable Nitrate to Ammonia Electroreduction
|
Electrochemical nitrate reduction is considered a promising energy efficient approach to remove environmentally harmful nitrate from various types of wastewater while simultaneously producing a product with high added value: ammonia. One important factor to be accounted for is the choice of the catalyst, which is required not only to accelerate nitrate reduction but also to direct the product selectivity of the electrolysis toward ammonia production. To this end, herein, we demonstrate the fabrication of novel Ni foam catalysts produced by means of a dynamic hydrogen bubble template and additive assisted electrodeposition process. The resulting 3D foam morphology of the catalyst is demonstrated to crucially govern its overall catalytic performance. Post-electrolysis cross-sectional SEM-EDX analysis (K mapping) demonstrated complete wetting of the 3D foam structure by the electrolyte. Ni foams deposited within 20 s exhibited outstanding selectivity toward nitrate electroreduction: more than 95% of the Faradaic efficiency of ammonia production was achieved in the particularly low potential range from -0.1 to -0.3 V vs. RHE. Hydrogen was found to be the only minor by-product of the nitrate reduction. Intriguingly, no other nitrogen containing products (e.g., NO, N2O, and N2) formed during electrolysis, thus indicating a highly efficient nitrate-to-ammonia conversion process. This significant improvement over the use of a planar Ni foil reference (33% FE at -0.3 V vs. RHE) is attributable to (i) the effective suppression of the HER in this potential regime and (ii) a high surface density of active sites for the nitrate reduction formed during Ni foam electrodeposition under extreme experimental conditions, e.g., at an applied geometric current density of -3 A cm-2. Trapping intermediates inside the primary macroporosity contributed to the excellent catalytic performance of the Ni foams. Identical location (IL) SEM analyses demonstrated the excellent structural stability of the novel Ni foam during extended catalyst stressing. These superior characteristics have not previously been reported for Ni and Ni rich catalysts, thus making the novel foam type of catalyst a highly promising candidate for truly selective and energy efficient nitrate-to-ammonia electroreduction and a promising alternative to mature copper-based catalysts.
|
Anna Iarchuk; Abhijit Dutta; Peter Broekmann
|
Catalysis; Energy; Earth, Space, and Environmental Chemistry; Environmental Science; Electrocatalysis; Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-02-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620f6a30cbb4f4c804c52c8e/original/beyond-copper-novel-ni-foam-catalysts-for-sustainable-nitrate-to-ammonia-electroreduction.pdf
|
60cb3121a5b6affa07753207
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10.26434/chemrxiv-2021-8gznz
|
Dual stimuli-responsive dynamic covalent peptide tags: Towards sequence-controlled release in tumor-like microenvironments
|
Dynamic covalent chemistry has emerged as a versatile synthetic tool for devising stable, stimuli-responsive bioconjugates. Nevertheless, dynamic covalent interactions often exhibit fast binding and dissociation events or vice versa, affecting their conversion rates or stabilities. To overcome this, we designed dual responsive peptide tags combining: (1) a pH responsive boronate ester with fast association and dissociation rates, and (2) a redox-active disulfide with slow formation and dissociation rate. Pre-coordination by boronic acid–catechol interaction improves self-sorting and selectivity in disulfide formation into heterodimers. The resulting bis-peptide conjugate exhibited improved complex stability in aqueous solution and acidic tumor-like extracellular microenvironment. The conjugate responds to pH changes and to a redox environment that is similar to certain conditions inside cancer cells. Such tags hold great promise for controlling the stability of bioconjugates under dilution in aqueous media, as well as designing intelligent pharmaceutics that react to distinct biological stimuli in cells.
|
Maksymilian M. Zegota; Michael Andreas Müller; Bellinda Lantzberg; Gönül Kizilsavas ; Jaime A. S. Coelho; Pierpaolo Moscariello; María Martínez-Negro; Svenja Morsbach; Pedro M. P. Gois; Manfred Wagner; David Y. W. Ng; Seah Ling Kuan; Tanja Weil
|
Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-06-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60cb3121a5b6affa07753207/original/dual-stimuli-responsive-dynamic-covalent-peptide-tags-towards-sequence-controlled-release-in-tumor-like-microenvironments.pdf
|
6696671a5101a2ffa8887b7d
|
10.26434/chemrxiv-2024-k8qr8
|
EFFECT OF AIR CARBON ARC GOUGING AND SUBMERGED ARC WELDING ON THE ELECTROCHEMICAL PROPERTIES OF AISI 316L AND 321 STAINLESS STEELS
|
The paper aims to evaluate the use of air carbon arc gouging-ACAG followed by submerged arc welding-SAW to repair two types of austenitic stainless steels, AISI 316L and AISI 321, verifying the effects on the resulting electrochemical properties: degree of sensitization and susceptibility to intergranular corrosion. The weld grooves of the 19,05 mm thick plate were prepared by machining (V-shape, with 2 mm weld root face thickness) and processed by SAW. Aiming at to simulate a repair operation a gouged groove (~6-7mm deep) was produced on the top of the weld metal, close to the Thermally Affected Zone by ACAG and rewelded by SAW. The welded joints were studied in three different situations regarding the joint preparation treatment after gouging, namely: i) without any type of cleaning, ii) brushing and iii) rectifying. The degree of sensitization of the welded joint was evaluated using the double loop potentiokinetic reactivation (DL-EPR) technique according to ISO 12732 Corrosion of metals and alloys — Electrochemical potentiokinetic reactivation measurement using the double loop method (based on Cihal's method), and susceptibility to intergranular corrosion in accordance with ASTM A262-15 Standard Practices for Detecting Susceptibility to Intergranular Attack in Austenitic Stainless Steels, Practice A. The results showed that the ACAG procedure does not affect the corrosion resistance of the steels studied even if no cleaning procedure was used to eliminate the contaminants left in the gouged groove surface. Therefore, the use of the gouging process presents an interesting alternative to repair welding in the field as well as to remove defect root pass and guarantee full penetration of the weld. Besides higher material removal yield, less effort from the operator, low cost, and ease of use in the field are attractive advantages of the technique.
|
Gabriel Campesan; Arthur Guerra; Guilherme Koga; Claudemiro Bolfarini
|
Energy; Power
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CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6696671a5101a2ffa8887b7d/original/effect-of-air-carbon-arc-gouging-and-submerged-arc-welding-on-the-electrochemical-properties-of-aisi-316l-and-321-stainless-steels.pdf
|
60c74e3e842e656496db35e3
|
10.26434/chemrxiv.12412694.v2
|
Improved Scaffold Hopping in Ligand-based Virtual Screening Using Neural Representation Learning
|
<pre><pre>Deep learning has demonstrated significant potential in advancing state of the art in many problem domains, especially those benefiting from automated feature extraction. Yet the methodology has seen limited adoption in the field of ligand-based virtual screening (LBVS), as traditional approaches typically require large, target-specific training sets, which limits their value in most prospective applications. Here, we report the development of a neural network architecture, and a learning framework designed to yield a generally applicable tool for LBVS. Our approach uses the molecular graph as input, and involves learning a representation that places compounds of similar biological profiles in close proximity within a hyperdimensional feature space; this is achieved by simultaneously leveraging historical screening data against a multitude of targets during training. Cosine distance between molecules in this space becomes a general similarity metric, and can readily be used to rank order database compounds in LBVS workflows. We demonstrate the resulting model generalizes exceptionally well to compounds and targets not used in its training. In three commonly employed LBVS benchmarks, our method outperforms popular fingerprinting algorithms without the need for any target-specific training. Moreover, we show the learned representation yields superior performance in scaffold hopping tasks, and is largely orthogonal to existing fingerprints. Summarily, we have developed and validated a framework for learning a molecular representation that is applicable to LBVS in a target-agnostic fashion, with as few as one query compound. Our approach can also enable organizations to generate additional value from large screening data repositories, and to this end we are making its implementation freely available at https://github.com/totient-bio/gatnn-vs</pre></pre>
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Luka Stojanovic; Milos Popovic; Nebojsa Tijanic; Goran Rakocevic; Marko Kalinic
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Chemoinformatics; Machine Learning; Artificial Intelligence
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e3e842e656496db35e3/original/improved-scaffold-hopping-in-ligand-based-virtual-screening-using-neural-representation-learning.pdf
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631f37eabe03b23be6f3014d
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10.26434/chemrxiv-2022-sl8d0
|
Data-Driven Design of Protein-Like Single-Chain Polymer Nanoparticles
|
The functional structure of proteins is heavily influenced by their folding behavior. AlphaFold, a powerful artificial intelligence (AI) program trained on information from the Protein Data Bank (PDB), was developed to predict the 3D structure of proteins from its amino acid sequence. Inspired by this, we aim to elucidate structural features of synthetic single-chain polymer nanoparticles (SCNPs) based on compositional information (monomers, chain length, molecular weight, charge, and valency) by machine learning (ML). Specifically, we demonstrate the effectiveness of ML to improve the efficiency of SCNP design and uncover important polymer design attributes to mimic protein-like structural features. To start, we randomly screened over 1000 synthesized SCNPs through a combination of high-throughput dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS) and compared these results to simulated protein data from the PDB. Then, utilizing evidential neural networks (ENets), we predicted, synthesized, and characterized 30 novel compact SCNPs. Incredibly, this data-driven approach yielded 58% of the predicted SCNPs with Porod exponent ≥ 3.5 as opposed to 5% of SCNPs from the random screen. Using Shapely additive explanation (SHAP) values, we further uncovered interesting contributions of monomer content on Porod exponent and radius of gyration. From this work, we have shown that an ML-guided approach proves effective for the challenging, unintuitive problem of nanoparticle design.
|
Rahul Upadhya; Matthew Tamasi; Elena Di Mare; Sanjeeva Murthy; Adam Gormley
|
Polymer Science; Nanoscience; Polymer chains; Polymer morphology; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2022-09-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631f37eabe03b23be6f3014d/original/data-driven-design-of-protein-like-single-chain-polymer-nanoparticles.pdf
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67c8fdd16dde43c908ac4462
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10.26434/chemrxiv-2025-59lfh
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Enantioselective Michael Spirocyclization of Palladium Enolates.
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ABSTRACT: We report an enantio- and diastereoselective Michael spirocyclization reaction of tetrasubstituted palladium enolates. This allows for the formation of adjacent all-carbon quaternary and tertiary stereocenters in good yield, dr, and ee. Various subsequent cyclization reactions enable access to a diverse range of tricyclic scaffolds. The mechanism of this trans-formation is evaluated via quantum mechanics calculations to elucidate the origins of stereoselectivity and the mechanism of catalyst turnover.
|
Christian S. Strong ; Peng-Jui Chen ; Sanzhar Bissenali ; William A. Goddard III; Brian M. Stoltz
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Theoretical and Computational Chemistry; Organic Chemistry; Organometallic Chemistry; Organic Synthesis and Reactions; Computational Chemistry and Modeling; Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c8fdd16dde43c908ac4462/original/enantioselective-michael-spirocyclization-of-palladium-enolates.pdf
|
60c74c194c891948f0ad3589
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10.26434/chemrxiv.12425267.v1
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Successful Design of a Multivalent Bifunctional Chelator for Diagnostic 64Cu PET Imaging in Alzheimer’s Disease
|
Herein, we report to the best of our knowledge the
first <sup>64</sup>Cu PET imaging agent that shows appreciable <i>in vivo</i> brain uptake and exhibits high
specific affinity for beta-amyloid (Aβ) aggregates, leading to the successful PET
imaging of amyloid plaques in the brains of 5xFAD mice versus those of WT mice.
The employed approach uses a bifunctional chelator with two Aβ-interacting
fragments that dramatically improves the Aβ-binding affinity and lipophilicity
for favorable BBB penetration, while the use of optimized-length spacers between
the Cu-chelating group and the Aβ-interacting fragments further improves the <i>in vivo</i> Aβ-binding specificity and brain
uptake of the corresponding <sup>64</sup>Cu PET imaging agent.
|
Hong-Jun Cho; Truc T. Huynh; Buck E. Rogers; Liviu M. Mirica
|
Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c194c891948f0ad3589/original/successful-design-of-a-multivalent-bifunctional-chelator-for-diagnostic-64cu-pet-imaging-in-alzheimer-s-disease.pdf
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657ca805e9ebbb4db9f9990b
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10.26434/chemrxiv-2022-s3cr2-v3
|
Evolution of Complex Chemical Mixtures Reveals Combinatorial Compression and Population Synchronicity
|
Some of the most interesting open questions about the origins of life and molecular sciences center on chemical evolution and the spontaneous generation of complex and functional chemical species. The processes that generated the spectacular biopolymers that underlay biology demonstrate an untapped, by modern science, creative potential. We have established a robust, facile, and generally applicable platform for observing and analyzing chemical evolution using complex mixtures. While previous studies have characterized the formation of proto-polymers via chemical reactions, we systematically studied the process itself. We report empirical outcomes that were not foreseen or predicted. We have constructed an experimental platform to study the evolution of chemical systems that: (i) undergoes continuous recursive change with transitions to new chemical spaces while not converging throughout the course of the experiment, (ii) demonstrates chemical selection, during which combinatorial explosion is avoided, (iii) maintains synchronicity of molecular sub-populations, and (iv) harvests environmental energy that is stored in chemical energy. We have established some general guidelines for conducting chemical evolution. Our results suggest that chemical evolution can be adapted to produce a broad array of molecules with novel structures and functions.
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Kavita Matange; Vahab Rajaei; Pau Capera-Aragonès; John T Costner; Adelaide Robertson; Jennifer Seoyoung Kim; Anton S Petrov; Jessica C. Bowman; Loren Dean Williams; Moran Frenkel Pinter
|
Organic Chemistry; Combinatorial Chemistry; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657ca805e9ebbb4db9f9990b/original/evolution-of-complex-chemical-mixtures-reveals-combinatorial-compression-and-population-synchronicity.pdf
|
62e8dcfa04c85fd4c480d0bf
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10.26434/chemrxiv-2022-zrm6p
|
Automated pH Adjustment Driven by Robotic Workflows and Active Machine Learning
|
Buffer solutions have tremendous importance in biological systems and in formulated products. Whilst the pH response upon acid/base addition to a mixture containing a single buffer can be described by the Henderson-Hasselbalch equation, modelling the pH response for multi-buffered poly-protic systems after acid/base addition, a common task in all chemical laboratories and many industrial plants, is a challenge. Combining predictive modelling and experimental pH adjustment, we present an active machine learning (ML)-driven closed-loop optimization strategy for automating small scale batch pH adjustment relevant for complex samples (e.g., formulated products in the chemical industry). Several ML models were compared on a generated dataset of binary-buffered poly-protic systems and it was found that Gaussian processes (GP) served as the best performing models. Moreover, the implementation of transfer learning into the optimization protocol proved to be a successful strategy in making the process even more efficient. Finally, practical usability of the developed algorithm was demonstrated experimentally with a liquid handling robot where the pH of different buffered systems was adjusted, offering a versatile and efficient strategy for a pH adjustment processes.
|
Alexander Pomberger; Nicholas Jose; David Walz; Jens Meissner; Christian Holtze; Matthaeus Kopczynski; Philipp Müller-Bischof; Alexei Lapkin
|
Physical Chemistry; Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Process Control; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2022-08-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e8dcfa04c85fd4c480d0bf/original/automated-p-h-adjustment-driven-by-robotic-workflows-and-active-machine-learning.pdf
|
60c7422cbdbb89a833a3846a
|
10.26434/chemrxiv.8236547.v1
|
Facile Size-Controlled Synthesis of Fluorescent Carbon Nanoparticles with Size-Independent Optical Properties
|
Nanoparticle imaging probes and drug delivery systems have distinct advantages over free or diffusive delivery in that they can concentrate the imaging contrast agent and/or drug, elicit controlled release/degradation, and have a high surface area to volume ratio beneficial for attaching targeting ligands. The size of these nanoparticles affects delivery, retention, degradation rate, and sometimes the radiological properties of the particles. For many optically active nanoparticles (such as gold, silver, and quantum dots), the optical properties are directly dependent on the size and shape of the nanoparticles. While this provides a simplistic outlet for modifying the optical properties of those nanoparticles, it is limiting in that their applications are also dependent on morphology. In these works, we aim to determine if the optical properties of fluorescent carbon nanoparticles are dependent on size through variations in synthetic parameters. Fluorescent carbon nanoparticles with hydrodynamic diameters ranging from 10 – 500 nm were prepared through variations of sugar source, concentration of agave (as a sugar source) and incubation time. Through comparisons made between these nanoparticles, we found no change in the local absorbance maxima and refractive index, with < 5 nm shifting in fluorescence maxima location. We have observed that fluorescent carbon nanoparticles can be prepared within a large range of sizes (10 – 500 nm) without considerable shift in optical properties. Because of this observation, we can infer that the optical properties of fluorescent carbon nanoparticles are largely size independent.
|
Aaron Schwartz-Duval; Neal Mistry; Indrajit Srivastava; Jasleena Singh; Kelsey Golk; Dipanjan Pan
|
Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-06-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7422cbdbb89a833a3846a/original/facile-size-controlled-synthesis-of-fluorescent-carbon-nanoparticles-with-size-independent-optical-properties.pdf
|
648a84ffbe16ad5c57f1e0d4
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10.26434/chemrxiv-2023-rczrv
|
The semisynthesis of nucleolar human selenoprotein H
|
The human selenoprotein H is the only selenocysteine-containing protein that is located in the cell’s nucleolus. In vivo studies have suggested that it plays some role in DNA binding, consumption of reactive oxygen species, and may serve as a safeguard against cancers. However, the protein has never been isolated and, as a result, not yet fully characterized. Here, we used a semi-synthetic approach to obtain the full selenoprotein H with a S43T mutation. Using biolayer interferometry, we also show that the Cys-containing mutant of selenoprotein H is capable of binding DNA with sub-micromolar affinity.
|
Norman Metanis; Rebecca Notis Dardashti
|
Biological and Medicinal Chemistry; Organic Chemistry; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-06-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648a84ffbe16ad5c57f1e0d4/original/the-semisynthesis-of-nucleolar-human-selenoprotein-h.pdf
|
60c74aa6bb8c1a60203db050
|
10.26434/chemrxiv.12235880.v1
|
Stimuli-Responsive Cycloaurated ‘OFF-ON’ Switchable Anion Transporters
|
Anion transporters have shown potential application as anti-cancer agents that function by disrupting homeostasis and triggering cell death. In this research article we report switchable anion transport by gold complexes of anion transporters that are ‘switched on’ in the presence of the reducing agent GSH by decomplexation of gold. GSH is found in higher concentrations in tumours than in healthy tissue and hence offers a strategy to target these systems to tumours.
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Mohamed Fares; Xin Wu; Deepthi Ramesh; William Lewis; Paul Keller; Ethan Howe; Ricardo Pérez-Tomás; Philip Gale
|
Supramolecular Chemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74aa6bb8c1a60203db050/original/stimuli-responsive-cycloaurated-off-on-switchable-anion-transporters.pdf
|
670d8e3051558a15ef130631
|
10.26434/chemrxiv-2024-kr41w
|
Analysis of adenosine phosphonucleotides in blood by nh-PHIP
|
The sensitivity of conventional NMR is limited to metabolites at mid-micromolar concentrations, however diagnostically relevant metabolites are often found at lower concentrations. nh-PHIP has shown promise for analyzing complex biological samples like urine, but adapting it to blood presents additional challenges due to its complex matrix. Herein we successfully demonstrate the use of nh-PHIP for detecting adenine phosphonucleotides in blood.
|
Helen Pais; Indrek Reile; Kerti Ausmees
|
Analytical Chemistry; Spectroscopy (Anal. Chem.)
|
CC BY 4.0
|
CHEMRXIV
|
2024-10-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670d8e3051558a15ef130631/original/analysis-of-adenosine-phosphonucleotides-in-blood-by-nh-phip.pdf
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60c74bfc702a9ba6b618b589
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10.26434/chemrxiv.12407288.v1
|
Influence of Solar Activity on Water Clusters. Annual Variations 2015-2019
|
The variations of solar activity and distribution of solar energy due to the rotation of the Earth around its axis and around the Sun exert a strong influence on water clusters, as a result of which their chemical reactivity in hydrolytic processes can vary in a very wide range. This phenomenon is well manifested in the hydrolysis of the phosphoric acid esters. 5-Year regular investigations (2015-2019) of the hydrolysis of triethylphosphite in acetonitrile show that the rate of this reaction with all other conditions being equal displays diurnal and annual variations, and is also modulated by the 11-year cycles of solar activity.
|
Igor Shevchenko
|
Hydrology and Water Chemistry
|
CC BY NC ND 4.0
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CHEMRXIV
|
2020-06-03
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bfc702a9ba6b618b589/original/influence-of-solar-activity-on-water-clusters-annual-variations-2015-2019.pdf
|
6184be8c7a00215f6547002e
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10.26434/chemrxiv-2021-d9fsx
|
Doubly linked chiral phenanthrene oligomers for homogeneously π-extended helicenes with large effective conjugation length
|
Helically twisted conductive nanocarbon materials are applicable to optoelectronic and electromagnetic molecular devices working on the nanometer scale. Herein, we report the synthesis of per-peri-perbenzo[5]- and [9]helicenes in addition to previously reported π-extended [7]helicene. The homogeneously π-extended helicenes can be regarded as helically fused oligo-phenanthrenes. The HOMO−LUMO gap decreased significantly from 2.14 to 1.15 eV with increasing helical length, suggesting the large effective conjugation length (ECL) of the π-extended helical framework. The large ECL of π-extended helicenes is attributed to the large orbital interactions between the phenanthrene subunits at the 9- and 10-positions, which form a polyene-like electronic structure. Based on the experimental results and DFT calculations, the ultrafast decay dynamics on the sub-picosecond timescale were attributed to the low-lying conical intersection.
|
Yusuke Nakakuki; Takashi Hirose; Hikaru Sotome; Min Gao; Daiki Shimizu; Ruiji Li; Jun-ya Hasegawa; Hiroshi Miyasaka; Kenji Matsuda
|
Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.); Materials Chemistry
|
CC BY NC ND 4.0
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CHEMRXIV
|
2021-11-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6184be8c7a00215f6547002e/original/doubly-linked-chiral-phenanthrene-oligomers-for-homogeneously-extended-helicenes-with-large-effective-conjugation-length.pdf
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64ee239bdd1a73847fc87129
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10.26434/chemrxiv-2023-ks784
|
Secondary-Sphere Preorganization by an NHC-Pyridonate Ligand Enables Nickel-Catalyzed Hydroboration of Nitriles
|
Herein, we describe nickel-catalyzed nitrile hydroboration with pinacolborane, wherein a tethered pyridonate ligand enables efficient catalysis (5 mol% [Ni], ≤6 h reaction time) at room temperature. Mechanistic studies, including isolation of the catalytically relevant intermediates, shed light on the cooperative role of the NHC-pyridonate ligand in the reaction.
|
Medina Afandiyeva; Xijue Wu; William Brennessel; Abhishek Kadam; Caitlyn Rose Kennedy
|
Catalysis; Organometallic Chemistry; Kinetics and Mechanism - Organometallic Reactions; Ligand Design
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ee239bdd1a73847fc87129/original/secondary-sphere-preorganization-by-an-nhc-pyridonate-ligand-enables-nickel-catalyzed-hydroboration-of-nitriles.pdf
|
6445f94b83fa35f8f62786fa
|
10.26434/chemrxiv-2023-f5mcr
|
Enantioselective NiH-Catalyzed Syn-Hydrometalative Cyclization of Alkyne-tethered Ketoamides to α-Hydroxy-γ-Lactams
|
An enantioselective NiH-catalyzed syn-hydrocyclization of alkyne-tethered ketoamides for the synthesis of α-hydroxy γ-lactams is reported. Using Ni(OTs)2•6H2O/(S,S)-Me-Duphos as a precatalyst and (EtO)2MeSiH as a hydride source, a broad range of enantioenriched γ-lactams with a fully substituted stereogenic center are obtained in 32–84% yields with 89.5:10.5–96.5:3.5 er. Synthetic utilities, including scale-up reaction and product derivatization, are also demonstrated. This research represents a ligand-enabled regioselective functionalization of alkynes and provides an efficient strategy to access functional group-enriched chiral heterocycles.
|
Hai-Xiang Zeng; Xiao-Wen Zhang; Qi-Yang Li; Wen-Bo Liu
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6445f94b83fa35f8f62786fa/original/enantioselective-ni-h-catalyzed-syn-hydrometalative-cyclization-of-alkyne-tethered-ketoamides-to-hydroxy-lactams.pdf
|
60c74db1567dfe280bec53be
|
10.26434/chemrxiv.12651017.v1
|
Peritectic Phase Transition of Benzene and Acetonitrile and Formation of a Cocrystal Relevant to Titan, Saturn’s Icy Moon
|
Benzene and acetonitrile are two of the most commonly used solvents found in almost every chemical laboratory. Titan, Saturn’s icy moon, is one
other place in the Solar system that has even larger amounts of these compounds, together with many other hydrocarbons. On Titan, organic molecules
are produced in the atmosphere and carried by methane rainfall to the surface, where they either dissolve in the lakes, deposit as sandy dunes, or solidify
as minerals with complex composition and structure. In order to untangle these structural complexities a reliable model of the phase behavior of these
compounds at temperatures relevant to Titan is crucial. We therefore report the composition–temperature binary phase diagram of acetonitrile and
benzene, and provide a detailed account of the structure and composition of the phases. This work is based on differential scanning calorimetry and in
situ powder diffraction analyses with synchrotron X-ray radiation and supported by theoretical modeling. Benzene and acetonitrile were found to
undergo a peritectic reaction into a cocrystal with a 1:3 acetonitrile:benzene stoichiometry. The crystal structure was solved and refined in the polar
space group, R3, and the solution was confirmed and optimized by energy minimization calculations. To mimic the environment on Titan more
accurately, we tested the stability of the structure under liquid ethane. The diffraction data indicate that the cocrystal undergoes further change upon
contact with ethane. These results provide new insights into the structure and stability of a potential mineral on Titan, and contribute to the fundamental
knowledge of some of the smallest organic molecules
|
Christina McConville; Yunwen Tao; hayden evans; Benjamin A. Trump; Jonathan B Lefton; Wenqian Xu; Andrey Yakovenko; Elfi Kraka; Craig M. Brown; Tomce Runcevski
|
Physical Organic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74db1567dfe280bec53be/original/peritectic-phase-transition-of-benzene-and-acetonitrile-and-formation-of-a-cocrystal-relevant-to-titan-saturn-s-icy-moon.pdf
|
6772a0de6dde43c908cb2490
|
10.26434/chemrxiv-2024-q7dcv
|
Effects of Lipid Headgroups on the Mechanical Properties and In Vitro Cellular Internalization of Liposomes
|
We performed all-atom and coarse-grained simulations of lipid bilayers mixtures of the unsaturated lipid DOPC, with saturated lipids having the same 18-carbon acyl tails and different headgroups, to understand their mechanical properties. The secondary lipids were DSPG, DSPA, DSPS, DSPC and DSPE. The DOPC:DSPG system with 65:35 molar ratio was the softest, with area compressibility modulus KA ~22% smaller than the pure DOPC value. Raising the mole% of DOPC leads to increases in KA, yet at any given composition the KA trend is DSPG < DSPA < DSPS < DSPC < DSPE. Lipid-lipid interactions are weaker in DOPC:DSPG mixtures and stronger in DSPE systems. The head and phosphate groups of the secondary lipids DSPG, DSPA and DSPS interact strongly with salt ions. Adding secondary lipids lead to DOPC having more ordered acyl tails relative to pure DOPC systems. No evidence of phase separation or inhomogeneities was observed in our simulations. We synthesized three liposomal formulations, L-DOPC (pure DOPC), and L-DOPC/DSPG and L-DOPC/DSPA, both with 15 mol% of secondary lipid. L-DOPC/DSPA had approximately 3- and 2-times higher in vitro internalization by normal epithelial (EpH4-Ev) and metastatic breast cancer (4T1) cells, compared with L-DOPC. The uptake of L-DOPC/DSPG by EpH4-Ev cells was almost 2-fold compared to L-DOPC, but both liposomes had similar uptakes by cancer cells. As L-DOPC/DSPG and L-DOPC/DSPA have similar KA values, we presumed that the mechanical properties, possibly in combination with higher negative surface charges in L-DOPC/DSPA and differences in effective liposome diameters and diffusivities, contributed to these observations.
|
Jiaming Xu; Stephen Adepoju; Simran Pandey; Jimena Pérez Tetuán; Mary Williams; Rudolf Abdelmessih; Debra Auguste; Francisco Hung
|
Physical Chemistry; Biological and Medicinal Chemistry; Chemical Engineering and Industrial Chemistry; Bioengineering and Biotechnology; Interfaces; Thermodynamics (Physical Chem.)
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-12-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6772a0de6dde43c908cb2490/original/effects-of-lipid-headgroups-on-the-mechanical-properties-and-in-vitro-cellular-internalization-of-liposomes.pdf
|
6349e15b86473a39231368a9
|
10.26434/chemrxiv-2022-w3t9p-v3
|
Impacts of Polarizable Continuum Models on the SCF Convergence and DFT Delocalization Error of Large Molecules
|
Advances in algorithm developments have enabled density functional theory (DFT) description of large molecules, including whole proteins, but the self-consistent field (SCF) convergence issues often hamper practical applications. The conductor-like polarizable continuum model (CPCM), although initially introduced as an implicit solvent model, was reported to improve SCF convergence in some large molecules. However, the underlying mechanisms and applicable use cases were unclear. We investigated the impacts of CPCM on the SCF convergence of 25 peptides and found that the CPCM only effectively reduced the SCF iterations for molecules with charge separations (e.g., the zwitterionic form of peptides) but had little effect on non-charge-separated molecules. We observed that CPCM increased the HOMO-LUMO gap of both the zwitterionic and non-charge-separated molecules, but only the charge-separated molecules suffered from the vanishing HOMO-LUMO gap problem in the gas phase which is the origin of the convergence issue. We revealed CPCM’s gap-opening mechanism as the selective stabilization/destabilization of molecular orbitals (MO) based on their local electrostatic environment. Compared to level-shifting, a traditional SCF improvement technique, CPCM has superior performance because the stabilization/destabilization of MOs is consistent through SCF iterations. Finally, we examined CPCM’s impacts on DFT density delocalization error (DDE) when used as an SCF accelerator. CPCM can mitigate the DDE and reproduce the density-derived properties (e.g., dipole moments) matching high-level methods when a very low dielectric constant is used but tends to over-localize the electron density at higher dielectric constants.
|
Fangning Ren; Fang Liu
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2022-10-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6349e15b86473a39231368a9/original/impacts-of-polarizable-continuum-models-on-the-scf-convergence-and-dft-delocalization-error-of-large-molecules.pdf
|
63affa32b9c5f60c64e59d10
|
10.26434/chemrxiv-2023-nfmhr
|
Unraveling the Mechanism of Phase Transformation and Structural Evolution in Si Anode with Deep-Potential Molecular Dynamics
|
Silicon has been extensively studied as one of the most promising anode materials for next-generation lithium-ion batteries because of its high specific capacity. However, a direct understanding of the atomic-scale mechanism associated with the charging and discharging processes for the Silicon anode is still lacking, partly due to the fact that the electrochemical reaction and structural evolution in the silicon anode involve complex phase transformation between crystalline (c-) and amorphous (a-) phases. In the past, such theoretical studies were limited by the capability of ab initio molecular dynamics. In this work, employing a newly developed deep potential model, we calculate and analyze voltage curves and microstructure evolution pathways starting from c-Si/a-Si/c-Li3.75Si/a-Li4.5Si with lithium insertion/extraction. Our simulations not only reproduce the key experimental phenomena, but also allow us to study the atomic scale mechanism associated with these phenomena. In particular, the voltage plateaus in both of the c-Si and a-Si lithiation processes are reproduced with a predicted plateau difference close to experimental measurements, which indicates the two-phase reaction mechanism at the initial lithiation stage. The latent heat of the phase transformation from c-Li15-δSi4 to a-Li15-δSi4 phases along the delithiation paths is evaluated, and agrees well with experimental value. Furthermore, the structural evolution from the crystal Si to the Li-Si solid solution and subsequently to the a-LixSi phase is captured, and the change of Si-Si bond distribution matches well with experiments. The simulation shows that the stress in the a-Si lithiation is lower than that in the c-Si lithiation, which is consistent with the experimental observation that the a-Si phase exhibits better stability than the c-Si phase. Our results provide much-needed insights into the thermodynamics of the phase transitions and structural evolution between the crystalline and amorphous LixSi phases, which play a key role in silicon anode optimization for battery applications.
|
Fangjia Fu; Xiaoxu Wang; Linfeng Zhang; Yifang Yang; Jianhui Chen; Bo Xu; Chuying Ouyang; Shenzhen Xu; Fu-Zhi Dai; Weinan E
|
Theoretical and Computational Chemistry; Theory - Computational; Machine Learning; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-01-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63affa32b9c5f60c64e59d10/original/unraveling-the-mechanism-of-phase-transformation-and-structural-evolution-in-si-anode-with-deep-potential-molecular-dynamics.pdf
|
64b9269ab053dad33a96cab0
|
10.26434/chemrxiv-2023-fvp05
|
Hypervalent λ3-Fluoro Iodane Triggered Semipinacol Rearrange-ments: Efficient Synthesis of Quaternary α-Fluoro Ketones
|
Hypervalent λ3-fluoro iodanes have emerged as versatile reagents, providing unusual fluorination selectivities under mild reac-tion conditions. Here, we report on adding a semipinacol rearrangement to the fluorination, aryl migration cascade reaction of styrene derivatives. Thus, various cyclopentanones became accessible in up to 96% yield all bearing quaternary C,F-carbon center adjacent to the ketone group. Such fluorinated structural motifs are difficult to build with previously established meth-ods. Preliminary experiments on enantioselective processes validated that asymmetric transformations are likewise feasible.
|
Pengyuan Zhao; Wanying Wang; Tanja Gulder
|
Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-07-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b9269ab053dad33a96cab0/original/hypervalent-3-fluoro-iodane-triggered-semipinacol-rearrange-ments-efficient-synthesis-of-quaternary-fluoro-ketones.pdf
|
60c753384c89192fc4ad429a
|
10.26434/chemrxiv.13443392.v1
|
Water-SARS-CoV-2 Interaction-Based Mechanism Inhibiting Virus Attachment to Host Cells
|
Many studies showed that the enveloped viruses, including coronaviruses, HIV-1, and influenza inactivate significantly faster in water than the non-enveloped viruses. It looks that there is a certain mechanism controlling this phenomenon. However, the epidemic spread of SARS-CoV-2 indicates that this virus – water interaction mechanism is not effective enough to fully inhibit coronavirus reproduction. We hypothesized that a spatially extended layer of the ordered water molecules, formed around CoV due to the spike’s glycans – surrounding water interaction acts as a buffer inhibiting CoV motion and its attachment to the host cell receptor. There is experimental evidence that water molecules while interacting with glucans experience the long-range ordering and repulsive forces. Our findings revealed new features that can promote its interaction. It was shown that the glycans and water molecules have the same far ultraviolet (UV) absorbance peak at ~185 nm. This peak is a manifestation of the still little-known physical properties possessed by hydroxyl (OH) groups, including those contained in glycans and water molecules. Many studies show that the carbohydrate hydroxyl groups are a key element in the long-range antifreeze glycoproteins activity which is closely correlated with our issue. To further increase ice inhibition, a sugar-based (usually trehalose) water solution, further slowing down the water dynamics is commonly used. Our experiments with sugar-based compounds dissolved in water showed that in such solutions the UV absorbance at ~185 nm (activity of the OH groups) can be essentially increased with respect to the bulk water. The spike’s glycans – water long-range interaction, activated due to the dissolved sugar-based compound, creates the glass-like stabilizing hydration layer (like in case of the trehalose) effectively inhibiting the virus – host cell binding. It was shown that the chemical structures of the known compounds with proven inhibition of SARS-CoV-2 entry into host cells agree with our findings. The described approach can be effective against human immunodeficiency viruses, influenza viruses, and possibly other enveloped viruses. <br />
|
Valery Shalatonin
|
Physical Organic Chemistry; Biophysics; Biophysical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-12-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753384c89192fc4ad429a/original/water-sars-co-v-2-interaction-based-mechanism-inhibiting-virus-attachment-to-host-cells.pdf
|
66a4eaccc9c6a5c07a1fc8d8
|
10.26434/chemrxiv-2024-sv81t
|
Monomer activity solely induces collapse of polymer chain in a good solvent
|
Ability of particles to transform absorbed energy into translational movements brings peculiar orderings into the nonequilibrium matter. Connected together into the chain, these particles collectively behave completely different from well-known equilibrium polymers. Interestingly, one can find examples of active chains within cells. It is now proposed that activity, induced by molecular motor proteins play a key role in packing of chromatin within the cell nucleus. Here we demonstrate the ability of the self-propulsion monomer units to cause polymer collapse under conditions where there is no explicit attraction between particles. The resulting conformation is heterogeneous and is characterized by a dense condensed core surrounded by elongated loops. The polymer segments in the condense phase have crumpled packing. Using molecular dynamics analysis, we show that this effect is similar to well-known motility induced phase separation, but more pronounced in active chains due to the polymers lack of entropy.
|
Aleksandr Buglakov; Vasilisa Lelecova; Aleksandr Chertovich
|
Theoretical and Computational Chemistry; Materials Science; Polymer Science; Biopolymers; Polymer chains; Polymer morphology
|
CC BY 4.0
|
CHEMRXIV
|
2024-07-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a4eaccc9c6a5c07a1fc8d8/original/monomer-activity-solely-induces-collapse-of-polymer-chain-in-a-good-solvent.pdf
|
63069d7ceadd9a0be380796d
|
10.26434/chemrxiv-2022-753l0
|
Remote Formation of Arynes via Formal Dehydrogenation of Arenes
|
Arynes offer immense potential for diversification of benezenoid cores, which occur in pharmaceuticals, agrochemicals, and liquid crystals. However, accessing these high-energy intermediates requires either harsh conditions or multi-step syntheses of designer reagents, and alternative methods with simpler substrates and milder conditions remain under- developed. Here, we describe a two-step formal dehydrogenation of simple arenes to generate arynes at a remote position relative to traditionally reactive groups, i.e., halides. This approach is enabled by regioselective installation and ejection of an “onium” leaving group, and we demonstrate the compatibility of simple arenes (20 examples) and arynophiles (6 examples). The mildness of this strategy is highlighted by formal dehydrogenation of clofibrate, an active pharmaceutical ingredient, and demonstrates that arynes are viable intermediates for late-stage functionalization. Finally, we show that aryne intermediates offer opportunities for orthogonal C-H amination relative to other methods.
|
Riley Roberts; Bryan Metze; Aleksandra Nilova; David Stuart
|
Organic Chemistry; Organic Synthesis and Reactions
|
CC BY 4.0
|
CHEMRXIV
|
2022-08-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63069d7ceadd9a0be380796d/original/remote-formation-of-arynes-via-formal-dehydrogenation-of-arenes.pdf
|
60f085e88ae3a7499b78400f
|
10.26434/chemrxiv-2021-k0qx5
|
Routescore: Punching the Ticket to More Efficient Materials Development
|
Self-driving labs, in the form of automated experimentation platforms guided by machine learning algorithms have emerged as a potential solution to the need for accelerated science. While new tools for automated analysis and characterization are being developed at a steady rate, automated synthesis remains the bottleneck in the chemical space accessible to self-driving labs. Combining automated and manual synthesis efforts immediately significantly expands the explorable chemical space. To effectively direct the different capabilities of automated (higher throughput and less labor) and manual synthesis (greater chemical versatility), we describe a protocol, the RouteScore, that quantifies the cost of combined synthetic routes. In this work, the RouteScore is used to determine the most efficient synthetic route to a well-known pharmaceutical (structure-oriented optimization), and to simulate a self-driving lab that finds the most easily synthesizable organic laser molecule with specific photophysical properties from a space of ~3500 possible molecules (property-oriented optimization). These two examples demonstrate the power and generality of our approach in mixed synthetic planning and optimization.
|
Martin Seifrid; Riley J. Hickman; Andrés Aguilar-Granda; Cyrille Lavigne; Jenya Vestfrid; Tony C. Wu; Théophile Gaudin; Emily J. Hopkins; Alán Aspuru-Guzik
|
Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Machine Learning; Artificial Intelligence; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-07-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f085e88ae3a7499b78400f/original/routescore-punching-the-ticket-to-more-efficient-materials-development.pdf
|
60c74baa337d6c4eb4e27b06
|
10.26434/chemrxiv.12041904.v2
|
Probing the Electronic Structure of Bulk Water at the Molecular Lengthscale with Angle-Resolved Photoelectron Spectroscopy
|
<div>We report a combined experimental and theoretical study of bulk water photoionization. Angular distributions of photoelectrons produced by ionizing the valence band of neat water using X-ray radiation (250-750 eV) show a limited (<30 %) decrease in the beta anisotropy parameter compared to the gas phase, indicating that the electronic structure of the individual water molecules can be probed. By theoretical modeling using high-level electronic structure methods, we show that in a high-energy regime photoionization of bulk can be described as an incoherent superposition of individual molecules, in contrast to a low-energy regime where photoionization probes delocalized entangled states of molecular aggregates. The two regimes-low energy versus high energy-are defined as limiting cases where the de Broglie wavelength of the photoelectron is either larger or smaller than the intermolecular distance between water molecules, respectively. The comparison of the measured and computed anisotropies reveals that at high kinetic energies the observed reduction in beta is mostly due to scattering rather than rehybridization due to solvation.</div>
|
Samer Gozem; Robert Seidel; Uwe Hergenhahn; Evgeny Lugovoy; Bernd Abel; Bernd Winter; Anna I. Krylov; Stephen
E. Bradforth
|
Physical and Chemical Properties; Quantum Mechanics; Solution Chemistry; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74baa337d6c4eb4e27b06/original/probing-the-electronic-structure-of-bulk-water-at-the-molecular-lengthscale-with-angle-resolved-photoelectron-spectroscopy.pdf
|
65117a2860c37f4f766b3827
|
10.26434/chemrxiv-2023-6vxj5-v2
|
On the role of Water-as-Additive in Lithium Electrodeposition
|
Electroplating of flat and smooth lithium layers is key for batteries using metallic lithium as the anode, where a major failure mechanism is the self-enhancing uneven or ramified growth of lithium metal leading to capacity fading or even short-circuiting during cycling. In that regard we shed new light on an intriguing growth mode for electrodeposited lithium in this work, where lithium self-assembles in a compact columnar morphology. Such growth results in topographically smooth layers and a particular stripping behavior along the length of these nanorods, rather than from the top down. Here, we demonstrate the electroplating of smooth layers of columnar lithium using LiTFSI and LiClO4 salts, which rules out the commonly found explanation of a LiF interface layer directing growth. Rather, we find that the addition of water to these (non-hydrolising) electrolytes is key for the guided growth. We investigate its effect both during electrochemical formation (applied potentials > Li+/Li), and growth (applied potentials < Li+/Li), and observe that the presence of water is required during the whole process. We use a rotating ring disk electrode (RRDE) to study the process in-situ, and find that hydrogen is continuously generated. Notably, hydrogen is generally considered as a side-product in the LiF based mechanism, and we therefore suggest that the evolution of hydrogen is in fact the critical component for the directed growth. Such an explanation homogenizes our results with earlier reports and provides mechanistic insights for the role of water during lithium electrodeposition, which is invariably present in lithium metal batteries.
|
Mark Aarts; Sai Gourang Patnaik; Toon Van Roy; Stefanie Sergeant; Maarten Debucquoy; Philippe Vereecken
|
Physical Chemistry; Energy; Energy Storage; Electrochemistry - Mechanisms, Theory & Study
|
CC BY 4.0
|
CHEMRXIV
|
2023-09-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65117a2860c37f4f766b3827/original/on-the-role-of-water-as-additive-in-lithium-electrodeposition.pdf
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60e77cd2b95bddddd4604574
|
10.26434/chemrxiv-2021-9ww0c-v2
|
Communication: Multi-reference Approach to the Computation of Double-Core-Hole Spectra
|
Double-Core Hole (DCH) states of small molecules are assessed with the restricted<br />active space self-consistent field (RASSCF) and multi-state restricted active space perturbation<br />theory of second order (MS-RASPT2) approximations. To ensure an unbiased<br />description of the relaxation and correlation effects on the DCH states, the neutral<br />ground state and DCH wave functions are optimized separately, whereas the spectral<br />intensities are computed with a biorthonormalized set of molecular orbitals within the<br />state-interaction (SI) approximation. Accurate shake-up satellites binding energies and<br />intensities of double-core-ionized states (K<sup>-2</sup>) are obtained for H<sub>2</sub>O, N<sub>2</sub>, CO and C<sub>2</sub>H<sub>2n</sub><br />(n=1–3). The results are analyzed in detail and show excellent
agreement with recent theoretical and experimental data. The K^{-2} shake-up spectra
of H2O and the C2H2n molecules are here completely characterized for the first time.
|
Bruno Nunes Cabral Tenorio; Piero Decleva; Sonia Coriani
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-07-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e77cd2b95bddddd4604574/original/communication-multi-reference-approach-to-the-computation-of-double-core-hole-spectra.pdf
|
60c74fc0bb8c1a6a733db9e3
|
10.26434/chemrxiv.12890810.v1
|
Analysis of Multicomponent Exponential Magnetic Resonance Relaxation Data: Automatable Parameterization and Interpretable Display Protocols
|
This report describes and illustrates a set of automatable multicomponent exponential relaxation analysis protocols that are model-agnostic and suited to extracting information under circumstances when little prior knowledge about the underlying system is used. Methods are illustrated and mathematical and physical underpinnings of the methods are provided.
|
Charles Eads
|
Imaging; Spectroscopy (Anal. Chem.); Process Control; Physical and Chemical Properties
|
CC BY 4.0
|
CHEMRXIV
|
2020-09-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fc0bb8c1a6a733db9e3/original/analysis-of-multicomponent-exponential-magnetic-resonance-relaxation-data-automatable-parameterization-and-interpretable-display-protocols.pdf
|
6708f1f212ff75c3a11f9d92
|
10.26434/chemrxiv-2024-qqh2s
|
Use of Resonant Acoustic Fields as Atmospheric-Pressure Ion Gates
|
Ion optics are crucial for spectrometric methods such as mass spectrometry (MS) and ion mobility spectrometry (IMS). Among the wide selection of ion optics, temporal ion gates are of particular importance for time-of-flight MS (TOF-MS) and drift-tube IMS. Commonly implemented as electrostatic ion gates, these optics offer a rapid, efficient means to block ion beams and form discrete ion packets for subsequent analysis. Unfortunately, these devices rely on pulsed high-voltage sources and are not fully transparent, even in their open state, which can lead to ion losses and contamination. Here, a novel atmospheric-pressure ion gate based on a resonant acoustic field structure is described. This effect was accomplished through the formation of a resonant, standing acoustic wave of alternating nodes and antinodes. Alignment of an atmospheric-pressure gaseous ion beam with an antinode, i.e. a region of transient pressure, of the acoustic structure acted as a gate and blocked ions from impinging ion-selective detectors, such as a mass spectrometer and a Faraday plate. The velocity of the ion stream and acoustic power were found to be critical parameters for gating efficiency. In the presence of an acoustic field (i.e. a closed gate), ion signals were decreased by as much as 99.8% with a response time faster than the readout of the ion-measurement devices used here (ca. 75 ms). This work demonstrates the basis for a low-cost, acoustic ion gate, which is optically transparent and easily constructed with low-power, off-the-shelf components, that can be used in MS and IMS instrumentation.
|
Julia Danischewski; Yi You; Lauren Bauer; Jens Riedel; Jacob Shelley
|
Physical Chemistry; Analytical Chemistry; Mass Spectrometry; Spectroscopy (Anal. Chem.); Transport phenomena (Physical Chem.)
|
CC BY NC ND 4.0
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CHEMRXIV
|
2024-10-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6708f1f212ff75c3a11f9d92/original/use-of-resonant-acoustic-fields-as-atmospheric-pressure-ion-gates.pdf
|
677d0b29fa469535b9114cef
|
10.26434/chemrxiv-2025-k3g05
|
Measuring Size and Shape Heterogeneity in AAVs with Ion Mobility Mass Spectrometry
|
Adeno-associated viruses (AAVs) are at the forefront of biopharmaceutical development as gene therapy vectors. The successful approval of these medicines requires robust characterization including an assessment of therapeutic gene content. Using ion mobility–mass spectrometry (IM-MS) techniques, we determine empty:full capsid ratios and explore structural differences in AAV particles relevant to payload. With drift tube IM-MS, we demonstrate that empty capsids, while slightly smaller, present more conformational variability than full capsids. This method also resolves two partially filled capsid species with intermediate masses, between that of empty and full capsids wherein the lower mass feature is conformationally more like empty and the higher mass feature appears highly similar to the full capsid. We present data using travelling wave ion mobility (TWIM) operated under conditions that limit or favour the mass-to-charge ratio (m/z) dependence on ion transit time through the drift cell via the velocity relaxation effect. This permits separation of empty and full capsids in the absence of mass spectrometry information, providing a new approach to study conformational and mass differences in super massive particles.
|
Ellen Liggett; Keith Richardson; David Langridge; Kevin Giles; Ian Anderson; Kamila Pacholarz; Paul Getty; Michael Walker; Jakub Ujma; Perdita Barran
|
Physical Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Apparatus; Cell and Molecular Biology; Biophysical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677d0b29fa469535b9114cef/original/measuring-size-and-shape-heterogeneity-in-aa-vs-with-ion-mobility-mass-spectrometry.pdf
|
62ab7ce8ecd7cd1e7dc6eb9d
|
10.26434/chemrxiv-2022-3vbdn
|
Revisiting the Stereoselectivity in Organoborane Rearrangement
|
Hydroboration of 1,2-dimethylcyclohexene (A) and successive rearrangements yield not only tertiary alkylboranes but also primary and secondary ones. In addition, nontypical anti-addition products are detected, whose formation mechanism is not apparent. Herein, we revisit three mechanisms proposed in the literature: an elimination and readdition, an intramolecular process involving an intermediate π-complex, and an intramolecular migration. According to our computations, the formation of all products starts from the tertiary alkylborane obtained by hydroboration of olefin A. This alkylborane then undergoes a sequence of further retrohydroborations and hydroborations in a syn fashion. Interestingly, the conformational changes on the ring affect these transformations and decide the rearrangement mechanism. Free olefin intermediates are generated during these reactions, which are then rehydroborated from their opposite faces, explaining the formation of anti-addition products. Moreover, the temperature effect on the rearrangement reactions is also analyzed.
|
Fernando Murillo; Alan Quintal; Jair García-Méndez; Eugenia Dzib; María A. Fernández-Herrera; Gabriel Merino
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-06-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ab7ce8ecd7cd1e7dc6eb9d/original/revisiting-the-stereoselectivity-in-organoborane-rearrangement.pdf
|
6668211d409abc034525220e
|
10.26434/chemrxiv-2024-3ws9d
|
Identifying and Filling the Chemobiological Gaps of Gut Microbial Metabolites
|
Human gut microbial metabolites are currently undergoing much research due to their involvement in multiple biological processes important for health, including immunity, metabolism, nutrition, and the nervous system. Metabolites exert their effect through the interaction with host and bacterial proteins, suggesting the use of “metabolite-mimetic” molecules as drugs and nutraceutics. In the present work, we retrieve and analyze the full set of published interactions of these compounds with human and microbiome-relevant proteins, and find patterns in their structure, chemical class, target class, and biological origins. In addition, we use virtual screening to expand (> 4-fold) the interactions, validate them with retrospective analyses, and use bioinformatic tools to prioritize them based on biological relevance. In this way, we fill many of the chemobiological gaps observed in the published data. By providing these interactions we expect to speed up the full clarification of the chemobiological space of these compounds, by suggesting many reliable predictions for fast, focused experimental testing.
|
Cristian Orgaz; Andrés Sánchez-Ruiz; Gonzalo Colmenarejo
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Agriculture and Food Chemistry; Drug Discovery and Drug Delivery Systems; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-06-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6668211d409abc034525220e/original/identifying-and-filling-the-chemobiological-gaps-of-gut-microbial-metabolites.pdf
|
66755acec9c6a5c07a061d5d
|
10.26434/chemrxiv-2024-nlm1k
|
Adaptable synthesis of chondroitin sulfate disaccharide subtypes preprogrammed for regiospecific O-sulfation
|
A divergent synthetic route to chondroitin sulfate (CS) disaccharide precursors, including rarer subtypes such as CS-D, has been developed. From common intermediates, a series of thioglycoside D-glucose donors and 4,6-O-benzylidene protected D-galactosamine acceptors are utilised in a robust glycosylation reaction, achieving β-selectivity and consistent yields (60-75%) on scales >2.0 g. A post-glycosylation oxidation to D-glucuronic acid and orthogonal protecting groups delivers access to CS-A, CS-C, CS-D, CS-E and CS-O precursor subtypes. Of further note is a 4-O-benzyl regioselective reductive ring opening of a 4,6-O- benzylidene protected disaccharide using PhBCl2 and Et3SiH to access a CS-D precursor, in 73% yield over two steps. Finally, synthesis of a 6-O-sulfated CS-C disaccharide containing a conjugable anomeric allyl tether is completed. These materials will provide a benchmark to further synthesise and study chondroitin sulfates.
|
Hannah Wootton; Sian Berry; Elaine Ferguson; Clare Mahon; Gavin Miller
|
Organic Chemistry; Natural Products; Organic Synthesis and Reactions
|
CC BY 4.0
|
CHEMRXIV
|
2024-06-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66755acec9c6a5c07a061d5d/original/adaptable-synthesis-of-chondroitin-sulfate-disaccharide-subtypes-preprogrammed-for-regiospecific-o-sulfation.pdf
|
61419613ac321977537c3856
|
10.26434/chemrxiv-2021-nlw4s
|
Electrocatalytic CO2 hydrogenation to C2 based products through C–C coupling over Cu(100) nanocube
|
In this study, we have considered a Cu nanocube (Cu-NC) based catalyst exposed with (100) facets for CO2 hydrogenation reactions. All the feasible mechanistic pathways for the formations of C1 (HCOOH, CH3OH and CH4) and C2 (C2H4 and C2H5OH) based products have been explored using the density functional theoretical calculations and the most plausible pathways have been identified. The calculated results are compared with the previous reports on the periodic Cu(100) and Cu(111) surfaces, and also on the surface of Cu85 nanocluster and Cu(111) monolayer. The in-depth mechanistic investigation shows that Cu-NC can be very selective towards the C2 based products with a lower limiting potential (calculated) compared to the periodic surfaces. The underlying reasons for such findings have been explained and compared that with the periodic surfaces. We therefore, propose that the Cu-NC based catalysts can be more promising for C2 based products.
|
Shyama Charan Mandal; Biswarup Pathak
|
Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational; Heterogeneous Catalysis
|
CC BY NC 4.0
|
CHEMRXIV
|
2021-10-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61419613ac321977537c3856/original/electrocatalytic-co2-hydrogenation-to-c2-based-products-through-c-c-coupling-over-cu-100-nanocube.pdf
|
66f1b9f7cec5d6c142fd7271
|
10.26434/chemrxiv-2024-1pzk5
|
Room temperature nucleophilic aromatic substitution of 2-halopyridinium ketene hemiaminals with sulfur nucleophiles
|
2-Thiopyridines and their derivatives are a valuable class of bioactive compounds for drug discovery. Herein we report preliminary results of a simple mix-and-stir protocol for the synthesis of novel 2-thiopyridiniums leveraging the recently developed reagent, 2-chloro-1-(1-ethoxyvinyl)pyridinium triflate, and readily accessible thiol or thiolate nucleophiles.
|
Jordan Merklin; Beau Sinardo; Max Majireck
|
Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-09-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f1b9f7cec5d6c142fd7271/original/room-temperature-nucleophilic-aromatic-substitution-of-2-halopyridinium-ketene-hemiaminals-with-sulfur-nucleophiles.pdf
|
61269d6342198e76cc642291
|
10.26434/chemrxiv-2021-jkn0b
|
Diindolocarbazole – Achieving Multiresonant Thermally Activated Delayed Fluorescence Without The Need for Acceptor Units
|
In this work we present a new multi-resonance thermally activated delayed fluorescence (MR-TADF) emitter paradigm, demonstrating that the structure need not require the presence of acceptor atoms. Based on an in-silico design, the compound DiICzMes4 possesses a red-shifted emission, enhanced photoluminescence quantum yield, and smaller ΔEST than the parent indolocarbazole that induces MR-TADF properties. Coupled cluster calculations accurately predict the magnitude of the singlet-triplet energy gap, ΔEST, when the optimized singlet and triplet geometries are used. Slow yet optically detectable reverse intersystem crossing contributes to low efficiency in organic light-emitting diodes using DiICzMes4 as then emitter. However, when used as a terminal emitter in combination with a TADF assistant dopant within a hyperfluorescence device architecture, maximum external quantum efficiencies of up to 16.9% were achieved at CIE (0.15,0.11). This represents one of the bluest hyperfluorescent devices reported to date. Simultaneously, recognising that MR-TADF emitters do not require acceptor atoms reveals an unexplored frontier in materials design, where yet greater performance may yet be discovered.
|
David Hall; Kleitos Stavrou; EImantas Duda; Andrew Danos; Sergey Bagnich; Stuart Warriner; Alexandra Slawin; David Beljonne; Anna Koehler; Andrew Monkman; Yoann Olivier; Eli Zysman-Colman
|
Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Spectroscopy (Physical Chem.); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-08-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61269d6342198e76cc642291/original/diindolocarbazole-achieving-multiresonant-thermally-activated-delayed-fluorescence-without-the-need-for-acceptor-units.pdf
|
60c7515a567dfe1223ec5a4d
|
10.26434/chemrxiv.13157522.v1
|
Gauge Dependence of the S Molecular Orbital Space Decomposition of Optical Rotation
|
<div>
<div>
<div>
<p>Optical rotation (OR) is a foundational technique for the detection and characterization of chiral
molecules, but it is poorly understood how the observed
property relates to the structure of the molecule. Over
the years, several schemes have been developed to de-
compose the OR into more chemically intuitive contributions. In this paper, we introduce two alternative formulations of our previously developed S molecular orbital space decomposition. These new expressions use
the Modified Velocity Gauge-Magnetic (MVG-M) and
-Electric (MVG-E) definitions of OR, rather than the
Length Gauge Magnetic (LG-M) definition used in the
original paper. Comparing these formulations across a
small set of previously studied chiral molecules, we find
that these different definitions produce consistent physical interpretations of the OR. These results further confirm the robustness of the S methodology for the investigation of structure-property relationships in chiral molecules.</p>
</div>
</div>
</div>
|
Ty Balduf; Marco Caricato
|
Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-10-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7515a567dfe1223ec5a4d/original/gauge-dependence-of-the-s-molecular-orbital-space-decomposition-of-optical-rotation.pdf
|
61b2a6659e56b83477b53490
|
10.26434/chemrxiv-2021-l53j3
|
Solvent controlled selective photocatalytic oxidation of benzyl alcohol over Ni@C/TiO2
|
The oxidation of aromatic alcohols to produce carbonyl compounds is of great significance in fine chemical production. The traditional oxidation produces waste gas and pollutes the environment during the reaction. As a new field, photocatalysis has attracted people's attention because of its environmental friendliness. At present, there have been much research on TiO2, or noble metal modified TiO2 to catalyze alcohol oxidation, but the high cost is not conducive to large-scale production. Herein, a Ni@C/TiO2 catalyst was prepared by in-situ hydrothermal synthesis. This catalyst has a better oxidation effect on benzyl alcohol than Ni@C supported on TiO2 on the market and has a good catalytic effect on aromatic alcohols with different substituents. It is more interesting that the selectivity of the product can be adjusted by choosing different reaction solvents. The highly active catalyst with low cost and wide applicability has certain significance for the large-scale use of photocatalytic alcohol oxidation.
|
Song Zhenlong; Jianguo Liu; Qi Zhang
|
Catalysis; Chemical Engineering and Industrial Chemistry; Heterogeneous Catalysis; Photocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2021-12-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b2a6659e56b83477b53490/original/solvent-controlled-selective-photocatalytic-oxidation-of-benzyl-alcohol-over-ni-c-ti-o2.pdf
|
60c751440f50dbcb0b397740
|
10.26434/chemrxiv.13143302.v1
|
Utilization of Biowaste-derived Catalyst for Biodiesel Production: Process Optimization Using Response Surface Methodology and Particle Swarm Optimization Method
|
In this experimental and optimization study,
banana (<i>Musa acuminata)</i> flower petals
ash has been considered as an effective catalyst in the room temperature (28
°C) assisted transesterification to produce biodiesel from waste cooking oil
(WCO). The transformation of <i>Musa acuminata</i>
flower petals to ash catalyst has been performed by simple conventional open-air
burning process. Three important parameters (catalyst concentration,
methanol/oil (M/O) molar ratio and time) that play significant role in
conversion of WCO to waste cooking methyl ester (WCME) were investigated. In
order to maximize the conversion rate these key transesterification parameters
were optimized using central composite rotatable design (CCRD) of response
surface methodology (RSM). A metaheuristic algorithm popularly known as
Particle swarm algorithm (PSO) has been used to observe a clear picture of the
global optimum points scattered around the search domain. PSO has also been
used to validate the results obtained from CCRD. The chemical composition and
morphology of ash catalyst has been investigated using several analytical
techniques such as X-Ray Diffraction (XRD), Fourier Transformation Infrared
Spectroscopy (FTIR), X-Ray Fluorescence Spectroscopy (XRF), X-ray Photoelectron Spectroscopy
(XPS), Thermal Gravimetric Analysis (TGA), Energy Dispersive Spectroscopy (EDS),
Brunauer-Emmett-Teller (BET), Scanning Electron Microscope (SEM), Transmission
Electron Microscope (TEM) and Hammett Indicator method. It was observed that
the catalyst remained active till 4<sup>th</sup> reaction cycle. The catalyst’s
reusability, renewability and robust activity in the reaction makes it
efficient, economic, green and industrially applicable.
|
Ikbal Bahar Laskar; Tuhin Deshmukhya; Aayushi Biswas; Bappi Paul; Bishwajit Changmai; Rajat Gupta; Sushovan Chatterjee; Samuel Lalthazuala Rokhum
|
Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-10-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751440f50dbcb0b397740/original/utilization-of-biowaste-derived-catalyst-for-biodiesel-production-process-optimization-using-response-surface-methodology-and-particle-swarm-optimization-method.pdf
|
6515e878006594091210824f
|
10.26434/chemrxiv-2023-fhhr4
|
An Interpretable and Transferrable Vision Transformer Model for Rapid Materials Spectra Classification
|
Rapid analysis of materials characterization spectra is pivotal for preventing accumulation of unwieldy datasets, thus accelerating subsequent decision-making. However, current methods heavily rely on experience and domain knowledge, which not only proves tedious but also is hard to keep up with the pace of data acquisition. In this context, we introduce a transferable Vision Transformer (ViT) model for identification of materials from their spectra, including XRD and FTIR. First, an optimal ViT model was trained to predict metal organic frameworks (MOFs) from their XRD spectra. It attains prediction accuracies of 70%, 93%, and 94.9% for Top-1, Top-3, and Top-5, respectively, and a shorter training time of 269 seconds in comparison to a convolutional neural network model. The dimension reduction and attention weight map underline its adeptness at capturing relevant features in the XRD spectra for determining the prediction outcome. Moreover, the model can be transferred to a new one for prediction of organic molecules from their FTIR spectra, attaining remarkable Top-1, Top-3, and Top-5 prediction accuracies of 84%, 94.1%, and 96.7%, respectively. The introduced ViT based model would set a new revenue to handling diverse types of spectroscopic data, thus expediting the materials characterization processes.
|
Zhenru Chen; Yunchao Xie; Yuchao Wu; Yuyi Lin; Shigetaka Tomiya; Jian Lin
|
Analytical Chemistry; Chemoinformatics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-09-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6515e878006594091210824f/original/an-interpretable-and-transferrable-vision-transformer-model-for-rapid-materials-spectra-classification.pdf
|
60c74661469df4720ef43634
|
10.26434/chemrxiv.8378405.v2
|
Photocontrolled Synthesis of N-Type Conjugated Polymers
|
Current approaches to synthesize π-conjugated polymers are dominated by thermally driven, transition metal-mediated methods. Herein we show that electron-deficient Grignard monomers readily polymerize under visible light irradiation at room temperature in the absence of a catalyst. The product distribution can be tuned by the wavelength of irradiation based on the absorption of the polymer. Conversion studies are consistent with an uncontrolled chain-growth process; correspondingly, chain extension produces all-conjugated n-type block copolymers. Preliminary results demonstrate that the polymerization can be expanded to donor-acceptor alternating copolymers. We anticipate that this method can serve as a platform to access new architectures of n-type conjugated polymers without the need for transition metal catalysis.
|
Eliot Woods; Alexandra Berl; Julia Kalow
|
Photochemistry (Org.); Organic Polymers; Polymerization (Polymers)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-11-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74661469df4720ef43634/original/photocontrolled-synthesis-of-n-type-conjugated-polymers.pdf
|
60c746b09abda2bcecf8c7a7
|
10.26434/chemrxiv.11369382.v1
|
What Makes an Explosion Happen?
|
<p>The combination of intermolecular hydrogen bond (X:H–Y) tension and the anti-HB (H↔H) or super-HB (X⇔Y) compression not only stabilizes the structure but also stores energy by shortening the intramolecular covalent bonds. The X:H tension constrains and the X⇔Y compression fosters explosion.<br /></p><p><b></b></p>
|
Chang Sun
|
Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-12-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746b09abda2bcecf8c7a7/original/what-makes-an-explosion-happen.pdf
|
60c73d0e9abda289e2f8b670
|
10.26434/chemrxiv.5411197.v1
|
CHEMICAL BONDS DISSOCIATION ENERGY
|
<p>In previous
publications dealing with experimental mass spectrometry of tungsten
hexacarbonyl, hexafluoroacetylacetone and
its bidentate metal complexes M(hfac)<sub>2</sub>;
M = Cu, Pd the obtained data have been not adequately systematized. In this paper, we
analyze the
previously published
experimental data of the
various bond
dissociation energy.<b> </b>A
modified Yukawa
potential, which is the exact solution of
the problem dependence the chemical bond energy of its length,
is used to analyze the experimental data.<b>
</b>Experimental
results of
the formation of ions
can be interpreted
only in terms of
the formation of
fractionally charged
quasi-particles. <b>
</b>As an experimental technique, mass
spectrometry of negative ions in electron resonance capture mode
ranks next to the fractional quantum Hall effect in which fractional
values of the charge quantization are observed. Also noted the
possibility capture of
electron with “negative” kinetic energy.</p>
|
Adel Iakubov
|
Physical and Chemical Properties; Thermodynamics (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2017-09-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0e9abda289e2f8b670/original/chemical-bonds-dissociation-energy.pdf
|
61475d9caeaa6ed146f18063
|
10.26434/chemrxiv-2021-d5ksj
|
Stabilizing Highly Dispersed Halo Sites in Thermally Restructured Palladium Core@shell Nanoparticles for Improved Catalyst Activity and Durability
|
Stabilizing high dispersions of catalytically active metals is integral to improving the lifetime, activity, and material utilization of catalysts that are periodically exposed to high temperatures during operation or maintenance. We have found that annealing palladium-based core@shell catalysts in air at elevated temperature (800°C) promotes the redispersion of active metal into highly dispersed sites, which we refer to as halo sites. Here, we examine the restructuring of Pd@SiO2 and Pd@CeO2 core@shell catalysts over successive 800°C aging cycles to understand the formation, activity, nanoscale structure and stability of these palladium halo sites. While encapsulation generally improves metal utilization by providing a physical barrier that promotes redispersion over agglomeration, our cycled aging experiments demonstrate that halo sites are not stable in all catalysts. Halo sites continue to migrate in Pd@SiO2 due to poor metal-support bonding, which leads to palladium agglomeration. In contrast, halo sites formed in Pd@CeO2 remain stable. The dispersed palladium also synergistically stabilizes the ceria from agglomerating. We attribute this stability, in addition to an observed improvement in catalytic activity, to the coordination between palladium and reducible ceria that arises during the formation of halo sites. We probe the importance of ceria oxidation state on the stability of halo sites by aging Pd@CeO2 after it has been reduced. While some halo sites agglomerate, we find that returning to air aging mitigates the loss of these sites and catalytic activity. Our findings illustrate how nanoscale catalyst structures can be designed to promote the formation of highly stable and dispersed metal sites.
|
Alexander Hill; Adarsh Bhat; Zachary Berquist; Galen Fisher; Andrej Lenert; Johannes Schwank
|
Materials Science; Catalysis; Nanoscience; Core-Shell Materials; Nanocatalysis - Catalysts & Materials; Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-09-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61475d9caeaa6ed146f18063/original/stabilizing-highly-dispersed-halo-sites-in-thermally-restructured-palladium-core-shell-nanoparticles-for-improved-catalyst-activity-and-durability.pdf
|
65d426a39138d231617ecd96
|
10.26434/chemrxiv-2024-x4wbl
|
CNSMolGen: a bidirectional recurrent neural networks based generative model for de novo central nervous system drug design
|
Central nervous system (CNS) drugs have had a significant impact on human health, e.g., treating a wide range of neurodegenerative and psychiatric disorders. In recent years, deep learning-based generative models, particularly those for designing drugs from scratch, have shown great potential for accelerating drug discovery, reducing costs and improving efficacy. However, specific applications of these techniques in CNS drug discovery have not been widely reported. In this study, we developed the CNSMolGen model, which uses a bidirectional recurrent neural networks (Bi-RNNs) system for de novo molecular design of CNS drugs by learning from compounds with CNS drug properties. Result shown that the pre-trained model was able to generate more than 90% of completely new molecular structures, and these new molecules possessed the properties of CNS drug molecules and synthesizable. In addition, transfer learning was performed on small datasets with specific biological activities to evaluate the potential application of the model for CNS drug optimization. Here, we used drugs against the classical CNS disease target serotonin transporter (SERT) as a fine-tuned dataset and generated a Focused database against the target protein. The potential biological activities of the generated molecules were verified using the physics-based induced fit docking study. The success of this model demonstrates its potential in CNS drug design and optimization, which provides a new impetus for future CNS drug development.
|
Rongpei Gou; Jingyi Yang; Menghan Guo; Yingjun Chen; Weiwei Xue
|
Theoretical and Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-02-22
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d426a39138d231617ecd96/original/cns-mol-gen-a-bidirectional-recurrent-neural-networks-based-generative-model-for-de-novo-central-nervous-system-drug-design.pdf
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657e4ce066c13817295c55e3
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10.26434/chemrxiv-2023-b3k7g
|
N–Cα Bond Cleavage Catalyzed by a Multinuclear Iron Oxygenase from a Divergent Methanobactin-like RiPP Gene Cluster
|
DUF692 multinuclear iron oxygenases (MNIOs) are an emerging family of tailoring enzymes involved in the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs). Three members, MbnB, TglH, and ChrH, have been characterized to date and shown to catalyze unusual and complex transformations. Using a co-occurrence-based bioinformatic search strategy, we recently generated a sequence similarity network of MNIO-RiPP operons that encode one or more MNIOs adjacent to a transporter. The network revealed >1,000 unique gene clusters, evidence of an unexplored biosynthetic landscape. In this work, we assess an MNIO-RiPP cluster from the network that is encoded in proteobacteria and actinobacteria. The cluster, which we have termed mov (for methanobactin-like operon in Vibrio), encodes a 23-residue precursor peptide, two MNIOs, a RiPP recognition element, and a transporter. Using both in vivo and in vitro methods, we show that one MNIO, homologous to MbnB, installs an oxazolone-thioamide at a Thr-Cys dyad in the precursor. Subsequently, the second MNIO catalyzes N–Cα bond cleavage of the penultimate Asn to generate a C-terminally amidated peptide. This transformation expands the reaction scope of the enzyme family, marks the first ex-ample of an MNIO-catalyzed modification that does not involve Cys, and sets the stage for future exploration of other MNIO-RiPPs
|
Vasiliki T. Chioti; Kenzie A. Clark; Mohammad R. Seyedsayamdost
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Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Microbiology
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-12-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657e4ce066c13817295c55e3/original/n-c-bond-cleavage-catalyzed-by-a-multinuclear-iron-oxygenase-from-a-divergent-methanobactin-like-ri-pp-gene-cluster.pdf
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60c75508842e654b00db4290
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10.26434/chemrxiv.14012888.v1
|
Theoretical Studies on the Reactions of Aryl and Hetaryl Thioketones with Nitrilimines
|
<p>Many synthetic routes to constructing biologically-active
heterocyclic compounds are made feasible through the (3 + 2) cycloaddition 32CA
reactions. Due to a large number of
possible combinations of several heteroatoms from either the three-atom
components (TACs) or the ethylene
derivatives, the potential of the 32CA
reactions in heterocyclic syntheses is versatile.
Herein, the 32CA of thiophene-2-carbothialdehyde derivatives
and <i>C</i>,<i>N</i>-disubstituted nitrilimines have been studied through
density functional theory (DFT) calculations at the B3LYP/6-311G(d,p) level of
theory. In the present study, one-step (3 + 2) and two-step (4 + 3) mechanisms
of the addition of the TAC and ethylene derivative have been investigated. In all reactions considered,
the one-step (3 + 2) cycloaddition is preferred over the two-step (4 + 3)
cycloaddition. The TAC chemoselectively adds across the thiocarbonyl group
present in the ethylene derivative in a (3 + 2) fashion to form the corresponding cycloadduct. Analysis
of the electrophilic (
and nucleophilic (
Parr functions at the various reaction centers
in the ethylene
derivative show that the TAC adds
across the atomic centers with the largest Mulliken atomic spin densities, which is in total agreement with the
experimental observation. The selectivities observed in the title reaction are
kinetically controlled.</p>
|
George Baffour Pipim; Ernest Opoku
|
Computational Chemistry and Modeling; Theory - Computational
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-02-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75508842e654b00db4290/original/theoretical-studies-on-the-reactions-of-aryl-and-hetaryl-thioketones-with-nitrilimines.pdf
|
60c74c46702a9b2b0118b610
|
10.26434/chemrxiv.11495811.v7
|
Surface curvature-quantized energy and forcefield in spacetime-warped chemical physics
|
<p><b>Surface curvatures-quantized spacetime’s
energy, forcefield, uncertainty and coupling were introduced consistently for geometrizing
chemical physics generally to support well-established theories, tackle
longstanding problems, predict new chemistry and chemical biology, geometrize Heisenberg’s
Uncertainty, and quantize and generalize Einstein’s spacetime.</b></p>
|
Zheng Tian
|
Interfaces; Physical and Chemical Properties; Quantum Mechanics; Surface
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c46702a9b2b0118b610/original/surface-curvature-quantized-energy-and-forcefield-in-spacetime-warped-chemical-physics.pdf
|
65a00dcbe9ebbb4db9f004b3
|
10.26434/chemrxiv-2024-2mr95-v2
|
Will We Witness Enzymatic or Pd-(Oligo)peptide Catalysis in Suzuki Cross-Coupling Reactions?
|
Despite the development of numerous advanced ligands for Pd-catalyzed Suzuki cross-coupling reactions, the potential of (oligo)peptides serving as ligands has remained largely unexplored. This study demonstrates, via DFT modeling, that (oligo)peptide ligands can exhibit superior activity compared to classic phosphines in these reactions. The utilization of natural amino acids such as Met, SeMet, and His offers strong binding of the Pd center, thereby ensuring substantial stability of the system. The increasing sustainability and economic viability of (oligo)peptide synthesis open new prospects for applying Pd-(oligo)peptide systems as greener catalysts. The feasibility of de novo engineering an artificial Pd-based enzyme for Suzuki cross-coupling is discussed, laying the groundwork for future innovations in catalytic systems.
|
Vlada V. Petrova; Yaroslav V. Solovev; Yuri B. Porozov; Mikhail V. Polynski
|
Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry; Computational Chemistry and Modeling; Homogeneous Catalysis; Transition Metal Complexes (Organomet.)
|
CC BY NC ND 4.0
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CHEMRXIV
|
2024-01-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a00dcbe9ebbb4db9f004b3/original/will-we-witness-enzymatic-or-pd-oligo-peptide-catalysis-in-suzuki-cross-coupling-reactions.pdf
|
635fd1402e0c637a6c437b1b
|
10.26434/chemrxiv-2022-96vc8
|
Synthesis of gem-diboromethyl substituted bicyclo[1.1.1]pentanes and their application in palladium-catalysed cross couplings
|
We describe a general transition-metal free synthesis of gem-diboromethyl substituted bicyclo[1.1.1]pentane (BCP) and other related C(sp3)-rich carbocyclic benzene bioisosteres from their corresponding p-tosylhydrazones. These novel functionalized benzene bioisosteres demonstrated unique reactivities towards palladium-catalyzed C(sp2)-C(sp3) cross couplings. The overall transformation can be applied to relatively complex substrates with potential utility in drug discovery.
|
Xiaoshen Ma; Yuan Jiang
|
Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-11-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635fd1402e0c637a6c437b1b/original/synthesis-of-gem-diboromethyl-substituted-bicyclo-1-1-1-pentanes-and-their-application-in-palladium-catalysed-cross-couplings.pdf
|
63e1abc6f1da89c6837f1209
|
10.26434/chemrxiv-2023-79285
|
Using Density Functional Theory to analyse hydrogen adsorption onto a lithium decorated BeN2 nanolayer
|
Reliable storage of hydrogen is an important area of research. Many different methods of storage are being researched. These novel materials can be used in a pure graphene form, as differently arranged allotropes, or using different substances such as beryllium nitride. However, issues of stability and synthesis are relevant for theoretical arrangements. Inclusion of a metallic atom onto the surface can also alter the adsorption profile. Although graphene-like materials can have a wide range of structures, this review will focus on 2D nanosheets. VASP software was used to analyse the hydrogen adsorption of a lithium decorated BeN2 layer. Stable arrangements demonstrated a 9.7 wt% storage capacity.
|
Ryan Brady
|
Materials Science; Hydrogen Storage Materials
|
CC BY NC ND 4.0
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CHEMRXIV
|
2023-02-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e1abc6f1da89c6837f1209/original/using-density-functional-theory-to-analyse-hydrogen-adsorption-onto-a-lithium-decorated-be-n2-nanolayer.pdf
|
66aa5c4a01103d79c5593cc0
|
10.26434/chemrxiv-2024-sjgg2-v2
|
Absolute Binding Free Energies with OneOPES
|
The calculation of absolute binding free energies (ABFEs) for protein-ligand systems has long been a challenge. Recently, refined force fields and algorithms have improved the quality of ABFE calculations. However, achieving the level of accuracy required to inform drug discovery efforts remains difficult. Here, we present a transferable enhanced sampling strategy to accurately calculate absolute binding free energies using OneOPES with simple geometric collective variables. We tested the strategy on two protein targets, BRD4 and Hsp90, complexed with a total of 17 chemically diverse ligands, including both molecular fragments and drug-like molecules. Our results show that OneOPES accurately predicts protein–ligand binding affinities with a mean unsigned error within 1 kcal mol-1 of experimentally determined free energies, without the need to tailor the collective variables to each system. Furthermore, our strategy effectively samples different ligand binding modes, and consistently matches the experimentally determined structures regardless of the initial protein-ligand configuration. Our results suggest that the proposed OneOPES strategy can be used to inform lead optimization campaigns in drug discovery and to study protein-ligand binding and unbinding mechanisms.
|
Maurice Karrenbrock; Alberto Borsatto; Valerio Rizzi; Dominykas Lukauskis; Simone Aureli; Francesco Luigi Gervasio
|
Theoretical and Computational Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-08-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66aa5c4a01103d79c5593cc0/original/absolute-binding-free-energies-with-one-opes.pdf
|
643e891e83fa35f8f6d8fa3d
|
10.26434/chemrxiv-2023-j1rj6
|
High-throughput screening of cationic lipidoids reveals how molecular conformation affects membrane-targeting antimicrobial activity
|
The search for next-generation antibacterial compounds that overcome the development of resistance can be facilitated by identifying how to target the cell membrane of bacteria. Understanding the key molecular features that enable interactions with lipids and lead to membrane disruption is therefore crucial. Here we employ a library of lipid-like compounds (lipidoids) comprising modular structures with tunable hydrophobic and hydrophilic architecture, to shed light on how the chemical functionality and molecular shape of synthetic amphiphilic compounds determine their activity against bacterial membranes. Synthesized from combinations of 8 different polyamines as headgroups and 13 acrylates as tails, 104 different lipidoids are tested for activity against a model Gram-positive bacterial strain (Bacillus subtilis). Results from the high-throughput antimicrobial screening assay show that lipidoids with the most potent antimicrobial properties (down to 2 μM) have intermediate tail hydrophobicity (i.e. logP values between 3 and 4), and lower headgroup charge density (i.e. longer spacer groups between charged amines). However, the most important factor appeared to be the ability of a lipidoid to self-assemble into an inverse hexagonal liquid crystalline phase, as observed by small angle X-ray scattering (SAXS) analysis. The lipidoids active at lowest concentrations, and which induced the most significant membrane damage during propidium iodide (PI) permeabilization assays, were those that aggregated into highly-curved inverse hexagonal liquid crystal phases. These observations suggest that the introduction of strong curvature stress into the membrane is one way to maximize membrane disruption and lipidoid antimicrobial activity. Lipidoids that demonstrated the ability to furnish this phase consisted of either i) branched or linear headgroups with shorter linear tails, or ii) cyclic headgroups with 4 bulky non-linear tails. On the contrary, lipidoids previously observed to adopt disc-like conformations that pack into bicontinuous cubic phases were significantly less effective against B. subtilis. The discovery of these structure-property relationships demonstrates that it is not simply a balance of hydrophobic and hydrophilic moieties that governs membrane-active antibacterial activity, but also their intrinsic curvature and collective behavior.
|
James Jennings; Dunja Ašćerić; Enrico Semeraro; Karl Lohner; Nermina Malanovic; Georg Pabst
|
Biological and Medicinal Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Drug Discovery and Drug Delivery Systems; Microbiology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643e891e83fa35f8f6d8fa3d/original/high-throughput-screening-of-cationic-lipidoids-reveals-how-molecular-conformation-affects-membrane-targeting-antimicrobial-activity.pdf
|
66edb3fe51558a15ef983ccd
|
10.26434/chemrxiv-2024-5bqml
|
Thermodynamics of Polyethylene Glycol Intrusion in Microporous Water
|
Polymers can be used to augment the properties of microporous materials, affording enhanced processability, stability, and compatibility. Manipulating polymers to target specific properties requires detailed knowledge of how different polymer and microporous materials interact, including the factors that determine whether a given polymer intrudes into framework micropores or remains on the external particle surface in different environments. Here, we report a study of the thermodynamics of polyethylene glycol (PEG) intrusion into a representative hydrophobic zeolite (silicalite-1) and metal–organic framework [ZIF-67; Co(2-methylimidazolate)2] in water, both of which can be formed into colloidally stable aqueous dispersions—termed "microporous water"—with dry, guest-accessible pore networks. Through a combination of O2 carrying capacity measurements and isothermal titration calorimetry (ITC), we establish relationships between PEG intrusion behavior, polymer length, polymer end groups, and the structure of the microporous framework. In particular, we find that PEG intrusion is exothermic for silicalite-1 but endothermic for ZIF-67. Our results provide fundamental insights into polymer intrusion in microporous materials that should inform efforts to design composite solids and fluids with enhanced functionality.
|
Jason Calvin; Christopher DelRe; Daniel Erdosy; Joy Cho; Hyukhun Hong; Jarad Mason
|
Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-09-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66edb3fe51558a15ef983ccd/original/thermodynamics-of-polyethylene-glycol-intrusion-in-microporous-water.pdf
|
60c747a79abda2aa68f8c978
|
10.26434/chemrxiv.11608782.v2
|
Mechanochemical Synthesis of Short DNA Fragments
|
We report the general and rapid synthesis of short DNA fragments of controllable sequence and length using multi-step, one-pot mechanochemical reactions, without bulk solvent or the need to isolate intermediates. We demonstrate, for the first time, the multi-step ball milling synthesis of DNA dimers and trimers via phosphoramidite and H-phosphonate chemistries. The use of mechanochemistry allowed for coupling of phosphoramidite monomers to the 5'-hydroxyl group of nucleosides, iodine/water oxidation of the resulting phosphite triester linkage, and removal of the 5'-dimethoxy (DMTr) protecting group in situ and in good yields (up to 60% over three steps) to produce DNA dimers in one-pot manner. Sulphurization of phosphite triester linkages was possible using elemental sulfur yielding the corresponding phosphorothioate DNA dimers in good yield (up to 80% over two steps). By using H-phosphonate chemistry under milling conditions, it was possible to couple, protect the H-phosphonate linkage, and remove the 5'-DMTr protecting group in situ, enabling an one-pot process with good yields comparable to existing solvent-based procedures (up to 65% over three steps, or ca. 87% per step). This work opens the door to creation of solvent-free methodologies for the assembly of complex DNA and RNA therapeutics.<br />
|
James Thorpe; Daniel O'Reilly; Tomislav Friscic; Masad J. Damha
|
Bioorganic Chemistry; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-01-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747a79abda2aa68f8c978/original/mechanochemical-synthesis-of-short-dna-fragments.pdf
|
60c74adc0f50db4062396b2f
|
10.26434/chemrxiv.12264110.v1
|
Diagnosing Surface Versus Bulk Reactivity for Molecular Catalysis Within Metal-Organic Frameworks Using a Quantitative Kinetic Model
|
<div>
<p>Metal-organic frameworks (MOFs) are
becoming increasingly popular as heterogenous support matrices for molecular
catalysts. Given that reactants, or potentially holes/electrons, need to
diffuse into the porous framework as the reaction proceeds, the reaction can
possibly take place within the bulk of the particle or be confined to a thin
layer at the surface due to transport limitations. Herein, a simple
steady-state reaction-diffusion kinetic model is developed to diagnose these
two mutually exclusive behaviors in MOF-based systems. The oxygen evolution
reaction (OER) driven by a chemical oxidant is presented as an example
mechanism. Quantitative metrics for assigning either bulk or surface reactivity
are delineated over a wide variety of conditions, and numerical simulations are
employed to verify these results. For each case, expressions for the turnover frequency
(TOF) are outlined, and it is shown that surface reactivity can influence
measured TOFs. Importantly, this report shows how to transition from surface to
bulk reactivity and thus identifies which experimental parameters to target for
optimizing the efficiency of MOF-based molecular catalyst systems.</p>
</div>
<br />
|
Ben A Johnson; Sascha Ott
|
Electrocatalysis; Heterogeneous Catalysis; Chemical Kinetics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74adc0f50db4062396b2f/original/diagnosing-surface-versus-bulk-reactivity-for-molecular-catalysis-within-metal-organic-frameworks-using-a-quantitative-kinetic-model.pdf
|
66277dba91aefa6ce12d0a56
|
10.26434/chemrxiv-2024-020gt
|
Does Machine Learning Learn the Physics for Pose Ranking of Fragment-Sized Ligands? A Comparison between Machine Learning and Physics-based Methods
|
In fragment-based drug discovery using in silico methods, predicting the binding pose is a crucial step to ensure the accurate prediction of binding affinities. Recent studies have focused on the challenges of docking fragments compared to drug-like molecules, with findings suggesting that more sophisticated scoring functions can improve the accuracy of identifying correct binding poses. In this work, we conducted extensive ABFEP (Alchemical Binding Free Energy Perturbation) calculations on a fragment benchmarking dataset to evaluate the accuracy of ABFEP in ranking binding poses of fragments and compared ABFEP rescoring with Vina and two machine learning (ML)-based scoring functions. Indeed, ABFEP, which has a theoretically more rigorous scoring function, significantly outperforms Vina. In-depth comparison between ML-based scoring functions and ABFEP shows that ML-based scoring functions behave similarly to ABFEP on the prediction accuracy and failed cases, indicating that ML is capable of increasing the prediction accuracy over traditional scoring functions through learning the underlying physics rather than memorizing the coordinates in the training data.
|
xiao wan; Bai Xue; Michael Bellucci; Zhixiong Lin; Mingjun Yang; Junjie Zou
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66277dba91aefa6ce12d0a56/original/does-machine-learning-learn-the-physics-for-pose-ranking-of-fragment-sized-ligands-a-comparison-between-machine-learning-and-physics-based-methods.pdf
|
6556f32a6e0ec7777f1c66fb
|
10.26434/chemrxiv-2023-5510r-v3
|
Investigating the Non-Electrostatic Component of Substrate Positioning Dynamics
|
Substrate positioning dynamics (SPD) orients the substrate to reactive conformations in the active site, accelerating enzymatic reactions. However, it remains unknown whether SPD effects originate primarily from electrostatic perturbation inside the enzyme or can independently mediate catalysis with a significant non-electrostatic component. Here we investigated how the non-electrostatic component of SPD affects transition state stabilization. Using high-throughput enzyme modeling, we selected Kemp eliminase variants with similar electrostatics inside the enzyme but significantly different SPD. The kinetic parameters of these selected mutants were experimentally characterized. We observed a valley-shaped, two-segment linear correlation between the TS stabilization free energy (converted from kinetic parameters) and an index used to quantify SPD. Favorable SPD was observed for a distal mutant R154W, leading to the lowest activation free energy among the mutants tested. R154W involves an increased proportion of reactive conformations. These results indicate the contribution of the non-electrostatic component of SPD to mediating enzyme catalytic efficiency.
|
Yaoyukun Jiang; Ning Ding; Qianzhen Shao; Sebastian Stull; Zihao Cheng; Zhongyue Yang
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Biochemistry; Computational Chemistry and Modeling; Biocatalysis
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-11-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6556f32a6e0ec7777f1c66fb/original/investigating-the-non-electrostatic-component-of-substrate-positioning-dynamics.pdf
|
60c73cc9f96a006c8b285ca4
|
10.26434/chemrxiv.14750823.v1
|
A General Approach to 2,2-Disubstituted Indoxyls: Total Synthesis of Brevianamide A and Trigonoliimine C
|
The indoxyl unit is a common structural motif in alkaloid natural products and bioactive compounds. Here, we report a general method that transforms readily available 2-substituted indoles into 2,2-disubstituted indoxyls via nucleophile coupling with a 2-alkoxyindoxyl intermediate and showcase its utility in short total syntheses of the alkaloids brevianamide A (7 steps) and trigonoliimine C (6 steps). The developed method is operationally simple and demonstrates broad scope in terms of nucleophile identity and indole substitution, tolerating 2-alkyl substituents and free indole N–H groups, elements beyond the scope of most prior approaches. Spirocyclic indoxyl products are also accessible via intramolecular nucleophilic trapping.
|
Fan Xu; Myles Smith
|
Natural Products; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-06-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc9f96a006c8b285ca4/original/a-general-approach-to-2-2-disubstituted-indoxyls-total-synthesis-of-brevianamide-a-and-trigonoliimine-c.pdf
|
6727ddc8f9980725cffc6f36
|
10.26434/chemrxiv-2024-kbdg6-v2
|
Simultaneous use of bacteriophages and UV irradiation for targeted control of bacterial pathogens using biocompatible food colorant brilliant blue FCF for selective protection of virions
|
Compared to the standard methods for treating bacterial diseases, bacteriophages are eco-friendly and chemical-free. Exposure to UV or sunlight hampers the efficacy of phage-based approaches. This is crucial when phages are i) exposed to sunlight (e.g., in agriculture) or ii) are to be used simultaneously with UV for sterilization. Here, we develop a method utilizing a food dye, brilliant blue FCF (BB), that selectively stabilizes bacteriophages against exposure to UV irradiation without protecting Gram-negative bacteria. Simultaneous action of BB-stabilized bacteriophages and UV allow for the removal of up to 99.99% of bacteria within only 30 to 60 minutes. We explain the mechanism of protection, which requires selective binding of BB to the capsid. We demonstrated the method's applicability in combating biofouling of membranes and food sterilization. We envision using the developed approach against biofouling in industrial processes, in agriculture (e.g., against Erwinia amylovora, Pseudomonas syringae, and Xylella fastidiosa), and the food industry.
|
Mateusz Wdowiak; Aneta Magiera; Magdalena Tomczyńska; Witold Adamkiewicz; Francesco Stellacci; Jan Paczesny
|
Biological and Medicinal Chemistry; Bioengineering and Biotechnology; Chemical Biology; Microbiology
|
CC BY 4.0
|
CHEMRXIV
|
2024-11-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6727ddc8f9980725cffc6f36/original/simultaneous-use-of-bacteriophages-and-uv-irradiation-for-targeted-control-of-bacterial-pathogens-using-biocompatible-food-colorant-brilliant-blue-fcf-for-selective-protection-of-virions.pdf
|
66f9f118cec5d6c142a04477
|
10.26434/chemrxiv-2024-5k2b8-v2
|
Substituent and heteroatom effects on parallel-displaced pi-stacking: Further evidence that short-range pi-pi interactions are not under electrostatic control
|
Stacking interactions are a recurring motif in supramolecular chemistry and biochemistry, where a persistent theme is a preference for parallel-displaced aromatic rings over face-to-face pi-stacking. The Hunter-Sanders model purports to explain this preference in terms of quadrupolar electrostatics but that interpretation is inconsistent with accurate quantum-mechanical calculations. Here, we apply symmetry-adapted perturbation theory to dimers composed of substituted benzene and to dimers of heterocycles including pyridine, pyrimidine, triazine, and thiophene. These systems display a wide range of electrostatic interactions, allowing us to investigate the generality of an alternative explanation for offset pi-stacking in which this phenomenon is driven by competition between Pauli repulsion and dispersion, not by electrostatics. Profiles of energy components along cofacial slip-stacking coordinates support this "van der Waals" model, even in cases where dipolar forces are significant. We find no evidence to support continued invocation of the Hunter-Sanders or quadrupolar electrostatics model. Our results suggest that chemical substitutions that primarily affect electrostatic interactions are unlikely to alter the short-range driving forces that contribute to offset-stacking. This has implications for rational design of soft materials and other supramolecular architectures.
|
Brandon Schramm; Montgomery Gray; John Herbert
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Supramolecular Chemistry (Org.)
|
CC BY 4.0
|
CHEMRXIV
|
2024-09-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f9f118cec5d6c142a04477/original/substituent-and-heteroatom-effects-on-parallel-displaced-pi-stacking-further-evidence-that-short-range-pi-pi-interactions-are-not-under-electrostatic-control.pdf
|
60c74eba4c8919bc02ad3ab0
|
10.26434/chemrxiv.12003186.v2
|
Vapour Pressure Isotope Effect on Evaporation from Pure Organic Phases - a PIMD Approach
|
<p></p><p>Very
often in order to understand physical and chemical processes taking place among
several phases fractionation of naturally abundant isotopes is monitored. Its measurement can
be accompanied by theoretical determination to provide a more insightful interpretation of observed
phenomena. Predictions are challenging due to the complexity of the effects involved in fractionation such as solvent
effects and non-covalent interactions governing the behavior of the system
which results in the necessity of using large models of those systems. This is
sometimes a bottleneck and limits the theoretical description to only a few methods.<br />
In this work vapour pressure isotope effects on evaporation from various
organic solvents (ethanol, bromobenzene, dibromomethane, and trichloromethane)
in the pure phase are estimated by combining force field or self-consistent charge density-functional tight-binding (SCC-DFTB)
atomistic simulations with path integral principle. Furthermore, the recently developed Suzuki-Chin path
integral is tested. In general, isotope effects are predicted qualitatively for most of the cases, however, the
distinction between position-specific isotope effects observed for ethanol was only reproduced by SCC-DFTB, which
indicates the importance of using non-harmonic bond approximations.<br />
Energy decomposition analysis performed using the symmetry-adapted perturbation
theory (SAPT) revealed sometimes quite substantial differences in interaction energy depending on
whether the studied system was treated classically or quantum mechanically. Those observed differences might
be the source of different magnitudes of isotope effects predicted using these two different levels of
theory which is of special importance for the systems governed by non-covalent interactions.</p><br /><p></p>
|
Luis Vasquez; Agnieszka Dybala-Defratyka
|
Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74eba4c8919bc02ad3ab0/original/vapour-pressure-isotope-effect-on-evaporation-from-pure-organic-phases-a-pimd-approach.pdf
|
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