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60c7422e842e65ff15db2020 | 10.26434/chemrxiv.7685654.v3 | Polymer supported carbon for safe and effective remediation of PFOA and PFOS-contaminated water | <div>
<div>
<div>
<p>Powdered activated carbon (PAC) is an economical sorbent for removing micropollutants from water,
but it generates hazardous dust that is flammable and a respiration hazard. Additionally, the fine particles of PAC can
cake and block filters and membranes, complicating its use in continuous processes. In this study, we present a sulfur
polymer support for PAC that overcomes these problems. The blend of the sulfur polymer and PAC generates low dust
and it does not block filters. The utility of the sorbent is demonstrated in the remediation of water contaminated with
perfluorinated alkyl substances (PFASs)—persistent micropollutants that currently threaten water safety worldwide.
Fundamental discoveries of PFAS self-assembly are reported, as well as testing on field samples. </p>
</div>
</div>
</div> | Nicholas Lundquist; Martin Sweetman; Kymberley Scroggie; Max Worthington; Louisa Esdaile; Salah Alboaiji; Sally Plush; John Hayball; Justin Chalker | Hydrology and Water Chemistry; Polymers | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7422e842e65ff15db2020/original/polymer-supported-carbon-for-safe-and-effective-remediation-of-pfoa-and-pfos-contaminated-water.pdf |
63238ba5ba8a6d1fe6509a48 | 10.26434/chemrxiv-2022-ql75g | A Sulfoxide Reagent for One-Pot, Three-Component Syntheses of Sulfoxides and Sulfinamides
| Sulfoxides and sulfinamides represent versatile sulfur functional groups found in ligands, chiral auxiliaries, and bioactive molecules. However, canonical two-component syntheses relying on substrates with a preinstalled C–S bond impede efficient and modular access to these sulfur motifs. Herein is presented the application of an easily prepared, bench stable sulfoxide reagent for one-pot, three-component syntheses of sulfoxides and sulfinamides. The sulfoxide reagent donates the SO unit upon the reaction with a Grignard reagent (RMgX) as a sulfenate anion (RSO–). While subsequent trapping reactions of this key intermediate with carbon electrophiles provide sulfoxides, a range of tertiary, secondary, and primary sulfinamides can be prepared by substitution reactions with electrophilic amines. The syntheses of sulfinamide analogs of amide- and sulfonamide-containing drugs illustrate the utility of the method for the rapid preparation of medicinally relevant molecules. | Fumito Saito | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63238ba5ba8a6d1fe6509a48/original/a-sulfoxide-reagent-for-one-pot-three-component-syntheses-of-sulfoxides-and-sulfinamides.pdf |
60db063d01b3e07223ea9ea9 | 10.26434/chemrxiv-2021-w18g2 | Solvation of anthraquinone and Tempo redox-active species in acetonitrile using a polarizable force field | Redox active molecules are of interest in many fields such as medicine, catalysis or energy storage. In particular, in supercapacitor applications, they can be grafted to ionic liquids to form so-called biredox ionic liquids. To completely understand the structural and transport properties of such systems, an insight at the molecular scale is often required but few force fields are developed ad hoc for these molecules. Moreover, they do not include polarization effects, which can lead to inaccurate solvation and dynamical properties. In this work, we developed polarizable force fields for redox-active species anthraquinone (AQ) and 2,2,6,6-tetra-methylpiperidinyl-1-oxyl (TEMPO) in their oxidized and reduced states, as well as for acetonitrile. We validate structural properties of AQ, AQ$^{\bullet-}$, AQ$^{2-}$, TEMPO$^{\bullet}$ and TEMPO$^{+}$ in acetonitrile against density functional theory-based molecular dynamics simulations and we study the solvation of these redox molecules in acetonitrile. This work is a first step toward the characterization of the role played by AQ and TEMPO in electrochemical and catalytic devices. | Roxanne Berthin; Alessandra Serva; Kyle Reeves; Esther Heid; Christian Schroeder; Mathieu Salanne | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Electrochemistry - Mechanisms, Theory & Study; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60db063d01b3e07223ea9ea9/original/solvation-of-anthraquinone-and-tempo-redox-active-species-in-acetonitrile-using-a-polarizable-force-field.pdf |
642b2df9db1a20696e781809 | 10.26434/chemrxiv-2023-b9mtd | Solvation of furfural at metal|water interfaces: Implications for aqueous phase hydrogenation reactions | Metal|water interfaces are central to understanding aqueous phase heterogeneous catalytic processes. However, it is challenging to model the interactions between metal surfaces, adsorbates and the solvent water molecules at the interface. Herein, we use ab-initio molecular dynamics (AIMD) simulations to study the adsorption of furfural, a platform biomass chemical on several catalytically relevant metal|water interfaces (Pt, Rh, Pd, Cu and Au) at low coverages. We find that furfural adsorption is destabilized on all the metal|water interfaces compared to the metal|vacuum interfaces considered in this work. This destabilization is a result of the energetic penalty associated with the displacement of water molecules near the surface upon adsorption of furfural. This is evidenced by a linear correlation between solvation energy and the change in surface water coverage. To predict solvation energies without the need for computationally expensive AIMD simulations, we demonstrate OH binding energy in vacuum to be a good descriptor to estimate the solvation energies of furfural on different metal|water interfaces. Using microkinetic modeling, we further explain the origin of the activity for furfural hydrogenation on intrinsically strong-binding metals, such as Rh and Pt, under aqueous conditions, i.e., the endothermic solvation energies for furfural adsorption helps prevent surface poisoning. Our work sheds light on the development of active aqueous-phase catalytic systems via rationally tuning the solvation energies of reaction intermediates. | Sihang Liu; Sudarshan Vijay; Mianle Xu; Ang Cao; Hector Prats; Georg Kastlunger; Hendrik Heenen; Nitish Govindarajan | Theoretical and Computational Chemistry; Catalysis; Theory - Computational; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642b2df9db1a20696e781809/original/solvation-of-furfural-at-metal-water-interfaces-implications-for-aqueous-phase-hydrogenation-reactions.pdf |
6503119c99918fe537f1121d | 10.26434/chemrxiv-2023-dwd6b | Proton-exchange membrane fuel cell design for in-situ depth-sensitive X-ray absorption spectroscopy | We have built a proton exchange membrane hydrogen fuel cell optimized for angle-resolved X-ray absorption spectroscopy. This cell allows in-situ fluorescence measurements during electrochemical operation with minimal trade-offs in cell performance while reaching automotive current densities. The fluorescence signal can be collected from wide angles to extract depth information from the probed atomic species such as Pt, Co, and Ni, crucial to highly efficient FC. This cell is designed to assess the connection between the ionic drag/diffusion and the performance loss by following the real-time movement of the species through the membrane electrode assembly. | Michal Ronovský; Mila Myllymaki; Yves Watier; Pieter Glatzel; Peter Strasser; Alex Martinez Bonastre; Jakub Drnec | Materials Science; Catalysis; Energy; Alloys; Electrocatalysis; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6503119c99918fe537f1121d/original/proton-exchange-membrane-fuel-cell-design-for-in-situ-depth-sensitive-x-ray-absorption-spectroscopy.pdf |
622632e457a9d2d9ff764de4 | 10.26434/chemrxiv-2022-z1sk3 | The role of asymmetry on the photoisomerization of dithienylethene molecule photoswitch | Dithienylethene (DTE) molecular photoswitches have shown to be excellent candidates in the design of efficient optoelectronic devices, due to their high photoisomerization quantum yield (QY), for which symmetry is suggested to play a crucial role. Here, we present a theoretical study on the photochemistry of a non-symmetric dithienylethene photoswitch, with a special emphasis on the effect of asymmetric substitution on the photocyclization and photoreversion mechanisms. We used the Spin-Flip Time Dependent Density Functional Theory (SF-TDDFT) method to locate and characterize the main structures (conical intersections and minima) of the ground state and the first two excited states, S1 and S2, along the ring opening/closure reaction coordinate of the photocyclization
and photoreversion processes, and to identify the important coordinates governing the radiationless decay pathways. Our results suggest that while the main features that characterize the photoisomerization of symmetric DTEs are also present for the photoisomerization of the non-symmetric DTE, the lower energy barrier on S1 along the cycloreversion reaction speaks in favor of a more efficient and therefore a higher cycloreversion QY for the non-symmetric DTEs, making them a better candidate for molecular optoelectronic devices than their symmetric counterparts. | Edison Salazar; Suzanne Reinink; Shirin Faraji | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622632e457a9d2d9ff764de4/original/the-role-of-asymmetry-on-the-photoisomerization-of-dithienylethene-molecule-photoswitch.pdf |
60c7477e469df44663f4381a | 10.26434/chemrxiv.10084715.v2 | The Reaction of Sulfur Dioxide Radical Cation with Hydrogen and Its Relevance in Solar Geoengineering Models | <p>In
recent years solar geoengineering has been proposed as
a
promising strategy to contrast global warming induced by anthropogenic CO<sub>2</sub>
emissions.
These technologies design to inject in the stratosphere
massive
amounts of molecular species, which can act as precursors for aerosol
formation able to partially reflect sunlight. SO<sub>2</sub>
is
one of these species. Since
in
the atmosphere
several
natural ionization sources, such as cosmic rays and corona discharge,
are active, we have considered that SO<sub>2</sub><sup>+</sup>
ions
can be formed in the stratosphere in a significant amount
after
being injected by balloons or
aircrafts. The
SO<sub>2</sub><sup>+
</sup>chemistry
could play a role in the dynamics of
aerosol formation as a cooling agent. We
have studied theoretically and experimentally
the
reaction of SO<sub>2</sub><sup>+</sup>,
produced by tunable synchrotron radiation, with H<sub>2</sub>
leading
to HSO<sub>2</sub><sup>+</sup>
and
H, the latter being
involved
in the ozone depletion by producing O<sub>2
</sub>and
OH. This is an ionic possible alternative
to OH formation during the nighttime, when
the common sunlight process of OH generation cannot
occur. In
order to explain the experimental reactivity we propose a new
non-thermal version of the Variational Transition State Theory. We
provide
analytic
expressions
for
the
temperature
dependent
rate
coefficients, which
should
be tested in
atmospheric kinetic models to fully explore the stratospheric solar
geoengineering strategies.</p> | Mauro Satta; Antonella Cartoni; Daniele Catone; Mattea Carmen Castrovilli; Paola Bolognesi; Nicola Zema; Lorenzo Avaldi | Atmospheric Chemistry; Computational Chemistry and Modeling; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7477e469df44663f4381a/original/the-reaction-of-sulfur-dioxide-radical-cation-with-hydrogen-and-its-relevance-in-solar-geoengineering-models.pdf |
6172f639913a741ff6650772 | 10.26434/chemrxiv-2021-03nzq | Efficient Synthesis and Functionalization of 3-Bromo Naphtho[2,3b]thiophene | Naphtho[2,3b]thiophene is a linear sulfur containing polycyclic aromatic hydrocarbon. Naphtho[2,3b]thiophene and its derivatives are commonly accessed by a Bradsher cyclization. Synthesis of the Bradsher cyclization substrate typically requires harsh conditions, including several oxidation state changes. Here we report an improved, multigram synthesis of 3-bromonaphtho[2,3b]thiophene, exploiting a copper-catalyzed cross coupling to prepare the Bradsher substrate in 3 steps from commercial materials while minimizing redox reactions. Modification of the naphthothiophene scaffold in the 3-position has not previously been reported. In this work, the 3-bromonaphthothiophene is further functionalized via lithium-halogen exchange, with the key finding being a specific order of addition in lithiation is required to avoid undesired rearrangement reactions. A small yet versatile set of derivatives, including a naphthothiophene-containing chiral amine are prepared. | Emily Burke; Erin Welsh; Katherine Robertson; Alexander Speed | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6172f639913a741ff6650772/original/efficient-synthesis-and-functionalization-of-3-bromo-naphtho-2-3b-thiophene.pdf |
60c74aadee301c6420c79ca3 | 10.26434/chemrxiv.12238967.v1 | Clickable Azide-Functionalized Bromo-Aryl-Aldehydes – Synthesis and Photophysical Characterization | In this article we describe the functionalization of bromo aryl aldehyde-based fluorophores with azide functionalities, their Cu-catalyzed attachment to alkynes and the effect of these functionalizations on their emission properties.<br /> | Dominik Göbel; Marius Friedrich; Enno Lork; Boris Nachtsheim | Organic Compounds and Functional Groups; Dyes and Chromophores | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74aadee301c6420c79ca3/original/clickable-azide-functionalized-bromo-aryl-aldehydes-synthesis-and-photophysical-characterization.pdf |
60c75217ee301cb9f6c7ab4c | 10.26434/chemrxiv.13244906.v1 | Electron Transfer Limitation in Carbon Dioxide Reduction Revealed by Data-Driven Tafel Analysis | Carbon dioxide (CO<sub>2</sub>) recycling holds
promise to mitigate anthropogenic emissions and to increase the sustainability of
many chemical and fuel production processes. Despite marked advances in catalyst
activity and selectivity at laboratory scale, fundamental understanding of the
electrocatalytic reduction of CO<sub>2</sub> remains limited, resulting in
great uncertainty when extrapolating data to industrially relevant reaction
rates. Importantly, the predominant models apply linear Tafel extrapolation,
which drastically overpredicts the current density at large overpotentials. Researchers
have posited several models to explain the curvature in Tafel behavior for CO<sub>2</sub>
reduction catalysis. Here we compare the ability of select models using Bayesian
inference to explain curvature in Tafel behavior within the context of CO<sub>2</sub>
reduction to CO catalyzed by gold surfaces. By harvesting Tafel data on gold
surfaces from multiple literature sources in a variety of reactor
configurations, we identify three important features common to the aggregate
data on Au-mediated CO<sub>2</sub> reduction: (1) curvature in the Tafel plot at
high overpotentials is only partly caused by mass transfer limitations; (2) the
Marcus-Hush-Chidsey model for rate-limiting single-electron transfer kinetics provides
the best fit to the data of the models tested; and finally, (3) the highly
varied data collapse onto a single curve governed by the maximum predicted
current in the electron-transfer-limited model. This analysis sets a foundation
for determining more accurate activity-driving force relationships for CO<sub>2</sub>
reduction on electrocatalytic surfaces, both improving the quality of
system-level analyses and motivating further research into the underlying mechanisms
of CO<sub>2</sub> reduction catalysis. | Steven M. Brown; Michael Orella; Yung Wei Hsiao; Yuriy Román-Leshkov; Yogesh Surendranath; Martin Z. Bazant; Fikile Brushett | Electrocatalysis; Heterogeneous Catalysis; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75217ee301cb9f6c7ab4c/original/electron-transfer-limitation-in-carbon-dioxide-reduction-revealed-by-data-driven-tafel-analysis.pdf |
60c750a0ee301c1afcc7a8d5 | 10.26434/chemrxiv.13063916.v1 | Charge-Transfer Intermediates in the Electrochemical Doping Mechanism of Conjugated Polymers | In this work, we address the nature of electrochemically induced charged states in conjugated polymers, their evolution as a function of electrochemical potential, and their coupling to their local environment by means of transient absorption and Raman spectroscopies synergistically performed in situ throughout the electrochemical doping process. In particular, we investigate the fundamental mechanism of electrochemical doping in an oligoether-functionalized 3,4-propylenedioxythiophene (ProDOT) copolymer. The changes embedded in both linear and transient absorption features allow us to identify a precursor electronic state with charge-transfer (CT) character that precedes polaron formation and bulk electronic conductivity. This state is shown to contribute to the ultrafast quenching of both neutral molecular excitations and polarons. Raman spectra relate the electronic transition of this precursor state predominantly to the C<sub>β</sub> -C<sub>β</sub> stretching mode of the thiophene heterocycle. We characterize the coupling of the CT-like state with primary excitons and electrochemically induced charge separated states, providing insight into the energetic landscape of a heterogeneous polymer-electrolyte system and demonstrate how such coupling depends on environmental parameters, such as polymer structure, electrolyte composition, and environmental polarity.<br /> | Ilaria Bargigia; Lisa R. Savagian; Anna M. Österholm; John R. Reynolds; Carlos Silva | Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750a0ee301c1afcc7a8d5/original/charge-transfer-intermediates-in-the-electrochemical-doping-mechanism-of-conjugated-polymers.pdf |
63d36c041fe14210ba5b5220 | 10.26434/chemrxiv-2023-mxhgx | Quantifying the Influence of C-H···pi Interactions on Non-Aqueous Electrolyte Solubility | For redox active organic molecules (ROMs) used in grid-scale energy storage applications, such as redox flow batteries, solubility is an essential physicochemical property. Specifically, solubility is directly proportional to the volumetric energy density of an energy storage device and thus affects its corresponding spatial footprint. Recently pyridiniums have been introduced as a class of ROMs with high persistence in multiple redox states at low potentials. Unfortunately, solubility of pyridinium salts in non-aqueous media remains low (generally less than 1 M), and relatively few practical molecular design strategies exist for generalized improvement of ROM solubility. Herein, we convey the extent to which discrete, attractive interactions between C-H groups and the p-electrons of an aromatic ring (C-H···pi interactions) can describe the solubility of N-substituted pyridinium salts in a non-aqueous solvent (acetonitrile). We find a direct correlation between the extent of crystalline C-H···pi interactions for each pyridinium salt and its solubility in acetonitrile (R2 = 0.93, solubility range = 0.3 – 2.1 M). The presence of C-H···pi interactions reveals how large disparities in solubility between (e.g.) N-(p-tolyl)-4-phenyl-2,6-dimethylpyridinium (0.32 ± 0.03 M) and N-(p-tolyl)-4-(p-tolyl)-2,6-dimethylpyridinium (1.06 ± 0.03 M) tetrafluoroborate may arise despite differing in structure by only three atoms. The correlation presented in this work highlights a surprising consequence of disrupting strong electrostatic interactions with weak dispersion interactions, showing how minimal structural change can have dramatic effects on ROM solubility. | Sharmila Samaroo; Charley Hengesbach; Chase Bruggeman; Nunzio Carducci; Lincoln Mtemeri; Thomas Guarr; David Hickey | Organic Chemistry; Analytical Chemistry; Energy; Organic Compounds and Functional Groups; Physical Organic Chemistry; Energy Storage | CC BY NC 4.0 | CHEMRXIV | 2023-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d36c041fe14210ba5b5220/original/quantifying-the-influence-of-c-h-pi-interactions-on-non-aqueous-electrolyte-solubility.pdf |
60c754cfbb8c1af6f73dc2ed | 10.26434/chemrxiv.13729063.v1 | Size Isn’t Everything - Compositional Variation in Hybrid Organic-Inorganic Lead Halide Perovskites: Kinetically- versus Thermodynamically-controlled Synthesis | <p>The formation and study of a partial solid solution <a></a><a>Az<sub>1-<i>x</i></sub>FA<i><sub>x</sub></i>PbBr<sub>3</sub></a>, using ‘similar’ sized cations azetidinium (Az<sup>+</sup>) and formamidinium (FA<sup>+</sup>), was explored via mechanosynthesis and precipitation synthesis. The composition and lattice parameters of samples from both syntheses were analysed by <sup>1</sup>H NMR and Rietveld refinement of the powder X-ray diffraction. A clear mismatch in the composition of the perovskite was found between the precipitated samples and the corresponding solutions. Such a mismatch was not observed for samples obtained via mechanosynthesis. The discrepancy suggests products are kinetically-controlled during precipitation, compared to thermodynamically-controlled mechanosynthesis. Furthermore, the cell volume as a function of composition in both 6H (Az-rich) and 3C (FA-rich) solid solutions suggests that FA<sup>+</sup> is actually smaller than Az<sup>+</sup>, contradicting the literature. In the 3C (Az-poor) solid solutions, the extent of Az<sub>1-<i>x</i></sub>FA<i><sub>x</sub></i>PbBr<sub>3 </sub>is unexpectedly smaller than Az<sub>1-<i>x</i></sub>MA<i><sub>x</sub></i>PbBr<sub>3</sub>, again in contradiction to the expectation based on the reported cation sizes. These results indicate that other factors, as yet unidentified, must also contribute to the solid solution formation of organic-inorganic hybrid perovskites, not simply the relative sizes of the A-site cations.</p> | Jiyu Tian; Eli Zysman-Colman; Finlay Morrison | Hybrid Organic-Inorganic Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754cfbb8c1af6f73dc2ed/original/size-isn-t-everything-compositional-variation-in-hybrid-organic-inorganic-lead-halide-perovskites-kinetically-versus-thermodynamically-controlled-synthesis.pdf |
60c74706469df45edaf43775 | 10.26434/chemrxiv.11483178.v1 | Thermodynamic Insights of Base Flipping in TNA Duplex: Force Fields, Salt Concentrations, and Free Energy Simulation Methods | <p>Threofuranosyl nucleic
acid (TNA) is an analogue of DNA. Its inter-nucleotide linkages are shifted
from the wild-type 5'-to-3' one to the 3'-to-2' one. As a result, the number of
covalent bonds between consecutive phosphates is reduced from 6 to 5. This
leads to higher chemical stability, less reactive groups, and lower
conformational flexibility. Experimental observations indicate that the
interaction network is perturbed at the minimal level and the thermodynamic
stability of the duplex is unaltered upon the TNA mutation. Whether
computational modelling could reproduce this result will be studied in the base
flipping of the middle T (DNA) residue or its T-to-TFT mutation (TNA). We
applied the equilibrium free energy simulation and the nonequilibrium
stratification method proposed previously in the base flipping case, proving
the applicability of alternative free energy simulation protocols. As the force
field is the main accuracy-limiting factor when converged phase space sampling
is obtained, we benchmarked three popular AMBER force fields for nucleotides.
The last-generation force fields include bsc1 and OL15, both of which perform
similarly in reproducing the structures near the crystal conformation in
previous benchmark studies. Our results indicate that all these three force
fields provide similar descriptions of the base-paired state. However, with
free energy simulation constructing the free energy profiles along the
conformational change pathway, high-energy regions are explored and these three
force fields behave differently. The bsc1 force field is found to perform best
in reproducing the similarity of stabilities of DNA and TNA duplexes. The free
energy barrier of base flipping under the OL15 force field is lowered modestly
in TNA, and thus this force field is also usable. However, the bsc0 force field
provides wrong results. The TNA duplex is significantly less stable than the DNA
duplex. Therefore, the bsc0 force field is not recommended in any application
in modern nucleotide simulations. The salt concentration in nucleotide
simulations is another factor influencing the thermodynamics of the system.
Previous reports conclude that the net-neutral and excess-salt simulations
provide similar results. However, the simulation method limits the phase space
region explored in previous computational modelling. Our free energy simulation
explores high-energy regions, where the excess salt does affect the
thermodynamic stability. The free energy barrier along the base flipping pathway
is generally elevated upon the addition of excess salts, but the relative
height of the free energy barriers in DNA and TNA duplexes is not significantly
changed. This phenomenon emphasizes the importance of adding sufficient salts
to reproduce the experimental condition. </p> | Zhaoxi Sun; John Z. H. Zhang | Bioinformatics and Computational Biology; Biophysics; Computational Chemistry and Modeling; Theory - Computational; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74706469df45edaf43775/original/thermodynamic-insights-of-base-flipping-in-tna-duplex-force-fields-salt-concentrations-and-free-energy-simulation-methods.pdf |
634de6a12a70913a4d6055cd | 10.26434/chemrxiv-2022-c585m | Machine Learning Identification of Active Sites in Graphite-Conjugated Catalysts | Graphite-conjugated catalysts (GCCs) are a promising class of materials that combine many of the advantages of heterogenous and homogeneous catalysts. In particular, GCCs containing an aryl-pyridinium active site appear to be effective nonmetal catalysts for the oxygen reduction reaction (ORR). In this study, we analyzed both structural and electronic properties of a dataset of molecules containing nitrogen atoms embedded in aromatic molecules in order to understand which properties enable a particular site to bind O2, which is a necessary step for the initiation of ORR. We found that carbon atoms ortho or para to nitrogen and at the edge of aromatic systems are especially likely to be active. Using both structural and electronic features to describe the individual atoms in each catalyst, we trained machine learning models capable of identifying catalyst active sites. Although permutation importance of the features used to train these models indicates that several key electronic features have the greatest impact on model performance, the model trained only on structural features still proved effective in simulated catalyst discovery scenarios where the objective is affected more by false positives than false negatives. | Kunal Lodaya; Nathan Ricke; Kelly Chen; Troy Van Voorhis | Theoretical and Computational Chemistry; Catalysis; Energy; Computational Chemistry and Modeling; Machine Learning; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2022-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634de6a12a70913a4d6055cd/original/machine-learning-identification-of-active-sites-in-graphite-conjugated-catalysts.pdf |
62979af480f81cd93798699a | 10.26434/chemrxiv-2022-0cfdj | Stabilized lignin nanoparticles for templated assembly of silver nanoparticles and covalent functionalization in dispersion state | Spherical lignin nanoparticles are emerging biobased nanomaterials, but instability and dissolution in organic solvents and aqueous alkali restricts their applicability. Here we report synthesis of hydroxymethylated lignin nanoparticles and their hydrothermal curing to stabilize the particles by internal crosslinking reactions. These colloidally stable particles contain a high bio-based content of 97% with a tunable particle size distribution and structural stability in aqueous media (pH 3 to 12) and organic solvents such as acetone, ethanol, dimethylformamide, and tetrahydrofuran. We demonstrate that the free phenolic hydroxyl groups that are preserved in the cured particles function as efficient reducing sites for silver ions, giving rise to hybrid lignin-silver nanoparticles that can be used for quick and facile sensing of hydrogen peroxide. The stabilized lignin particles can also be directly modified using base-catalyzed reactions such as the ring-opening of cationic epoxides that renders the particles with pH-dependent agglomeration and redispersion properties. Combining scalable synthesis, solvent-stability, and reusability these new class of lignin nanoparticles pave the way for a new era in circular bio-based nanomaterials. | Mohammad Morsali; Adrian Moreno; Andriana Loukovitou; Ievgen Pylypchuk; Mika Sipponen | Polymer Science; Nanoscience; Biopolymers; Cellulosic materials; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62979af480f81cd93798699a/original/stabilized-lignin-nanoparticles-for-templated-assembly-of-silver-nanoparticles-and-covalent-functionalization-in-dispersion-state.pdf |
61e15cfa6afbefe57f6438d4 | 10.26434/chemrxiv-2022-0cbms-v2 | We Are Never Ever Getting (back to) Ideal Symmetry:
Structure and Luminescence in a Ten-Coordinated Europium(III) Sulfate Crystal | Our theoretical treatment of electronic structure in coordination complexes often rests on assumptions of symmetry. Experiments rarely provide fully symmetric systems to study. In solution, fluctuation in solvation, variations in conformation, and even changes in constitution occur and complicates the picture. In crystals, lattice distortion, energy transfer, and phonon quenching is in play, but we are able to have distinct symmetries. Yet the question remains: How is the real symmetry in a crystal compared to ideal symmetries? Moreover, at what level of detail do we need to study a system to determine, if the electronic structure behaves as if it has ideal symmetry? Here, we have revisited the Continues Shape Measurement (CShM) approach developed by Ruiz-Martínez and Alvarez to evaluate the structure of ten-coordinated europium(III) ions in a K5Na[Eu2(SO4)6] structure. By comparing the result of the symmetry deviation analysis to luminescence data, we are able to show the effect of small deviations from ideal symmetry. We suggest using a symmetry deviation value, σideal, determined by using our updated approach to Continues Shape Measurements, where we also align the structure via our AlignIt code. AlignIt includes normalization and relative orientation in the symmetry comparison, and by combining the calculated values with the experimentally determined energy level splitting, we were able create the first point on a scale that can show how close to ideal an experimental structure actually is. | Maria Storm Thomsen; Andy Sode Anker; Laura Kacenauskaite; Thomas Just Sørensen | Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Crystallography – Inorganic | CC BY NC 4.0 | CHEMRXIV | 2022-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e15cfa6afbefe57f6438d4/original/we-are-never-ever-getting-back-to-ideal-symmetry-structure-and-luminescence-in-a-ten-coordinated-europium-iii-sulfate-crystal.pdf |
642d823f0784a63aee949898 | 10.26434/chemrxiv-2023-gbchq | DeepDelta: Predicting Pharmacokinetic Improvements of Molecular Derivatives with Deep Learning | Established molecular machine learning models process individual molecules as inputs to predict their biological, chemical, or physical properties. However, such algorithms require large datasets and have not been optimized to predict property differences between molecules. Many drug and material development tasks would benefit from an algorithm that can directly compare two molecules to guide molecular optimization and prioritization. Here, we develop DeepDelta, a pairwise deep learning approach that processes two molecules simultaneously and learns to predict property differences between two molecules from small datasets. On 10 pharmacokinetic benchmark tasks, our DeepDelta approach outperforms two established molecular machine learning algorithms, the message passing neural network (MPNN) ChemProp and Random Forest using radial fingerprints. We further analyze our performance and find that DeepDelta is particularly outperforming established approaches at predicting large differences in molecular properties and can perform scaffold hopping. Furthermore, we derive simple computational tests of our models based on mathematical invariants and show that compliance to these tests correlate with overall model performance – providing an innovative, unsupervised, and easily computable measure of expected model performance and applicability. Taken together, DeepDelta provides an accurate approach to predict molecular property differences and will allow for higher fidelity and transparency in molecular optimization for drug development and the chemical sciences. | Zachary Fralish; Ashley Chen; Paul Skaluba; Daniel Reker | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-04-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642d823f0784a63aee949898/original/deep-delta-predicting-pharmacokinetic-improvements-of-molecular-derivatives-with-deep-learning.pdf |
62c400fe9195492110dfa5c5 | 10.26434/chemrxiv-2022-3gfbx | Pd–H species on electrode stabilized by solvent co-adsorption: Observation by operando IR spectroscopy | On-top hydrogen on a Pd cathode (Pd–H) was observed for the first time by operando infrared (IR) spectroscopy at 2030 cm−1, being stabilized by co-adsorbed solvent (n-alkane) molecules. A proton-exchange membrane (PEM) reactor with Pt/C (anode) and Pd/C (cathode) catalysts was modified to transmit an infrared (IR) beam for operando observation. Pd–H species was observed when 1) H+ was supplied to the cathodic chamber through the PEM, 2) solvent was flowed at the cathode, and 3) an appropriate bias was applied to the cathode. Because atomic H on Pd surfaces interacts with multiple Pd atoms, on-top Pd–H is proposed to be stabilized by co-adsorbed solvent molecules. Spectra of the solvent were deformed when Pd–H species were present: the peak intensity increased and nonfundamental bands at 2800–2500 cm−1 became pronounced. The intensification of these bands was caused by resonance with free-electron absorption bands in the IR region. | Junko N. Kondo; Shuo Ge; Tomohiro Suzuki; Ryota Osuga; Takeshi Matsumoto; Toshiyuki Yokoi; Yugo Shimizu; Atsushi Fukazawa; Naoki Shida; Mahito Atobe | Catalysis; Electrocatalysis | CC BY NC 4.0 | CHEMRXIV | 2022-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c400fe9195492110dfa5c5/original/pd-h-species-on-electrode-stabilized-by-solvent-co-adsorption-observation-by-operando-ir-spectroscopy.pdf |
60c7442d567dfe535fec4215 | 10.26434/chemrxiv.9750872.v1 | Relaxation Dynamics of Hydrated Thymine, Thymidine, and Thymidine Monophosphate Probed by Liquid Jet Time-Resolved Photoelectron Spectroscopy | <p>The relaxation dynamics
of thymine and its derivatives thymidine and thymidine monophosphate were
studied using time-resolved photoelectron spectroscopy applied to a water
microjet. Two absorption bands were studied, the first is a bright ππ* state
which was populated using tunable-ultraviolet light in the range of 4.74 – 5.17
eV and probed using a 6.20 eV probe pulse. By reversing the order of these
pulses, a band containing multiple ππ* states was populated by the 6.20 eV
pulse and the lower energy pulse served as the probe. The lower lying ππ* state
was found to decay in ~400 fs in both thymine and thymidine independent of pump
photon energy while thymidine monophosphate decays varied from 670-840 fs with
some pump energy dependence. </p><p>The application of a computational QM/MM scheme at
the XMS-CASPT2//CASSCF/AMBER level of theory suggests
that conformational differences existing between thymidine and thymidine
monophosphate in solution accounts for this difference. The
higher lying ππ* band was found to decay in ~600 fs in all three cases, but was
only able to be characterized when using the 5.17 eV probe pulse. Notably, no
long-lived signal from an np* state could be identified in either
experiment on any of the three molecules.</p> | Blake Erickson; Zachary Heim; Elisa Pieri; Erica Liu; Todd J. Martínez; Daniel Neumark | Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7442d567dfe535fec4215/original/relaxation-dynamics-of-hydrated-thymine-thymidine-and-thymidine-monophosphate-probed-by-liquid-jet-time-resolved-photoelectron-spectroscopy.pdf |
616e5c81aa918d2d3b2ff64c | 10.26434/chemrxiv-2021-33jp3 | Cross-Electrophile Coupling of Alcohols with Aryl and Vinyl Halides | Although alcohols represent one of the largest pools of commercially available alkyl substrates, approaches to di-rectly utilize them in cross-coupling and cross-electrophile coupling are limited. We report the use of alcohols in cross-electrophile coupling with aryl and vinyl halides to form C(sp3)–C(sp2) bonds in a one-pot strategy. This strategy allows the use of primary and secondary alcohols through their very fast (<1 min) in situ conversion to the corre-sponding alkyl bromides with compatible phosphonium activating reagents. The utility of the reaction is exempli-fied by its simple reaction setup, scalability, and broad scope (41 examples, 57% ± 15% ave yield). The reaction can be performed on the benchtop without the need for electro-chemical or photochemical equipment. Finally, translation to standard parallel synthesis techniques is demonstrated by successfully coupling all combinations of 8 alcohols with 12 aryl cores in a 96-well plate using only one (99% cover-age) or two (100% coverage) sets of conditions. | Benjamin Chi; Jonas Widness; Michael Gilbert; Daniel Salgueiro; Kevin Garcia; Daniel Weix | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616e5c81aa918d2d3b2ff64c/original/cross-electrophile-coupling-of-alcohols-with-aryl-and-vinyl-halides.pdf |
65697a2729a13c4d4767bc57 | 10.26434/chemrxiv-2023-1d3lx | Effect of Interfacial Potential on Elementary Exciton Processes in InP-based Core/shell Quantum Dots | Suppression of Auger recombination rate in semiconductor quantum dots (QDs) is essential for various applications such as LEDs and lasers. We investigate the effect of interfacial potential on Auger recombination processes in InP-based core/shell quantum dots (c/s QDs) using femtosecond transient absorption spectroscopy (fs-TAS). We have synthesized c/s QDs with diverse interfacial potentials: steep ones (InP/ZnS and InP/ZnSe QDs) and a smoothed counterpart (InP/ZnSexS1-x/ZnS QDs). The steady-state absorption and luminescence spectra obtained from aliquots extracted during the synthesis of InP/ZnSexS1-x/ZnS QDs and the EDS line profile revealed the formation of a compositional gradient shell (smoothed interfacial potential). The Auger recombination processes in InP/ZnSexS1-x/ZnS QDs QDs were ~ 8 times slower than those in InP/ZnS QDs in the same volume. These suppressions can be explained by the effective electron wavefunction penetration from the core into the shell and reduced carrier momentum in the final state resulted from the smoothed interfacial potential. These findings provide an important guideline for the rational design of the interfacial potentials in InP-based c/s QDs for various applications such as LED and laser devices. | Kazuki Inada; Daichi Eguchi; Naoto Tamai | Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65697a2729a13c4d4767bc57/original/effect-of-interfacial-potential-on-elementary-exciton-processes-in-in-p-based-core-shell-quantum-dots.pdf |
6685767bc9c6a5c07a2d34b1 | 10.26434/chemrxiv-2024-8q740 | Pellet dispensomixer and pellet distributor: Open hardware for nanocomposite space exploration via automated material compounding | The development of novel polymer-based nanocomposites necessitates the experimental preparation and characterization of numerous compositions to identify optimal formulations. For thermoplastic-based materials, the compounding process typically involves the labor-intensive tasks of dispensing, weighing, mixing, and extruding solid components such as polymers and additives. Herein, we present an open hardware solution that aims to automate this process. Our setup system is designed to streamline material surveying tasks associated with experimental design or closed-loop, self-driving laboratories. Our hardware setup consists of two main components: a multi-material pellet dispenser, which simplifies the preparation of targeted compositions from a range of master batches, and a pellet collector-distributor, which efficiently gathers and distributes processed materials into various containers throughout the experiment. | Miguel Hernández-del-Valle; Jorge Ilarraza-Zuazo; Enrique Dios-Lázaro; Javier Rubio; Joris Audoux; Maciej Haranczyk | Polymer Science; Biopolymers; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6685767bc9c6a5c07a2d34b1/original/pellet-dispensomixer-and-pellet-distributor-open-hardware-for-nanocomposite-space-exploration-via-automated-material-compounding.pdf |
63a4584a81e4ba7c9256aec2 | 10.26434/chemrxiv-2022-42m73 | Carbon–Carbon Bond Formation from CO and H–
The Role of Metal Formyl Intermediates
| In this mini-review, we summarise the current examples of carbon chain production from metal formyl intermediates with homogeneous metal complexes. To date, the formation of both unsaturated and saturated C2 motifs along with cyclic C3 products has been reported. We discuss the mechanistic aspects of these reactions and the challenges and opportunities in using this understanding to underpin future FT chemistry. | Joseph Parr; Mark Crimmin | Organometallic Chemistry; Kinetics and Mechanism - Organometallic Reactions; Small Molecule Activation (Organomet.); Theory - Organometallic | CC BY 4.0 | CHEMRXIV | 2022-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a4584a81e4ba7c9256aec2/original/carbon-carbon-bond-formation-from-co-and-h-the-role-of-metal-formyl-intermediates.pdf |
60c73ff9bb8c1a77233d9c77 | 10.26434/chemrxiv.7577597.v1 | Directed, Palladium(II)-Catalyzed Enantioselective anti-Carboboration of Alkenyl Carbonyl Compounds | A substrate-directed enantioselective <i>anti</i>-carboboration reaction of alkenes has been developed, wherein a carbon based nucleophile and a boron moiety are installed across the C=C bond through a 5- or 6-membered palladacycle intermediate. The reaction is promoted by a palladium(II) catalyst and a mondentate oxzazoline ligand. A range of enantioenriched secondary alkylboronate products were obtained with moderate to high enantioselectivity that could be further upgraded by recrystallization. This work represents a new method to synthesize versatile and valuable alkylboronate building blocks. Building on an earlier mechanistic proposal by Peng, He, and Chen, a revised model is proposed to account for the stereoconvergent nature of this transformation. | Zhen Liu; Xiaohan Li; Tian Zeng; Keary Engle | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ff9bb8c1a77233d9c77/original/directed-palladium-ii-catalyzed-enantioselective-anti-carboboration-of-alkenyl-carbonyl-compounds.pdf |
66c0bb8320ac769e5feb4a82 | 10.26434/chemrxiv-2024-pjztm | Distinguishing Surface and Bulk Reactivity: Concentration Dependent Kinetics of Iodide Oxidation by Ozone in Microdroplets | Iodine oxidation reactions play an important role in environmental, biological, and industrial contexts. The multiphase reaction between aqueous iodide and ozone is of particular interest due to its prevalence in the marine atmosphere and unique reactivity at the air-water interface. Here, we explore the concentration dependence of the I- + O3 reaction in levitated microdroplets under both acidic and basic conditions. To interpret the experimental kinetics, molecular simulations are used to benchmark a kinetic model, which enables insight into the reactivity of the interface, the nanometer-scale sub-surface region, and the bulk interior of the droplet. For all experiments, a kinetic description of gas- and liquid-phase diffusion is critical to interpreting the results. We find that the surface dominates the iodide oxidation kinetics under concentrated and acidic conditions, with the reactive uptake coefficient approaching an upper limit of 10-2 at pH 3. In contrast, reactions in the sub-surface dominate under more dilute and alkaline conditions, with inhibition of the surface reaction at pH 12 and an uptake coefficient that is 10x smaller. The origin of a changing surface mechanism with pH is explored and compared to previous ozone-dependent measurements. | Alexander Prophet; Kritanjan Polley; Emily Brown; David Limmer; Kevin Wilson | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Chemical Kinetics; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c0bb8320ac769e5feb4a82/original/distinguishing-surface-and-bulk-reactivity-concentration-dependent-kinetics-of-iodide-oxidation-by-ozone-in-microdroplets.pdf |
65786541bec7913d276f7216 | 10.26434/chemrxiv-2023-bc339 | Studying Cation Exchange in {Cr7Co} Pseudorotaxanes: Preparatory Studies for Making Hybrid Molecular Machines | In the design of dynamic supramolecular systems used in molecular machines, it is important to understand the binding preferences between the macrocycle and stations along the thread. Here, we apply 1H NMR spectroscopy to investigate the relative stabilities of a series of linear alkylammonium templated pseudorotaxanes with the general formula [H2NRR’][Cr7CoF8(O2CCH2tBu)16] by exchanging the cation in solution. Our results show that the pseudorotaxanes are able to exchange threads via a dissociative mechanism. The position of equilibrium is dependent upon the ammonium cation and solvent used. Short chain primary ammonium cations are shown to be far less favourable macrocycle stations than secondary ammonium cations. Collision-induced dissociation mass spectrometry (CID-MS) has been used to look at disassembly of the pseudorotaxanes in a solvent-free environment and stability trends compared to those in acetone-d6. The energy needed to induce 50% of the precursor ion loss (E50) is used shows a similar trend to the equilibria measured by NMR. Comparing the relative stabilities of these hybrid inorganic-organic pseudo-rotaxanes with host-guest compounds involving crown ethers shows significant differences that may be valuable for the design of molecular machines. | Tom Bennett; Niklas Geue; Grigore Timco; George Whitehead; Inigo Vitorica-Yrezabal; Perdita Barran; Eric McInnes; Richard Winpenny | Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2023-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65786541bec7913d276f7216/original/studying-cation-exchange-in-cr7co-pseudorotaxanes-preparatory-studies-for-making-hybrid-molecular-machines.pdf |
6724b1fa5a82cea2fab73adb | 10.26434/chemrxiv-2024-4cn2m | Sustained growth of nanotubes by self-assembly of DNA strands at room temperature
| Artificial biomolecular nanotubes are a promising approach to build materials mimicking the capacity of the cellular cytoskeleton to grow and self-organize dynamically. Nucleic acid nanotechnology has demonstrated a variety of self-assembling nanotubes with programmable, robust features, and morphological similarities to actual cytoskeleton components. However their production typically requires thermal annealing that is not only incompatible with physiological conditions but also hinders the possibility for continuous growth and dynamic self-organization. Here we report DNA nanotubes that self-assemble from a simple mixture of five short DNA strands at constant room temperature, with remarkable capability to sustainably grow over prolonged time. The assembly, done in a monovalent salt buffer (here, 100 mM NaCl), ensures that the nanoscale features of the nanotubes are preserved under these isothermal conditions, enabling continuous growth up to 20 days and the formation of individual nanotubes with near flawless arrangement, a diameter of 22 ± 4 nm, and length of several tens of micrometers. We demonstrate the crucial role of the monovalent cation to achieve such properties. We finally encapsulate the strands in micro-sized compartments, such as water-in-oil microdroplets and giant unilamellar vesicles serving as simple cell models. Notably, nanotubes not only isothermally grow in these conditions, but also self-organize into dynamic higher-order structures, such as rings and dynamic networks, demonstrating that cytoskeleton-like properties can emerge from a combination of sustained growth and confinement. Our study suggests a method for engineering biomolecular scaffolds and materials that display sustained dynamic and life-like properties. | Laura Bourdon; Syed Pavel Afrose; Siddharth Agarwal; Aurélie Di Cicco; Daniel Lévy; Ayako Yamada; Damien Baigl; Elisa Franco | Physical Chemistry; Materials Science; Nanoscience | CC BY 4.0 | CHEMRXIV | 2024-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6724b1fa5a82cea2fab73adb/original/sustained-growth-of-nanotubes-by-self-assembly-of-dna-strands-at-room-temperature.pdf |
641073eae53eff1af31d21c1 | 10.26434/chemrxiv-2023-l2vkp | Probing the dynamical interaction of the para-sulfonato-calix[4]arene with an antifungal protein | Calixarenes are hallmark molecules in supramolecular chemistry as guest cages for small ligands. They have also conversely proved their interest as auxiliary ligands toward assisted co-crystallization of proteins. These functionalized macromolecular cages target positively-charges residues, and notably surface-exposed lysines, with a site-selectivity finely characterized experimentally, but that remains to be assessed. Relying on a tailored molecular dynamics simulations protocol, we explore the association of para-sulfonato-calix[4]arenes with an antifungal protein, as a small yet most competitive system with 13 surface-exposed lysines. Our computational approach probe "de novo" the electrostatically-driven interaction, ruled out by a competition with salt bridges, not only corroborating the main binding site probed by X-ray, but also characterizing a second binding site that can act as a transient hub spot. The attach-pull-release (APR) method provides a very good assessment of the overall binding free energy measured experimentally (-6.42+-0.5 vs -5.45 kcal.mol-1 by isothermal titration calorimetry). This work also probes dynamical allosteric modifications upon ligand binding, and our computational protocol could be generalized to situate the supramolecular forces ruling out the calixarene-assisted co-crystallization of proteins. | Alessio Bartocci; Elise Dumont | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Chemical Biology; Computational Chemistry and Modeling; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641073eae53eff1af31d21c1/original/probing-the-dynamical-interaction-of-the-para-sulfonato-calix-4-arene-with-an-antifungal-protein.pdf |
612dce3f42198e099468a7ac | 10.26434/chemrxiv-2021-08j01-v4 | Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteria | Catabolism of sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose), the ubiquitous sulfosugar produced by photosynthetic organisms, is an important component of the biogeochemical carbon and sulfur cycles. Here, we describe a new pathway for SQ degradation that involves oxidative desulfurization to release sulfite and enable utilization of the entire carbon skeleton of the sugar to support the growth of the plant pathogen Agrobacterium tumefaciens. SQ or its glycoside sulfoquinovosyl glycerol (SQGro) are imported into the cell by an ABC transporter system with an associated SQ binding protein. A sulfoquinovosidase hydrolyses the SQ glycoside and the liberated SQ is acted on by a flavin mononucleotide-dependent sulfoquinovose monooxygenase, in concert with an NADH-dependent flavin reductase, to release sulfite and 6-oxo-glucose. An NADPH-dependent oxidoreductase reduces the 6-oxo-glucose to glucose, enabling entry into primary metabolic pathways. Structural and biochemical studies provide detailed insights into the recognition of key metabolites by proteins in this pathway. Bioinformatic analyses reveal that the sulfoquinovose monooxygenase (smo) pathway is distributed across Alpha- and Betaproteobacteria and is especially prevalent within the Rhizobiales order. This strategy for SQ catabolism is distinct from previously described pathways as it enables the complete utilization of all carbons within SQ by a single organism with concomitant production of inorganic sulfite. | Mahima Sharma; James Lingford; Marija Petricevic; Alexander Snow; Yunyang Zhang; Michael Jarva; Janice Mui; Nichollas Scott; Eleanor Saunders; Runyao Mao; Ruwan Epa; Bruna da Silva; Douglas Pires; David Ascher; Malcolm McConville; Gideon Davies; Spencer Williams; Ethan Goddard-Borger | Biological and Medicinal Chemistry; Catalysis; Chemical Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612dce3f42198e099468a7ac/original/oxidative-desulfurization-pathway-for-complete-catabolism-of-sulfoquinovose-by-bacteria.pdf |
641e0c3591074bccd03bb433 | 10.26434/chemrxiv-2023-wq9t3 | ∆-Learning for Coarse-Grained Potentials | Coarse-grained molecular dynamics (CGMD) simulations address lengthscales and timescales that are critical to many chemical and material applications. Nevertheless, contemporary CGMD modeling is relatively bespoke and there are no black-box CGMD methodologies available that could play a comparable role in discovery applications that density functional theory plays for electronic structure. This gap might be filled by machine learning (ML) based CGMD potentials that simplify model development, but these methods are still in their early stages and have yet to demonstrate a significant advantage over existing physics-based CGMD methods. Here we explore the potential of $\Delta$-learning models to leverage the advantages of these two approaches. This is implemented by using ML-based potentials to learn the difference between the target CGMD variable and the predictions of physics-based potentials. The $\Delta$-models are benchmarked against the baseline models in reproducing on-target and off-target atomistic properties as a function of CG resolution, mapping operator, and system topology. The $\Delta$-models outperform the reference ML-only CGMD models in nearly all scenarios. In several cases, the ML-only models also manage to minimize training error while still producing qualitatively incorrect dynamics, which is corrected by the $\Delta$-models. Given their negligible added cost, $\Delta$-models provide essentially free gains over their ML-only counterparts. Nevertheless, an unexpected finding is that neither the $\Delta$-learning models nor ML-only models significantly outperform the elementary pair-wise models in reproducing atomistic properties. This fundamental failure is attributed to the relatively large irreducible force errors associated with coarse-graining that produces little benefit from using more complex potentials. | Aditi Khot; Brett Savoie | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Statistical Mechanics | CC BY 4.0 | CHEMRXIV | 2023-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641e0c3591074bccd03bb433/original/learning-for-coarse-grained-potentials.pdf |
66503509418a5379b0269cc5 | 10.26434/chemrxiv-2024-h6882 | Transducing chemical energy through catalysis by an artificial molecular motor | Cells display a range of mechanical activities enabled by the cytoskeleton, a viscoelastic hydrogel manipulated by motor proteins powered through catalysis. This raises the question of how the acceleration of a chemical reaction can enable the energy released from that reaction to be transduced, and thereby work to be done, by a molecular catalyst. Here we demonstrate the molecular-level transduction of chemical energy to mechanical force in the form of the powered contraction and powered re-expansion of a crosslinked polymer gel driven by the directional rotation of embedded artificial catalysis-driven molecular motors. Continuous 360° rotation of the rotor about the stator of motor-molecules incorporated within the polymeric framework of the gel, twists the polymer chains of the crosslinked network around one another (either clockwise or anti-clockwise, depending on the chirality of the fuelling system). This progressively increases writhe and tightens entanglements, causing macroscopic contraction of the gel to ~70% of its original volume. The limit of contraction corresponds to the stall force of the motor; the point at which, despite catalysis continuing, the untwisting force exerted by the entwined strands balances conformation selection in the motor’s catalytic cycle. Subsequent addition of the opposite enantiomeric fuelling system powers rotation of the motor-molecules of the contracted gel in the reverse direction, unwinding the entanglements and causing the gel to re-expand. Continued powered twisting of the strands in the new direction causes the gel to contract once again. The experimental demonstration of work against a load by a synthetic catalyst, and the mechanism of the transduction of energy by a catalyst through kinetic asymmetry in its acceleration of a fuel-to-waste reaction, informs both the debate surrounding the mechanism of force generation by biological motors and the design principles for artificial molecular nanotechnology. | Peng-Lai Wang; Stefan Borsley; Martin Power; Alessandro Cavasso; Nicolas Giuseppone; David Leigh | Organic Chemistry; Catalysis; Nanoscience; Physical Organic Chemistry; Supramolecular Chemistry (Org.); Nanodevices | CC BY NC 4.0 | CHEMRXIV | 2024-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66503509418a5379b0269cc5/original/transducing-chemical-energy-through-catalysis-by-an-artificial-molecular-motor.pdf |
6473a7e7be16ad5c570f27b5 | 10.26434/chemrxiv-2023-94zd8 | Catalysis distillation neural network for the few-shot open catalyst challenge | The integration of artificial intelligence and science has resulted in substantial progress in computational chemistry methods for the design and discovery of novel catalysts. Nonetheless, the challenges of electrocatalytic reactions and developing a “large-scale language model” in catalysis persist, and the recent success of ChatGPT's (Chat Generative Pre-trained Transformer) few-shot methods surpassing BERT (Bidirectional Encoder Representation from Transformers) underscores the importance of addressing limited data, expensive computations, time constraints and structure-activity relationship in research. Hence, the development of few-shot techniques for catalysis is critical and essential, regardless of present and future requirements. This paper introduces the Few-Shot Open Catalyst Challenge 2023, a competition aimed at advancing the application of machine learning technology for predicting catalytic reactions on catalytic surfaces, with a specific focus on dual-atom catalysts in hydrogen peroxide electrocatalysis. To address the challenge of limited data in catalysis, we propose a machine learning approach based on MLP-Like and a framework called Catalysis Distillation Graph Neural Network (CDGNN). Our results demonstrate that CDGNN effectively learns embeddings from catalytic structures, enabling the capture of structure-adsorption relationships. This accomplishment has resulted in the utmost advanced and efficient determination of the reaction pathway for hydrogen peroxide, surpassing the current graph neural network approach by 16.1%. Consequently, CDGNN presents a promising approach for few-shot learning in catalysis. | Bowen Deng | Theoretical and Computational Chemistry; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6473a7e7be16ad5c570f27b5/original/catalysis-distillation-neural-network-for-the-few-shot-open-catalyst-challenge.pdf |
6718180312ff75c3a13a58bf | 10.26434/chemrxiv-2024-q8kqx-v2 | Distinguishing Potential Organic Biosignatures on Ocean Worlds from Abiotic Geochemical Products using Thermodynamic Calculations | The search for life in our solar system often involves efforts to detect organic molecules, which have been found on many extraterrestrial bodies, including planets, moons, meteorites, comets, and asteroids. These chemical signatures are not typically thought of as biosignatures because we know that organic synthesis can occur through abiotic processes. Therefore, development of methods for distinguishing biotic and abiotic biosignatures would enable interpretation of data collected from habitability and life-detection missions. Life on Earth harnesses energy-releasing reactions to power biosynthesis reactions, which often require energy. Using thermodynamic data, we can quantify the energy required for organic synthesis. If an organic molecule is detected in an abundance that is thermodynamically unstable, then it is possible that life coupled its synthesis to other energy-releasing reactions. On the other hand, if an organic molecule is detected in an abundance that is thermodynamically stable, then abiotic synthesis was plausible. This sorting framework can be applied to the search for life wherever we have geochemical data. One such example is Saturn’s moon Enceladus. Small compounds involving the elements that comprise the majority of biomass were detected by the Cassini spacecraft in the plume gas erupting from the subsurface ocean. Using Enceladus as an example, we demonstrate the utility of thermodynamic calculations for distinguishing biosignatures and show that organic synthesis is often favorable using the carbon sources available on Enceladus. While these results may lead us to conclude that hypothetical organic signatures on Enceladus are abiotic, this framework can be applied to other environments in the search for genuine biosignatures. | Jordyn Robare; Everett Shock | Organic Chemistry; Earth, Space, and Environmental Chemistry; Organic Synthesis and Reactions; Space Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6718180312ff75c3a13a58bf/original/distinguishing-potential-organic-biosignatures-on-ocean-worlds-from-abiotic-geochemical-products-using-thermodynamic-calculations.pdf |
60c75552702a9b374b18c69f | 10.26434/chemrxiv.14080028.v1 | Nontargeted Mass Spectrometry of Dried Blood Spots for Interrogation of the Human Circulating Metabolome | Advances in high resolution, nontargeted mass
spectrometry allow for the simultaneous measure of thousands of metabolites in
a single biosample. Application of these analytical approaches to population-scale
human studies has been limited by the need for resource-intensive blood sample collection,
preparation, and storage. Dried blood spotting, a technique developed decades
ago for newborn screening, may offer a simple approach to overcome barriers in
human blood acquisition and storage. In this study, we find that over 4,000 spectral
features across diverse chemical classes may be efficiently and reproducibly extracted
and relatively quantified from human dried blood spots using nontargeted mass
spectrometry-based metabolomics. Moreover, over 80% of metabolites were found
to be chemically stable in dried blood spots stored at room temperature for up
to a week. In direct relation to plasma samples, dried blood spots exhibited comparable
representation of the human circulating metabolome, capturing both known and previously
uncharacterized metabolites. Dried blood spot approaches provide an opportunity
for rapid and facile human biosampling and storage, and will enable widespread
metabolomics study of populations, particularly in resource-limited areas. | Casey Ward; Shriram Nallamshetty; Jeramie D. Wartrous; Eowyn Acres; Tao Long; Ian T Mathews; Sonia Sharma; Susan Cheng; Farhad Imam; Mohit Jain | Analytical Chemistry - General; Biochemical Analysis; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75552702a9b374b18c69f/original/nontargeted-mass-spectrometry-of-dried-blood-spots-for-interrogation-of-the-human-circulating-metabolome.pdf |
66f1a3cbcec5d6c142faf3f9 | 10.26434/chemrxiv-2024-w5wnb-v2 | Selective dissolution and re-precipitation by pH cycling enables recovery of manganese from surface nodules | Meeting global sustainable development and climate goals requires a rapid transition to renewable energy technologies. However, these emerging technologies rely on critical elements whose sourcing presents geopolitical and environmental challenges. In this study, we explore ferromanganese nodules from the Oacoma Site in South Dakota as a viable feedstock for sourcing manganese, a critical element used in the production of battery cathodes, consumer electronics, and steel. The nodules are readily accessible from the surface site and primarily consist of rhombohedral metal carbonates, including manganese at 3.5–5.4 at% (9.2– 14.1 wt%) relative to all the elements present in the nodules. Based on titration experiments and an equilibrium speciation model, we developed a strategy for extracting the manganese by selectively dissolving carbonate phases in acidic conditions, followed by selectively re-precipitating manganese oxide in alkaline conditions. Specifically, exposing the samples to pH 1.5–2 dissolved almost all the calcium and manganese ions, while retaining a significant portion of the iron and magnesium in the residual nodule powders. Subsequently, increasing the pH of the leachate to 5.7 resulted in the selective re-precipitation of predominantly iron hydroxide. Further increasing the pH of the leachate solution to 10.9 finally produced a relatively pure manganese oxide product. Our pH cycling approach recovered 65.7–74.2% of the manganese in the nodules at 70.3–85.4 at% (81.5–91.0 wt%) purity relative to the other metals, without the need for specialty chemicals, membranes, ligands, or resins, and without generating highly acidic wastes. We further performed a preliminary assessment of the scalability and industrial relevance of this process to explore these nodules as a feedstock for sustainable sourcing of manganese. | Pravalika Butreddy; Sebastian Mergelsberg; Jennifer N Jocz; Dongsheng Li; Venkateshkumar Prabhakaran; Andrew J Ritchhart ; Chinmayee V Subban; Jon Kellar; Scott R Beeler ; Sarah W Keenan; Elias Nakouzi | Materials Science; Energy | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f1a3cbcec5d6c142faf3f9/original/selective-dissolution-and-re-precipitation-by-p-h-cycling-enables-recovery-of-manganese-from-surface-nodules.pdf |
60c74021f96a0036fc286232 | 10.26434/chemrxiv.7636004.v1 | Halide Ion Micro-Hydration: Structure, Energetics, and Spectroscopy of Small Halide–Water Clusters | <div>
<div>
<div>
<p>Replica exchange molecular dynamics simulations and vibrational spectroscopy calculations
are performed using halide-water many-body potential energy functions to provide a bottom-up
analysis of the structures, energetics, and hydrogen-bonding arrangements in X−(H2O)n=3−6
clusters, with X = F, Cl, Br, and I. Independently of the cluster size, it is found that all four
halides prefer surface-type structures in which they occupy one of the vertices in the underlying three-dimensional hydrogen-bond networks. For fluoride-water clusters, this is in contrast
with previous reports suggesting that fluoride prefers interior-type arrangements, where the ion
is fully hydrated. These differences can be ascribed to the variability in how various molecular
models are capable to reproduce the subtle interplay between halide-water and water-water interactions. Our results thus emphasize the importance of a correct representation of individual
many-body contributions to the molecular interactions for a quantitative description of halide
ion hydration.
</p>
</div>
</div>
</div> | Pushp Bajaj; Marc Riera; Jason K. Lin; Yaira E. Mendoza Montijo; Jessica Gazca; Paesani Lab | Computational Chemistry and Modeling; Theory - Computational; Clusters; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Statistical Mechanics; Structure; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74021f96a0036fc286232/original/halide-ion-micro-hydration-structure-energetics-and-spectroscopy-of-small-halide-water-clusters.pdf |
679068a381d2151a02402b51 | 10.26434/chemrxiv-2025-2zr3l | Extending the MMPBSA method to membrane proteins: Addressing conformational changes upon ligand binding to P2Y12R | Membrane proteins play crucial roles in biological signaling and represent key targets in drug discovery, garnering significant experimental and computational attention. Recent advances in computational screening techniques have enabled the development of more accurate and efficient binding affinity calculation methods. Among these, the Molecular Mechanics Poisson Boltzmann Surface Area (MMPBSA) method has gained widespread adoption in large-scale simulations due to its computational efficiency. However, its application to membrane protein-ligand systems remains less developed compared to globular protein systems, primarily due to the additional complexity introduced by the membrane environment. In this study, we present enhanced capabilities in Amber that provide flexible and automatic options for calculating membrane placement parameters. Furthermore, we present the first application of ensemble simulations, combined with a multi-trajectory approach and entropy corrections, to enhance MMPBSA calculations for membrane protein systems. This novel methodology is particularly advantageous for systems exhibiting large ligand-induced conformational changes, significantly improving accuracy and sampling depth compared to traditional single-trajectory methods. We validate our approach using the human purinergic platelet receptor P2Y12R as a model system, chosen for its well-documented agonist-induced conformational changes and extensive experimental data, making it an ideal candidate for evaluating our enhanced simulation protocol. | Cizhang Zhao; Tianhong Wang; Ray Luo | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679068a381d2151a02402b51/original/extending-the-mmpbsa-method-to-membrane-proteins-addressing-conformational-changes-upon-ligand-binding-to-p2y12r.pdf |
60c73f5b0f50dbe9e139577f | 10.26434/chemrxiv.7325126.v1 | Improved Synthesis of β-Ketoenamine-Linked Covalent Organic Frameworks via Monomer Exchange Reactions | <div>
<div>
<div>
<p>β-ketoenamine-linked covalent organic frameworks (COFs) offer
excellent structural versatility and outstanding aqueous stability,
but their less dynamic linkages complicate obtaining samples with
high crystallinity and surface areas that approach theoretical
values. In contrast, imine-linked COFs are often isolated with
superior materials quality. Here we synthesize several β-
ketoenamine-linked COFs, including two unreported structures,
with unmatched crystallinity and high surface areas by preparing
the topologically equivalent imine-linked COF and exchanging its
triformylbenzene monomers with triformylphloroglucinol.
</p>
</div>
</div>
</div> | Michael Daugherty; Edon Vitaku; Rebecca Li; Austin Evans; Anton Chavez; William Dichtel | Organic Synthesis and Reactions; Organic Polymers; Polymerization (Polymers); Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f5b0f50dbe9e139577f/original/improved-synthesis-of-ketoenamine-linked-covalent-organic-frameworks-via-monomer-exchange-reactions.pdf |
60c9e3b1059ce27b3076bb42 | 10.26434/chemrxiv.14766849.v1 | Viewpoint: Reply to Comment on 'Using NMR to Test Molecular Mobility During a Chemical Reaction' | Reports of boosted diffusion during chemical and enzymatic reactions have inspired a loyal community of scientists who find them so counter-intuitive that they must be artifact. This second Comment on the subject by these authors is about technicalities of how to analyze data we deposited online regarding J. Phys. Chem. Lett. (2021) 12, 2370 and Science (2020) 369, 537. Now that their own data is also online, one apparent discrepancy can be resolved: we demonstrate that the authors’ data agrees with ours because their first Comment on this subject reported only truncated short-time excerpts of the longer time series they deposited online (zenodo.org/record/4628353). This second Comment adds 5 additional objections, 4 of which are too technical to change the qualitative conclusion. The 5th objection errs because it omits to recognize intermediate states of the click reaction during which one reactant complexes with the catalyst to form an object of larger size. Elsewhere we analyzed in great detail the respective influences of boosted diffusion and this hydrodynamic effect (doi.org/10.26434/chemrxiv.14740563.v1). The factual evidence and reasoning in this Reply strongly support this laboratory’s earlier conclusions regarding boosted diffusion during common chemical reactions. | Tian Huang; Huan Wang; Steve Granick | Chemical Kinetics; Physical and Chemical Processes; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c9e3b1059ce27b3076bb42/original/viewpoint-reply-to-comment-on-using-nmr-to-test-molecular-mobility-during-a-chemical-reaction.pdf |
60c74b9dbdbb896e3ea3960d | 10.26434/chemrxiv.12360788.v1 | A Study of Hybridization Understanding from Algorithmic to Conceptual – Is Algorithmic an End Point for Students? | <p>This paper details the results of a qualitative study examining the reasoning students use to solve common hybridization theory assessment questions and their mental images of hybrid and atomic orbitals. The data were collected through think-aloud interviews as students worked through a five-question questionnaire. Prior to recruitment, the study was deemed to be exempt from IRB review by Sterling IRB. Prior to start of interviews participants provided verbal consent. The resulting transcripts and answers were analyzed following the practices of grounded theory and constant comparative analysis. Coding schemes can be found in the Supplementary Information section. Results, conclusions, and implications for teaching are presented in the manuscript.</p> | Gianna J. Manchester; Julia Winter; Sean P. Hickey; Sarah Wegwerth | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b9dbdbb896e3ea3960d/original/a-study-of-hybridization-understanding-from-algorithmic-to-conceptual-is-algorithmic-an-end-point-for-students.pdf |
62ddb1d94e76bf8b1b9e3a35 | 10.26434/chemrxiv-2022-p9grn | Tuning the Physical Properties of Carboxylated Cellulose Nanocrystal (cCNC) Microspheres by Hybridizing with Silk Fibroin (SF) | A new class of hydrophobic/lipophilic cellulose microspheres are made from carboxylated cellulose nanocrystals (cCNC) by adding silk fibroin (SF) protein in the course of spray-drying from aqueous suspension. We found mere 2% SF addition could leverage the surface energy with an increase of contact angle from 27.5° to 60.4°. Besides the complete altered surface energy from cellulose beads, the hybrid SF-cCNC microspheres also show improved mechanical properties and prolonged diffusion kinetics for transporting water-soluble ions / molecules (e.g., methylene blue). Depth profiling of the SF-cCNC microspheres reveals that SF is more concentrated at the surface in comparison with the core, and this surface localization is the reason for the tuned properties. Moreover, post methanol treatment of the SF-cCNC hybrid microspheres induces a β-sheet phase transition to the Silk II structure, which can further enhance the mechanical properties and slow down the small molecule transport of the microspheres. Therefore, a new method has been established that could tune the physical properties of functional cellulose microspheres through the control of SF structural transformation, which could significantly benefit for controlled drug release and microplastic beads replacement applications. | Junqi Wu; Amelia Loesch-Zhang ; Mark Andrews | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ddb1d94e76bf8b1b9e3a35/original/tuning-the-physical-properties-of-carboxylated-cellulose-nanocrystal-c-cnc-microspheres-by-hybridizing-with-silk-fibroin-sf.pdf |
6351ae3bee31867fd76b6222 | 10.26434/chemrxiv-2022-ht25q | Highly stable amorphous silica-alumina catalysts for continuous bio-derived mesitylene production under solvent-free conditions | Aromatization of alkyl methyl ketones obtained from biorefinery streams is a viable and attractive catalytic pathway to renewable aromatics, precursors for various important monomers and chemicals. To achieve high catalytic activity and stability under continuous conditions, mesoporous amorphous silica-alumina (ASA) catalysts are studied for the acid-catalyzed self-condensation of biomass-derived acetone to mesitylene in solvent-free continuous conditions using a fixed-bed reactor. The catalytic efficiency of ASA catalysts depends on their structure and intrinsic acidity. In comparison to pure alumina, ASA Siralox 30 exhibits a 2.2 times higher catalytic activity for acetone conversion and 3.8 times higher mesitylene yield, demonstrating the importance of Brønsted acid sites (BAS) generated in ASA catalysts. The detailed kinetic studies and catalyst characterization indicate that mesitylene formation is favored over BAS and that the formation rate is enhanced with the relative strength of BAS. We demonstrate here that Siralox 30 (total product selectivity = 66 %, W/F = 12.5 gcat h mol 1) is an adequate and highly active catalyst for the continuous mesitylene synthesis with remarkable long-term operational stability (> 50 hours-on-stream). | Phillip Reif; Navneet Kumar Gupta; Marcus Rose | Catalysis; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Acid Catalysis; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2022-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6351ae3bee31867fd76b6222/original/highly-stable-amorphous-silica-alumina-catalysts-for-continuous-bio-derived-mesitylene-production-under-solvent-free-conditions.pdf |
60c75503469df44322f4506a | 10.26434/chemrxiv.13954415.v1 | Assembly of Model Membrane Nanodiscs for Native Mass Spectrometry | Native mass spectrometry (MS) with nanodiscs is a promising technique for characterizing membrane protein and peptide interactions in lipid bilayers. However, prior studies have used nanodiscs made of only one or two lipids, which lack the complexity of a natural lipid bilayer. To better model specific biological membranes, we developed model mammalian, bacterial, and mitochondrial nanodiscs with up to four different phospholipids. Careful selection of lipids with similar masses that balance the fluidity and curvature enabled these complex nanodiscs to be assembled and resolved with native MS. We then applied this approach to characterize the specificity and incorporation of LL-37, a human antimicrobial peptide, in single lipid nanodiscs versus model bacterial nanodiscs. Overall, development of these model membrane nanodiscs reveals new insights into the assembly of complex nanodiscs and provides a useful toolkit for studying membrane protein, peptide, and lipid interactions in model biological membranes. | Marius Kostelic; Ciara K. Zak; Hiruni Jayasekera; Michael Marty | Biochemical Analysis; Mass Spectrometry; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75503469df44322f4506a/original/assembly-of-model-membrane-nanodiscs-for-native-mass-spectrometry.pdf |
60c7438b469df43d7ef431f5 | 10.26434/chemrxiv.9250340.v1 | Total Synthesis and Structural Revision of a Harziane Diterpenoid | The first total synthesis of nominal harziane
diterpenoid is disclosed, whose spectral
characteristics did not match those of the reported natural product. Stereochemical
analysis and subsequent synthesis of the epimeric tertiary alcohol led to
reassignment of configuration of the natural product. At the heart of the synthesis is an
enyne cycloisomerization that sets a key quaternary stereocenter within a
cyclobutane with high diastereocontrol. The route features strategies for the synthesis
of the highly congested 6–5–7–4 carbon skeleton characteristic of the caged harziane
diterpenoids. | Moritz Honig; Erick Carreira | Natural Products | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7438b469df43d7ef431f5/original/total-synthesis-and-structural-revision-of-a-harziane-diterpenoid.pdf |
646c8e3cccabde9f6e390aea | 10.26434/chemrxiv-2023-c5q6w-v2 | Density functional theory study of hydrophobic zeolites for the removal of triclosan from aqueous solution | The chlorinated biphenyl ether triclosan (TCS), used as a disinfectant in health care settings and in various personal care products, is an emerging organic contaminant of significant concern. Adsorption-based methods have been proposed as one potential pathway for the removal of TCS from wastewaters. Hydrophobic high-silica zeolites could constitute suitable adsorbent materials for such applications. In order to gauge the impact of pore size, topology, and framework composition, the adsorption of TCS in six different all-silica zeolites (AFI, BEA, CFI, FAU, IFR, MOR frameworks) and two highly siliceous protonated zeolites (H-FAU, H-MOR) was investigated using dispersion-corrected density functional theory (DFT). While pore size was found to affect the interaction strength, the rather flexible TCS molecule can adjust to different pore shapes, resulting in very similar adsorption energies for most all-silica zeolites. Although the interaction with TCS is enhanced in protonated zeolites, the affinity towards water increases even more. In DFT-based molecular dynamics simulations of TCS and water co-adsorption, H2O molecules quickly replace TCS in the vicinity of the framework protons, deprotonating the framework and forming positively charged clusters. In addition to delivering atomic-level insights into TCS adsorption, the calculations indicate that a fine-tuning of pore size with a concurrent maximization of hydrophobicity should constitute a promising strategy to develop optimized zeolite adsorbents for TCS removal. | Michael Fischer | Theoretical and Computational Chemistry; Earth, Space, and Environmental Chemistry; Hydrology and Water Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646c8e3cccabde9f6e390aea/original/density-functional-theory-study-of-hydrophobic-zeolites-for-the-removal-of-triclosan-from-aqueous-solution.pdf |
61a93dfc63557c8a5294a8af | 10.26434/chemrxiv-2022-gb47v | Deep eutectic solvents comprising creatine and citric acid and their hydrated mixtures | We report the phase diagram for the binary creatine–citric acid mixture which features a stable and broad eutectic region. Combinations containing 10–60 mol% creatine yield a deep eutectic solvent with a glass transition temperature at 270 K. Addition of up to 70 mol% water to the binary mixture affords retention of the eutectic nature and a handle to vary solvent viscosity and polarity. | Matthew Heaney; Laxmi Adhikari; Asher Siegel ; Kyle Pekar; Jonathan Lefton; Claire Lamberti ; Pokpong Rungthanaphatsophon ; Justin R. Walensky ; Gary Baker; Tomce Runcevski | Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Thermodynamics (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a93dfc63557c8a5294a8af/original/deep-eutectic-solvents-comprising-creatine-and-citric-acid-and-their-hydrated-mixtures.pdf |
6601902ce9ebbb4db97eb362 | 10.26434/chemrxiv-2024-r58cx | Atomically smooth CeO2(001) films on YSZ(001) | CeO2 is a non-inert support material for heterogeneous catalysis applications. Here, we present a facile growth procedure for the preparation of CeO2(0 0 1) thin films supported by YSZ(0 0 1) suitable for combined catalytic and structural investigations. Detailed structural and chemical analysis of the films was conducted directly after UHV preparation and after a tube furnace annealing step giving rise to significant restructuring of the film. Complete characterization using AFM, cross-section HR-STEM, GIXRD, XPS, and polarization-resolved IRRAS showed that the film is fully oxidized and atomically flat with a coherent crystal lattice over the full film thickness. A dislocation network at the interface compensates the lattice mismatch between film and the YSZ support, yielding a film with bulk in plane lattice parameters and small tensile out of plane strain. The surface of the CeO2 film is bulk terminated, and stabilized by the presence of hydroxyl groups for polarity compensation. | Jan-Christian Schober; Esko Erik Beck; Ming-Chao Kao; Mona Kohantorabi; Marcus Creutzburg; Dmitry Novikov; Birger Holtermann; Nadejda Firman; Lachlan Caulfield; Eric Sauter; Vedran Vonk; Christof Wöll; Yuemin Wang; Heshmat Noei; Yolita Eggeler; Andreas Stierle | Materials Science; Nanoscience; Catalysts; Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6601902ce9ebbb4db97eb362/original/atomically-smooth-ce-o2-001-films-on-ysz-001.pdf |
672f4886f9980725cfa57997 | 10.26434/chemrxiv-2024-z2k6b-v2 | Synthesis and Reactivity of an Olefin Metathesis-Catalyzing Ruthenium Complex with a Selenoether Moiety in the Benzylidene Ligand | A Hoveyda-Grubbs (HG)-type olefin metathesis complex with a selenoether moiety at the terminal of phenoxy moiety was synthesized. The complex showed a Se-coordination to the ruthenium center, resulting in its higher thermostability than the parent HG catalyst. The Se-coordinative property enhanced product yields in the ring-closing metathesis of N-tosyldiallylamine in the presence of methanol. The large activation enthalpy observed in the reaction with butyl vinyl ether indicated an increased contribution of “dissociative mechanism” during the initiation of the catalytic cycle. Introducing coordinative atoms or functional groups at the terminal of the phenoxy moiety is a useful strategy to regulate the thermostability of HG-type olefin metathesis catalysts. | Tsubasa Kinugawa; Seishu Mitsusada; Naoki Orito; Takashi Matsuo | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Organometallic Compounds; Coordination Chemistry (Organomet.); Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672f4886f9980725cfa57997/original/synthesis-and-reactivity-of-an-olefin-metathesis-catalyzing-ruthenium-complex-with-a-selenoether-moiety-in-the-benzylidene-ligand.pdf |
60c740de567dfe6ba8ec3c6d | 10.26434/chemrxiv.7848179.v1 | Chemical Reaction Stoichiometry: A Key Link between Thermodynamics and Kinetics, and an Excel Implementation | <div>The Law of Conservation of Mass (LCM) is one of the most important principles in chemistry. It applies to both closed and steady-state open flow systems undergoing chemical change. Various special methods are generally taught for its implementation, including inspection, oxidation-reduction, and ion-electron approaches, which typically fall under the topic of "balancing a chemical equation". However, apart from the simplest case described by a single such equation, only matrix methods are applicable.</div><div><br /></div><div>This paper describes Chemical Reaction Stoichiometry (CRS), and its implementation of the LCM for chemically reacting systems by its expression in terms of a nonunique set of independent chemical equations of the appropriate number. Such equations have the superficial appearance of, but are distinct from, an actual chemical reaction mechanism. The underlying matrix method is based on ideas from basic linear algebra; in addition to being generally applicable to systems of any complexity, it obviates the need for the aforementioned special methods in single-reaction systems.</div><div><br /></div><div>We provide an easy-to-use spreadsheet implementation of CRS that includes many worked examples.</div> | Leslie Glasser; William Smith | Chemical Education - General; Bioinformatics and Computational Biology; Thermodynamics (Chem. Eng.); Chemical Kinetics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740de567dfe6ba8ec3c6d/original/chemical-reaction-stoichiometry-a-key-link-between-thermodynamics-and-kinetics-and-an-excel-implementation.pdf |
60c74885567dfe6065ec49fb | 10.26434/chemrxiv.11914992.v1 | Artificially Produced UV Light and Challenging Photoreactions Enabled by Upconversion in Water | Sensitized triplet-triplet annihilation is the most promising mechanism for pooling the energy of two visible photons, but its applications in solution were so far limited to organic solvents, with a current maximum of the excited-singlet state energy of 3.6 eV. By combining tailor-made iridium complexes with naphthalenes, we demonstrate blue-light driven upconversion in water with unprecedented singlet-state energies approaching 4 eV. The annihilators have outstanding excited-state reactivities enabling challenging photoreductions driven by sTTA. Specifically, we found that an aryl-bromide bond activation can be achieved with blue photons, and we obtained full conversion for the very energy-demanding decomposition of a persistent ammonium compound as typical water pollutant, not only with a cw laser but also with an LED light source. These results provide the first proof-of-concept for the usage of low-power light sources for challenging reactions employing blue-to-UV upconversion in water, and pave the way for the further development of sustainable light-harvesting applications. | Björn Pfund; Debora M. Steffen; Mirjam R. Schreier; Maria-Sophie Bertrams; Chen Ye; Karl Börjesson; Oliver S. Wenger; Christoph Kerzig | Transition Metal Complexes (Inorg.); Photocatalysis; Catalysis; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74885567dfe6065ec49fb/original/artificially-produced-uv-light-and-challenging-photoreactions-enabled-by-upconversion-in-water.pdf |
60c742af469df4a179f43023 | 10.26434/chemrxiv.8427116.v1 | Chemically Accurate Excitation Energies With Small Basis Sets | <p>By combining extrapolated selected configuration interaction (sCI) energies obtained with the CIPSI (Configuration Interaction using a Perturbative Selection made Iteratively) algorithm with the recently proposed short-range density-functional correction for basis-set incompleteness [Giner et al., J. Chem. Phys. 2018, 149, 194301], we show that one can get chemically accurate vertical and adiabatic excitation energies with, typically, augmented double-ζ basis sets. We illustrate the present approach on various types of excited states (valence, Rydberg, and double excitations) in several small organic molecules (methylene, water, ammonia, carbon dimer and ethylene). The present study clearly evidences that special care has to be taken with very diffuse excited states where the present correction does not catch the radial incompleteness of the one-electron basis set.</p> | Emmanuel Giner; Anthony Scemama; Julien Toulouse; Pierre-Francois Loos | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742af469df4a179f43023/original/chemically-accurate-excitation-energies-with-small-basis-sets.pdf |
60c75899bb8c1a1df83dca6b | 10.26434/chemrxiv.14564529.v1 | Acoustofluidic Medium Exchange for Preparation of Electrocompetent Bacteria Using Channel Wall Trapping | Transformation, i.e. reprogramming of bacteria by delivering exogenous genetic material (such as DNA) into the cytoplasm, is a key process in molecular engineering and modern biotechnology in general. Transformation is often performed by electroporation, i.e. creating pores in the membrane using electric shocks in a low conductivity environment. However, cell preparation for electroporation can be cumbersome as it requires the exchange of growth medium (high-conductivity) for low-conductivity medium, typically performed via multiple time-intensive centrifugation steps. To simplify and miniaturize this step, we developed an acoustofluidic device capable of trapping the bacterium <i>Escherichia coli </i>non-invasively for subsequent exchange of medium, which is challenging in acoustofludic devices due to detrimental acoustic streaming effects. <br />With an improved etching process, we were able to produce a thin wall between two microfluidic channels, which, upon excitation, can generate streaming fields that complement the acoustic radiation force and therefore can be utilized for trapping of bacteria. Our novel design robustly traps <i>Escherichia coli</i> at a flow rate of 10 µL minute<sup>-1</sup> and has a cell recovery performance of 47 ± 3 % after washing the trapped cells.<br />To verify that the performance of the medium exchange device is sufficient, we tested the electrocompetence of the recovered cells in a standard transformation procedure and found a transformation efficiency of 8∙10<sup>5</sup> CFU per µg of plasmid DNA. Our device is a viable low-volume alternative to centrifugation-based methods and opens the door for miniaturization of a plethora of microbiological and molecular engineering protocols.<br /> | Michael Gerlt; Peter Ruppen; Moritz Leuthner; Sven Panke; Jürg Dual | Bioengineering and Biotechnology; Microbiology | CC BY 4.0 | CHEMRXIV | 2021-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75899bb8c1a1df83dca6b/original/acoustofluidic-medium-exchange-for-preparation-of-electrocompetent-bacteria-using-channel-wall-trapping.pdf |
60c750b7567dfe345eec58f8 | 10.26434/chemrxiv.13076030.v1 | Accurate, Automated Density Functional Theory for Complex Molecules Using On-the-fly Error Correction | High-throughput density functional theory (DFT) has been widely utilized to study a variety of materials and molecular properties. However, its application to complex molecular systems, including those relevant to electrochemical reactivity and decomposition, has been limited by insufficient automation.Here, we report a broadly applicable, automated framework for the accurate and robust DFT calculation of molecules, capable of addressing species relevant to electrochemistry. This framework is specifically designed to study molecules with different charge states, open-shell electronic structure, metal coordination, and implicit solvation. We first identify appropriate levels of theory that avoid calculation failures and accurately predict molecular redox potentials. We then describe our framework, including methods to automatically detect and correct errors and to optimize structures from saddle points to potential energy surface minima. To demonstrate the efficacy of this framework, we examine a case study including over 12,000 calculations of reactive molecular fragments. This framework is able to reduce the rate of failure for DFT calculations from 25.1% to 1.2%, significantly improving the degree of automation possible for high-throughput molecular DFT. | Samuel Blau; Evan Walter Clark Spotte-Smith; Brandon Wood; Shyam Dwaraknath; Kristin Persson | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750b7567dfe345eec58f8/original/accurate-automated-density-functional-theory-for-complex-molecules-using-on-the-fly-error-correction.pdf |
620d044749bd3231585236d2 | 10.26434/chemrxiv-2022-mzdpm | Bright Room-Temperature Phosphorescence from Mixed Mothballs Enabling Specific Identification of the Illegal Component | Ultralong organic room-temperature phosphorescence (RTP) with high brightness was rarely achieved to date despite their huge potential in various applications such as lighting, sensing, anti-counterfeiting and imaging. Herein, by exploiting π-π* nature of the lowest excited triplet state of naphthalene (NL, the traditional active ingredient for mothball) and intersystem crossingpromoting factors from 1,4-dichlorobenzene (DCB, a safer alternative to NL as mothball), we report a simple and novel guest/host
system, namely NL/DCB, that could produce strong green RTP with quantum yield > 20% and lifetime > 0.76 s (afterglow duration > 10 s) at ambient conditions. The RTP performance with simultaneous high efficiency and ultralong lifetime is superior to that of most purely organic (metal-free) RTP materials reported so far. Control experiments with different hosts and first-principle theoretical calculations revealed that the robust RTP behavior in the unique NL/DCB system was mainly attributed to a combination of clusterexciton formation and external heavy atom effect. Meanwhile, the remarkable “turn-on” type RTP to naked eyes allows fast and
specific detection of illegal NL mothball using DCB as a sensor, which is valuable in household as well as industrial applications. | Xuepeng Zhang; Junkai Liu; Biao Chen; Xuewen He; Xueyu Li; Peifa Wei; Peng Fei Gao; Guoqing Zhang; Jacky W. Y. Lam; Ben Zhong Tang | Physical Chemistry; Clusters; Interfaces; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620d044749bd3231585236d2/original/bright-room-temperature-phosphorescence-from-mixed-mothballs-enabling-specific-identification-of-the-illegal-component.pdf |
67dac9066dde43c9086a88d2 | 10.26434/chemrxiv-2025-zlh66-v2 | Catalytic Glutathione Oxidation and Platinum(IV) Prodrug Activation via a Ruthenium-Flavin Catalyst | Cyclopentadienyl (Cp) Ru(IV) quinoline complexes are known for their role in bioorthogonal catalysis within cellular environments, where they use endogenous GSH to deprotect profluorescent and prodrug substrates. However, their reactivity toward GSH and potential for redox-mediated therapies remain underexplored. This study presents RuQ-TARF, a Cp-Ru(IV) complex with a quinoline ligand linked to 2',3',4',5'-tetraacetylriboflavin (TARF) as a redox-active moiety. Its catalytic activity in oxidizing GSH and activating a Pt(IV) prodrug of oxaliplatin was investigated. RuQ-TARF catalyzes the oxidation of GSH to GSSG, improving electron transfer compared to RuQ, its flavin-free analogue. LC-MS analysis showed that activating the Pt(IV) prodrug with GSH produces multinuclear Pt(II)-GS species. RuQ-TARF was additionally evaluated during co-incubation with GSH and NADH under blue light, where NADH enabled faster activation of the prodrug, producing oxaliplatin as confirmed by 195Pt NMR. Cyclic voltammetry showed that linking TARF to RuQ improves the reversibility of redox processes, enhancing catalytic performance and supporting its use in combined GSH oxidation and prodrug activation strategies. | Juan Sánchez-Camacho; Ana C. Carrasco; German E. Pieslinger; Álvaro Martínez; Ryszard Lobinski; Luisa Ronga; Luca Salassa | Biological and Medicinal Chemistry; Inorganic Chemistry; Catalysis; Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Redox Catalysis | CC BY NC 4.0 | CHEMRXIV | 2025-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dac9066dde43c9086a88d2/original/catalytic-glutathione-oxidation-and-platinum-iv-prodrug-activation-via-a-ruthenium-flavin-catalyst.pdf |
60c74356ee301c7f49c78f97 | 10.26434/chemrxiv.9104858.v1 | Nanoscale Mapping of Non-Uniform Heterogeneous Nucleation Kinetics Mediated by Surface Chemistry | <p>Nucleation underlies the formation of many liquid-phase
synthetic and natural materials with applications in materials chemistry, geochemistry,
biophysics, and structural biology. Most liquid-phase nucleation processes are
heterogeneous, occurring at specific nucleation sites at a solid-liquid
interface; however, the chemical and topographical identity of these nucleation
sites and how nucleation kinetics vary from site-to-site remains mysterious. Here
we utilize <i>in situ</i> liquid cell electron
microscopy to unveil counterintuitive nanoscale non-uniformities in
heterogeneous nucleation kinetics on a macroscopically uniform solid-liquid
interface. Time-resolved <i>in situ</i> electron
microscopy imaging of silver nanoparticle nucleation at a water-silicon nitride
interface showed apparently randomly-located nucleation events at the interface.
However, nanometric maps of local nucleation kinetics uncovered nanoscale interfacial
domains with either slow or rapid nucleation. Interestingly, the interfacial
domains vanished at high supersaturation ratio, giving way to rapid spatially
uniform nucleation kinetics. Atomic force microscopy and nanoparticle labeling
experiments revealed a topographically flat, chemically heterogeneous interface
with nanoscale interfacial domains of functional groups similar in size to those
observed in the nanometric nucleation maps. These results, along with a
semi-quantitative nucleation model, indicate that a chemically non-uniform
interface presenting different free energy barriers to heterogeneous nucleation
underlies our observations of non-uniform nucleation kinetics. Overall, our
results introduce a new imaging modality, nanometric nucleation mapping, and
provide important new insights into the impact of surface chemistry on microscopic
spatial variations in heterogeneous nucleation kinetics that have not been
previously observed.</p> | Mei Wang; Thilini Umesha Dissanayake; Chiwoo Park; Karen J. Gaskell; Taylor Woehl | Nanostructured Materials - Materials; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74356ee301c7f49c78f97/original/nanoscale-mapping-of-non-uniform-heterogeneous-nucleation-kinetics-mediated-by-surface-chemistry.pdf |
633c6993f764e654610e2779 | 10.26434/chemrxiv-2022-20mll | Plasma-Enhanced Molecular Layer Deposition of Phosphane-ene Polymer Films | A vapour phase molecular layer deposition (MLD) process generating phosphorus-rich phosphane-ene polymer networks was adapted from known solution phase methods and successfully used in a commercial atomic layer deposition tool. By using plasma-enhanced MLD on Si/SiO2 and Al2O3 substrates, film deposition was carried out with a commercially available primary phosphine, iBuPH2, paired with a known volatile cyclic siloxane precursor, tetramethyltetravinylcyclotetrasiloxane (D4Vinyl). The deposition process used radicals generated by an Ar plasma source to facilitate P-H addition to vinyl functionalities on D4Vinyl which yielded a growth per cycle of 0.6 – 2.0 Å, generating 10-120 nm films as determined by AFM and SEM measurements. Characterization of the films were carried out using X-ray photoelectron spectroscopy and oxygen scavenging capabilities were studied using a quartz crystal microbalance, showing an uptake of oxygen by a 12 nm depth of a freshly deposited polymer film. | Justin Lomax; Eden Goodwin; Peter Gordon; Christine McGuiness; Floryan Decampo; Sean Barry; Paul Ragogna | Polymer Science; Nanoscience; Inorganic Polymers; Nanofabrication; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633c6993f764e654610e2779/original/plasma-enhanced-molecular-layer-deposition-of-phosphane-ene-polymer-films.pdf |
62f1caa15f6870398bb16448 | 10.26434/chemrxiv-2022-d9l0f | β-NiOOH is An Active Electrocatalyst for the Ammonia Oxidation Reaction Predicted by Density Functional Theory | The electrocatalyzed ammonia oxidation reaction (AOR) is an ambient temperature and pressure process with potential applications for sustainable energy generation and waste ammonia treatment. In this work, we study the mechanism of ammonia oxidation towards N2, NO2– , and NO3– on the (0001) β-NiOOH surface and compare the computed free energy of reaction intermediates to results previously obtained on (0001) β-Ni(OH)2. NiOOH surfaces with a hydroxide vacancy favoured NH2–NH2 coupling and reduced the theoretical onset potential for N2, NO2–, and NO3– relative to the β-Ni(OH)2 surface. The surface with an oxygen vacancy favoured NH–NH coupling, and had lower onset potentials for N2 and NO2– formation relative to the β-Ni(OH)2 surface, while NO3– formation was slightly hindered due to its increased stabilization of the precursor adsorbate, *NO2. In general, the NiOOH surface had lower computed onset potentials compared to the Ni(OH)2 surface due to the destabilization of certain adsorbates which form thermodynamic sinks in the AOR pathway, leading to differences in the potential-determining step for the formation of N2 and NO2–. This work sheds light on the ammonia electrooxidation mechanism on β-NiOOH and predicts the material to be a much more active electrocatalyst compared to β-Ni(OH)2. | Rachelle M. Choueiri; Leanne D. Chen | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f1caa15f6870398bb16448/original/ni-ooh-is-an-active-electrocatalyst-for-the-ammonia-oxidation-reaction-predicted-by-density-functional-theory.pdf |
6271188311b146be8a39966d | 10.26434/chemrxiv-2022-mpgk2 | Two types of liquid phase separation induced by soft centrifugation in aqueous ethyl acetate using ethanol as co-solvent | Water-ethyl acetate-ethanol is widely used as “green” extractant system. We show that two different types of phase separation can be induced upon centrifugation in this ternary system using ethanol as a co-solvent of water and ethyl acetate (EA): centrifuge-induced criticality and centrifuge-induced emulsification. The expected composition profiles of samples after centrifugation can be represented by bent lines in a ternary phase diagram when gravitational energy is added to the free energy of mixing. The experimental equilibrium composition profiles behave qualitatively as expected and can be predicted using a phenomenological theory of mixing. The concentration gradients are small except near the critical point, as expected for small molecules. Nevertheless, they are usable when accompanied by temperature cycles. These findings open new possibilities of centrifugal separation, even if control is delicate during temperature cycles. These schemes are accessible even at relatively low centrifugation speed for molecules that float and sediment with apparent molar masses several hundred times larger than the molecular mass. | Helmut Coelfen; Rose Rosenberg; Dirk Haffke; Simon Stemplinger; Thomas Zemb; Dominik Horinek | Physical Chemistry; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6271188311b146be8a39966d/original/two-types-of-liquid-phase-separation-induced-by-soft-centrifugation-in-aqueous-ethyl-acetate-using-ethanol-as-co-solvent.pdf |
667017c701103d79c56499b9 | 10.26434/chemrxiv-2024-b713v-v2 | Modular Open-access and Open-source julia language Toolbox for Processing of HRMS Data: jHRMSToolBox | There is a growing need for understanding the exposome chemical space. Non-target analysis is, generally, used for the analysis of the thousand of known and unknown chemicals in environmentally and biologically relevant samples. However, algorithm limitations arise with regard to flexibility and suitability for the processing of such data. Hence, the modular open-access and open-source jHRMS toolbox was developed, providing both a user-interface and the freedom to modify and add workflows as required. The default implemented algorithms have been developed for high-resolution mass spectrometry data and can handle MS1 and various data-dependent and data-independent analysis data types both in profile and centroided formats. Moreover, the identification algorithm provides extensive match quality reporting. Besides the data processing workflow, the toolbox comes with built in post processing (i.e., visualization) for individual steps of the workflow and statistical analysis. Finally, the results are reported step-by-step, parameters can be saved, and it is operating system agnostic. To showcase the potential of the jHRMS toolbox, two datasets from different origins environmental and biological were analyzed and reported. For the environmental case study the trends of some pharmaceuticals in river waters were evaluated. While for the biological samples it was possible to differentiate between liver and brain tissues based on the extracted information. | Denice van Herwerden; Etienne Kant; Miranda Jackson; Chloe Fender; Manuel Garcia-Jaramillo; Jake O'Brien; Kevin Thomas; Saer Samanipour | Analytical Chemistry; Chemoinformatics; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2024-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667017c701103d79c56499b9/original/modular-open-access-and-open-source-julia-language-toolbox-for-processing-of-hrms-data-j-hrms-tool-box.pdf |
667a7f9001103d79c5143610 | 10.26434/chemrxiv-2024-x5ggt | Nanoconfinement geometry of pillared V2O5 determines electrochemical ion intercalation mechanism and diffusion pathway | Improving electrochemical ion intercalation capacity and kinetics in layered host materials is a critical challenge to further develop lithium-ion batteries, as well as emerging cell chemistries based on ions beyond lithium. Modification of the nanoconfined interlayer space within host materials by synthetic pillaring approaches has emerged as a promising strategy, however, the resulting structural properties of host materials, host-pillar interaction, as well as evolving structure-functionality relations remain poorly understood. Herein, a series of bilayered V2O5 host materials pillared with alkyldiamine molecules of different lengths is systematically studied, resulting in tunable nanoconfinement geometry with interlayer spacings in the range of 1.0-1.9 nm. The electrochemical Li+ intercalation capacity is increased from approx. 1 to 1.5 Li+ per V2O5 in expanded host materials, and the intercalation kinetics improve with larger expansion. Operando X-ray diffraction reveals a transition of the charge storage mechanism from solid-solution Li+ intercalation in V2O5 hosts with small and medium interlayer spacings, to cointercalation of Li+ and solvent in V2O5 with the largest interlayer spacing. Density functional theory reveals a transition in Li+ diffusion pathways from 1D to 2D diffusional networks for expanded interlayers. The work reveals the impact of nanoconfinement geometry within bilayered V2O5 on the resulting Li+ intercalation properties, providing insights into both the microstructure and related functionality of pillared materials. | Jameela Karol; Charles O. Ogolla; Manuel Dillenz; Mohsen Sotoudeh; Ellen Vollmer; Maider Zarrabeitia; Axel Groß; Benjamin Butz; Simon Fleischmann | Theoretical and Computational Chemistry; Energy; Energy Storage; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-06-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667a7f9001103d79c5143610/original/nanoconfinement-geometry-of-pillared-v2o5-determines-electrochemical-ion-intercalation-mechanism-and-diffusion-pathway.pdf |
63ac27a7518c16a2bc3b2a54 | 10.26434/chemrxiv-2022-gdmdh-v2 | Exploring battery cathode materials in the Li-Ni-O phase diagrams using structure prediction | The Li-Ni-O phase diagram contains several electrochemically active ternary phases. Many compositions and structures in this phase space can easily be altered by (electro-)chemical processes, yielding many more (meta-)stable structures with interesting properties. In this study, we use ab initio random structure searching (AIRSS) to accelerate materials discovery of the Li-Ni-O phase space. We demonstrate that AIRSS can efficiently explore structures (e.g. LiNiO2) displaying dynamic Jahn-Teller effects. A thermodynamically stable Li2Ni2O3 phase which reduces the thermodynamic stability window of LiNiO2 was discovered. AIRSS also encountered many dynamically stable structures close to the convex hull. Therefore, we confirm the presence of metastable Li-Ni-O phases by revealing their structures and properties. This work will allow Li-Ni-O phases to be more easily identified in future experiments and help to combat the challenges in synthesizing Li-Ni-O phases. | Jiayi Cen; Bonan Zhu; David Scanlon | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ac27a7518c16a2bc3b2a54/original/exploring-battery-cathode-materials-in-the-li-ni-o-phase-diagrams-using-structure-prediction.pdf |
639231b57b7c916379e8fb7a | 10.26434/chemrxiv-2022-k6wft | A machine learning approach to model interaction effects: development and application to alcohol deoxyfluorination | The application of machine learning (ML) techniques to model high-throughput experimentation (HTE) datasets has seen a recent rise in popularity. Nevertheless, the ability to model the interplay between reaction components, known as interaction effects, with ML remains an outstanding challenge. Using a simulated HTE dataset, we find that the presence of irrelevant features poses a strong obstacle to learning interaction effects with common ML algorithms. To address this problem, we propose a two-part statistical modeling approach for HTE datasets: classical analysis of variance (ANOVA) of the experiment to identify systematic effects that impact reaction yield across the experiment, followed by regression of individual effects using chemistry-informed features. To illustrate this methodology, we use our previously published alcohol deoxyfluorination dataset comprising 740 reactions to build compact, interpretable regression models that account for each significant effect observed in the dataset. We achieve a sizeable performance boost compared to our previously published Random Forest model, reducing mean absolute error (MAE) from 18.1% to 13.4% and root mean squared error (RMSE) from 21.7% to 16.5% on a newly generated test set. Finally, we demonstrate that this approach can facilitate the generation of new mechanistic hypotheses which, when probed experimentally, can lead to a deeper understanding of chemical reactivity. | Andrzej Zuranski; Shivaani Gandhi; Abigail Doyle | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Physical Organic Chemistry; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2022-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639231b57b7c916379e8fb7a/original/a-machine-learning-approach-to-model-interaction-effects-development-and-application-to-alcohol-deoxyfluorination.pdf |
60c7544ef96a00d0a128862e | 10.26434/chemrxiv.13643432.v1 | One Step Photochemical Synthesis of Surface-Supported Naked Gold Nanoparticles and Its Application as a SERS Substrate | <p>A direct and straightforward method is proposed to synthetize a surface-supported gold nanoparticles mediated by pulsed laser irradiation of quartz surfaces in contact with a gold precursor solutions. The substrates´ performance as SERS sensors is tested by the Rhodamine 6G (R6G) Raman signal enhancement.</p> | Pablo A. Mercadal; Sergio David Garcia Schejtman; Fernando P. Cometto; Alicia V. Veglia; Eduardo A. Coronado | Nanostructured Materials - Materials; Spectroscopy (Anal. Chem.); Nanodevices; Nanofabrication; Nanostructured Materials - Nanoscience; Sensors; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7544ef96a00d0a128862e/original/one-step-photochemical-synthesis-of-surface-supported-naked-gold-nanoparticles-and-its-application-as-a-sers-substrate.pdf |
61acc8fd48e4bc0633fc27f9 | 10.26434/chemrxiv-2021-mk8zv | Variation between Antiferromagnetism and Ferrimagnetism in NiPS3 by Electron Doping | How to electrically control magnetic properties of a magnetic material is promising towards spintronic applications, where the investigation of carrier doping effects on antiferromagnetic (AFM) materials remains challenging due to their zero net magnetization. In this work, we found electron doping dependent variation of magnetic orders of a two-dimensional (2D) AFM insulator NiPS3, where doping concentration is tuned by intercalating various organic cations into the van der Waals gaps of NiPS3 without introduction of defects and impurity phases. The doped NiPS3 shows an AFM-ferrimagnetic (FIM) transition at doping level of 0.2-0.5 electrons/cell and a FIM-AFM transition at doping level of ≥0.6 electrons/cell. We propose that the found phenomenon is due to competition between Stoner exchange dominated inter-chain ferromagnetic order and super-exchange dominated inter-chain AFM order at different doping level. Our studies provide a viable way to exploit correlation between electronic structures and magnetic properties of 2D magnetic materials for realization of magnetoelectric effect. | Mengjuan Mi; Xingwen Zheng; Shilei Wang; Yang Zhou; Lixuan Yu; Han Xiao; Houning Song; Bing Shen; Fangsen Li; Lihui Bai; Yanxue Chen; Shanpeng Wang; Xiaohui Liu; Yilin Wang | Materials Science; Nanoscience; Magnetic Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61acc8fd48e4bc0633fc27f9/original/variation-between-antiferromagnetism-and-ferrimagnetism-in-ni-ps3-by-electron-doping.pdf |
60c74224bdbb89d972a3843a | 10.26434/chemrxiv.8209304.v1 | Electrically Enhanced Hydrogen Adsorption in Metal-Organic Frameworks | <p>Using a multiscale approach, we show that
applied electric field does not affect significantly the hydrogen
uptake of weakly polarizable metal-organic frameworks (MOFs).
Nonetheless, we show that, for large MOF polarizabilities, the
hydrogen uptake can double in applied electric field. We propose
searching for a novel class of hydrogen storage materials, that of
highly polarizable porous MOFs. Hydrogen uptake in such materials would
be controlled by electric field, a much easier to adjust parameter
than pressure or temperature.</p> | Liviu Zarbo; Marius Oancea; Emmanuel Klontzas; Emmanuel Tylianakis; Ioana G. Grosu; George E. Froudakis | Hydrogen Storage Materials; Computational Chemistry and Modeling; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74224bdbb89d972a3843a/original/electrically-enhanced-hydrogen-adsorption-in-metal-organic-frameworks.pdf |
657979dcfd283d7904e521d5 | 10.26434/chemrxiv-2023-lvc7w-v2 | Azole reagents enabled ligation of peptide acyl pyrazoles for chemical protein synthesis | Native chemical ligation (NCL) has been playing an increasingly important role in chemical protein synthesis (CPS), more efficient ligation methods that circumvent the requirement of peptidyl thioester and thiol additive—which allow the following desulfurization or refolding in one pot—are urgently needed for the synthesis of more complex protein targets and in large quantities. Herein, we discover that the weak acyl donor peptidyl N-acylpyrazole can be activated by azole reagents like 3-methylpyrazole or imidazole to facilitate its ligation directly with an N-terminal cysteine peptide. As it requires no thioester and thiol additive, this ligation strategy can be conveniently combined with metal-free desulfurization (MFD) or oxidative protein folding to allow various one-pot protocols. The utility and generality of the strategy are showcased by the total synthesis of ubiquitin via an N-to-C sequential ligation-MFD strategy, the semi-synthesis of a copper protein azurin, and the efficient assembly of a sulfated hirudin variant and the cyclotide kalata B1, all in a one-pot fashion. | Peisi Liao; Chunmao He | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657979dcfd283d7904e521d5/original/azole-reagents-enabled-ligation-of-peptide-acyl-pyrazoles-for-chemical-protein-synthesis.pdf |
642c0169a029a26b4ce4a296 | 10.26434/chemrxiv-2022-dt0lk-v2 | Dual Chalcogen-bonding interactions for the conformational control of urea | Dual chalcogen-bonding interactions is proposed as a novel means for the conformational control of urea derivatives. The formation of a chalcogen-bonding interaction at both sides of the urea carbonyl group was unambiguously confirmed by X-ray diffraction and natural bond orbital (NBO) analysis via DFT calculations. By virtue of this dual interaction, urea derivatives that bear chalcogen atoms (X = S and Se) adopt a planar structure via the carbonyl oxygen (O) with an X•••O•••X arrangement on the same side of the molecule. The rigidity of the conformational lock was evaluated using the molecular arrangement in the crystal and the rotational barrier of benzochalcogenophene ring, which indicated a stronger conformational lock in benzoselenophene than in benzothiophene urea derivatives. Furthermore, the acidity of the urea derivatives increases according to the Lewis-acidic properties of the chalcogen-bonding interactions, whereby benzoselenophene urea is more acidic than benzothiophene urea. Tweezer-shaped urea derivatives were prepared, and their stereostructure proved the viability of the conformational control for defining the location of the substituents on the urea framework. | Takumi Furuta; Takumi Inoue; Moe Ota; Yui Amijima; Haru Takahashi; Shohei Hamada; Yusuke Kobayashi; Takahiro Sasamori | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642c0169a029a26b4ce4a296/original/dual-chalcogen-bonding-interactions-for-the-conformational-control-of-urea.pdf |
62718ce2ed4d886934228c41 | 10.26434/chemrxiv-2022-bmhx1 | Unraveling the Electrocatalytic Reduction Mechanism of Enols on Copper in Aqueous Media | A mechanism is proposed for the direct electrochemical deoxygenation of aldehydes to alkenes and alkanes which has implications in refining biomass-derived fuels for use as transportation fuel, as a potential green synthesis strategy for terminal olefins in aqueous, ambient conditions, and in understanding the reaction pathway for CO2 to C2 and C3 products. Here we report the electrochemical conversion of vinyl alcohol and acetaldehyde on polycrystalline Cu to ethanol, ethylene and ethane; and propenol and propionaldehyde to propanol, propene and propane. Sensitive detection was achieved using a rotating disk electrode coupled with gas chromatography-mass spectrometry (RDE-GC-MS). In situ attenuated total reflection surface-enhanced infrared absorption spectroscopy (ATR-SEIRAS), and in situ Raman spectroscopy confirmed the adsorption of the vinyl alcohol. Calculations using canonical and grand-canonical density functional theory (DFT and GC-DFT), along with experimental findings suggest that the rate-determining step (RDS) for ethylene and ethane formation is an electron transfer step to the adsorbed vinyl alcohol. Finally, we extend our conclusions to enols resulting from higher-order soluble aldehyde and ketone. | Zhihao Cui; Xing'an Dong; Sung Gu Cho; Weidong Dai; Fan Dong; Anne C. Co | Catalysis; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62718ce2ed4d886934228c41/original/unraveling-the-electrocatalytic-reduction-mechanism-of-enols-on-copper-in-aqueous-media.pdf |
63dca891cdb6a7f57b37d7ee | 10.26434/chemrxiv-2023-qfrc0 | Tailoring Dynamic Hydrogels by Controlling Associative Exchange Rates | Dithioalkylidenes are a recently-developed class of conjugate acceptors that undergo thiol exchange via an associative mechanism and have been used for reprocessable vitrimers, amine sensors, and degradable networks. Here, we show that the exchange rate of the reaction in aqueous environments is highly sensitive to the structure of the acceptor and may be varied over four orders of magnitude. Cyclic acceptors exchange rapidly, from 0.95 to 15.6 M-1s-1, while acyclic acceptors exchange between 3.77x10-3 and 2.17x10-2 M-1s-1. Computational, spectroscopic, and structural data suggest that the cyclic acceptors are more reactive than their linear counterparts because of resonance stabilization of the tetrahedral intermediate. We leverage this insight to design a compound with reactivity intermediate to that of the cyclic and linear analogs. Lastly, we incorporate this dynamic bond into hydrogels and demonstrate that molecular kex correlates with the hydrogels characteristic stress relaxation time; furthermore, these values may be parametrized with respect to computed descriptors of the electrophilic site. This work opens new avenues to design and control hydrogel viscoelasticity with an associative exchange mechanism. | Vivian Zhang; Joseph Accardo; Ilia Kevlishvili; Eliot Woods; Steven Chapman; Christopher Eckdahl; Heather Kulik; Julia Kalow | Organic Chemistry; Polymer Science; Physical Organic Chemistry; Hydrogels | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63dca891cdb6a7f57b37d7ee/original/tailoring-dynamic-hydrogels-by-controlling-associative-exchange-rates.pdf |
67157049b91c6e99719d084a | 10.26434/chemrxiv-2024-gm3h4 | Graphene-Based Single-Atom Catalysts for Electrochemical CO2 Reduction: Unraveling the Roles of Metals and Dopants in Tuning Activity | Discovering electrocatalysts that can efficiently convert carbon dioxide (CO2) to valuable fuels and feedstocks using excess renewable electricity is an emergent carbon-neutral technology. A single metal atom embedded in doped graphene, i.e., single-atom catalyst (SAC), possesses high activity and selectivity for electrochemical CO2 reduction (CO2R) to CO, yet further reduction to hydrocarbons is challenging. Here, using density functional theory calculations, we investigate stability and reactivity of a broad SAC chemical space with various metal centers (3d transition metals) and dopants (2p dopants of B, N, O; 3p dopants of P, S) as electrocatalysts for CO2R to methane and methanol. We observe that the rigidities of these SACs depend on the type of dopants, with 3p-coordinating SACs exhibiting more severe out-of-plane distortion than 2p-coordinating SACs. Using CO adsorption energy as a descriptor for CO2R reactivity, we narrow down the candidates and identify seven SACs with near-optimal CO binding strength. We then elucidate full reaction mechanisms towards methane and methanol generation on these identified candidates and observe highly dopant-dependent activity and rate-limiting steps, divergent from conventional mechanistic understanding on metallic surfaces, calling into question whether previous design principles established on metals are directly transferrable to SACs. Consequently, we find that zinc embedded in boron-doped graphene (Zn-B-C) is a highly active catalyst for electrochemical CO2R to C1 hydrocarbons. Our work reveals the opportunities of tuning SAC reactivity via engineering dopants and metals and highlights the importance of re-elucidating CO2R reaction mechanisms on SACs towards unearthing new design principles for SAC chemistry. | Colin Gallagher; Manish Kothakonda; Qing Zhao | Theoretical and Computational Chemistry; Catalysis; Theory - Computational; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67157049b91c6e99719d084a/original/graphene-based-single-atom-catalysts-for-electrochemical-co2-reduction-unraveling-the-roles-of-metals-and-dopants-in-tuning-activity.pdf |
63b6a4aa4ba57312d56b7641 | 10.26434/chemrxiv-2023-kwmdh-v2 | Synthesis and characterization of J and H aggregate-forming carbazole-based diketopyrrolopyrrole materials | The aggregation of molecules in devices plays a central role in determining their functional properties. In the aggregated state, p conjugated chromophores can exhibit enhanced emission in comparison to their dilute solution. Here we synthesize and characterize a diketopyrrolopyrrole (DPP) based donor-acceptor molecule in terms of its optical properties in solution and thin film. Temperature and concentration dependent photoluminescence studies reveal the presence of both H and J aggregates in thin film, which is corroborated by computational investigations of the coulombic coupling in the crystal structure of the DPP derivative. We find that the type of aggregate formed is extremely sensitive to the relative arrangement of the monomers in the crystal structure geometry. | Aritrajit Gupta; Ashish Sarkalya; Ramesh Ganduri; Jayashree Nagesh; Satish Patil | Organic Chemistry; Physical Organic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b6a4aa4ba57312d56b7641/original/synthesis-and-characterization-of-j-and-h-aggregate-forming-carbazole-based-diketopyrrolopyrrole-materials.pdf |
60c742acee301c412dc78ea9 | 10.26434/chemrxiv.8275358.v1 | How to Analyse Chemical Compounds? A Guide to Compositional Data Analysis Demonstrated with Beer Data | <p>In recent years, a lot of analysis was carried out to investigate data on chemical compositions of (non-)alcoholic beverages (whiskey, wine, beer, etc.) and food. However, no study has ever considered the compositional pitfalls inherent in such studies, which may lead to arbitrary results. Two approaches were compared, compositional data analysis (CoDa) and classical statistical analyses. The outcome of compositional data analysis methods provided very well-interpretable results. The method we are proposing is novel in the field of food chemistry, with demonstrated ability to analyse the chemical composition of drinks and food.</p> | Matthias Templ; Barbara Templ | Chemoinformatics; Food | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742acee301c412dc78ea9/original/how-to-analyse-chemical-compounds-a-guide-to-compositional-data-analysis-demonstrated-with-beer-data.pdf |
60c75931842e65ca39db49ab | 10.26434/chemrxiv.14671575.v1 | In0.5Ga0.5N Layers by Atomic Layer Deposition | <p><b>We present an ALD
approach to metastable In<sub>1‑x</sub>Ga<sub>x</sub>N with 0.1 < x < 0.5
based on co-sublimed solid In- and Ga-precursors that were co-sublimed into the
deposition chamber in one pulse. A near In<sub>0.5</sub>Ga<sub>0.5</sub>N film
with a bandgap of 1.94 eV was achieved on Si (100) substrate. Epitaxial In<sub>1‑x</sub>Ga<sub>x</sub>N
(0002) was successfully grown directly on 4H-SiC (0001). </b></p> | Polla Rouf; Justinas Palisaitis; Babak Bakhit; Nathan O'Brien; Henrik Pedersen | Materials Processing; Thin Films; Ligands (Inorg.); Main Group Chemistry (Inorg.); Solid State Chemistry; Surface; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75931842e65ca39db49ab/original/in0-5ga0-5n-layers-by-atomic-layer-deposition.pdf |
674623947be152b1d0f24867 | 10.26434/chemrxiv-2024-2v1nx | HEPOM: Using Graph Neural Networks for the accelerated predictions of Hydrolysis Free Energies in different pH conditions. | Hydrolysis is a fundamental family of chemical reactions where water facilitates the cleavage of bonds. The process is ubiquitous in biological and chemical systems, owing to water's remarkable versatility as a solvent. However, accurately predicting the feasibility of hydrolysis through computational techniques is a difficult task, as subtle changes in reactant structure like heteroatom substitutions or neighboring functional groups can influence the reaction outcome. Furthermore, hydrolysis is sensitive to the pH of the aqueous medium, and the same reaction can have different reaction properties at different pH conditions. In this work, we have combined reaction templates and high-throughput ab-initio calculations to construct a diverse dataset of hydrolysis free energies. The developed framework automatically identifies reaction centers, generates hydrolysis products, and utilizes a trained Graph Neural Network(GNN) model to predict values for all potential hydrolysis reactions in a given molecule. The long-term goal of the work is to develop a data-driven, computational tool for high-throughput screening of pH-specific hydrolytic stability and the rapid prediction of reaction products, which can then be applied in a wide array of applications including chemical recycling of polymers and ion-conducting membranes for clean energy generation and storage. | Rishabh D. Guha; Santiago Vargas; Evan Walter Clark Spotte-Smith; Alexander Rizzolo Epstein; Maxwell Venetos; Ryan Kingsbury; Mingjian Wen; Samuel Blau; Kristin A. Persson | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674623947be152b1d0f24867/original/hepom-using-graph-neural-networks-for-the-accelerated-predictions-of-hydrolysis-free-energies-in-different-p-h-conditions.pdf |
676050a56dde43c9085b4ccd | 10.26434/chemrxiv-2024-c660p | SMILES All Around: Structure to SMILES conversion for Transition Metal Complexes | We present a method for creating RDKit parsable SMILES for transition metal complexes (TMCs) based on xyz-coordinates and overall charge of the complex. This can be viewed as an extension to the program xyz2mol that does the same for organic molecules. The only dependency is RDKit, which makes it widely applicable. One thing that has been lacking when it comes to generating SMILES from structure for TMCs is an existing SMILES dataset to compare with. Therefore, sanity-checking a method has required manual work. Therefore, we also generate SMILES two other ways; one where ligand charges and TMC connectivity are based on natural bond orbital (NBO) analysis from density functional theory (DFT) calculations utilizing recent work by Kneiding et al. (Digital Discovery 2023, 2, 618-633). Another one fixes SMILES available through the Cambridge Structural Database (CSD), making them parsable by RDKit. We compare these three different ways of obtaining SMILES for a subset of the CSD (tmQMg) and find >70% agreement for all three pairs. We utilize these SMILES to make simple molecular fingerprint (FP) and graph-based representations of the molecules to be used in the context of machine learning. Comparing with the graphs made by Kneiding et al. where nodes and edges are featurized with DFT properties, we find that depending on the target property (polarizability, HOMO-LUMO gap or dipole moment) the SMILES based representations can perform equally well. This makes them very suitable as baseline-models. Finally we present a dataset of 227k RDKit parsable SMILES for mononuclear TMCs in the CSD. | Maria H. Rasmussen; Magnus Strandgaard; Julius Seumer; Laura K. Hemmingsen; Angelo Frei; David Balcells; Jan H. Jensen | Theoretical and Computational Chemistry; Organometallic Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676050a56dde43c9085b4ccd/original/smiles-all-around-structure-to-smiles-conversion-for-transition-metal-complexes.pdf |
60f337c48ae3a7520978c0bd | 10.26434/chemrxiv-2021-zg1d4 | Guided Inquiry in Sophomore Organic Lecture: Deducing Mechanisms by Reaction Mapping | Arrow-pushing mechanisms can be understood more readily if the changes from starting material to product are systematically charted. This can be done by labeling the relevant atoms in the starting material and in the product, then making lists of the bonds to be broken and the bonds to be formed. | Douglass Taber | Organic Chemistry; Chemical Education | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f337c48ae3a7520978c0bd/original/guided-inquiry-in-sophomore-organic-lecture-deducing-mechanisms-by-reaction-mapping.pdf |
63d7ffca5391e5d2ea6bd177 | 10.26434/chemrxiv-2023-m8w37 | DFT Studies of Pt8V4Fe14 Nanoparticles and the O2 Adsorption | The ability to produce cheap and efficient catalysts for oxygen reduction is essential for cost reduction in fuel cells. This work reports the density functional theory (DFT) results of the investigation of ~1 nm trimetallic nanocatalysts of 26 atoms with a composition of Pt8V4Fe14. The relative stability of ~50 Pt8V4Fe14 nanoparticles (NPs) were analyzed to conclude that the most stable NPs had vanadium atoms located at the center of the NP with scattered platinum atoms attached to them from the outside. Adsorption of O2 on the most stable nanocatalyst was also analyzed at 14 various adsorption sites; it was determined that oxygen preferred to bond to vanadium and iron atoms located at the surface of the NP. Compared to the small sub-nanometer PtVFe clusters of the same composition, the O2 adsorption strength is slightly decreased on the ~1nm PtVFe NPs. These findings provided important insights into the effectiveness of PtVFe nanocatalysts towards oxygen reduction. | Kristof Toth; Lichang Wang | Theoretical and Computational Chemistry; Catalysis; Energy; Computational Chemistry and Modeling; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d7ffca5391e5d2ea6bd177/original/dft-studies-of-pt8v4fe14-nanoparticles-and-the-o2-adsorption.pdf |
60c74920bb8c1aac2d3dadc4 | 10.26434/chemrxiv.12033630.v1 | Enhanced Performance Induced by Phase Transition of Li2FeSiO4 upon Cycling at High Temperature | <p>Owing to its low cost, thermal
stability and theoretically high capacity, Li<sub>2</sub>FeSiO<sub>4 </sub>has
been a promising cathode material for high-energy-density Li-ion (Li<sup>+</sup>)
battery system. However, its poor rate performance and high voltage polarisation
attributed to innately slow Li<sup>+</sup> kinetics at room temperature, has
fundamentally curbed its ascent into prominence. Here, the rate performance of
Li<sub>2</sub>FeSiO<sub>4</sub> at high temperatures in electrolyte comprising
molten salt (ionic liquid) was investigated. Subsequently, a comparison of the
phase transition behaviour observed at both high-temperature and room-temperature
cycling was elucidated. Our results show that remarkable rate performance with
good cyclability in conjunction with low voltage polarisation is attained upon
cycling of Li<sub>2</sub>FeSiO<sub>4</sub> at high temperatures, due to the
faster phase transformation from unstable monoclinic structures to
thermodynamically stable orthorhombic structures triggered by elevated
temperature. What this study adds to the burgeoning body of research work
relating to the silicates is that the initially slow phase transformation behaviour
observed at room temperature can significantly be enhanced upon cycling at
elevated temperatures.</p> | Titus Masese; Yuki Orikasa; Kentaro Yamamoto; Yosuke Horie; Rika Hagiwara; Yoshiharu Uchimoto | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74920bb8c1aac2d3dadc4/original/enhanced-performance-induced-by-phase-transition-of-li2fe-si-o4-upon-cycling-at-high-temperature.pdf |
6448d41183fa35f8f644e712 | 10.26434/chemrxiv-2023-jk4h5 | Enzymatic Synthesis of L-Methionine Analogues and Application in a Methyltransferase Catalysed Alkylation Cascade | Chemical modification of small molecules is a key step for the development of pharmaceuticals. S-adenosyl-L-methionine (SAM) analogues are used by methyltransferases (MTs) to transfer alkyl, allyl and benzyl moieties chemo-, stereo- and regioselectively onto substrates, enabling an enzymatic way for specific derivatization of a wide range of molecules. L-Methionine analogues are required for the synthesis of SAM analogues. Most of these are not commercially available. In nature, O-acetyl-L-homoserine sulfhydrolases (OAHS) catalyse the synthesis of L methionine from O-acetyl-L-homoserine or L homocysteine, and methyl mercaptan. Here, we investigated the substrate scope of ScOAHS from Saccharomyces cerevisiae for the production of L methionine analogues from L homocysteine and organic thiols. The promiscuous enzyme was used to synthesise nine different L methionine analogues with modifications on the thioether residue up to a conversion of 75%. ScOAHS was combined with an established MT dependent three-enzyme alkylation cascade, allowing transfer of in total seven moieties onto two MT substrates. Ethylation was nearly doubled with the new four-enzyme cascade, indicating a beneficial effect of the in situ production of L methionine analogues with ScOAHS. | Michael Mohr; Raspudin Saleem-Batcha; Nicolas Cornelissen; Jennifer Andexer | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6448d41183fa35f8f644e712/original/enzymatic-synthesis-of-l-methionine-analogues-and-application-in-a-methyltransferase-catalysed-alkylation-cascade.pdf |
60c74127469df4be3af42dc6 | 10.26434/chemrxiv.7979717.v1 | Automated Detection and Characterization of Surface Restructuring Events in Bimetallic Catalysts | <div>Surface restructuring in bimetallic systems has recently been shown to play a crucial role in heterogeneous catalysis. In particular, the segregation in binary alloys can be reversed in the presence of strongly bound adsorbates. Mechanistic characterization of such restructuring phenomena at the atomic level remains scarce and challenging due to the large configurational space that must be explored. To this end, we propose an automated method to discover elementary surface restructuring processes in an unbiased fashion, using Pd/Ag as an example. We employ high-temperature classical molecular dynamics (MD) to rapidly detect restructuring events, isolate them, and optimize using density functional theory (DFT). In addition to confirming the known exchange descent mechanism, our systematic approach has revealed three new predominant classes of events at step edges of close-packed surfaces that have not been considered before: (1) vacancy insertion; (2) direct exchange; (3) interlayer exchange. The discovered events enable us to construct the complete set of mechanistic pathways by which Pd is incorporated into the Ag host in vacuum. These atomistic insights provide a step toward systematic understanding and engineering of surface segregation dynamics in bimetallic catalysts.</div> | Jin Soo Lim; Nicola Molinari; Kaining Duanmu; Philippe Sautet; Boris Kozinsky | Alloys; Computational Chemistry and Modeling; Theory - Computational; Heterogeneous Catalysis; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74127469df4be3af42dc6/original/automated-detection-and-characterization-of-surface-restructuring-events-in-bimetallic-catalysts.pdf |
60c73dd8702a9be289189c71 | 10.26434/chemrxiv.6213701.v1 | Synthesis of 1,2,5,6- and 1,4,5,8-Anthracenetetrone: Building Blocks for π-Conjugated Small Molecules and Polymers | Reliable
reactions for the synthesis of two interesting
anthracenetetrones have been identified and optimized. Both syntheses
start from dihydroxy-9,10-anthraquinones and were selected for
maximized efficiency and minimized work load. Work-up of all
reactions can be achieved without column chromatography, which
facilitates further scale-up. So far, both target compounds are
considerably underexplored despite their promising molecular
structure for use in devices and in organic
synthesis, especially as building blocks for π-conjugated compounds.
The crystal structure of 1,4,5,8-anthracentetrone is reported. | Florian Glöcklhofer; Berthold Stöger; Johannes Fröhlich | Organic Synthesis and Reactions; Organic Polymers | CC BY 4.0 | CHEMRXIV | 2018-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd8702a9be289189c71/original/synthesis-of-1-2-5-6-and-1-4-5-8-anthracenetetrone-building-blocks-for-conjugated-small-molecules-and-polymers.pdf |
676fe2c8fa469535b90fa1c3 | 10.26434/chemrxiv-2024-mgsgh | Capturing the sol and gel states of thermoresponsive polyoxazoline / -oxazine hydrogels by ambient and subambient solid-state NMR | Recently it was shown that ABA-type triblock copolymers with pPheOzi as central B-block undergo a cooling induced order-order transition from spherical to worm-like micelles accompanied by inverse thermogelation. Previous attempts to modulate the chemical structure of the pPheOzi block prevented worm-formation or even thermogelation. Here, two novel polymer variants were synthesized bearing -CH3 or -OCH3 at the para-position of the phenyl group of pMeOx-b-pPheOzi-b-pMeOx. Rheological, µDSC and AFM analyses proved thermogelation and formation of worm-like micelles of pMeOx-b-pMeOPheOzi-b-pMeOx, while pMeOx-b-pMePheOzi-b-pMeOx remains a sol of spherical micelles. In order to understand the macroscopic phenomena at the molecular level, a detailed NMR study has been carried out. NMR spectroscopy in solution was used to visualize the subset of mobile polymer moieties in the corona, whereas rigid moieties were analysed in-detail by solid-state NMR. Intermediate motions can interfere with classical solid-state NMR analyses, but freezing the samples successfully improved the visibility of moieties in this dynamic regime. Combining solid-state NMR of frozen samples with DSC revealed three types of water —non-freezable bound, freezable-bound, and free water— with indications for water also being present in the core of micelles and worms. Based on the complementary insights due to the additional frozen sol- and gel-state NMR experiments, the -OCH3 within the B-block could also be identified to stabilize the core-water interaction leading to prolonged thermal stability for the new pMeOx-b-pMeOPheOzi-b-pMeOx gels. | Theresa Zorn; Stephanie Bachmann; Lando Polzin; Johannes Greiner; Robert Luxenhofer; Ann-Christin Pöppler | Materials Science; Analytical Chemistry; Polymer Science; Core-Shell Materials; Hydrogels | CC BY NC 4.0 | CHEMRXIV | 2024-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676fe2c8fa469535b90fa1c3/original/capturing-the-sol-and-gel-states-of-thermoresponsive-polyoxazoline-oxazine-hydrogels-by-ambient-and-subambient-solid-state-nmr.pdf |
60c74333bb8c1a2b573da2b6 | 10.26434/chemrxiv.8976881.v1 | Modeling Interfacial Electron Transfer in the Double Layer: The Interplay Between Electrode Coupling and Electrostatic Driving | This manuscript presents a theoretical model for simulating interfacial electron transfer reactions within the electrical double layer. This model resolves the population density of redox active species and simulated electron transfer at the level of Marcus theory, with a fluctuating solvent polarization coordinate. In this model, the kinetics and thermodynamics of electron transfer depend on the values of the electronic coupling of species (to the electrode) and the electrical potential drop, respectively. | Aditya Limaye; Adam Willard | Electrochemistry - Mechanisms, Theory & Study; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74333bb8c1a2b573da2b6/original/modeling-interfacial-electron-transfer-in-the-double-layer-the-interplay-between-electrode-coupling-and-electrostatic-driving.pdf |
60c7529a0f50dbd8743979f9 | 10.26434/chemrxiv.13325690.v1 | Molecular Docking Approaches to Suggest the Anti-Mycobacterial Targets of Natural Products | Tuberculosis (TB) is a major global threat mostly due to the development of antibiotic resistant forms of Mycobacterium tuberculosis, the causal agent of the disease. Driven by the pressing need for new anti-mycobacterial agents, several natural products (NPs) have been shown to have in vitro activities against M. tuberculosis. The utility of any NP as a drug lead is augmented when the anti-mycobacterial target(s) is unknown. To suggest these, we used a molecular docking approach to predict the interactions of 53 selected anti-mycobacterial NPs against known ‘druggable’ mycobacterial targets ClpP1P2, DprE1, InhA, KasA, PanK, PknB and Pks13. The docking scores / binding free energies were predicted and calculated using AutoDock Vina along with physicochemical and structural properties of the NPs, using PaDEL descriptors. These were compared to the established inhibitor (control) drugs for each mycobacterial target. The specific interactions of the bisbenzylisoquinoline alkaloids 2-nortiliacorinine, tiliacorine and 13’-bromotiliacorinine against the targets PknB and DprE1
(-11.4, -10.9 and -9.8 kcal.mol-1
; -12.7, -10.9 and -10.3 kcal.mol-1 , respectively) and the lignan αcubebin and Pks13 (-11.0 kcal.mol-1 ) had significantly superior docking scores compared to controls. Our approach can be used to suggest predicted targets for the NP to be validated experimentally but these in silico steps are likely to facilitate drug optimisation. | Rafael Baptista; Sumana Bhowmick; Shen Jianying; Luis Mur | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7529a0f50dbd8743979f9/original/molecular-docking-approaches-to-suggest-the-anti-mycobacterial-targets-of-natural-products.pdf |
67a9b25d6dde43c908419f8f | 10.26434/chemrxiv-2025-vwxfq | Microalgae as source for SLA 3D printing resin | 3D printers are becoming common household and laboratory appliances thanks to the possibility of producing physical objects in a short time, at low cost, low waste and tailored to the needs of each user. One of the most widely used types of 3D printers is the stereolithography SLA or the masked stereolithography (m)SLA, which uses light to photo crosslink a liquid resin to solid objects layer by layer. 3D printable resins consist of numerous components, with the biggest part consisting of usually methacrylates or acrylates. However, contrary to the trend of reducing plastic consumption, the methacrylates used for SLA resins are mainly petroleum derivatives. Bio-based options made with soybean oil have become commercially available in the last few years. These oils are not very sustainable as soybeans have a high demand for land and water use, and there is competition for using soy as food/feed or for materials. In contrast to soybeans, microalgae have simple nutrient requirements and do not need arable land or freshwater, excluding them from competition with crops. They also have a high CO₂ fixation and can produce and store a high oil content of up to 75% by biomass weight, which can be used for the production of the resin. Here, we show how to produce 3D printable resins based on microalgal oil. Starting from a commercial microalgal oil, we perform epoxidation and methacrylation reactions on it to obtain reactive groups usable for polymerization. Subsequently, we formulated an SLA resin that we 3D printed and analyzed the mechanical performance. | Sabrina Fonzo; Antigoni Bougatsia; Alfredo de la Peña Gonzales; Iulian Boboescu; Carl Safi; Lambertus Antonius Maria van den Broek; Herman de Beukelaer; Aldrik H Velders; vittorio saggiomo | Polymer Science | CC BY 4.0 | CHEMRXIV | 2025-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a9b25d6dde43c908419f8f/original/microalgae-as-source-for-sla-3d-printing-resin.pdf |
664cc02e91aefa6ce19894ae | 10.26434/chemrxiv-2024-0ls3m | Computational Screening of Putative Catalyst Transition Metal Complexes as Guests in a Ga4L6–12 Nanocage | Metal-organic cages form well-defined microenvironments that can enhance the catalytic proficiency of encapsulated transition metal catalysts (TMCs). We introduce a screening protocol to efficiently identify TMCs that are promising candidates for encapsulation in the Ga4L6-12 nanocage. We obtain TMCs from the Cambridge Structural Database with geometric and electronic characteristics amenable to encapsulation and mine the text of associated manuscripts to curate TMCs with documented catalytic functionality. By docking candidate TMCs inside the nanocage cavity and carrying out electronic structure calculations, we identify a subset of successfully optimized candidates (TMC-34) and observe that encapsulated guests occupy an average of 60% of the cavity volume, in line with previous observations. Notably, highly charged guests occupy as much as 72% of the cavity as a result of linker rotation. Encapsulation has a universal effect on the electrostatic potential, systematically decreasing the electrostatic potential at the metal center of each TMC in the TMC-34 dataset, while minimally altering TMC metal partial charges. Collectively these observations support geometry-based screening of potential guests and suggest that encapsulation in Ga4L6 cages could electrostatically stabilize diverse cationic or electropositive intermediates. We highlight candidate guests with associated known reactivity and solubility most amenable for encapsulation in experimental follow-up studies. | Clorice Reinhardt; Melissa Manetsch; Wanlu Li; Teresa Head-Gordon; Heather Kulik | Theoretical and Computational Chemistry; Inorganic Chemistry; Supramolecular Chemistry (Inorg.); Transition Metal Complexes (Inorg.); Theory - Computational; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664cc02e91aefa6ce19894ae/original/computational-screening-of-putative-catalyst-transition-metal-complexes-as-guests-in-a-ga4l6-12-nanocage.pdf |
67581b47085116a133ed6b0b | 10.26434/chemrxiv-2024-0jn77 | Assessing the performance of coupled-trajectory schemes on full-dimensional two-state linear vibronic coupling models | We investigate the performance of coupled-trajectory methods for nonadiabatic molecular dynamics in simu- lating the photodynamics of 4-(dimethylamino)benzonitrile (DMABN) and fulvene, with electronic structure provided by linear vibrational coupling models. We focus on the coupled-trajectory mixed quantum-classical (CTMQC) algorithm and on the (combined) coupled-trajectory Tully surface hopping (C)CTTSH in com- parison to independent-trajectory approaches, such as multi-trajectory Ehrenfest and Tully surface hopping. Our analysis includes not only electronic populations but also additional electronic and nuclear properties in position and momentum space. For both DMABN and fulvene, the recently-developed CCTTSH algorithm successfully resolves the internal inconsistencies of CTTSH. Instead, we find that DMABN highlights a sig- nificant weakness of CTMQC, which arises when the trajectories remain for long time in the vicinity of a region of strong nonadiabaticity. | Peter Schürger; Lea Ibele; David Lauvergnat; Federica Agostini | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67581b47085116a133ed6b0b/original/assessing-the-performance-of-coupled-trajectory-schemes-on-full-dimensional-two-state-linear-vibronic-coupling-models.pdf |
60c74c36842e654139db3283 | 10.26434/chemrxiv.12449297.v1 | Correlation Between Water Molecules Identified in Atomic Models of Beta-Galactosidase Determined by Cryo-EM and X-Ray Crystallography | <p>We start from the water placement in cryo-EM maps and in X-ray crystal structures of beta-galactosidase. We apply MD simulations to analyze the behavior of the placed water, and how they are bound to the protein residues. We analyze the solvent exposure of binding sites for water, and the water residence time at these locations. Through a statistical analysis, we conclude that water placed by cryo-EM has a similar behavior to conserved water across multiple crystal structures.</p> | Florentina Tofoleanu; Lesley Earl; Frank Pickard; Bernard Brooks | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c36842e654139db3283/original/correlation-between-water-molecules-identified-in-atomic-models-of-beta-galactosidase-determined-by-cryo-em-and-x-ray-crystallography.pdf |
62ac20f520a4ed149541e02d | 10.26434/chemrxiv-2022-rfbhd | Comparison and risk assessment of trace metal content in factory-farmed broiler and free-range chicken meat sold in Laguna, Philippines | Chicken meat consumption remains high in the Philippines, and consequently, annual chicken production has risen steadily over the years. Although most of the chicken meat available in the market are sourced from factory farms, there has been growing popularity of free-range chicken production, largely driven by its perceived health benefits and sanitation concerns in factory farms, among others. In this work, we aimed at comparing the trace metal (copper, iron, lead, manganese, and zinc) content of free-range and factory-farmed broiler chicken meat that are being sold in Laguna, Philippines. The samples were subjected to acid digestion and analysis was done using atomic absorption spectrometry. Results showed an average concentration between 0.17 – 0.24 mg/kg, 2.22 – 2.34 mg/kg, 0.12 – 0.15 mg/kg, 0.95 – 1.32 mg/kg, and 1.81 – 1.96 mg/kg for copper, iron, lead, manganese, and zinc, respectively. Statistical analysis using one-way ANOVA and Tukey multiple comparison test (p < 0.05) showed no significant differences in the trace metal content of free-range and factory-farmed chicken meats, suggesting that in terms of the levels of these trace metals, not much differentiates the two varieties. Analysis of the health hazards, reported as target hazard quotient (THQ) and hazardous index (HI), associated with the consumption of the said chicken breast meat indicated no potential health risks. | Monique Estrella; Aileen Fritz Samson; Rafael Espiritu | Agriculture and Food Chemistry; Food | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ac20f520a4ed149541e02d/original/comparison-and-risk-assessment-of-trace-metal-content-in-factory-farmed-broiler-and-free-range-chicken-meat-sold-in-laguna-philippines.pdf |
62d0b915a7d17ed0a85b7a2c | 10.26434/chemrxiv-2022-hkd5f | Towards High-Performance Metal-Organic-Framework-Based Solid-State Electrolytes: Tunable Structures and Electrochemical Properties | Metal–organic frameworks (MOFs) have been reported as promising solid-state electrolytes owing to their tunable porous structures and ion-sieving capability. However, it remains challenging to rationally design high-performance MOF electrolytes. Herein, we controllably synthesized a series of MOFs to study the effects of pore apertures and open metal sites on ion-transport properties and electrochemical stability of MOF electrolytes. We demonstrate that MOFs with non-redox-active metal centers can lead to a wider electrochemical stability window than those with redox-active centers. Pore aperture of MOFs dominates the uptake of lithium salt and thus ionic conductivity. Ab initio molecular dynamics simulations further demonstrate that open metal sites of MOFs can immobilize anions of lithium salt via Lewis acid–base interaction, leading to a high lithium-ion transference number. This work provides not only a platform for studying ion-transport properties in tunable MOF electrolytes, but also a design strategy for MOF electrolytes with the guide of structure–property relationships. | Panpan Dong; Xiahui Zhang; William Hiscox; Xiaoyu Li; Qiang Zhang; Min-Kyu Song | Theoretical and Computational Chemistry; Materials Science; Composites; Hybrid Organic-Inorganic Materials; Theory - Computational; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d0b915a7d17ed0a85b7a2c/original/towards-high-performance-metal-organic-framework-based-solid-state-electrolytes-tunable-structures-and-electrochemical-properties.pdf |
67d49dd6fa469535b940dbfe | 10.26434/chemrxiv-2025-67l8k | Descriptor of Non-Local Effects in Oxidative Surface Bonding in Metal-Oxides | The catalytic properties of transition metal oxides (TMOs) are largely defined by their surface bonding. However, an accurate description of adsorption in these systems remains elusive. In this study, we focus on the descriptors of catalytic activity oxygen evolution and reduction reactions using Integrated Crystal Orbital Hamiltonian Population (ICOHP), which was found to be a good descriptor recently.1,2 We use bond-decomposed analysis and expansion beyond the active site to propose an improved ICOHP descriptor which now includes non-local effects of adsorption. This approach is very effective for all systems including previously excluded d0-cases. The size extrapolated change in ICOHP leads to strong linear correlation which is close to unity for 4d and 5d and half of that for 3d. We assign this difference due to adsorption-induced changes in magnetic moments. We argue that non-bonding characteristic of 3d high-spin metals cannot be captured by ICOHP alone and propose tentative solution by adding contributions from crystal field energies. Overall, the size extrapolated approach to ICOHP descriptor not only improves the overall prediction accuracy but also highlights the importance of considering both local and more extended bonding environments in catalytic design of pure oxides and mixed oxides. | Neha Bothra; Ara Cho; Benjamin Comer; Kirsten Winther; Michal Bajdich | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d49dd6fa469535b940dbfe/original/descriptor-of-non-local-effects-in-oxidative-surface-bonding-in-metal-oxides.pdf |
60c7484d469df4a419f439c2 | 10.26434/chemrxiv.11886789.v1 | Urea-Catalyzed Functionalization of Unactivated C–H Bonds | Herein we report the 3,5bistrifluoromethylphenyl urea-catalyzed functionalization of unactivated C–H bonds. In this system, the urea catalyst mediates the formation of high-energy vinyl carbocations that undergo facile C–H insertion and Friedel–Crafts reactions. We introduce a new paradigm for these privileged scaffolds where the combination of hydrogen bonding motifs and strong bases affords highly active Lewis acid catalysts capable of ionizing strong C–O bonds. Despite the highly Lewis acidic nature of these catalysts that enables triflate abstraction from sp<sup>2</sup> carbons, these newly found reaction conditions allow for the formation of heterocycles and tolerate highly Lewis basic heteroaromatic substrates. This strategy showcases the potential utility of dicoordinated vinyl carbocations in organic synthesis.<br /> | Alex L. Bagdasarian; Stasik Popov; Benjamin Wigman; Wenjing Wei; woojin lee; Hosea Nelson | Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7484d469df4a419f439c2/original/urea-catalyzed-functionalization-of-unactivated-c-h-bonds.pdf |
669da75101103d79c502125d | 10.26434/chemrxiv-2024-j5dcn | Utilizing Reanalysis Datasets to Improve the Performance of Low-Cost Air Sensors in the Global South | A Low-cost sensors for particulate matter can provide high spatiotemporal resolution monitoring of air quality, especially in much of the Global South, and sub-Saharan Africa (SSA) in particular, where reference-grade instrumentation is often not available. However, ensuring high-quality data from low-cost sensor (LCS) platforms is essential. Until now, LCS required calibration by collocation with a reference-grade monitor to be used for more than qualitative studies of air quality, but reference-grade monitors are not available in many countries of the Global South. Since a key artifact in optical PM sensors is aerosol hygroscopic growth, we explore the viability of an alternative LCS calibration method: a hygroscopic growth correction factor using particle composition data from the MERRA-2 reanalysis dataset. We compare 3 different LCS located in 3 different areas of SSA – Kenya, Ghana, and South Africa - with 3 different calibration techniques: traditional linear calibrations with a reference-grade monitor, a κ-Köhler-derived correction with MERRA-2 data, and a random forest machine learning regression utilizing MERRA-2 and the regulatory-grade monitor. Random forest regressions using MERRA-2 particle composition data and collocation with a reference-grade monitor improve sensor performance to near that of regulatory-grade monitors. But even without collocation, a hygroscopic growth correction based on MERRA-2 particle composition alone can improve LCS PM2.5 performance by reducing mean-normalized bias to near-zero and reducing error by up to 40%. | Michael R Giordano; Matthias Beekmann; Emmanuel Appoh; Allison Hughes; Michael J Gatari; James Nimo; Moses N Njeru; Stuart Piketh; Albert Presto; Nyaga Waiguru; Daniel M. Westervelt; R Subramanian | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669da75101103d79c502125d/original/utilizing-reanalysis-datasets-to-improve-the-performance-of-low-cost-air-sensors-in-the-global-south.pdf |
60c751bff96a00111a2880a4 | 10.26434/chemrxiv.13198688.v1 | Automated Solubility Screening Platform Using Computer Vision | <p>Solubility screening is an essential, routine process that is often labour intensive. Robotic platforms have been developed to automate some aspects of the manual labour involved. However, many of the existing systems rely on traditional analytic techniques such as High Performance Liquid Chromatography or HPLC, which require pre-calibration for each compound and can be prohibitively expensive. In addition, automation is not typically end-to-end, requiring user intervention to move vials, establish analytical methods for each compound and interpret the raw data. We developed a closed-loop, flexible robotics system with integrated solid and liquid dosing capabilities that relies on computer vision and iterative feedback to successfully measure caffeine solubility in multiple solvents. After initial researcher input (<2 min), the system ran autonomously, screening five different solvent systems (20-80 min each). The resulting data matched values obtained using traditional manual techniques.</p> | Parisa Shiri; Veronica Lai; Tara Zepel; Daniel Griffin; Jonathan Reifman; Sean Clark; Shad Grunert; Lars Yunker; Sebastian Steiner; Henry Situ; Fan Yang; Paloma Prieto; Jason Hein | Solution Chemistry; Robotics | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751bff96a00111a2880a4/original/automated-solubility-screening-platform-using-computer-vision.pdf |
620a9479cbb4f402b0c0acd2 | 10.26434/chemrxiv-2022-2zq0r | Stable, π-conjugated radical anions of boron-nitrogen dihydroindeno[1,2-b]fluorenes | We have recently reported the synthesis and application of boron-nitrogen dihydroindeno[1,2-b]fluorene derivatives as acceptors in organic photovoltaic (OPV) devices. Their modest observed efficiencies may be related to the properties of their reduced congeners. In this work, we report two new members of this family of compounds prepared via the electrophilic borylation of 2,5-di-p-tolylpyrazine followed by an arylation of the boron centre with ZnAr2 reagents. Two derivatives, 1 (Ar = 2,4,6-F3C6H2) and 2 (Ar = C6F5) were synthesized, and their radical anions, 1•− and 2•−, were formed via chemical reductions with CoCp*2 and CoCp2, respectively. Through comparison of structural parameters, as well as spectroscopic and computational data, the unpaired electron in the radical anions is localized in the planar core of the molecule, and dimerization is disfavored as a result. However, unlike the neutral starting materials, 1•− and 2•− are reactive towards ambient atmosphere. These observations suggest that the reduced compounds are stable towards intrinsic degradation pathways but subject to extrinsic degradation in device operation. | Tony Nguyen; Tyler Hannah; Warren Piers; Benjamin Gelfand | Organic Chemistry; Inorganic Chemistry; Electrochemistry; Main Group Chemistry (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620a9479cbb4f402b0c0acd2/original/stable-conjugated-radical-anions-of-boron-nitrogen-dihydroindeno-1-2-b-fluorenes.pdf |
678fd8af6dde43c9089362ce | 10.26434/chemrxiv-2025-zvmvn | Watching Pseudomonas mevalonii HMG-CoA Reductase in Action | HMG CoA Reductase catalyzed the interconversion of a thioester, HMG CoA, and mevalonic acid, a key step in the isoprenoid pathway, through a complex reaction mechanism involving three distinct chemical steps with two molecules of cofactor and large-scale rearrangements of the enzyme. Here, we investigate the second step, the formation of a thiohemiacetal from CoA and mevaldehyde, using time resolved crystallography and molecular dynamics (MD) simulations. After triggering the reaction by a pH jump from pH 6.7 to pH9, the formation of the carbon-sulfur bond can be observed in the two structures at 2.5 and 4 minutes. The structures obtained close to the activated complex of the reaction serve as the starting point for MD simulations of different possible protonation states of the catalytically active residues. Changes to the active site geometry, specifically the residues Ser 85, Glu 83 and His 381 that are important for catalysis of the reaction are discussed in detail. This work demonstrates the applicability of the combination of time resolved crystallography using a pH trigger with D simulations to obtain a detailed view of a complex reaction in an enzyme active site. | Himani Patel; Vatsal Purohit; Calvin Steussy; Timothy Schmidt; Paul Helquist; Cynthia Stauffacher; Olaf Wiest | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Biophysics; Computational Chemistry and Modeling; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678fd8af6dde43c9089362ce/original/watching-pseudomonas-mevalonii-hmg-co-a-reductase-in-action.pdf |
67bfadfcfa469535b9169224 | 10.26434/chemrxiv-2024-4n4jc-v2 | Mechanical, Thermal, and Rheological Properties of Fish-Porcine Gelatin Microparticle Composites for Advanced 3D Biofabrication | Driven by the increasing need for the biofabrication of complex hydrogels, this work introduces a class of fish–porcine composite hydrogels that combine rapid, tunable photo-crosslinking with microparticle reinforcement for advanced 3D printing. Here, pre-crosslinked porcine gelatin (methacrylated porcine gelatin, MPG) microparticles are incorporated into a methacrylated fish gelatin (MFG) matrix to produce robust yet easily processable hydrogels. Nuclear Magnetic Resonance (NMR) confirmed the degree of methacrylation, while scanning electron microscopy (SEM) revealed the hierarchical porosity vital for tissue integration. Detailed Mastersizer measurements characterized the size distributions of the MPG microparticles, and rheological tests demonstrated the composite hydrogels’ strong shear-thinning behavior an essential trait for extrusion-based and embedded 3D printing. Thermal (TGA, DSC) and mechanical (compression) analyses show that the microparticle-reinforced hydrogels achieve improved thermal stability, adjustable mass swelling ratio, and customizable compressive moduli. As a proof of concept, these composites are validated in digital light processing (DLP) printing of microfluidic constructs and as a support bath for embedded printing of complex geometries. This platform provides a unique synergy of easy UV crosslinkability, tunable mechanical features, and 3D printing versatility. This advancement underscores the potential of these materials as a foundational platform in tissue engineering, opening new avenues for creating complex, biocompatible structures with customizable properties. | Syed M. Q. Bokhari; Mecit A. Alioglu; Grace L. Voronin; Jeffrey M. Catchmark | Biological and Medicinal Chemistry; Materials Science; Biological Materials; Composites; Granular Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bfadfcfa469535b9169224/original/mechanical-thermal-and-rheological-properties-of-fish-porcine-gelatin-microparticle-composites-for-advanced-3d-biofabrication.pdf |
67457201f9980725cff50fe6 | 10.26434/chemrxiv-2024-lqn9z | Operando Characterization of Porous
Nickel Foam Water Splitting Electrodes using Near Ambient Pressure X-ray Photoelectron
Spectroscopy | This study presents a practical approach for characterizing industrial water-splitting nickel foam electrodes under both cathodic and anodic conditions by employing synchrotron radiation near-ambient pressure X-ray photoelectron spectroscopy (NAP-XPS). The in-situ studies reveal quantitatively reduced and oxidized Ni species on the electrode surface by recording the Ni 2p3/2 signals after cycling the potential in cathodic and anodic regions, respectively. Operando studies demonstrate that a stable electrolyte film forms, allowing the probing of the solid/liquid interface under applied potentials. We attribute this stability to capillary forces within the porous structure of the foam, which enables the monitoring of surface deprotonation under anodic potentials and surface protonation under cathodic potentials. Given that the most common industrial alkaline water electrolyzer electrodes are based on nickel foams similar to the samples measured in this study, the demonstrated method offers a valuable approach for fundamental NAP-XPS examination directly on industrially employed electrodes. | Ramadan Chalil Oglou; Morten Linding Frederiksen; Zhaozong Sun; Marcel Ceccato; Andrey Shavorskiy; Jeppe Vang Lauritsen | Physical Chemistry; Catalysis; Nanoscience; Electrocatalysis; Spectroscopy (Physical Chem.); Surface | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67457201f9980725cff50fe6/original/operando-characterization-of-porous-nickel-foam-water-splitting-electrodes-using-near-ambient-pressure-x-ray-photoelectron-spectroscopy.pdf |
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