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61ae33680e35eb9ef796c3c6
|
10.26434/chemrxiv-2021-0wc9g-v3
|
Quantitative profiling and dynamics of mRNA modifications in Escherichia coli
|
mRNA methylation is an important regulator of many physiological processes in eukaryotes but has not been studied in depth in prokaryotes. In contrast to the large number of eukaryotic mRNA modifications that have been described, N6-methyladenosine (m6A) is the only modification of bacterial mRNA identified to date. Here, we used a gel electrophoresis-based RNA separation method and quantitatively analyzed the mRNA-specific modification profile of Escherichia coli using mass spectrometry. In addition to m6A, we provide evidence for the presence of 7-methylguanosine (m7G), and we found first hints for 5-methylcytidine (m5C), N6,N6-dimethyladenosine (m6,6A), 1-methylguanosine (m1G), 5-methyluridine (m5U), and pseudouridine (Ψ) in the mRNA of E. coli, which implies that E. coli has a complex mRNA modification pattern. Furthermore, we observed changes in the abundance of some mRNA modifications during the transition of E. coli from the exponential growth to the stationary phase as well as upon exposure to stress. This study reveals a previously underestimated level of regulation between transcription and translation in bacteria.
|
Dimitar Plamenov Petrov; Steffen Kaiser; Stefanie Kaiser; Kirsten Jung
|
Biological and Medicinal Chemistry; Microbiology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-12-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ae33680e35eb9ef796c3c6/original/quantitative-profiling-and-dynamics-of-m-rna-modifications-in-escherichia-coli.pdf
|
6707403051558a15efa71276
|
10.26434/chemrxiv-2024-5wpgn
|
Synthesis of D-glucono-1,4-lactones modified with linear saturated fatty acids and evaluation of their physical properties
|
To develop a novel low molecular–weight organogelator, D-glucono-1,4-lactones, in which all hydroxy groups were esterified with linear saturated fatty acids, were synthesized, and their gelation ability was evaluated. When a fatty acid was introduced, the six-membered ring D-glucono-1,5-lactone changed to a five-membered ring D-glucono-1,4-lactone, regardless of the length of the fatty acid. However, the gelation ability depended on the length of the fatty acid, and compounds esterified with palmitic acid (16 carbons) and stearic acid (18 carbons) showed a better gelation ability. Electron microscopy showed that the structure of the xerogels varied with the length of the fatty acids, with some forming a fiber structure and others forming plate-like crystals building up to a porous structure. In addition, their emulsification ability and crystal polymorphism were confirmed, and detailed polymorphic crystal analysis by FT-IR was performed to estimate the intermolecular packing structure at the molecular level.
|
Shiro Komba
|
Organic Chemistry; Supramolecular Chemistry (Org.)
|
CC BY 4.0
|
CHEMRXIV
|
2024-10-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6707403051558a15efa71276/original/synthesis-of-d-glucono-1-4-lactones-modified-with-linear-saturated-fatty-acids-and-evaluation-of-their-physical-properties.pdf
|
64a6aeb16e1c4c986be8bc73
|
10.26434/chemrxiv-2023-lg3cw
|
Systems chemistry of aminoacyl phosphates: Spontaneous and selective peptide oligomerisation in water driven by phase changes
|
The pathways and mechanisms that allow spontaneous and selective peptide elongation in aqueous abiotic systems remain unclear. Herein we work to uncover those pathways by following the systems chemistry of aminoacyl phosphates, the synthetic counterpart of aminoacyl adenylates. Thus, oligomers up to dodecamers were synthesized in one flask and on the minute time scale, where consecutive additions activated autonomous phase changes. The resulting phases arose from the high polar and reactive nature of the aminoacyl phosphates, which can be dissolved in water in concentrations of up to 300 mM. Upon elongation, short oligomers are prevalent in solution, while in the aggregated phase, longer oligomers are selected based on their aggregation propensity. We furthermore demonstrated that the solution phases can be isolated and act as a new environment for continuous elongation, by adding various phosphates. These findings suggest that the systems chemistry of aminoacyl phosphates can activate a selection mechanism for peptide formation, by merging aqueous synthesis and self-assembly.
|
Kun Dai; Mahesh Pol; Lenard Saile; Arti Sharma; Bin Liu; Ralf Thomann; Johanna Trefs; Danye Qiu; Sandra Moser; Stefan Wiesler; Bizan Balzer; Thorsten Hugel; Henning Jessen; charalampos Pappas
|
Organic Chemistry; Nanoscience
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-07-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a6aeb16e1c4c986be8bc73/original/systems-chemistry-of-aminoacyl-phosphates-spontaneous-and-selective-peptide-oligomerisation-in-water-driven-by-phase-changes.pdf
|
66c4376c20ac769e5f22ac9e
|
10.26434/chemrxiv-2024-fvgdq
|
Mixed1-ethyl-3-methylimidazoliumbis(trifluoromethylsulfonyl)imide/lithium bis(fluoromethylsulfonyl)imide based ionic liquid and carbonate co-solvents for Li-ion battery applications– analysis of transport properties using MD simulation
|
In this work, we examined the transport properties for different mixing ratios of 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide/lithium bis(fluoromethylsulfonyl)imide based ionic liquid and carbonate co-solvents using OPLS/AA force field. No single-solvent electrolyte can satisfy all the requirements of LIB electrolytes. For this reason, therefore, LIB electrolytes are often complex mixtures of multiple co-solvents with optimized properties. Our study finds that the addition of EC/DMC carbonate co-solvent mixtures into [EMI][TFSI]/1M LiFSI results in reduction in the values of the density of the mixture. By comparing the organic solvents EC/DMC with the IL solvents, the computed density of the pure IL/1M LiFSI system (no EC/DMC content) is higher than that of the EC/DMC/1M LiFSI system (no [EMI][TFSI] content). The relative increase in density with higher contents of IL/1M LiFSI system is suggestive of arising from the stronger interactions of [TFSI]- and [FSI]- anions with the Li+ ions as compared to the interaction of EC/DMC with Li+ ions. The behavior of the MSDs for the center-of-mass of the ions as a function of IL/carbonate co-solvent mixtures indicated that the ions exhibited slow dynamics (diffusivity) with higher carbonate content. Our study on the diffusion coefficient analysis of Li+, [FSI]- and [TFSI]- ions have revealed that the organic solvents restrict the free motion of the ions, reducing the dynamics (diffusivity) of the electrolytes. The simulation results also revealed that the total molar ionic conductivity for the different mixing ratios of IL/carbonate blends decrease with higher contents of EC/DMC co-solvents. Furthermore, the relative ionic contribution to the total molar conductivity of each individual cationic and anionic species increase with higher contents of IL in the IL/carbonate mixture, showing that higher carbonate co-solvents have the effects of reducing the molar ionic conductivity.
Key words: 1-ethyl-3-methylimidazolium, bis(trifluoromethylsulfonyl)imide, bis(fluoromethylsulfonyl)imide, DFT, MD, OPLS/AA.
|
Abraham Molla Wagaye; Henok Brehanu Abebe; Teketel Yohannes; Getachew Adam Workneh
|
Physical Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-08-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c4376c20ac769e5f22ac9e/original/mixed1-ethyl-3-methylimidazoliumbis-trifluoromethylsulfonyl-imide-lithium-bis-fluoromethylsulfonyl-imide-based-ionic-liquid-and-carbonate-co-solvents-for-li-ion-battery-applications-analysis-of-transport-properties-using-md-simulation.pdf
|
620fc43b7a054ab61c11ff75
|
10.26434/chemrxiv-2022-vw6vh-v2
|
On the Optical Properties of Colloidal Silver Nanowires
|
Silver nanowires are used in many applications, ranging from transparent conductive layers to Raman substrates and sensors. Their performance often relies on their unique optical properties that emerge from localized surface plasmon resonances in the ultraviolet. In order to tailor the nanowire geometry for a specific application, a correct understanding of the relationship between the wire’s structure and its optical properties is therefore necessary. However, while the colloidal synthesis of silver nanowires typically leads to structures with pentagonally-twinned geometries, their optical properties are often modeled assuming a cylindrical cross section. Here, we highlight the strengths and limitations of such an approximation by numerically calculating the optical and electrical response of pentagonally-twinned silver nanowires and nanowire networks. We find that our accurate modeling is crucial to deduce structural information from experimentally measured extinction spectra of colloidally-synthesized nanowire suspensions and to predict the performance of nanowire-based near-field sensors. On the contrary, the cylindrical approximation is fully capable of capturing the optical and electrical performance of nanowire networks used as transparent electrodes. Our results can help assess the quality of nanowire syntheses and guide in the design of optimized silver nanowire-based devices.
|
Ruben F. Hamans; Matteo Parente; Aitzol Garcia-Etxarri; Andrea Baldi
|
Physical Chemistry; Materials Science; Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-02-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620fc43b7a054ab61c11ff75/original/on-the-optical-properties-of-colloidal-silver-nanowires.pdf
|
60c749320f50db782f396892
|
10.26434/chemrxiv.12039888.v1
|
Nelfinavir Is Active Against SARS-CoV-2 in Vero E6 Cells
|
Utilizing
an integrative computational drug discovery approach, we predicted that
nelfinavir is a potential inhibitor of SARS-CoV-2 main protease. Further
docking nelfinavir to 30 potential target proteins of COVID-19, we found
that nelfinavir is most probably a multi-target agent. The half-maximal
effective concentration (EC<sub>50</sub>) of nelfinavir mesylate against
SARS-CoV-2 was 2.89±0.65 μM while that of remdesivir was 1.00±0.34 μM,
both drugs showed similar dose-response curves. Based on its high potency
against SARS-CoV-2 at cellular level, its higher exposure in lung than in
plasma, its good safe profile and its potential to reduce inflammation,
nelfinavir deserves further exploration for the treatment of COVID-19.
|
Zhijian Xu; Hangping Yao; Jingshan Shen; Nanping Wu; Yechun Xu; Xiangyun Lu; weiliang zhu; Lan-Juan Li
|
Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-03-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749320f50db782f396892/original/nelfinavir-is-active-against-sars-co-v-2-in-vero-e6-cells.pdf
|
60c749579abda286d3f8cbea
|
10.26434/chemrxiv.12053076.v1
|
Copper-Graphene-TiO2 Hybrid Materials for Photocatalytically Assisted H2 Generation
|
<p>Hydrogen, as energy carrier, is a
zero-emission fuel. Being green and clean, it is considered to play an
important role in energy and environmental issues. Photocatalytic water
splitting is a process used to generate hydrogen from the dissociation of
water. Titanium dioxide is still the archetype material for photocatalytic
water splitting. However, because of the fast recombination of the
photo-generated exciton, the yield of the reaction is typically low. In this
work, we have modified the surface of titanium dioxide with copper and
copper/graphene to sensitise it to visible light, and to increase the spatial
charge carrier separation, thus extending the quantum yield of H<sub>2</sub> production
from methanol/water mixtures. Results showed that, in the analysed system,
exists an optimum amount of copper plus graphene (<i>i.e.</i> 0.5 mol% copper plus 0.5 wt% graphene) to grant a two-fold
increase in the photocatalytic hydrogen generation compared to that of bare
titania. That system proved itself to be complex and dynamic. This was attributed to the increased spatial charge carrier separation exploited by graphene (under 365 and 405 nm irradiation), and to the continuous reduction of Cu(II) to Cu(I) due to IFCT that has proven to be an excellent visible-light sensitiser in the copper/graphene-titania system.</p><p>Hybrid titania-copper-graphene materials could therefore be exploited in
the field of light-to-energy applications.</p>
|
David Maria Tobaldi; Kamila Koci; Miroslava Edelmannova; Luc Lajaunie; Bruno Figueiredo; José Calvino; Maria Paula Seabra; Joao Antonio Labrincha
|
Composites; Hydrogen Storage Materials; Energy Storage; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.); Crystallography
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749579abda286d3f8cbea/original/copper-graphene-ti-o2-hybrid-materials-for-photocatalytically-assisted-h2-generation.pdf
|
60c74e87bdbb890df4a39bc6
|
10.26434/chemrxiv.12770813.v1
|
Spin Diffusion Transfer Difference (SDTD) NMR: An Advanced Method for the Characterisation of Water Structuration Within Particle Networks
|
<p>Saturation transfer difference (STD) NMR spectroscopy is a well‑known ligand‑based solution NMR technique used extensively for ligand epitope mapping, the identification of the nature of ligand binding sites, and the determination of ligand binding affinity. Recently, we have shown that STD NMR can be also applied to monitor changes in bound water during gelation of particulate dispersions. However, this technique is strongly dependent on gelator and solvent concentrations and does not report on the degree of organisation of the solvent within the particle network. This obscures the detailed understanding of the role of the solvent on gelation and precludes the comparison of solvation properties between dispersions prepared under different experimental conditions. In this work we report a novel STD NMR method to characterise the degree of solvent structuration in carbohydrate-based particulate dispersions by demonstrating for the first time that, for solvents interacting with large particles, the spin diffusion transfer build‑up curves can be modelled by the general one‑dimensional diffusion equation. Our novel approach, called Spin Diffusion Transfer Difference (SDTD) NMR, is independent of the gelator and solvent concentrations, allowing to monitor and compare the degree of solvent structuration in different gel networks. In addition, the simulation of SDTD build-up curves report on minimum distances (<i>r</i>) and spin diffusion rates (<i>D</i>) at the particle‑solvent interface. As a case study, we have characterised the degree of structuration of water and low molecular weight alcohols during the alcohol‑induced gelation of TEMPO-oxidised cellulose hydrogels by SDTD NMR, demonstrating the key role of water structuration on gel properties. SDTD NMR is a fast, robust and easy-to-implement solution NMR protocol that overcomes some of the limitations of the classical STD NMR approach when applied to the study of solvation. This technique can be readily extended to characterise the solvent(s) organisation in any type of particulate gels. Hence, the SDTD NMR method provides key insights on the role of water in the mechanism of gelation and the macroscopic properties of particulate gels, of fundamental importance for the design of soft matter materials with tuneable properties. </p>
|
Valeria Gabrielli; Agne Kuraite; Marcelo Alves da Silva; Karen J. Edler; Jesús Angulo; Ridvan Nepravishta; Juan C. Muñoz-García; Yaroslav Khimyak
|
Biopolymers; Hydrogels; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e87bdbb890df4a39bc6/original/spin-diffusion-transfer-difference-sdtd-nmr-an-advanced-method-for-the-characterisation-of-water-structuration-within-particle-networks.pdf
|
668c59d9c9c6a5c07aae2fa5
|
10.26434/chemrxiv-2024-xvjsw
|
Modelling MR-TADF emitters: excited-state decay rate constants and wavefunction descriptors
|
Multiresonance thermally-activated delayed fluorescence (MR-TADF) emitters have gained popularity given their potential of attaining negligible singlet-triplet energy gaps, i.e., ΔE_ST, without hindering emission, thus increasing the reverse and direct intersystem crossing rates without affecting fluorescence. This is achieved due to the singlet and triplet states' short-range charge transfer character (SRCT). Thus, obtaining quantitative information about SRCT would help developing new MR-TADF emitters. This work studies three different families of MR-TADF emitters: DOBOA, DiKTa and OQAO. First, we compute their adiabatic ΔE_ST with four different methods (TDA-CAM-B3LYP, STEOM-DLPNO-CCSD, ADC(2) and SCS-CC2). Then, we compute fluorescence (k_r), direct (k_ISC), and reverse (k_rISC) intersystem crossing rate constants. For k_r, we assess the effect of different levels of approximations on the rate calculations. We show that k_r do not depend significantly on the different harmonic models (adiabatic Hessian or vertical Hessian), coordinate systems, and broadening widths. Moreover, Herzberg-Teller effects are negligible for k_r but they are the main contribution for k_ISC and k_RISC. The computed rate constants agree well with the experimental results. Moreover, we propose the use of two wavefunction descriptors – Q_a^t and LOCa – based on the 1-particle transition density matrix, which assigns the amount of charge centered on the atoms. We compute these descriptors for three transitions: S0→S1, S0→T1, and S1→T1. For the studied cases, these descriptors are independent of the choice of electronic structure method and optimal geometry. We show that the adiabatic ΔE_ST decreases with the increase of S1→T1 Q_a^t, while ΔE_ST increases with an increase of the S0 →T1 Q_a^t. These trends showcase how the Q_a^t values can act as guiding descriptors to design new MR-TADF emitters with small ΔE_ST values.
|
Mariana Telles do Casal; Youssef Badawy; Daniel Escudero
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-07-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668c59d9c9c6a5c07aae2fa5/original/modelling-mr-tadf-emitters-excited-state-decay-rate-constants-and-wavefunction-descriptors.pdf
|
65f288dae9ebbb4db9aa70dd
|
10.26434/chemrxiv-2024-56121
|
NH3-SCR over Fe/SSZ-13 catalyst prepared by modification of natural chabazite
|
Natural zeolites are typically found in abundance in various geological formations, including volcanic and sedimentary rocks. The properties of these natural chabazites such as crystallinity, surface area, and composition can be tailored to enhance their catalytic properties. In this work, the low-crystalline natural chabazite containing iron was transformed into a highly crystalline Fe/SSZ-13 catalyst by hydrothermal synthesis. The initial and modified samples were subjected to various characterization techniques, including XRD, N2-physisorption, ICP-OES, and SEM, to measure their crystallinity, porosity, elemental composition and morphology. The characterization results reveal that the modification of natural chabazite enhanced the crystallinity and surface area of the sample, resulting in the incorporation of iron within the micropores of SSZ-13 zeolite. Their catalytic activities were evaluated at varying temperatures, and the resulting Fe/SSZ-13 catalyst showed high activity in the NH3-SCR reaction.
|
AMEEN SHAHID; Nabeel Ahmad; Nouman Ahmad; Sher Ahmad
|
Catalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Redox Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f288dae9ebbb4db9aa70dd/original/nh3-scr-over-fe-ssz-13-catalyst-prepared-by-modification-of-natural-chabazite.pdf
|
60c747889abda28b2ff8c91b
|
10.26434/chemrxiv.11653224.v1
|
Comment on ‘Multilayered Stable 2D Nano-Sheets of Ti2NTx MXene: Synthesis, Characterization, and Anticancer Activity’
|
<p>A
recent article entitled “Multilayered stable 2D nano-sheets of Ti<sub>2</sub>NT<sub>x</sub>
MXene: synthesis, characterization, and anticancer activity” published in
this journal, claimed that two-dimensional Ti<sub>2</sub>NT<sub>x</sub> MXene could be
synthesized by selectively etching Ti<sub>2</sub>AlN in concentrated
hydrofluoric acid at room temperature.
However, the X-ray diffraction pattern of Ti<sub>2</sub>NT<sub>x</sub> MXene reported in that paper is
completely different with those of other MXenes. In this comment, it is argued
that the samples synthesized in that paper were NOT Ti<sub>2</sub>NT<sub>x</sub>
MXene at all. Although carbide MXenes can be made by selectively etching A
layers from MAX phase, it is very difficult or impossible to make nitride
MXenes (Ti<sub>2</sub>NT<sub>x</sub>) by the same way.</p>
|
Yitong Guo; Qianku Hu; Libo Wang; Aiguo Zhou
|
Nanostructured Materials - Materials
|
CC BY 4.0
|
CHEMRXIV
|
2020-01-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747889abda28b2ff8c91b/original/comment-on-multilayered-stable-2d-nano-sheets-of-ti2n-tx-m-xene-synthesis-characterization-and-anticancer-activity.pdf
|
6555849c6e0ec7777f0853a7
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10.26434/chemrxiv-2023-npl8r
|
A G-quadruplex-binding platinum complex induces cancer mitochondrial dysfunction in vitro and in vivo independently of ROS induction
|
G-quadruplex DNA (G4) is a non-canonical structure forming in guanine-rich regions, which play a vital role in cancer biology and are now being acknowledged in both nuclear and mitochondrial (mt) genome. However, the impact of G4-based targeted therapy on both nuclear and mt genome, affecting mt function and its underlying mechanisms remain largely unexplored. Here, we first demonstrated that the G4-binding platinum(II) complex, Pt-ttpy, shows a highest accumulation in the mitochondria of A2780 cancer cells as compared with two other platinum(II) complexes with no/weak G4-binding properties, Pt-tpy and cisplatin. Pt-ttpy significantly induces deletion, copy number reduction and transcription inhibition of mt DNA, and it hinders the translation of mt proteins. Functional study shows that Pt-ttpy induces a potent mt dysfunction indicated by a high reduction of mt membrane potential, oxygen consumption rate and ATP synthesis, as well as toxic mt morphology switching, but without reactive oxygen species (ROS) induction. Mechanistic study by RNA-seq, Chip-seq and CUT-RUN shows Pt-ttpy impairs most nuclear-encoded mt ribosome genes’ transcription initiation through dampening the recruiting of TAF1 and NELFB to their promoter, which are highly enriched in G4 forming sequences. In vivo studies on a A2780 tumor xenograft mouse model suggest Pt-ttpy’s efficient anti-tumor effects, causing substantial disruption in mt genome function, while exhibiting less side effects compared to cisplatin. Overall, this study presents the first evidence that a G4-binding platinum(II) complex can harm cancer cell mitochondria potently without inducing ROS activity, potentially reducing side effects that shows promise in developing safer and effective platinum-based G4-binding molecules in cancer therapy.
|
Keli Kuang; Chunyan Li; Fatlinda Maksut; Deepanjan Ghosh; Robin Vinck; Maoling Wang; Joël Poupon; Run Xiang; Wen Li; Fei Li; Zhu Wang; Junrong Du; Marie-Paule Teulade-Fichou; Gilles Gasser; Sophie Bombard; Tao JIA
|
Biological and Medicinal Chemistry; Biochemistry; Cell and Molecular Biology; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-11-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6555849c6e0ec7777f0853a7/original/a-g-quadruplex-binding-platinum-complex-induces-cancer-mitochondrial-dysfunction-in-vitro-and-in-vivo-independently-of-ros-induction.pdf
|
626320f5ed4d8854c5155389
|
10.26434/chemrxiv-2021-lrqnx-v2
|
Modification of the Basic Dilution Equation for the Programming of Serial Dilutions
|
Stock solutions made with accurately weighable quantities of biologically active compounds often do not result in physically measurable delivery volumes, delivered to cell cultures, assay buffers etc., consequently requiring delineation of the serial dilution steps of the stock solution in a case by case manner. The basic dilution equation (C1V1 = C2V2) alone is not amenable for the programming and computerization of the serial dilutions. The best solution to this dilemma is to develop an equation with the delivery volume as one of the variables. We present here a modified dilution equation (MDE) that has the delivered volume as one of the variables. We demonstrate with examples how the equation can be used in delineating serial dilution steps either manually or through programming. The equation is D = C1p/C2V2, where D is the fold dilution required of a stock solution of C1 concentration which is diluted and delivered (pipetted) at a volume p to cell culture media, assay mixture etc., of volume (V2 – p), to achieve a final concentration of C2. The equation is useful when the volume of the stock solution made up to the final volume as calculated with basic dilution equation is not measurable physically. An Android application for the dilution/Serial dilution instructions, developed based on the MDE and named as “TheDilutionApp” is now available for free for a limited period at "github.com/bbassa9824/TheDilutions/releases". Downloading instructions are given under the “Results and Discussion” section of this preprint. A video demonstration of the downloading instructions and use of the Android application is available at https://youtu.be/3zuRvEz2HiA. A windows version of the same application is available as part of a larger program (8).
|
Babu Bassa; Rao Uppu
|
Biological and Medicinal Chemistry; Analytical Chemistry; Chemical Education; Biochemical Analysis; Biochemistry; Bioinformatics and Computational Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-04-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626320f5ed4d8854c5155389/original/modification-of-the-basic-dilution-equation-for-the-programming-of-serial-dilutions.pdf
|
666bce5bc9c6a5c07a702408
|
10.26434/chemrxiv-2024-4sv5h
|
Natural size variation amongst protocells leads to survival and growth under hypoosmotic conditions
|
Membrane growth is vital to the evolution of cellular life. For model protocells, this has most commonly been shown to occur through competition between different protocell populations or with the addition of extra amphiphiles. We find an alternative mechanism for protocell membrane growth that occurs as a consequence of hypoosmotic shocks that could have occurred naturally in the protocell environment. We show that nanoscale and giant fatty acid vesicles can withstand substantial osmotic pressures through membrane growth, whilst also retaining a significant portion of their contents. Notably, the giant vesicles retained contents following osmotic shocks ten times higher than that predicted to be tolerable. This is likely enabled by the membrane’s incorporation of additional amphiphiles from less tense vesicles. The dynamic nature of these fatty acid-based model protocells provides a mechanism through which not only membrane growth occurs, but a mechanism which enables protocell survival in hypoosmotic environments.
|
Lauren Lowe; Natasha Kaushik; Anna Wang
|
Physical Chemistry; Materials Science; Aggregates and Assemblies; Biophysical Chemistry; Self-Assembly
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666bce5bc9c6a5c07a702408/original/natural-size-variation-amongst-protocells-leads-to-survival-and-growth-under-hypoosmotic-conditions.pdf
|
67657e4181d2151a026310b1
|
10.26434/chemrxiv-2024-qqsnn
|
Design of radionuclide separations based on MD simulations
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The development of selective materials for radionuclide separation is often a long and costly process, requiring labor-intensive chemical separations and extensive optimization. To streamline the development of selective materials, this study explores MD simulations to accelerate the identification of optimal separation conditions, extractant-radionuclide affinity, reducing the need for extensive experimental trials.
We assessed the effectiveness of MD simulations using the challenging system of Sr²⁺ and Pb²⁺ with 18-crown-6 crown ether, focusing on the influence of different working media, including nitric, hydrochloric, formic, acetic, and perchloric acids, as well as potassium thiocyanate. The simulation results were validated experimentally by measuring the distribution weight ratios (Dw) of Sr²⁺ and Pb²⁺ using crown ether immobilized on a polymeric surface. Our findings demonstrate a strong correlation between MD predictions and experimental data, particularly highlighting acetic acid as a medium where Sr²⁺ forms stable complexes, while Pb²⁺ does not.
This study confirms the suitability of MD simulations as a reliable tool for predicting the selectivity of extractants, enabling faster development of new scintillating and non-scintillating resins. By reducing the time and resources needed for experimental optimization, this approach offers a more efficient pathway for the development of advanced materials for radionuclide separation.
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Isaac Giménez Guerra; Giulia Sormani; Alex Rodriguez; Ali Hassanali; Hector Bagán; Alex Tarancón
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Theoretical and Computational Chemistry; Analytical Chemistry; Environmental Analysis; Separation Science; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2024-12-24
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67657e4181d2151a026310b1/original/design-of-radionuclide-separations-based-on-md-simulations.pdf
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60c750e60f50db0d86397675
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10.26434/chemrxiv.13096121.v1
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Chiral Alkyl Amine Synthesis via Catalytic Enantioselective Hydroalkylation of Enamides
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Chiral alkyl amines are omnipresent as bio-active molecules and synthetic intermediates. Catalytic and enantioselective synthesis of alkyl amines from readily accessible precursors is challenging. Here we develop a nickel-catalyzed hydroalkylation method to assemble a wide range of chiral alkyl amines from enamides and alkyl halides in high regio- and enantioselectivity. The method works for both non-activated and activated alkyl halides, and is able to produce enantiomerically enriched amines with two minimally differentiated alpha-alkyl substituents. The mild conditions lead to high functional group tolerance, which is demonstrated in the post-product functionalization of many natural products and drug molecules, as well as the synthesis of chiral building blocks and key intermediates to bio-active compounds.
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Deyun Qian; Srikrishna Bera; Xile Hu
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Organic Synthesis and Reactions; Homogeneous Catalysis
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CC BY NC ND 4.0
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CHEMRXIV
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2020-10-16
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750e60f50db0d86397675/original/chiral-alkyl-amine-synthesis-via-catalytic-enantioselective-hydroalkylation-of-enamides.pdf
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67ab34fb81d2151a02f58bcc
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10.26434/chemrxiv-2025-hx2sd
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Zwitterionic Heavier Pnictinidenes in Redox Catalysis
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Herein we describe a new class of zwitterionic heavier pnictogen species with bis(NHC)borate as stabilizing ligands, enabling the isolation of Sb and Bi species in +1, +2, and +3 oxidation states. Computational analysis of zwitterionic pnictinidines revealed their cationis character, as well as unique electronic properties that contribute to their nucleophilicity and stability. These systems participate in key organometallic transformations, including oxidative addition and reductive elimination pro-cesses, and display redox catalytic activity in hydrodefluorination reactions, marking a rare example of pnictinidine-catalyzed redox transformation beyond the constraints of pincer ligands. Additionally, we report on a novel dehydrogenative thiolation of silanes. This work expands the scope of low-valent pnictogen chemistry, providing a novel platform for main group redox catalysis.
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Selwin Fernando; Yi Chen Chan; Sergio Fernandez; Enric Sabater; Graham Tizzard; Simon Coles; Diego M. Andrada; Oriol Planas
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Inorganic Chemistry; Catalysis; Organometallic Chemistry; Catalysis; Coordination Chemistry (Organomet.); Main Group Chemistry (Organomet.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2025-02-24
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ab34fb81d2151a02f58bcc/original/zwitterionic-heavier-pnictinidenes-in-redox-catalysis.pdf
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63c5da28aadd9584067464d0
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10.26434/chemrxiv-2023-tk505
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Model-Driven Design of Redox Mediators: Quantifying the Impact of Quinone Structure on Bioelectrocatalytic Activity with Glucose Oxidase
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Successful application of emerging bioelectrocatalysis technologies depends upon an efficient electrochemical interaction between redox enzymes as biocatalysts and conductive electrode surfaces. One approach to establishing such enzyme-electrode interfaces utilizes small redox-active molecules to act as electron mediators between an enzyme active site and electrode surface. While redox mediators have been successfully used in bioelectrocatalysis applications ranging from enzymatic electrosynthesis to enzymatic biofuel cells, they are often selected using a guess-and-check approach. Herein, we identify structure-function relationships in redox mediators that describe the bimolecular rate constant for its reaction with a model enzyme, glucose oxidase (GOx). Based on a library of quinone-based redox mediators, a quantitative structure-activity relationship (QSAR) model is developed to describe the importance of mediator redox potential and projected molecular area as two key parameters for predicting the activity of quinone/GOx-based electroenzymatic systems. Additionally, rapid scan stopped-flow spectrophotometry was used to provide fundamental insights into the kinetics and the stoichiometry of reactions between different quinones and the flavin adenine dinucleotide (FAD+/FADH2) cofactor of GOx. This work provides a critical foundation for both designing new enzyme-electrode interfaces and understanding the role that quinone structure plays in altering electron flux in electroenzymatic reactions.
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Lincoln Mtemeri; David Hickey
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Catalysis; Biocatalysis; Electrocatalysis; Redox Catalysis
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CC BY NC 4.0
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CHEMRXIV
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2023-01-18
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c5da28aadd9584067464d0/original/model-driven-design-of-redox-mediators-quantifying-the-impact-of-quinone-structure-on-bioelectrocatalytic-activity-with-glucose-oxidase.pdf
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64065326cc600523a3c2eae1
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10.26434/chemrxiv-2023-3zsvr
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Photocatalytic collection and degradation of microplastics by self-asymmetric Pac-Man TiO2
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Microplastics are a significant environmental threat as they are not regularly monitored or removed and the lack of efficient removal techniques further amplifies this crisis. In this direction and many other environmental remediation processes, photocatalytic micro/nanomotors hold vast potential to remove and degrade micropollutants. Unifying the different properties of a photocatalytic micromotor (self-propulsion, phoretic assembly with passive colloids and photocatalytic oxidation of contaminants), we present highly scale-able, inherently-asymmetric Pac-Man TiO2 particles that can actively collect and degrade polystyrene microplastics.
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Purnesh Chattopadhyay; Maria Camila Ariza Tarazona; Erika Iveth Cedillo-Gonzlez; Cristina Siligardi; Juliane Simmchen
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Catalysis; Earth, Space, and Environmental Chemistry; Environmental Science; Photocatalysis; Materials Chemistry
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CC BY 4.0
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CHEMRXIV
|
2023-03-07
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64065326cc600523a3c2eae1/original/photocatalytic-collection-and-degradation-of-microplastics-by-self-asymmetric-pac-man-ti-o2.pdf
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64f0e9eb3fdae147fa37142f
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10.26434/chemrxiv-2023-gq2zl
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Manganese Dissolution in alkaline medium with and without concurrent oxygen evolution in LiMn2O4
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Manganese dissolution during the oxygen evolution reaction (OER) has been a persistent challenge that impedes the practical implementation of Mn-based electrocatalysts including the LixMn2O4 system in aqueous alkaline electrolyte. The investigated LiMn2O4 particles exhibit two distinct Mn dissolution processes; one independent of OER and the other associated to OER. Combining the bulk sensitive X-ray absorption spectroscopy, surface sensitive X-ray photoelectron spectroscopy and electrochemical detection of Mn dissolution using rotating ring-disk electrode, we explore the less understood Mn dissolution mechanism during OER. We correlate near-surface oxidation with the charge attributed to dissolved Mn, which demonstrates increasing Mn dissolution with the formation of surface Mn4+ species under anodic potential. The observed stronger dissolution during the OER is attributed to the formation of additional Mn4+ from Mn3+ during OER. We show that control over the amount of Mn4+ in LixMn2O4 before the onset of the OER can partially mitigate the OER-triggered dissolution. Overall, our atomistic insights into the Mn dissolution processes are crucial for knowledge-guided mitigation of electrocatalyst degradation, which can be broadly extended to manganese-based oxide systems.
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Omeshwari Bisen; Max Baumung; Cynthia A. Vokert; Marcel Risch
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Materials Science; Catalysis; Energy; Fuels - Materials; Electrocatalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-09-01
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f0e9eb3fdae147fa37142f/original/manganese-dissolution-in-alkaline-medium-with-and-without-concurrent-oxygen-evolution-in-li-mn2o4.pdf
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60c74904bdbb895c07a390a1
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10.26434/chemrxiv.12012789.v1
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Ultrasensitive and Whole-Course Encapsulated Field Detection of 2019-nCoV Gene Applying Exponential Amplification from RNA Combined with Chemical Probes
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The newly identified 2019-nCoV (SARS-CoV-2) RNA virus has caused over 80,000 laboratory-confirmed human infections in China (as of Mar. 1st, 2020), and is now becoming a global epidemic issue. As a result, highly sensitive, reliable and field-deployable methods to detect 2019-nCoV that can be developed in a shortest possible time are urgently needed. In this work, we introduce whole-course encapsulated and ultrasensitive field detection methods against 2019-nCoV gene. We applied isothermal exponential amplification methods via reverse transcription plus subsequent enzymatic recombinase amplification (ERA), a modified recombinase polymerase amplification (RPA), to amplify trace level of 2019-nCoV RNA. We designed both exo FRET probe and nfo affinity probe for easy detection of the amplified nucleic acids. These methods can be developed within a few days and as low as 0.32 aM (i.e. 0.32×10-18 M) of RNA can be reliably detected.<b></b><br />
|
Simin Xia; Xi Chen
|
Cell and Molecular Biology; Chemical Biology
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-03-23
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74904bdbb895c07a390a1/original/ultrasensitive-and-whole-course-encapsulated-field-detection-of-2019-n-co-v-gene-applying-exponential-amplification-from-rna-combined-with-chemical-probes.pdf
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61d6f67b90fc8a297fec1739
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10.26434/chemrxiv-2022-n3f56
|
Nanoscale Chemical Imaging of Coadsorbed Thiolate Self-assembled Monolayers on Au(111) by Tip-Enhanced Raman Spectroscopy
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Self-assembled monolayers (SAMs) of thiolates on metal surfaces are of key importance for engineering surfaces with tunable properties. However, it remains challenging to understand binary thiolate SAMs on metals at the nanoscale under ambient conditions. Here we employ tip-enhanced Raman spectroscopy (TERS) and density functional theory (DFT) calculations to investigate local information of binary SAMs on Au(111) coadsorbed from an equimolar mixture of p-cyanobenzenethiol (pCTP) and p-aminothiophenol (pATP), including chemical composition, coadsorption behavior, phase segregation, plasmon-induced photocatalysis, and solvation effects. We found that upon competitive adsorption of pCTP and pATP on Au(111) from a methanolic solution, the coadsorption initially occurs randomly and homogeneously; eventually, pATP is replaced by pCTP through gradual growth of pCTP nanodomains. TERS imaging also allows for visualization of the plasmon-induced coupling of pATP to p,p’-dimercaptoazobenzene (DMAB) and the solvation-induced phase segregation of the binary SAMs into nanodomains, with a spatial resolution of ~9 nm under ambient conditions. According to DFT calculations, these aromatic thiolates differing only in their functional groups, -CN versus –NH2, show different adsorption energy on Au(111) in vacuum and methanol, and thus the solvation effect on adsorption energy of these thiolates in methanol can determine the dispersion state and replacement order of the binary thiolates on Au(111).
|
Feng Shao; Liqing Zheng; Jinggang Lan; Renato Zenobi
|
Analytical Chemistry; Spectroscopy (Anal. Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-01-07
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d6f67b90fc8a297fec1739/original/nanoscale-chemical-imaging-of-coadsorbed-thiolate-self-assembled-monolayers-on-au-111-by-tip-enhanced-raman-spectroscopy.pdf
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60c75195567dfe3212ec5ac1
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10.26434/chemrxiv.13182881.v1
|
Harnessing Photoelectrochemistry for Wastewater Nitrate Treatment Coupled with Resource Recovery
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<p>Wastewater is a misplaced resource well suited to recover nutrients, value-added chemicals, energy, and clean water. A photoelectrochemical device is proposed to transform wastewater nitrates to ammonia and nitrous oxide, coupled with water oxidation. Numerical models were developed to quantify the dependence of process efficiencies and nitrogen-removal rates on light absorber band gaps, electrocatalytic kinetic parameters, competing oxygen reduction and hydrogen evolution reactions, and the reacting nitrate species concentrations that affect the mass-transfer limited current densities. With a single light-absorber and state-of-the-art catalysts, optimal solar-to-chemical efficiencies of 7% and 10% and nitrogen-removal rates of 260 and 395 g<sub>N</sub> m<sup>-2</sup> day<sup>-1</sup> are predicted for nitrate reduction to ammonia and nitrous oxide respectively. The influence of competing reactions on the performance depends on the nitrate concentration and band gap of the light absorber modeled. Oxygen reduction is more dominant than hydrogen evolution to compete with the nitrate reduction reaction, but is mass-transfer limited. Even with kinetic parameters that enhanced the driving forces for the competing reactions, the performance is only minimally affected by these reactions for optimally selected band gaps and nitrate concentrations larger than 100 mM. Theoretically predicted peak nitrogen removal rates and specific energy intensities are competitive with reported estimates for bioelectrochemical and Sharon-Anammox processes for ammonia recovery and nitrogen removal respectively. This result, together with the added benefit of harnessing sunlight to produce value-added products, indicates promise in the photoelectrochemical approach as a tertiary pathway to recover nutrients and energy from wastewater nitrates.</p>
|
Luisa Barrera; Rohini Bala Chandran
|
Environmental Science; Wastes; Transport Phenomena (Chem. Eng.); Water Purification; Electrocatalysis; Photocatalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-11-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75195567dfe3212ec5ac1/original/harnessing-photoelectrochemistry-for-wastewater-nitrate-treatment-coupled-with-resource-recovery.pdf
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63790d5056c6f44fdd7403eb
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10.26434/chemrxiv-2022-407gd
|
Vitamin E-loaded polymeric nanoparticles from biocompatible adipate-based copolymer obtained using the nanoprecipitation method
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Despite the search for new biomaterials dedicated for biomedical applications intensified in recent decades, this field is still not fully explored. Therefore, the synthesis of novel aliphatic biopolyesters poly(butylene adipate-co-dilinoleic adipate) (PBA-DLA) was performed using monomers derived from natural sources and enzyme lipase B Candida antarctica (CALB) as biocatalyst in order to provide fully biobased and biodegradable material suitable for drug delivery systems. Proton nuclear magnetic spectroscopy (1H NMR) analysis confirmed chemical structure of PBA-DLA copolyester whereas in vitro cytotoxicity assay indicate on material biocompatibility. By applying a single-step nanoprecipitation method narrowly distributed PBA-DLA nanoparticles (NPs) with hydrodynamic diameter (HD) of ~200 nm were produced, however, after purification (centrifugation) step NPs tend to agglomerate. In order to eliminate this drawback suitable amount of stabilizer (Pluronic F127, 0.05 mg/ml) was selected and NPs with HD of ~149 nm were obtained. The PBA-DLA NPs could be loaded with the hydrophobic α-tocopherol (α-TP) – main ingredient of vitamin E, with encapsulation efficiency ranging from 48 to 74 % depending on tested α-TP concentration (2.5, 5, 10 mg/ml) as evidenced by combined dynamic light scattering (DLS), ultraviolet-visible spectroscopy (UV-VIS) and 1H NMR measurements.
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Martyna Sokołowska; Maja Marchwiana; Miroslawa El Fray
|
Materials Science; Polymer Science; Biocompatible Materials; Controlled-Release Systems; Drug delivery systems
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CC BY 4.0
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CHEMRXIV
|
2022-11-22
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63790d5056c6f44fdd7403eb/original/vitamin-e-loaded-polymeric-nanoparticles-from-biocompatible-adipate-based-copolymer-obtained-using-the-nanoprecipitation-method.pdf
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6177f10b4c04e8663892a119
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10.26434/chemrxiv-2021-34v44
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Exploring Polycrystalline Materials: High-throughput Phase Elucidation Using Serial Rotation Electron Diffraction
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Rapidly and reliably elucidating the phases in polycrystalline materials is essential for developing new materials. Yet, crystals of many materials of biological, pharmaceutical, chemical, or industrial interest are too small (<1 μm) for routine X-ray diffraction (XRD) analysis. For complex materials, this can result in workflow bottlenecks in high-throughput synthesis screenings favoured by industrial laboratories. With the increased prevalence of electron diffraction as an alternative technique for materials characterization, we explore a series of zeolite syntheses, resulting in typical polycrystalline products, via high-throughput phase identification using serial rotation electron diffraction (SerialRED). Five zeolite phases were identified in one product, the most complex mixture ever discovered in zeolite chemistry. Some of the phases are of ultra-low contents, similar unit cells, and/or identical morphologies. Via automatically examining hundreds of crystals, SerialRED enables the reliable and high-throughput phase analysis of products that XRD could not handle. It allows the exploration of more complex synthesis systems and provides new opportunities for rapidly developing novel polycrystalline materials, greatly benefiting synthesis chemistry and material science.
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Yi Luo; Bin Wang; Stef Smeets; Junliang Sun; Weimin Yang; Xiaodong Zou
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Materials Science; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-10-27
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6177f10b4c04e8663892a119/original/exploring-polycrystalline-materials-high-throughput-phase-elucidation-using-serial-rotation-electron-diffraction.pdf
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655fab3c5bc9fcb5c93a1acb
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10.26434/chemrxiv-2023-qmkqf
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Can tunneling current in molecular junctions be so strongly temperature dependent to challenge a hopping mechanism? Analytical formulas answer this question and provide important insight into large area junctions
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{Analytical equations like Richardson-Dushman's or Shockley's provided a general, if simplified conceptual background, which was widely accepted in conventional electronics and made a fundamental contribution to advances in the field. In the attempt to develop a (highly desirable, but so far missing) counterpart for molecular electronics, in this work, we deduce a general analytical formula for the tunneling current through molecular junctions mediated by a single level that is valid for any bias voltage and temperature. Starting from this expression, which is exact and obviates cumbersome numerical integration, in the low and high temperature limits we also provide analytical formulas expressing the current in terms of elementary functions. They are accurate for broad model parameter ranges relevant for real molecular junctions. Within this theoretical framework we show that: (i) by varying the temperature, the tunneling current can vary by several orders of magnitude, thus debunking the myth that a strong temperature dependence of the current is evidence for a hopping mechanism, (ii) real molecular junctions can undergo a gradual (Sommerfeld-Arrhenius) transition from a weakly temperature dependent to a strongly (``exponential'') temperature dependent current that can be tuned by the applied bias, and (iii) important insight into large area molecular junctions with eutectic gallium indium alloy (EGaIn) top electrodes can be gained. E.g., merely based on transport data, we estimate that the current carrying molecules represent only a fraction of f \approx 4 \times 10^{-4} out of the total number of molecules in a large area Au-S-(CH2)_13-CH_3 / EGaIn junction.
|
Ioan Baldea
|
Theoretical and Computational Chemistry; Materials Science; Nanoscience; Nanodevices; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling
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CC BY NC 4.0
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CHEMRXIV
|
2023-11-24
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655fab3c5bc9fcb5c93a1acb/original/can-tunneling-current-in-molecular-junctions-be-so-strongly-temperature-dependent-to-challenge-a-hopping-mechanism-analytical-formulas-answer-this-question-and-provide-important-insight-into-large-area-junctions.pdf
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667c2131c9c6a5c07a712920
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10.26434/chemrxiv-2024-xcjgq
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Automated One-pot Library Synthesis with Aldehydes as Radical Precursors
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The increased demand for the synthesis of enriched hybridized Csp3 motifs and the urgency of discovering new drug molecules require the development of more efficient technologies and synthetic tools to accelerate drug discovery processes. Herein, we report a fully automated strategy for the addition of Csp3 enriched building blocks onto olefins via Giese addition to forge Csp3-Csp3 bonds. The developed fully automated protocol allowed the conversion of aldehydes (non-redox-active species) in-situ to electroactive imidazolidines and to employ them as precursors of C-centered radicals under photoredox catalyzed conditions for the synthesis of enriched fraction sp3 (Fsp3) character building blocks and bioactive compound libraries.
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Adrián Luguera Ruiz; Brenda Pijper; Maria Lourdes Linares; Santiago Cañellas; Stefano Protti; Maurizio Fagnoni; Jesus Alcazar
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Biological and Medicinal Chemistry; Organic Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-06-27
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667c2131c9c6a5c07a712920/original/automated-one-pot-library-synthesis-with-aldehydes-as-radical-precursors.pdf
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60dc37ae6e388b388c702223
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10.26434/chemrxiv-2021-s7r6b
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Ball Milling Enabled Reactivity of Manganese Metal
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Efforts to generate organomanganese reagents under ball milling conditions have led to the serendipitous discovery that manganese metal can mediate the reductive dimerization of arylidene malonates. The newly uncovered process has been optimized and its mechanism explored using CV measurements, radical trapping experiments, EPR spectroscopy and solution control reactions. This unique reactivity can also be translated to solution where upon pre-milling of the manganese is required.
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Duncan Browne; William Nicholson; Joseph Howard; Giuseppina Magri; Alex Seastram; Adam Khan; Louis Morrill; Emma Richards
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Organic Chemistry; Organometallic Chemistry; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Reaction (Organomet.)
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CC BY NC 4.0
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CHEMRXIV
|
2021-06-30
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60dc37ae6e388b388c702223/original/ball-milling-enabled-reactivity-of-manganese-metal.pdf
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65de2336e9ebbb4db9669f89
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10.26434/chemrxiv-2024-2vxrq
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Directed Evolution of Protoglobin Optimizes the Enzyme Electric Field
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To unravel why computational design fails in creating viable enzymes, while directed evolution (DE) succeeds, our research delves into the laboratory evolution of Protoglobin. DE has adapted this protein to efficiently catalyze carbene transfer reactions. We show that the previously proposed enhanced substrate access and binding alone cannot account for increased yields during DE. The 3D electric field in the entire active site is tracked through protein dynamics, clustered using the affinity propagation algorithm, and subjected to principal component analysis. This analysis reveals notable changes in the electric field with DE, where distinct field topologies influence transition state energetics and mechanism. A chemically meaningful field component emerges and takes the lead during DE and facilitates crossing the barrier to carbene transfer. Our findings underscore intrinsic electric field dynamic's influence on enzyme function, the ability of the field to switch mechanisms within the same protein, and the crucial role of the field in enzyme design.
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Shobhit S. Chaturvedi; Santiago Vargas; Pujan Ajmera; Anastassia N. Alexandrova
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Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Biocatalysis; Quantum Mechanics
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CC BY NC 4.0
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CHEMRXIV
|
2024-02-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65de2336e9ebbb4db9669f89/original/directed-evolution-of-protoglobin-optimizes-the-enzyme-electric-field.pdf
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60c75003337d6c5222e28213
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10.26434/chemrxiv.12980306.v1
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Simeprevir and Eltrombopag as Potential Inhibitors of SARS-CoV2 Proteases: A Molecular Docking and Virtual Screening Approach to Combat COVID-19
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The present study investigates the binding affinities of 61 FDA approved drugs against two key proteases of SARS-COV2, 3-chymotrypsin-like protease and papain-like protease. We also investigated the ADMET properties of the top 10 best binding drugs to understand the druglikeness property.
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Ananta Swargiary; AKALESH Verma; Manita Daimari; Mritunjoy Kumar Roy
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Bioinformatics and Computational Biology
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-09-22
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75003337d6c5222e28213/original/simeprevir-and-eltrombopag-as-potential-inhibitors-of-sars-co-v2-proteases-a-molecular-docking-and-virtual-screening-approach-to-combat-covid-19.pdf
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60c74f694c891952a0ad3bc8
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10.26434/chemrxiv.12899831.v1
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Molecular Dynamics Simulations of Liquid-Liquid Interfaces in an Electric Field: the Water-1,2-Dichloroethane Interface
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Molecular dynamics simulations of the liquid-liquid interface between water and 1,2-Dichloroethane in the presence of weak external electric fields.<div>The effect of the use of 3D periodic Ewald summation and the effect of the simulation setup are discussed.</div><div>A new simple geometric method for designing the simulation cell is proposed. This method was thoroughly tested shown that it mitigates any artefacts to the use of 3D Ewald summation with external electric field.</div>
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Paolo Raiteri; Peter Kraus; Julian Gale
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Computational Chemistry and Modeling; Electrochemistry - Mechanisms, Theory & Study; Physical and Chemical Properties; Surface
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-09-01
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f694c891952a0ad3bc8/original/molecular-dynamics-simulations-of-liquid-liquid-interfaces-in-an-electric-field-the-water-1-2-dichloroethane-interface.pdf
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63e9711bfcfb27a31fa87ecd
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10.26434/chemrxiv-2023-gbrjb
|
Tuning the HOMO Energy of the Triarylamine Molecules with Orthogonal HOMO and LUMO Using Functional Groups
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Tuning the HOMO and LUMO energy strategically of triphenylamine derivatives plays an important role towards understanding and design of high performance organic photovoltaics. To improve on the charge separation and electron transfer properties, twenty one D-pi-A organic dyes with nitrostyryl triphenylamine-based structures (NTPAs) were designed and computationally studied, in which triphenylamine, carbazole, or indoline structures were used as donor and NO2 group as acceptor. The LUMOs of these dyes are more localized at the nitrostyryl moiety with almost the same energy and the HOMOs, which are orthogonal to the LUMOs, can be conveniently tuned by changing the donor structure and using different functional groups substituted on the donor. Compared with triphenylamine molecules, carbazole molecules decrease the HOMO energy of NTPA, whereas cis N-phenylindoline structure increase the HOMO energy. In addition, the exciton sizes generated by these dyes are also tuned in a range of 7.0-12.7 A. These results show that introduction of dimethylamino group on the triphenylamine moiety greatly increases the HOMO energy and prolongs the maximum absorption wavelength as well as increases the exciton size, indicating that NTPA dyes containing strong electron donating dimethylamino group on the donor part are promising candidates as sensitizers in the dye-sensitized solar cell applications. The results of the structural and spectral properties show good correlation with the experimental results, which confirms that the DFT method employed in this work is an effective way to design organic small molecule based sensitizers.
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Junpeng Zhuang; Noel Amaro; Thomas Testoff; Xueqin Zhou; Tianyang Wang; Lichang Wang
|
Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Dyes and Chromophores; Physical and Chemical Properties
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-02-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e9711bfcfb27a31fa87ecd/original/tuning-the-homo-energy-of-the-triarylamine-molecules-with-orthogonal-homo-and-lumo-using-functional-groups.pdf
|
649db6056e1c4c986b8c816e
|
10.26434/chemrxiv-2023-p11b2
|
Organophotocatalyzed Synthesis of Vinyl-SCF3 and Benzoyl-SCF3 Using a New Shelf-Stable PhPh-N-(SCF3)(CF3) Reagent.
|
We report the photocatalyzed C-SCF3 bond formation using a new shelf stable PhPh-N-(SCF3)(CF3) reagent I in combination with 4CzIPN as organophotocatalyst under blue LED irradiation. While the synthesis of vinyl-SCF3 is performed in the presence of bromide salts as an activator of reagent I, the synthesis of trifluoromethylthioesters was undertaken using aldehydes as starting material in the presence of a hydrogen atom transfer catalyst (HAT). Preliminary mechanistic investigations including EPR spectroscopy and cyclic voltammetry analysis shed the light on the reaction mechanisms.
|
Yi Yang; renhe tang; Seifallah Abid; Lhoussain Khrouz; JULIEN VANTOUROUT ; Anis Tlili
|
Organic Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-07-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649db6056e1c4c986b8c816e/original/organophotocatalyzed-synthesis-of-vinyl-scf3-and-benzoyl-scf3-using-a-new-shelf-stable-ph-ph-n-scf3-cf3-reagent.pdf
|
637e3ebeebc1c76513d02d12
|
10.26434/chemrxiv-2022-dp36t-v3
|
The cost of direct air capture and storage: the impact of technological learning, regional diversity, and policy.
|
Direct air capture and storage (DACS) is a carbon dioxide removal technology that is necessary to reach our climate targets. However, huge question marks remain regarding the cost. In contrast to previous studies, we use a costing methodology that is truly consistent with the technology readiness level of DACS to calculate cost trajectories for four example DACS technologies. Our analysis demonstrates the cost of DACS is unlikely to reach the $100 t-CO2-1 target, as costs fall to $100-600 t-CO2-1 at the Gt-CO2 year-1 scale. Rational siting and energy source selection will be critical, and importantly, coupling DACS to low capacity factor intermittent renewable electricity is uneconomical. Although, sites with high renewable capacity factors do exist. Furthermore, strong, holistic, technology-catered policy support is needed to aid market creation, scale-up, and long-term cost reductions. The results and conclusions outlined in this work have significant implications for academics, industry, policymakers, and investors alike.
|
John Young; Noah McQueen; Charithea Charalambous; Spyros Foteinis; Olivia Hawrot; Manuel Ojeda; Hélène Pilorgé; John Andresen; Peter Psarras; Phil Renforth; Susana Garcia; Mijndert van der Spek
|
Energy; Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Fuels - Energy Science; Power
|
CC BY 4.0
|
CHEMRXIV
|
2022-11-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637e3ebeebc1c76513d02d12/original/the-cost-of-direct-air-capture-and-storage-the-impact-of-technological-learning-regional-diversity-and-policy.pdf
|
628b71546b12b6bc007beb14
|
10.26434/chemrxiv-2022-1s760-v2
|
Flexible organic crystals. Understanding the tractable co-existence of elastic and plastic bending
|
As an emerging class of flexible materials, mechanically bendable molecular crystals are broadly classified as elastic or plastic. Nevertheless, flexible organic crystals with mutually exclusive elastic and plastic traits, with contrasting structural requirements, co-existing under different stress settings are exceptional; hence, it is imperative to establish the concurring factors that beget this rare occurrence. We report a series of halogen-substituted benzil crystals showing elastic bending (within ~ 2.45% strain), followed by elastoplastic deformation at ambient conditions. At higher stress settings, they display exceptional plastic flexibility that one could bend, twist, or even coil around a capillary tube. X-ray diffraction, microscopy, and computational data reveal the microscopic and macroscopic basis for the exciting co-existence of elastic, elastoplastic, and plastic properties in the crystals. The layered molecular arrangement and the weak dispersive interactions sustaining the interlayer region provide considerable tolerance towards the breaking and making upon engaging or releasing the external stress; it enables restoring the original state within the elastic strain. Comparative studies with oxalate compounds, wherein the twisted diketo moiety in benzil was replaced with a rigid and coplanar central oxalate moiety, enabled us to understand the effect of the anisotropy factor in the crystal packing induced by the C=O···C tetral interactions. The enhanced anisotropy depreciated the elastic domain, making the oxalate crystals more prone to plastic deformation. Three-point bending experiments and the determined Young's moduli further corroborate the co-existence of the elastic and plastic realm and highlights the critical role of the underlying structural elements that determine the elastic to plastic transformation. The work highlights the possible co-existence of orthogonal mechanical characteristics in molecular crystals and further construed the concurrent effect of the microscopic and macroscopic elements in attaining this exceptional mechanical trait.
|
SUNIL VARUGHESE, PhD; Krzysztof Woźniak; Indira S. Divya; Kandasamy Saravanan; Toshiyuki Sasaki; Hideko Koshima; Shodai Hasebe
|
Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-07-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628b71546b12b6bc007beb14/original/flexible-organic-crystals-understanding-the-tractable-co-existence-of-elastic-and-plastic-bending.pdf
|
60c74b354c89197239ad33cc
|
10.26434/chemrxiv.12307592.v1
|
Emergency Antiviral Drug Discovery During a Pandemic - a Case Study on the Application of Natural Compounds to Treat COVID-19
|
<p>The
spreading COVID-19 pandemic has brought the world to a halt in 2020. One of the
major challenges is the lack of effective antiviral drugs. Drug and vaccine
development typically takes years; a practical approach to formulate
knowledge-based prescriptions is to conduct <i>in
silico </i>screening for drugs and
compounds that has the potential to disrupt viral protein functions. By
evaluating the dataset from the “Shennong project”, an <i>in silico</i>
screening of the DrugBank library against SARS-CoV-2 proteins, we identified
chlorogenic acid and rutin displayed a strong affinity with diverse viral
proteins. Chlorogenic acid is naturally present in coffee in large quantity,
and rutin is available as nutraceutical products, both compounds are considered
safe to consume, hence could potentially aid the recovery or treatment for
COVID-19 patients at low health risk. We emphasise that the results require
further clinical clarification, the impact of this work shall be examined by professionals
carefully.</p>
|
Jianfeng Yu; Shengxi Shao; Bin Liu; Zhihao Wang; Yi-Zhou Jiang; Yunqing Li; Feng Chen; Bing Liu
|
Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b354c89197239ad33cc/original/emergency-antiviral-drug-discovery-during-a-pandemic-a-case-study-on-the-application-of-natural-compounds-to-treat-covid-19.pdf
|
66d32850a4e53c48763fc4f1
|
10.26434/chemrxiv-2024-9q0hj-v2
|
Constrained Nuclear-Electronic Orbital Transition State Theory Using Energy Surfaces with Nuclear Quantum Effects
|
Hydrogen-atom transfer is crucial in a myriad of chemical and biological processes, yet the accurate and efficient description of hydrogen-atom transfer reactions and kinetic isotope effects remains challenging due to significant quantum effects on hydrogenic motion, especially tunneling and zero-point energy. In this paper, we combine transition state theory (TST) with the recently developed constrained nuclear-electronic orbital (CNEO) theory to propose a new transition state theory denoted CNEO-TST. We use CNEO-TST with CNEO density functional theory (CNEO-DFT) to predict reaction rate constants for two prototypical gas-phase hydrogen-atom transfer reactions and their deuterated isotopologic reactions. The CNEO-TST is similar to conventional TST except that it employs constrained minimized energy surfaces to include zero-point energy and shallow tunneling effects in the effective potential. We find that the new theory predicts reaction rates quite accurately at room temperature. The effective potential surface must be generated by CNEO theory rather than by ordinary electronic structure theory, but because of the favorable computational scaling of CNEO-DFT, the cost will remain economical even for large systems. Our results show that dynamics calculations with this approach achieve accuracy comparable to variational TST with a semiclassical multidimensional tunneling transmission coefficient at and above room temperature. Therefore, CNEO-TST can be a useful tool for rate prediction, even for reactions involving highly quantal motion, such as many chemical and biochemical reactions involving transfers of hydrogen atoms, protons, or hydride ions.
|
Zehua Chen; Jingjing Zheng; Donald Truhlar; Yang Yang
|
Theoretical and Computational Chemistry; Theory - Computational
|
CC BY 4.0
|
CHEMRXIV
|
2024-09-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d32850a4e53c48763fc4f1/original/constrained-nuclear-electronic-orbital-transition-state-theory-using-energy-surfaces-with-nuclear-quantum-effects.pdf
|
60c75927702a9b304618ce4b
|
10.26434/chemrxiv.14663454.v1
|
Iron-Catalyzed Homogeneous Hydrogenation with Precise Temperature-Governed Chemoselectivity.
|
The chemoselective hydrogenation of unsaturated compounds has been a powerful tool for both synthetic chemistry and chemical industry. The achievement of chemoselectivity among different functionalities with a single catalyst has been a challenge for transition metal-catalyzed hydrogenation. In this paper, iron tetraphosphine complexes show high catalytic efficiency for a variety of polar unsaturated substrates such as aldehydes, ketones, enones, nitroarenes and N-heteroaromatics. Without an N-H group on the catalyst, the chemoselectivity was controlled precisely by the reaction temperature. The catalytic efficiency, chemoselectivity and robustness of this Fe/P4N2 catalyst found its merit in the preparation of several important drug intermediates. A diamagnetic trans-iron dihydride complex, formed under the reaction conditions, was supposed to be an on-cycle catalytically active species.<br />
|
Ya-Nan Duan; Yiqun Zeng; ZhiKai Cui; Jialin Wen; Xumu Zhang
|
Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75927702a9b304618ce4b/original/iron-catalyzed-homogeneous-hydrogenation-with-precise-temperature-governed-chemoselectivity.pdf
|
60c74703567dfe705eec471f
|
10.26434/chemrxiv.11374716.v1
|
From Electricity to Fuels: Descriptors for C1 Selectivity in Electrochemical CO2 Reduction
|
Electrochemical reduction of carbon dioxide (CO<sub>2</sub>)
over transition metals follows a complex reaction network. Even for products
with a single carbon atom (C<sub>1</sub> products), two bifurcated pathways
exist: initially between carboxyl (COOH*) and formate (HCOO*) intermediates and
the COOH* intermediate is further bifurcated by pathways involving either formyl
(CHO*) or COH*. In this study, we combine evidence from the experimental
literature with a theoretical analysis of energetics to rationalize that not
all steps in the reduction of CO<sub>2</sub> are electrochemical. This insight
enables us to create a selectivity map for two-electron products (carbon
monoxide (CO) and formate) on elemental metal surfaces using only the CO and OH
binding energies as descriptors. In the further reduction of CO<sup>*</sup>, we
find that CHO* is formed through a chemical step only whereas COH* follows from
an electrochemical step. Notably on Cu(100), the COH pathway becomes dominant
at an applied potential lower than −0.5V vs. RHE. For the
elemental metals selective towards CO formation, the variation of the CO
binding energy is sufficient to further subdivide the map into domains that
predominantly form H<sub>2</sub>, CO, and ultimately more reduced products. We
find Cu to be the only elemental metal capable of reducing CO<sub>2</sub> to
products beyond 2e<sup>− </sup>via the proposed COH pathway and we identify atomic
carbon as the key component leading to the production of methane. Our analysis also
rationalizes experimentally observed differences in products between thermal
and electrochemical reduction of CO<sub>2</sub> on Cu.
|
Michael Tang; Hongjie Peng; Philomena Schlexer Lamoureux; Michal Bajdich; Frank Abild-Pedersen
|
Electrocatalysis; Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-12-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74703567dfe705eec471f/original/from-electricity-to-fuels-descriptors-for-c1-selectivity-in-electrochemical-co2-reduction.pdf
|
673c5b4bf9980725cfb41633
|
10.26434/chemrxiv-2024-3nxtx
|
Fluorescent Rhodopsins: a challenging test for cost-effective QM/MM approaches
|
In this study, we evaluate the performance of two cost-effective models, namely TD-DFT and ∆SCF methods, combined with different Molecular Mechanics models, to predict photophysical and photochemical properties of a set of fluorescent mutants of the microbial rhodopsin Archaerhodopsin3. We investigate absorption energies and excited state isomerization barriers of the embedded retinal protonated Schiff-base chromophore by comparing different DFT functionals as well as different approximations of the embedding model. For absorption energies, CAM-B3LYP demonstrates the most consistent alignment with experiments among the functionals tested whereas the embedding potentials exhibit similar accuracy. However, incorporating linear response corrections within the polarizable TD-DFT/MM framework enhances accuracy. The photoisomerization barriers, instead, exhibit a pronounced sensitivity to the choice of embedding model, underscoring the complex role that environmental factors play in modulating predictions of excited-state processes. For the two properties here investigated, ∆SCF/MM presents a qualitatively similar behavior with respect to TD-DFT for all the tested embedding models.
|
Duccio Di Prima; Laura Milena Pedraza González; Peter Reinholdt; Jacob Kongsted; Benedetta Mennucci
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673c5b4bf9980725cfb41633/original/fluorescent-rhodopsins-a-challenging-test-for-cost-effective-qm-mm-approaches.pdf
|
6318b3c41856849c110d8a30
|
10.26434/chemrxiv-2022-p296f
|
Oxygen evolution at the BiVO4-water interface:
Mechanism of the water dehydrogenation
reaction
|
We study the water dehydrogenation reaction at the BiVO4(010)-water interface by combining nudged-elastic-band calculations and electronic structure calculations at
the hybrid functional level. We investigate the pathway and the kinetic barrier for the adiabatic reaction going from the hole polaron localized in BiVO4 to the dehydrogenation of the adsorbed water molecule at the interface. The reaction is found to involve the H2O•+ radical cation as intermediate, to have a kinetic barrier of 0.7 eV, and to be initiated by the electron transfer. The calculated kinetic barrier is in good agreement with experiment and is consistent with the slow hole transfer kinetics observed at the surface of BiVO4. To characterize the structural changes occurring during this process, we analyze the O-H distances for three relevant water molecules. We also examine the Wannier functions around the O atom of the adsorbate involved in the reaction to reveal the changes in the electronic structure during the hole hopping. The projected density of states of the lowest unoccupied molecular orbitals allows us to identify the atomic orbitals that are primarily involved in the reaction. We expect that the proposed reaction mechanism generally holds when the surface coverage is dominated by molecularly adsorbed water.
|
Sai Lyu; Julia Wiktor; Alfredo Pasquarello
|
Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6318b3c41856849c110d8a30/original/oxygen-evolution-at-the-bi-vo4-water-interface-mechanism-of-the-water-dehydrogenation-reaction.pdf
|
65c625c466c138172949303b
|
10.26434/chemrxiv-2024-6vrvq
|
Modulation of peripheral functional groups for the enhancement of electrochemical HER activity in bimetallic Ni-containing triply-fused porphyrins
|
We report here nickel(II) complexes (Ni-1 and Ni-2) of triply fused (covalently linked through β–β, meso–meso, β′–β′ linkages) porphyrins functionalized with tert-butyl and O-hexyl chains for the investigation of the electrocatalytic hydrogen evolution reaction (HER). The analogous monometallic porphyrins Ni-3 and Ni-4 were also synthesized for comparative analysis. Cyclic voltammetry of the bimetallic complexes functionalized with tert-butyl and O-hexyl chains showed an anodic shift in reduction potentials of Ni-1. The influence of the long alkyl chains was even more pronounced during electrochemical proton reduction with trifluoroacetic acid (TFA), as confirmed by the higher icat/ip and rate constants (kobs) of Ni-2 compared to Ni-1. Additionally, Faradaic efficiencies for the HER is more than 90 % for Ni-2, which is three times larger than Ni-1. Ni-2 also displays turnover numbers that are more than 200 times larger than Ni-1. A mechanistic investigation using UV-vis-NIR and EPR spectroscopy as well theoretical calculations indicate the involvement of the doubly reduced species as an active catalytic intermediate in the electrocatalytic process.
|
Arijit Singha Hazari; Shubhadeep Chandra; Patrick Becker; Hang Liu; Elias Klemm; Johannes Kästner; Biprajit Sarkar
|
Theoretical and Computational Chemistry; Inorganic Chemistry; Catalysis; Coordination Chemistry (Inorg.); Theory - Inorganic; Electrocatalysis
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-02-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c625c466c138172949303b/original/modulation-of-peripheral-functional-groups-for-the-enhancement-of-electrochemical-her-activity-in-bimetallic-ni-containing-triply-fused-porphyrins.pdf
|
67c6f279fa469535b9e66dec
|
10.26434/chemrxiv-2025-pd06r
|
Synthesis of Chroman Derivatives by Group Transposition and Atom Swap of 1-Tetralones. Single Atom Editing Enabled by Contractive Oxidation of Benzoxepine Silyl Ketene Acetals
|
Single-atom editing of complex molecules is steadily filling the chemical toolbox with site-selective modification reactions. Herein, a stepwise scheme for carbon-to-oxygen swap in tetralins leading to privileged chroman scaffolds is presented. Increasing the oxi-dation state at each stage, the substrate scope naturally extends: starting from tetralins via 1-tetralones and further via subsequently formed seven-membered lactones, the transformation results in diverse chroman-2-carboxylic acids and chroman-2-ols. The effi-ciency of this synthetic route is governed by the developed new oxidative ring-contractive transformations of tetrahydroben-zooxepinones, enabled by intermediate silylation into ketene acetals. The described carbon-to-oxygen swap is illustrated by 35+ examples, including skeletal editing of natural products and short formal synthesis of Heliannuol E. Formation of chroman-2-ols tentatively proceeds via a rare retro-[2+1]-cycloaddition accompanied by extrusion reaction of carbon monoxide..
|
Viktoria Ikonnikova; Pavel Solyev; Amir Al Mufti; Kirill Kungurtsev; Alexander Korlyukov; Mikhail Baranov; Andrey Mikhaylov
|
Organic Chemistry; Natural Products; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c6f279fa469535b9e66dec/original/synthesis-of-chroman-derivatives-by-group-transposition-and-atom-swap-of-1-tetralones-single-atom-editing-enabled-by-contractive-oxidation-of-benzoxepine-silyl-ketene-acetals.pdf
|
60c75a12bdbb892bc7a3b139
|
10.26434/chemrxiv.14229134.v3
|
Effect of Phase Transition on the Thermal Transport in Isoreticular DUT Materials
|
<p></p><p>Soft porous crystals (SPCs) or flexible metal-organic frameworks have great potential applications in gas storage and separation, in which SPCs can undergo phase transition due to external stimuli. Thus, understanding the effect of phase transition on the thermal transport in SPCs becomes extremely crucial, because the latent heat generated in aforementioned applications is needed to be effectively removed. In this paper, taking the isorecticular DUT series as an example, the thermal transport property of SPCs during the phase transition from the large pore (lp) phase to the narrow pore (np) phase is comprehensively investigated by molecular dynamics simulations together with the Green-Kubo method. According to our calculations, all DUT structures exhibit an ultralow thermal conductivity smaller than 0.2 Wm<sup>-1</sup>K<sup>-1</sup>. In addition, we find that the effect of phase transition on the thermal transport property of different DUT materials considered here strongly depends on their porosity. As for DUT-48, its lp phase has a thermal conductivity larger than that of its np phase. However, in other DUT materials, i.e, DUT-47, DUT-49, DUT-50, and DUT-151 the thermal transport property of their lp phase is found to be weaker than that of their np phase. This complicated effect of phase transition on the thermal transport in SPCs can be explained by a porosity-dominated competition mechanism between the increased volumetric heat capacity and the aggravated phonon scattering during the phase transition process.</p><p></p>
|
Penghua Ying; Jin Zhang; Zheng Zhong
|
Transport phenomena (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-06-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75a12bdbb892bc7a3b139/original/effect-of-phase-transition-on-the-thermal-transport-in-isoreticular-dut-materials.pdf
|
66a4321cc9c6a5c07a1027ff
|
10.26434/chemrxiv-2024-k0sgz-v2
|
Microplastic particles contain ice nucleation sites that can be inhibited by atmospheric aging
|
Recent research has shown that microplastics are widespread in the atmosphere. However, we know little about their ability to nucleate ice and their impact on ice formation in clouds. Ice nucleation by microplastics could also limit their long-range transport and global distribution. The present study explores the heterogeneous ice-nucleating ability of seven microplastic samples in the immersion-freezing mode. Two polypropylene samples and one polyethylene terephthalate sample froze heterogeneously with median freezing temperatures of -20.9°C, -23.2°C and -21.9°C, respectively. The number of ice nucleation sites per surface area, n_s (T), ranged from 10^-1 to 10^4 cm^-2 in a temperature interval of -15 to -25°C, which is comparable to that of volcanic ash and fungal spores. After exposure to ozone or a combination of UV light and ozone, simulating atmospheric aging, the ice nucleation activity decreased in some cases and remained unchanged in others. Our freezing data suggest that microplastics may promote ice formation in cloud droplets. In addition, based on a comparison of our freezing results and previous simulations using a global transport model, ice nucleation by microplastics will impact their long-range transport to faraway locations and global distribution.
|
Teresa M. Seifried; Sepehr Nikkho; Aurelio Morales Murillo; Lucas J. Andrew; Edward R. Grant; Allan K. Bertram
|
Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science
|
CC BY 4.0
|
CHEMRXIV
|
2024-07-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a4321cc9c6a5c07a1027ff/original/microplastic-particles-contain-ice-nucleation-sites-that-can-be-inhibited-by-atmospheric-aging.pdf
|
60c74f7bbb8c1ab4283db938
|
10.26434/chemrxiv.12897086.v1
|
Fragment-Based Identification of Ligands for Bromodomain-Containing Factor 3 of Trypanosoma Cruzi
|
The <i>Trypanosoma cruzi</i> (<i>T. cruzi</i>) parasite is the cause of Chagas disease, a neglected disease endemic in South America. The life cycle of the <i>T. cruzi</i> parasite is complex and includes transitions between distinct life stages. This change in phenotype (without a change in genotype) could be controlled by epigenetic regulation, and might involve the bromodomain-containing factors 1-5 (<i>Tc</i>BDF1-5). However, little is known about the function of the <i>Tc</i>BDF1-5. Here we describe a fragment-based approach to identify ligands for <i>T. cruzi</i> bromodomain-containing factor 3 (<i>Tc</i>BDF3). We expressed a soluble construct of <i>Tc</i>BDF3 in <i>E. coli</i>, and used this to develop a range of biophysical assays for this protein. Fragment screening identified twelve compounds that bind to the <i>Tc</i>BDF3 bromodomain. Based on this screen, we developed functional ligands containing a fluorescence or <sup>19</sup>F reporter group, and a photo-crosslinking probe for <i>Tc</i>BDF3. These tools compounds will be invaluable in future studies on the function of <i>Tc</i>BDF3 and will provide insight into the biology of <i>T. cruzi</i>.
|
Corentine Laurin; Joseph Bluck; Anthony Chan; Michelle Keller; Andrew Boczek; Amy Scorah; K. F. Larissa See; Laura Jennings; David Hewings; Fern Woodhouse; Matthias Schiedel; Philip Humphreys; Philip Biggin; Stuart Conway
|
Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-09-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f7bbb8c1ab4283db938/original/fragment-based-identification-of-ligands-for-bromodomain-containing-factor-3-of-trypanosoma-cruzi.pdf
|
60c7490a702a9b35cd18b0c8
|
10.26434/chemrxiv.12009636.v1
|
Identification of Key Interactions Between SARS-CoV-2 Main Protease and Inhibitor Drug Candidates
|
<p> The number of cases of severe acute respiratory syndrome coronavirus
2 (SARS-CoV-2) infection (COVID-19) has reached over 114,000. SARS-CoV-2 caused
a pandemic in Wuhan, China, in December 2019 and is rapidly spreading globally. It has been reported that peptide-like
anti-HIV-1 drugs are effective against <a>SARS-CoV </a>Main
protease (M<sup>pro</sup>). Due to the close phylogenetic relationship between
SARS-CoV and SARS-CoV-2, their main proteases share many structural and
functional features. Thus, these drugs are also regarded as potential drug
candidates targeting SARS-CoV-2 M<sup>pro</sup>. However, the mechanism of
action of SARS-CoV-2 M<sup>pro</sup> at the atomic-level is unknown. In the
present study, we revealed key interactions between SARS-CoV-2 M<sup>pro</sup>
and three drug candidates by performing pharmacophore modeling and 1μs molecular
dynamics (MD) simulations. His41, Gly143, and Glu166 formed interactions with the
functional groups that were common among peptide-like inhibitors in all MD
simulations. These interactions are important targets for potential drugs
against SARS-CoV-2 M<sup>pro</sup>.</p>
|
Ryunosuke Yoshino; Nobuaki Yasuo; Masakazu Sekijima
|
Bioinformatics and Computational Biology; Biophysics; Computational Chemistry and Modeling; Biophysical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-03-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7490a702a9b35cd18b0c8/original/identification-of-key-interactions-between-sars-co-v-2-main-protease-and-inhibitor-drug-candidates.pdf
|
67b4edd3fa469535b9e7a7fd
|
10.26434/chemrxiv-2025-hjjw6
|
Expedient construction of fused polycyclic skeletons via
palladium-catalyzed dearomatization of naphthalenes and
benzenes.
|
A novel palladium-catalyzed dearomative cyclization of naphthalenes and benzenes has been accomplished for expedient construction of fused polycyclic skeletons bearing an all-carbon quaternary center. Excellent functional group tolerance was demonstrated in the reaction of 2,2-phenylnaphthyl acetonitriles, in which cyano group can serve as linkage for potential applications. Further, the challenging dearomatization of benzenes was developed, offering a series of [6,5,6]-carbotricyclic scaffolds which may play a role as intermediate for the synthesis of fused tricyclic natural products and its analogues.
|
Jinbin Zhu; Jiaqi Li; Zhenyue Li; Yuan Yuan; Zelan Zhu; Yanyan Wang; Zhonghao Deng; Qiuyan Tu; Zhiyong Tan; Shaobin Tang; Zhengwang Chen; Zhong-Xia Wang
|
Organic Chemistry; Organometallic Chemistry; Organic Synthesis and Reactions; Reaction (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-02-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b4edd3fa469535b9e7a7fd/original/expedient-construction-of-fused-polycyclic-skeletons-via-palladium-catalyzed-dearomatization-of-naphthalenes-and-benzenes.pdf
|
615b32820ad1ff64b78a09f9
|
10.26434/chemrxiv-2021-tkzc6
|
MALDI TIMS IMS of Disialoganglioside Isomers – GD1a and GD1b in Murine Brain Tissue
|
Gangliosides are classified as acidic glycosphingolipids, containing ceramide moieties and oligosaccharide chains with one or multiple sialic acid residue(s). The presence of multiple sialylation sites gives rise to highly diverse isomeric structures with distinct biological roles. Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) enables the untargeted spatial analysis of gangliosides, among other biomolecules, directly from tissue sections. Integrating trapped ion mobility mass spectrometry (TIMS), a gas-phase separation technology, with MALDI IMS allows for the investi-gation of isomeric lipid structures in situ. Here we demonstrate the gas-phase separation of disialoganglioside isomers GD1a and GD1b that differ in the position of a sialic acid residue, in a standard mixture of both isomers, a total ganglioside extract, and directly from thin tissue sections. The unique spatial distributions of GD1a/b (d36:1) and GD1a/b (d38:1) were deter-mined from rat hippocampus, as well as in a spinal cord tissue section.
|
Katerina Djambazova; Martin Dufresne; Lukasz Migas; Angela Kruse; Raf Van de Plas; Richard Caprioli; Jeffrey Spraggins
|
Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Imaging; Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-10-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615b32820ad1ff64b78a09f9/original/maldi-tims-ims-of-disialoganglioside-isomers-gd1a-and-gd1b-in-murine-brain-tissue.pdf
|
60c7591bf96a0058f0288f5e
|
10.26434/chemrxiv.14644854.v1
|
A Deep Generative Model Enables Automated Structure Elucidation of Novel Psychoactive Substances
|
Over the past decade, the illicit drug market has been reshaped by the proliferation of clandestinely produced designer drugs. These agents, referred to as new psychoactive substances (NPSs), are designed to mimic the physiological actions of better-known drugs of abuse while skirting drug control laws. The public health burden of NPS abuse obliges toxicological, police, and customs laboratories to screen for them in law enforcement seizures and biological samples. However, the identification of emerging NPSs is challenging due to the chemical diversity of these substances and the fleeting nature of their appearance on the illicit market. Here, we present DarkNPS, a deep learning-enabled approach to automatically elucidate the structures of unidentified designer drugs using only mass spectrometric data. Our method employs a deep generative model to learn a statistical probability distribution over unobserved structures, which we term the structural prior. We show that the structural prior allows DarkNPS to elucidate the exact chemical structure of an unidentified NPS with an accuracy of 51%, and a top-10 accuracy of 78%. Our generative approach has the potential to enable de novo structure elucidation for other types of small molecules that are routinely analyzed by mass spectrometry.
|
Michael Skinnider; Fei Wang; Daniel Pasin; Russell Greiner; Leonard Foster; Petur Dalsgaard; David
S. Wishart
|
Analytical Chemistry - General; Chemoinformatics; Mass Spectrometry; Machine Learning; Artificial Intelligence
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7591bf96a0058f0288f5e/original/a-deep-generative-model-enables-automated-structure-elucidation-of-novel-psychoactive-substances.pdf
|
6657afe191aefa6ce14b7075
|
10.26434/chemrxiv-2024-5g8jg
|
An ex situ gaseous reagent for multicomponent amine bioconjugation
|
Bioconjugation is a large field with many diverse goals, needs, and challenges, that requires a broad toolbox of fundamentally different synthetic approaches. As nucleophilic groups are prevalent in biomolecules, the ability to crosslink two nucleophilic sites offers an attractive approach to construct useful bioconjugates. New technologies for crosslinking with gaseous reagents and with minimal perturbation of natural structure could provide new ways to think about bioconjugation in complex environments. We report a minimalist gaseous sulfonyl chloride-derived reagent for multicomponent bioconjugation with amine, phenol, or aniline reagents to afford urea or carbamate products. In utilizing a gas-phase reagent for a reaction mediated by metal ions, a variety of biologically relevant molecules such as saccharide, PEG, fluorophore, and affinity tag can be efficiently crosslinked to the N-terminus or lysine side chain amines on natural polypeptides or proteins. The application of this method to the production of functional, modified proteins was demonstrated by fluorescence imaging of a cancer cell line and by the facile preparation of a peptide–protein conjugate.
|
Yuxuan Ding; Simon Pedersen; Yixian Wang; Han Xiao; Zachary Ball
|
Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6657afe191aefa6ce14b7075/original/an-ex-situ-gaseous-reagent-for-multicomponent-amine-bioconjugation.pdf
|
65b614e2e9ebbb4db9237db9
|
10.26434/chemrxiv-2023-rvr9n-v2
|
MS²Rescore 3.0 is a modular, flexible, and
user-friendly platform to boost peptide
identifications, as showcased with MS Amanda 3.0
|
Rescoring of peptide-spectrum matches (PSMs) has emerged as a standard procedure for the analysis of tandem mass spectrometry data. This emphasizes the need for software maintenance and continuous improvement for such algorithms. We here introduce MS²Rescore 3.0, a versatile, modular, and user-friendly platform designed to increase peptide identifications. Researchers can install MS²Rescore across various platforms with minimal effort and benefit from a graphical user interface, a modular Python API, and extensive documentation.
To showcase this new version, we connected MS²Rescore 3.0 with MS Amanda 3.0, a new release of the well-established search engine, addressing previous limitations on automatic rescoring. Among new features, MS Amanda now contains additional output columns that can be used for rescoring. The full potential of rescoring is best revealed when applied on challenging data sets. We therefore evaluated the performance of these two tools on publicly available single-cell data sets, where the number of PSMs was substantially increased, thereby demonstrating that MS²Rescore offers a powerful solution to boost peptide identifications.
MS²Rescore's modular design and user-friendly interface make data-driven rescoring easily accessible, even for inexperienced users. We therefore expect MS²Rescore to be a valuable tool for the wider proteomics community. MS²Rescore is available at https://github.com/compomics/ms2rescore.
|
Louise Marie Buur; Arthur Declercq; Marina Strobl; Robbin Bouwmeester; Sven Degroeve; Lennart Martens; Viktoria Dorfer ; Ralf Gabriels
|
Biological and Medicinal Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-01-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b614e2e9ebbb4db9237db9/original/ms2rescore-3-0-is-a-modular-flexible-and-user-friendly-platform-to-boost-peptide-identifications-as-showcased-with-ms-amanda-3-0.pdf
|
660e517c418a5379b008b0d7
|
10.26434/chemrxiv-2024-rhl1f
|
Rhodium-Catalyzed [5 + 1 + 2] Cycloaddition of Yne-3-Acyloxy-1,4-Enynes (YACEs) and Carbon Monoxide: Reaction Development and Mechanism
|
Developing new reaction to synthesize challenging eight-membered carbocycles is a research frontier of organic synthesis. Reported here is the development of the first Rh-catalyzed [5 + 1 + 2] cycloaddition of yne-3-acyloxy-1,4-enyne (Yne-ACEs, short as YACEs) and CO, in which sequentially 5-carbon (generated from 3-acyloxy-1,4-enynes), 1-carbon (CO) and 2-carbon (alkynes) are embedded into the final 5/8 scaffold containing cyclooctatrienone structure. This reaction has broad scope and can be carried out under mild conditions. Keys to the success of the present [5 + 1 + 2] reaction, discovered and supported by experiments and ab initio calculations, include: using terminal alkyne in the 3-acyloxy-1,4-enyne moiety of the substrates so that 1,2-acyloxy migration (instead of 1,3-acyloxy migration, a step required for competing [4 + 2 + 1] reaction) can be realized; applying electron-rich aryl group (here is p-dimethylamino aryl) in the acyloxy group to make [5 + 1] pathway disfavored. Quantum chemical calculations have also been used to answer why this reaction is [5 + 1 + 2] but not [5 + 2 + 1] (where alkyne insertion is ahead of CO insertion), and the factors disfavoring the competitive [5 + 2], [5 + 1] and [4 + 2 + 1] reactions.
|
Qi Cui; Pan Zhang; Bing-Wen Li; Yi Jin; Qianwei Zhang; Hong-Xi Bai; Zhi-Xiang Yu
|
Organic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-04-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660e517c418a5379b008b0d7/original/rhodium-catalyzed-5-1-2-cycloaddition-of-yne-3-acyloxy-1-4-enynes-yac-es-and-carbon-monoxide-reaction-development-and-mechanism.pdf
|
61c165cc75c572fe8df2cb78
|
10.26434/chemrxiv-2021-czx0q
|
Unsymmetrical Growth Synthesis of Nontraditional Dendrimers
|
Developing highly complex molecules is of great significance in science and technology. Here we present an unprecedented type of dendrimer assembled from linear ABB-type monomer. The construction of this nontraditional ramified architecture was facilely achieved through one simple convergent strategy established on the iridium-catalyzed cycloaddition of organic azides with internal 1-thioalkynes (IrAAC). By virtue of the unsymmetrically growing fashion in this process, diverse functional groups could be conveniently distributed on both of its exterior and interior layers. Syntheses of two dendrons from the cooperation of one linear alkyne motif with different azides were presented to demonstrate the efficiency and fidelity of this protocol. Post-modifications on their core or periphery were further conducted, resulting in diverse newly functionalized dendrimers with up to ~16.0 kDa molecular weight. The identity and purity of these unsymmetrical dendritic macromolecules were well confirmed by 1H NMR, MS and SEC analysis.
|
Shengtao Ding; Lijiao Niu; Xueyan Zhang
|
Polymer Science; Organic Polymers
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-12-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c165cc75c572fe8df2cb78/original/unsymmetrical-growth-synthesis-of-nontraditional-dendrimers.pdf
|
619f3c107c89162f5f441e73
|
10.26434/chemrxiv-2021-t6lcq-v2
|
Construction of Stable Metal-Organic Framework Platforms Embedding N-Heterocyclic Carbene Metal Complexes for Selective Catalysis
|
We report a bottom-up approach to immobilize catalysts into MOFs, including copper halides and gold chloride in a predictable manner. Interestingly, the structures of MOFs bearing NHC metal complexes maintained a similar 4-fold interpenetrated cube. They exhibited exceptionally high porosity despite the interpenetrated structure and showed good stability in various solvents. Moreover, these MOFs possess high size activity depending on the size of the substrates in various reactions, compared to homogeneous catalysis. Also, the high catalytic activity of MOFs can be preserved 4 times without significant loss of crystallinity. Incorporation of the various metal complexes into MOFs allows for the preparation of functional MOFs for practical applications.
|
Hyunyong Kim; Hyunseok Kim; Kimoon Kim; Eunsung Lee
|
Inorganic Chemistry; Coordination Chemistry (Inorg.); Reaction (Inorg.); Crystallography – Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-11-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619f3c107c89162f5f441e73/original/construction-of-stable-metal-organic-framework-platforms-embedding-n-heterocyclic-carbene-metal-complexes-for-selective-catalysis.pdf
|
60c755fcee301c9c11c7b27a
|
10.26434/chemrxiv.14184830.v1
|
Efficient Solid-State Photon Upconversion Enabled by Spin Inversion at Organic Semiconductor Interface
|
We realized solid-state UC with 100
times higher efficiency than a conventional system by discovering a novel UC
mechanism in bilayer organic semiconductor heterojunctions. The UC occurred
through spin inversion during the charge separation and recombination at the
interface. The key to the success was the triplet formation at the interface,
as this could avoid the loss process during triplet diffusion, which is a
problematic issue in conventional systems. As a result of this finding,
efficient UC from near-infrared to visible light on flexible thin films under LED
light excitation was made possible.
|
Seiichiro Izawa; Masahiro Hiramoto
|
Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2021-03-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755fcee301c9c11c7b27a/original/efficient-solid-state-photon-upconversion-enabled-by-spin-inversion-at-organic-semiconductor-interface.pdf
|
623c49e413d47813bb9a2207
|
10.26434/chemrxiv-2022-7gcmd
|
Chemical Proteomics Reveals Antibiotic Targets of Oxadiazolones in MRSA
|
Phenotypic screening is a powerful approach to identify novel antibiotics against methicillin-resistant Staphylococcus aureus (MRSA) infection, but elucidation of the targets responsible for antimicrobial activity is often challenging in the case of compounds with a polypharmacological mode-of-action. Here, we show that activity-based protein profiling maps the target interaction landscape of a series of 1,3,4-oxadiazole-3-ones, identified in a phenotypic screen to have high antibacterial potency against multidrug resistant S. aureus. In situ competitive and comparative chemical proteomics with a tailor-made activity-based probe, in combination with transposon and resistance studies, revealed several cysteine and serine hydrolases as relevant targets. Our data showcase oxadiazolones as novel antibacterial chemotype with a polypharmacological mode-of-action, in which FabH, FphC and AdhE play a central role.
|
Alexander Bakker; Ioli Kotsogianni; Liza Mirenda; Verena Straub; Bogdan Florea; Richard van den Berg; Antonius Janssen; Nathaniel Martin; Mario van der Stelt
|
Biological and Medicinal Chemistry; Organic Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems; Microbiology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623c49e413d47813bb9a2207/original/chemical-proteomics-reveals-antibiotic-targets-of-oxadiazolones-in-mrsa.pdf
|
662865d921291e5d1d889ffa
|
10.26434/chemrxiv-2024-zj1w3-v2
|
Exploration of Multi-Label Classification Techniques for Modelling of Specialty Arabica Coffee Flavour Notes
|
Predicting the complex flavor profiles of specialty Arabica coffee is a challenging task due to the subjective nature of human sensory evaluations. This study investigates the application of visible-near-infrared (vis-NIR) spectroscopy coupled with multi-label classification techniques to simultaneously predict the presence of flavors described by the Specialty Coffee Association's Flavour Wheel in unroasted green coffee beans.
Sixty lots of green coffee beans from various origins were analyzed by vis-NIR spectroscopy, yielding spectral data from 400-1100 nm. Flavour notes for each lot were provided by a commercial coffee roaster based on sensory evaluations, which were binarized as present or absent labels. Nine flavour notes from the Flavour Wheel were modeled: Floral, Honey, Caramel, Fruits, Citrus, Berry, Cocoa, Nuts, and Spice.
Exploratory data analysis using principal component analysis and uniform manifold approximation and projection revealed no clear clustering based on flavor notes or origin. However, potential correlations between related flavors on the Flavour Wheel were observed.
Several multi-label classification approaches were explored, including binary relevance, classifier chains with various chaining strategies, and decomposed binary classifiers. Model performance was evaluated using Hamming loss and mean balanced accuracy across all labels.
The best results were achieved using a decomposed approach by extracting the best-performing binary models for each flavour note from the binary relevance experiments. This yielded a Hamming loss of 0.2778 and a mean balanced accuracy of 69%.
Classifier chain methods consistently underperformed, suggesting potential error propagation or that flavour note relationships may not directly translate to taste perception. Independently training binary classifiers achieved low Hamming loss but suffered from overfitting.
This study demonstrates the feasibility of using visible-NIR spectroscopy and the potential of multi-label classification to predict the flavor profiles of green coffee beans. With larger datasets and deeper investigations into flavor correlations, these techniques could enable efficient prediction of green coffee beans in the supply chain.
|
Sherman Ho
|
Analytical Chemistry; Agriculture and Food Chemistry; Spectroscopy (Anal. Chem.); Food
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-04-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662865d921291e5d1d889ffa/original/exploration-of-multi-label-classification-techniques-for-modelling-of-specialty-arabica-coffee-flavour-notes.pdf
|
66b0ba37c9c6a5c07a0e6b20
|
10.26434/chemrxiv-2024-zlrdj
|
Radical-Nucleophilicity Controlled Regiodivergent C-3 vs C-7 Functionalization of Quinoxalin-2(1H)-ones
|
Here in this article, we have addressed how radical nucleophilicity and temperature controlled the regiodiversity (C-3 vs C-7) of quinoxalin-2(1H)-one. Following the acquisition of the diversity product, PTSA and potassium carbonate were added within the reaction vessel to further address the selectivity issue for the same methods. And we encompassed an easy-to-follow guide explaining how to obtain 7-bromo-1-methylquinoxalin-2(1H)-one and 2-(4-methyl-3-oxo-3,4-dihydroquinoxalin-2-yl)benzo[d]isothiazol-3(2H)-one 1,1-dioxide using 1-methylquinoxalin-2(1H)-one and 2-bromobenzo[d]isothiazol-3(2H)-one 1,1-dioxide in acetonitrile solvent.
|
Buddhadeb Pal; Bikash Mandal; Soumyashree Priyadarshinee; Prasenjit Mal
|
Organic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b0ba37c9c6a5c07a0e6b20/original/radical-nucleophilicity-controlled-regiodivergent-c-3-vs-c-7-functionalization-of-quinoxalin-2-1h-ones.pdf
|
60c7470c842e652983db290a
|
10.26434/chemrxiv.11522418.v1
|
Electrochemical Deposition of Addressable N-Heterocyclic Carbene Monolayers
|
<div>Herein, we introduce an electrochemical based approach for surface-anchoring of N-heterocyclic carbene (NHC) monolayers. The deposition process is based on in-situ formation of hydroxide ions by water reduction under negative potential. The hydroxide ions function as a base for deprotonation of the imidazole cations for the formation of active carbenes that self-assemble on the electrode's surface. Therefore, the electrochemical deposition does not require dry conditions or the addition of external base for carbene activation. The high temporal and spatial proximity between the NHC's activation and surface anchoring enabled the formation of well-ordered monolayers of NHCs on Au surfaces with higher density and stability than those achieved using liquid-phase deposition.</div>
|
Einav Amit; Shahar Dery; Suhong Kim; Anirban Roy; Qichi Hu; F. Dean Toste; Elad Gross
|
Electrochemistry - Mechanisms, Theory & Study; Self-Assembly; Spectroscopy (Physical Chem.); Surface
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-01-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7470c842e652983db290a/original/electrochemical-deposition-of-addressable-n-heterocyclic-carbene-monolayers.pdf
|
67db2de1fa469535b9d6893d
|
10.26434/chemrxiv-2025-6d1f5
|
10-Step, Gram-Scale Total Synthesis of (–)-Bipinnatin J
|
A concise, scalable total synthesis of (–)-Bipinnatin J is disclosed. Commencing from inexpensive starting materials, this marine diterpenoid was fashioned through a highly convergent synthesis enabled by Ni-electrocatalytic decarboxylative cross–coupling (DCC) taking advantage of succinate as an ethylene 2-carbon bridge, a unique halogen dance-Zweifel sequence to rapidly access a trisubstituted furan, a Ni-mediated 1,6-conjugate addition, and an asymmetric proton transfer.
|
Phil Baran; Anthony Rodriguez; Maithili Pokle ; Griffin Barnes
|
Organic Chemistry; Natural Products; Organic Synthesis and Reactions
|
CC BY 4.0
|
CHEMRXIV
|
2025-03-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67db2de1fa469535b9d6893d/original/10-step-gram-scale-total-synthesis-of-bipinnatin-j.pdf
|
65f23acb9138d2316168a5ae
|
10.26434/chemrxiv-2024-hjcx6
|
Understanding Boron Chemistry as the Surface Modification and Electrolyte Additive for Co-free Lithium-Rich Layered Oxide
|
Lithium-rich layered oxide (LRLO) stands out as a highly promising cathode material for the next generation of Li-ion batteries, owing to its exceptional lithium storage capacity. The absence of cobalt in LRLO's composition provides an additional advantage, enabling cost-effective production and thereby improving the feasibility of large-scale manufacturing. Despite these promising attributes, LRLO has encountered challenges related to poor cycling performance and severe voltage decay, impeding its practical application. In addressing these challenges, we employ a surface modification technique involving lithium borate (LBO) through a dry coating method. The LBO-coated LRLO exhibits a uniform surface layer with a thickness of 15 nm. Furthermore, the performance of LBO-coated LRLO in a full cell is synergistically enhanced when combined with lithium bis(oxalato)borate (LiBOB) as an electrolyte additive. A discharge capacity retention of 82% is achieved after 400 cycles at room temperature. These substantial improvements are attributed to the continual reaction between boron species on the LRLO cathode surface and PF6- anions in the electrolyte. This reaction generates BF4- and suppresses HF acid formation during the high voltage charging process, demonstrating LRLO's potential for practical implementation.
|
Na Ri Park; Minghao Zhang; Bing Han; Bryant Dang; Weikang Li; Kun Qian; HongNam Nguyen; Shinichi Kumakura; Wendy Zhou; Ying Meng
|
Materials Science; Energy; Chemical Engineering and Industrial Chemistry; Coating Materials; Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f23acb9138d2316168a5ae/original/understanding-boron-chemistry-as-the-surface-modification-and-electrolyte-additive-for-co-free-lithium-rich-layered-oxide.pdf
|
636332c3cf6de90e2c2d50d3
|
10.26434/chemrxiv-2022-h8rjb
|
Water soluble chromenylium dyes for shortwave infrared imaging in mice
|
In vivo imaging using shortwave infrared light (SWIR, 1000-2000 nm) benefits from deeper penetration depths, decreased background autofluorescence, and high resolution. However, the development of biocompatible contrast agents for these low energy wavelengths has significant challenges. While there have been significant advances in SWIR chromophore scaffolds over the past 5 years, a major barrier for widespread utility of SWIR small molecule fluorophores is their hydrophobicity and tendency to form non-emissive aggregates. Here, we report a platform for generating a panel of soluble and functional dyes for SWIR imaging by late-stage functionalization of a fluorophore intermediate via click chemistry. The resulting fluorophores with sulfonate, ammonium or zwitterion functionalities are all water soluble with bright SWIR fluorescence in serum, allowing for fast imaging in mice. Specifically, the sulfonate-carrying derivative enables clear video-rate imaging of vasculature with as little as 0.05 nmol injected dye, and the ammonium-modified dye shows strong retention in cells that enables tracking of xenograft tumor growth. We further showcase the versatility of this design by incorporating phosphonate functionalities for imaging of bone in awake and moving mice. This modular design of functional SWIR fluorophores in water provides insights for facile derivatization of existing fluorophores to introduce solubility and bioactivity towards bioimaging applications.
|
Shang Jia; Eric Lin; Irene Lim; Emily Mobley; Lei Guo; Ellen Sletten
|
Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-11-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636332c3cf6de90e2c2d50d3/original/water-soluble-chromenylium-dyes-for-shortwave-infrared-imaging-in-mice.pdf
|
67d8381a6dde43c9082099a9
|
10.26434/chemrxiv-2025-rsqr9
|
How does the Ni-Ga Alloy Structure Tune Methanol Productivity and Selectivity?
|
In this work, we assess how the structure of SiO₂-supported, Ni-Ga alloys determines their activity and selectivity for the hydrogenation of CO₂ to methanol. Using a hydrothermal deposition-precipitation approach followed by activation at 700°C in H₂, we synthesize catalysts containing α-Ni, α-Ni₉Ga, α’-Ni₃Ga, or δ-Ni₅Ga₃ phases supported on amorphous SiO2. Operando X-ray pair distribution function analysis and X-ray absorption spectroscopy confirm unequivocally the structure of all phases and their stability under reaction conditions; additionally, all catalysts contain GaOx species in varying amounts. We observe that the catalysts α’-Ni₃Ga/SiO₂ and δ-Ni₅Ga₃/SiO₂ exhibit high methanol formation rates (~0.8 mmolMeOH molNi⁻¹ s⁻¹), which are 27 times greater than those of α-Ni₉Ga/SiO₂ and α-Ni/SiO₂. Notably, α’-Ni₃Ga/SiO₂ shows the highest selectivity for methanol at 71%, compared to 55% for δ-Ni₅Ga₃/SiO₂ and 11% for α-Ni₉Ga/SiO₂, which challenges the conventional view of α’-Ni₃Ga being a poor catalyst for methanol synthesis. To explain the high methanol selectivity and productivity of α’-Ni₃Ga/SiO₂ compared to the other alloy phases, DFT calculations were performed. It was found that the Ni-rich step sites in α’-Ni₃Ga effectively stabilize key reaction intermediates (HCOO* and CH₃O*) for the formation of methanol. However, such Ni-rich step sites in α’-Ni₃Ga also favour CO* dissociation, which could facilitate methane formation, yet the presence of GaOx decreases the stability of CO* on α’-Ni₃Ga, explaining ultimately the promotion of HCOO* formation. This study highlights the importance of Ga species (both metallic and oxidic) in modulating the electronic properties of heterogeneous catalysts, providing a versatile toolbox to stabilize key reaction intermediates, leading ultimately to high product selectivity.
|
Nora Zimmerli; Andres-Felipe Usuga ; Stefano Checchia; Aleix Comas Vives ; Christoph Müller ; Paula Abdala
|
Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d8381a6dde43c9082099a9/original/how-does-the-ni-ga-alloy-structure-tune-methanol-productivity-and-selectivity.pdf
|
60c73eda337d6c0e5be26437
|
10.26434/chemrxiv.7149281.v1
|
Separating the Effects of Experimental Noise from Inherent System Variability in Voltammetry: The [Fe(CN)_6]^3−/4− Process
|
<div>Recently, we have introduced the use of techniques drawn from Bayesian statistics to recover kinetic and thermodynamic parameters from voltammetric data, and were able to show that the technique of large amplitude ac voltammetry yielded significantly more accurate parameter values than the equivalent dc approach. In this paper we build on this work to show that this approach allows us, for the first time, to separate the effects of random experimental noise and inherent system variability in voltammetric</div><div>experiments. We analyse ten repeated experimental data sets for the [Fe(CN) 6 ] 3−/4− process, again using large-amplitude ac cyclic voltammetry. In each of the ten cases</div><div>we are able to obtain an extremely good fit to the experimental data and obtain very narrow distributions of the recovered parameters governing both the faradaic (the reversible formal faradaic potential, E_0, the standard heterogeneous charge transfer rate constant k_0, and the charge transfer coefficient α) and non-faradaic terms (uncompensated resistance, R_u , and double layer capacitance, C_dl). We then employ hierarchical</div><div>Bayesian methods to recover the underlying “hyperdistribution” of the faradaic and non-faradaic parameters, showing that in general the variation between the experimental data sets is significantly greater than suggested by individual experiments, except for α where the inter-experiment variation was relatively minor. Correlations between pairs of parameters are provided, and for example, reveal a weak link between k_0 and C_dl (surface activity of a glassy carbon electrode surface). Finally, we discuss the</div><div>implications of our findings for voltammetric experiments more generally.</div>
|
Martin Robinson; Alan Bond; Alexandr Simonov; Jie Zhang; David Gavaghan
|
Electrochemical Analysis; Computational Chemistry and Modeling
|
CC BY 4.0
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CHEMRXIV
|
2018-10-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73eda337d6c0e5be26437/original/separating-the-effects-of-experimental-noise-from-inherent-system-variability-in-voltammetry-the-fe-cn-6-3-4-process.pdf
|
674eadc67be152b1d0c510fd
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10.26434/chemrxiv-2024-9c8sr
|
Thiyl Chemistry: Cysteine-Catalyzed Maleate Isomerization via Nucleophilic Addition versus Aqueous Thiyl Radical Processes
|
Enzymatic systems catalyze the E/Z isomerization of C=C double bonds by thiol-based cysteine residues efficiently, while artificial reactions with thiol-based molecules have remained stoichiometric, not catalytic. Herein, we report a catalytic isomerization of maleate to fumarate at benign temperatures using molecular catalysts based on cysteine and its analogs via chemical or photochemical radical activation. Kinetic analysis and DFT study support the aqueous thiyl radical-catalyzed reaction. The reaction is first-order with respect to the reactant, zero-order with respect to the thiol molecules, and first-order with respect to the radical initiator concentration. The catalytic turnover number of 2,500 and catalytic turnover frequency of 1.1 s‒1 have been achieved in the presence of thiyl radicals, and chemical “mutational” studies reveal the importance of both the thiol unit and the intramolecular adjacent groups for efficient catalysis.
|
Satoru Kosaka; Kentaro Kurebayashi; Naoki Yamato; Hiroshi Tanaka; Naoki Haruta; Masanori Yamamoto
|
Biological and Medicinal Chemistry; Organic Chemistry; Catalysis
|
CC BY 4.0
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CHEMRXIV
|
2024-12-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674eadc67be152b1d0c510fd/original/thiyl-chemistry-cysteine-catalyzed-maleate-isomerization-via-nucleophilic-addition-versus-aqueous-thiyl-radical-processes.pdf
|
60fa70c2d03b3df2a4026dee
|
10.26434/chemrxiv-2021-dppsm-v2
|
Targeted Exploration of Bio-inspired Cascade Reactions: A One-Pot Total Synthesis of Nesteretal A
|
Nesteretal A was recently isolated from a marine actinomycete. An appealing and challenging cage-structure along with an unusual biosynthetic pathway prompted us to explore an expeditious bio-inspired total synthesis of nesteretal A. An unconventional strategy was chosen and a cascade reaction starting from diacetyl was studied. Under organocatalytic conditions mimicking an aldolase-type sequence with a cyclic secondary amine, nesteretal A was detected and targeted through LC-MS/MS and NMR analyses. Starting from a double aldolization of three units, an intramolecular succession of aldolizations and acetalizations probably drives the highly reproducible formation of nesteretal A. An easy isolation protocol has been devised to overcome a non-surprising low yield but largely counterbalanced by the straightforwardness and cost-effectiveness of this first total synthesis of nesteretal A.
|
Axel Leblond; Inès Houari; Karine Leblanc; Erwan Poupon; Mehdi Beniddir
|
Organic Chemistry; Analytical Chemistry; Natural Products; Organic Synthesis and Reactions; Mass Spectrometry
|
CC BY NC ND 4.0
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CHEMRXIV
|
2021-07-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60fa70c2d03b3df2a4026dee/original/targeted-exploration-of-bio-inspired-cascade-reactions-a-one-pot-total-synthesis-of-nesteretal-a.pdf
|
668ce7485101a2ffa8d4c5eb
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10.26434/chemrxiv-2024-qd42r
|
Synthesis by fast thiol-Michael click addition of biodegradable and potentially fully biobased architectures based on starch and polyester, towards sustainable and performing multiphase systems.
|
For short-term sustainable applications such as packaging and agriculture, new biodegradable and renewable macromolecular architectures based on polysaccharide and polyester have been developed with an original multistep pathway, and then characterized. In a first step, amylomaize starch (AMS), based on rather linear polysaccharides with very high amylose content, and poly(butylene adipate-co-terephthalate) (PBAT), a potential fully biobased and biodegradable co-polyester, were chemically modified. Reactive maleimide and thiol groups have been added to their chemical structures. They have undergone a thiol-Michael addition, yielding a cross-linked network based on AMS and PBAT oligomers. In this large study, the structures of the different AMS and PBAT derivatives were precisely determined by FTIR, 1H, 13C APT and 31P NMR. Nitrogen containing products were also analyzed by 1H-15N NMR, a useful but largely underutilized tool, to determine the chemical structures of these synthesized products. This study clearly shows the high potential of these macromolecular architectures based on AMS and PBAT obtained by a fast click reaction, to develop reactive additives in the case of rather incompatible multiphase materials (blends, multilayers,) for a large range of short-term and demanding applications (packaging, agriculture,) for a greener future.
|
Alexis Morinval; Luc Avérous
|
Polymer Science; Biopolymers
|
CC BY 4.0
|
CHEMRXIV
|
2024-07-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668ce7485101a2ffa8d4c5eb/original/synthesis-by-fast-thiol-michael-click-addition-of-biodegradable-and-potentially-fully-biobased-architectures-based-on-starch-and-polyester-towards-sustainable-and-performing-multiphase-systems.pdf
|
67225f9bf9980725cf994cc8
|
10.26434/chemrxiv-2024-t818f
|
Trajectory-based Non-adiabatic Simulations of the Polariton Relaxation Dynamics
|
We benchmark the accuracy of various trajectory-based non-adiabatic methods in simulating the polariton relaxation dynamics under the collective coupling regime. The Holstein-Tavis-Cummings (HTC) Hamiltonian is used to describe the hybrid light-matter system of N molecules coupled to a single cavity mode. We apply various recently developed trajectory-based methods to simulate the population relaxation dynamics by initially exciting the upper polariton state, and benchmark the results against populations computed from exact quantum dynamical propagation using the hierarchical equations of motion (HEOM) approach. In these benchmarks, we have systematically varied the number of molecules N , light-matter detunings, and the light-matter coupling strengths. Our results demonstrate that the symmetrical quasi-classical method with γ correction (γ-SQC) and spin-mapping linearized semi-classical (spin-LSC) approaches yield more accurate polariton population dynamics than traditional mixed quantum-classical (MQC) methods such as the Ehrenfest and surface hopping techniques.
|
Deping Hu; Benjamin Chng; Wenxiang Ying; Pengfei Huo
|
Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Physical and Chemical Processes
|
CC BY 4.0
|
CHEMRXIV
|
2024-11-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67225f9bf9980725cf994cc8/original/trajectory-based-non-adiabatic-simulations-of-the-polariton-relaxation-dynamics.pdf
|
655a9bc72c3c11ed71bce38c
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10.26434/chemrxiv-2023-87xb7
|
Simulating micelle self-assembly to assess potential for viscosity build in surfactant formulations
|
Self-assembly of surfactants into complex structures is key to the performance of many formulated products, which form a significant fraction of the world’s manufactured goods. Here we adopt the dissipative particle dynamics simulation approach to explore the self-assembly process of surfactants, with the aim of understanding what information can be obtained that may correlate with an increased zero-shear viscosity of products. To this end we experimentally measured the zero-shear viscosity of mixed micelle systems comprised of cocoamidopropyl betaine (CAPB) and sodium lauryl sarcosinate (SLSar), and characterised the early stages of self-assembly of the same systems in simulation, as a function of the CAPB / SLSar mole ratio and pH. From simulation we identify three distinct behaviors in the micellar self-assembly process (logarithmic, linear and cubic power law growth) which we find show some degree of correlation with the experimental zero-shear viscosity. Owing to the relatively short simulation times required, this may provide formulation scientists with a practical route to identify regions of interest (i. e. those with a desired zero-shear viscosity) prior to synthesising de novo (potentially natural) surfactants.
|
Ennio Lavagnini; Jonathan Booth; Katy Helm; Ferdaous El-Benni; Patrick Warren; David Bray; Richard Anderson
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties; Self-Assembly; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-11-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655a9bc72c3c11ed71bce38c/original/simulating-micelle-self-assembly-to-assess-potential-for-viscosity-build-in-surfactant-formulations.pdf
|
650606d9b338ec988a989093
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10.26434/chemrxiv-2023-vgz1r
|
Combining Donor Strength and Oxidative Stability in Scorpionates: A Strongly Donating Fluorinated Mesoionic Tris(imidazol-5-ylidene)borate Ligand
|
Strongly donating scorpionate ligands support the study of high-valent transition metal chemistry; however, their use is frequently limited by oxidative degradation. To address this concern, we report the synthesis of a tris(imidazol-5-ylidene)borate ligand featuring trifluoromethyl groups surrounding its coordination pocket. This ligand represents the first example of a chelating poly(imid- azol-5-ylidene) mesoionic carbene ligand, a scaffold which is expected to be extremely donating. The {NiNO}10 complex of this ligand, as well as that of a previously reported strongly donating tris(imidazol-2-ylidene)borate, have been synthesized and characterized. This new ligand’s strong donor properties, as measured by the υNO of its {NiNO}10 complex and natural bonding orbital second-order pertur- bative energy analysis, are on par with those of the well-studied alkyl substituted tris(imidazol-2-ylidene)borates which are known to effectively stabilize high-valent intermediates. The good donor properties of this ligand, despite the electron withdrawing trifluorome- thyl substituents, arise from the strongly donating imidazol-5-ylidene mesoionic carbene arms. These donor properties, when combined with the robustness of trifluoromethyl groups towards oxidative decomposition, suggest this ligand scaffold will be a useful platform in the study of oxidizing high-valent transition metal species.
|
Joseph Scott; Joseph Schneider; Eyob Tewelde; Joel Gardner; Sophie Anferov; Alex Filatov; John Anderson
|
Inorganic Chemistry; Coordination Chemistry (Inorg.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-09-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650606d9b338ec988a989093/original/combining-donor-strength-and-oxidative-stability-in-scorpionates-a-strongly-donating-fluorinated-mesoionic-tris-imidazol-5-ylidene-borate-ligand.pdf
|
60c75984702a9be8bf18ced5
|
10.26434/chemrxiv.14706009.v1
|
Tuning Reactivity of Micellar Nanoreactors by Precise Adjustments of the Amphiphiles and Substrates Hydrophobicity
|
<p>Polymeric assemblies, such as micelles, are gaining increasing attention due to their ability to serve as nanoreactors for the execution of organic reactions in aqueous media. The ability to conduct transformations, which have been limited to organic media, in water is essential for the further development of the important fields of green</p><p>catalysis and bioorthogonal chemistry, among other fields. In light of the recent progress in the expanding the scopes of reactions that can be conducted using nanoreactors, we aimed to gain deeper understanding of the roles of the hydrophobicity of both the core of micellar nanoreactors and the substrates on the reaction rates in water. Towards this goal we designed a set of metal-loaded micelles, composed of PEG-dendron amphiphiles and studied their ability to serve as nanoreactors for a palladium mediated depropargylation reaction of four substrates with different LogP values. Using dendrons as the hydrophobic block, allowed us to fine tune the lipophilicity of the dendritic end-groups and study how precise structural changes in the hydrophobicity of the amphiphiles affect the reaction rates. The kinetic data revealed linear relations between the rate constants and the hydrophobicity of the amphiphiles (estimated by the dendron’s</p><p>cLogP), while exponential dependence was obtained for the lipophilicity of the substrates (estimated by their LogP values). Our results demonstrate the vital contributions of the hydrophobicity of both the substrates and amphiphiles on the lipo-selectivity of nanoreactors, illustrating the potential of tuning hydrophobicity as a tool for optimizing</p><p>the reactivity and selectivity of nanoreactors.</p>
|
Shahar Tevet; Shreyas Shankar Wagle; Gadi Slor; Roey Amir
|
Nanocatalysis - Catalysts & Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-06-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75984702a9be8bf18ced5/original/tuning-reactivity-of-micellar-nanoreactors-by-precise-adjustments-of-the-amphiphiles-and-substrates-hydrophobicity.pdf
|
643f0c3771383d0921ed4ea7
|
10.26434/chemrxiv-2023-w0j0n
|
Total organic halogen (TOX) in treated wastewaters: Method development and comparison with target analysis
|
Wastewater effluents are complex mixtures that may potentially contain thousands of compounds that are not well removed from conventional wastewater treatment. There are more than 350,000 chemicals registered for production or use that can potentially end up in the environment. Quantification of emerging contaminants by target analysis has been extensively applied however, these methods are often limited by the availability of analytical standards and resources. The total organic halogen (TOX) method is a comprehensive evaluation of the total halogen content in water including emerging halogenated contaminants and disinfection by-products. In this study, an analytical method was developed to simultaneously quantify TOX as total organic fluorine (TOF), total organic chlorine (TOCl), total organic bromine (TOBr), and total organic iodine (TOI). Halophenol recovery experiments were performed in secondary wastewater effluents for TOF, TOCl, TOBr, and TOI with recoveries between 61-105%. Also, nine halogenated contaminants were spiked into ultrapure water with recoveries between 19-107%. The TOX method was used to evaluate four secondary wastewater effluents prior to disinfection across 2 cities in Alberta, Canada. It was observed that TOF, TOCl, and TOBr ranged from 4.9 - 10.5 µg/L, 67.5 - 80.0 µg/L, and 5.0 – 9.0 µg/L, respectively whereas TOI was only detected in two samples at 1.8 and 6.1 µg/L. A sample was analyzed for 196 emerging contaminants to characterize and identify TOX in wastewater for the first time. Target analysis with liquid chromatography tandem mass spectrometry only identified 1.5% of TOX which underlines the severe limitations of target analysis in wastewater samples. These results highlight the applicability of the TOX method in wastewater analysis.
|
Chad Verwold; Chris Tremblay; Miriam Patron; Susana Y. Kimura
|
Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Analytical Chemistry - General; Environmental Analysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643f0c3771383d0921ed4ea7/original/total-organic-halogen-tox-in-treated-wastewaters-method-development-and-comparison-with-target-analysis.pdf
|
656408fc5bc9fcb5c974ad1c
|
10.26434/chemrxiv-2023-1d5qx
|
Design, Synthesis, In Vitro and In Vivo Evaluation of Cereblon Binding Bruton’s Tyrosine Kinase (BTK) Degrader CD79b targeted Antibody Drug Conjugates
|
Antibody-drug conjugates (ADCs) are an established modality which allows for targeted delivery of a potent molecule, or payload, to a desired site of action. ADCs, wherein the payload is a targeted protein degrader is an emerging area in the field. Herein we describe our efforts of delivering a Bruton’s tyrosine kinase (BTK) bifunctional degrader 1 via a CD79b mAb where the degrader is linked at the ligase binding portion of the payload via a cleavable linker to the mAb. The resulting CD79b ADCs, 3 and 4, exhibit in vitro degradation and cytotoxicity comparable to 1 and ADC 3 can achieve more sustained in vivo degradation than iv administered 1 with markedly reduced systemic exposure of the payload.
|
Alan Zhang; Katherine Seiss; Sebastian Palacio-Ramirez; Laurent Laborde; Daniel Guthy; Mylene Lanter; Julien Lorber; Anna Vulpetti; Thomas Zoller; Christina Hebach; William R. Tschantz; Alexei Karpov; Gregory J. Hollingworth; Joseph A. D’Alessio; Stephane Ferretti; Matthew T. Burger
|
Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-11-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656408fc5bc9fcb5c974ad1c/original/design-synthesis-in-vitro-and-in-vivo-evaluation-of-cereblon-binding-bruton-s-tyrosine-kinase-btk-degrader-cd79b-targeted-antibody-drug-conjugates.pdf
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63483e02a2c790f93f461961
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10.26434/chemrxiv-2022-0k0jg
|
Emergent chemical behavior in mixed food and lignocellulosic green waste hydrothermal liquefaction
|
Hydrothermal liquefaction (HTL) is a promising strategy for conversion of energy-dense waste streams to fuels. Mixed-feed HTL aggregates multiple feed streams to achieve greater scales that capitalize on local resources, hence lowering costs. The potential for new pathways and products upon feedstock blending becomes a compounding level of complexity when unlocking emergent chemistries. Food and green waste streams were evaluated under HTL conditions (300 °C, 1 hr) to understand the effect of feed molecular composition on product distributions and mechanisms. Thousands of emergent chemical compounds were detected via FT-ICR MS, ultimately leading to the emergence of two dominant outcomes. First, the presence of small amounts of food waste into green waste results in substantial decarboxylation and subsequent polymerization to biocrude then chars. Second, in the other limit, small amounts of green waste promote capping of oxygenates into the biodiesel range, such as with the emergence of fatty acid methyl esters.
|
Heather LeClerc; Jeffrey Page; Geoffrey Tompsett; Sydney Niles; Amy McKenna; Julia Valla; Michael Timko; Andrew Teixeira
|
Energy; Chemical Engineering and Industrial Chemistry; Reaction Engineering
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63483e02a2c790f93f461961/original/emergent-chemical-behavior-in-mixed-food-and-lignocellulosic-green-waste-hydrothermal-liquefaction.pdf
|
67b4725b81d2151a02f96aab
|
10.26434/chemrxiv-2025-mhhdg
|
Synthesis of Au13-based building block clusters for programmed dimer formation and Au13 cluster dimer photoexcitation properties
|
Recently, there has been increasing attention on the fabrication of ligand-protected metal clusters composed of a finite number of noble metal atoms and on their precise assembly to elicit novel properties that are not observed in individual metal clusters. In the present study, we investigated (1) the behavior of ligand exchange reactions and (2) the selective and efficient formation of dimers composed of Au13 clusters. Specifically, we focused on a gold cluster consisting of 13 atoms coordinated to diphosphine ligands (dppe) and either chloride (Cl) or acetylide, i.e., [Au13(dppe)5X2]3+ (X = Cl or acetylide). The findings showed that Au13 clusters containing counter anion Cl− undergo a transformation under specific conditions, where Cl− acts as a ligand (rather than an anion) directly coordinated to the Au13 surface. The introduction of two types of ligands—chelating ligands that coordinate to the Au13 cluster surface and end-capping ligands that suppress polymerization—enabled the synthesis of a building block molecule which are programmed to selectively and spontaneously form Au13-based dimers upon the addition of metal ions. The designed building block clusters indeed selectively and efficiently formed stable dimers composed of two Au13 clusters in the presence of iron ions. Furthermore, in the Au13-based dimer, the phosphorescent Au13 moiety is directly connected to a coordination site that exhibits quenching effects, enabling rapid intramolecular photoinduced charge transfer even with a small driving force.
|
Taiga Kosaka; Yoshiki Niihori; Tokuhisa Kawawaki; Yuichi Negishi
|
Inorganic Chemistry; Supramolecular Chemistry (Inorg.)
|
CC BY 4.0
|
CHEMRXIV
|
2025-02-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b4725b81d2151a02f96aab/original/synthesis-of-au13-based-building-block-clusters-for-programmed-dimer-formation-and-au13-cluster-dimer-photoexcitation-properties.pdf
|
60c74a78567dfe20daec4da6
|
10.26434/chemrxiv.12205913.v1
|
Bright Blue Emitting Cu-doped Cs2ZnCl4 Colloidal Nanocrystals
|
We report here the synthesis
of undoped and Cu-doped Cs<sub>2</sub>ZnCl<sub>4</sub> nanocrystals (NCs), in
which we could tune the concentration of Cu from 0.7% to 7.5%. According to electron
paramagnetic resonance analysis, in 0.7% and 2.1% Cu-doped NCs the Cu ions were
present in the +1 oxidation state only, while in NCs at higher Cu
concentrations we could detect Cu(II) ions. The undoped Cs<sub>2</sub>ZnCl<sub>4
</sub>NCs were non emissive, while the Cu-doped samples had a bright intra-gap photoluminescence
(PL) at 2.6eV mediated by band-edge absorption. The PL quantum yield was maximum (~55%) for the samples with low Cu concentration (≤ 2.1%) and it systematically
decreased when further increasing the concentration of Cu, reaching 15%
for the NCs with the highest doping level (7.5%). Density functional theory calculations indicated that the
PL emission could be ascribed only to Cu(I) ions: these ions introduce intra-gap
states that promote the formation of
self-trapped excitons, through which an efficient emission takes place.
|
Dongxu Zhu; Valerio Pinchetti; Rosaria Brescia; Fabrizio Moro; Marco Fanciulli; Aiwei Tang; Ivan Infante; Luca De Trizio; Sergio Brovelli; Liberato Manna
|
Nanostructured Materials - Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a78567dfe20daec4da6/original/bright-blue-emitting-cu-doped-cs2zn-cl4-colloidal-nanocrystals.pdf
|
60c75267469df4344cf44b5e
|
10.26434/chemrxiv.13296143.v1
|
A Spotter's Guide to Dispersion in Surface-Confined Voltammetry Experiments
|
<div>This paper describes the effect of thermodynamic and kinetic dispersion
on numerical simulations of three different surface-confined
voltammetry experiments, ramped FTACV, Purely sinusoidal voltammetry
(PSV) and direct current voltammetry (DCV), and the differences between
the dispersed and non-dispersed cases. <br /></div><div>Dispersion in this case refers to a range of observed values for the thermodynamic driving force and
reaction rate of a redox reaction (thermodynamic and kinetic dispersion
respectively) . This has been acknowledged as a complicating factor of voltammetry experiments for some time. <br /></div><div>We demonstrate that thermodynamic
dispersion has a far stronger effect than kinetic
dispersion, and detail the ways in which kinetic dispersion can be
resolved under such conditions. The work is novel in its comparison of
three separate voltammetry techniques, and a focus on how to determine
the presence of dispersion through computational
analysis of experimental voltammetry data alone; previous work has
required specific experiments designed to distinguish between dispersed
and non-dispersed cases.</div>
|
Henry Lloyd-Laney; Martin Robinson; Alan Bond; Alison Parkin; David Gavaghan
|
Theory - Computational
|
CC BY NC 4.0
|
CHEMRXIV
|
2020-11-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75267469df4344cf44b5e/original/a-spotter-s-guide-to-dispersion-in-surface-confined-voltammetry-experiments.pdf
|
620e2e900aec1a43e320b19b
|
10.26434/chemrxiv-2021-50n0k-v2
|
Validating Experiments for the Reaction H2 + NH2- by Dynamical Calculations on an Accurate Full-Dimensional Potential Energy Surface
|
Ion-molecule reactions play key roles in the field of ion related chemistry. As a prototypical multi-channel ion-molecule reaction, the reaction H2 + NH2- → NH3 + H- has been studied for decades. In this work, we develop a globally accurate potential energy surface (PES) for the title system based on hundreds of thousands of sampled points over a wide dynamically relevant region that covers long-range interacting configuration space. The permutational invariant polynomial-neural network (PIP-NN) method is used for fitting and the resulting total root mean squared error (RMSE) is extremely small, 0.026 kcal mol-1. Extensive dynamical and kinetic calculations are carried out on this new PIP-NN PES by the quasi-classical trajectory (QCT) method. The calculated rate coefficients for H2 / D2 + NH2- agree well with the experimental results, which show an inverse temperature dependence from 50 to 300 K, consistent with the capture nature of this barrierless reaction. The significant kinetic isotope effect observed by experiment is well reproduced by the QCT computations as well. In addition, we report a unique phenomenon of significant reactivity suppression by exciting the rotational mode of H2, supported by both QCT and quantum dynamics (QD) calculations. Further analysis uncovers that exciting the H2 rotational mode would prevent the formation of the reactant complex and thus suppress reactivity.
|
Kaisheng Song; Hongwei Song; Jun Li
|
Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Machine Learning; Chemical Kinetics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-02-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620e2e900aec1a43e320b19b/original/validating-experiments-for-the-reaction-h2-nh2-by-dynamical-calculations-on-an-accurate-full-dimensional-potential-energy-surface.pdf
|
62f6bdd442ddf555d1b90a2c
|
10.26434/chemrxiv-2022-zjzb2
|
Uncertainty Informed Screening for Safer Solvents used in the Synthesis of Perovskite Based Solar Cells via Machine Learning
|
The objective of this paper is to do a multi-output binary classification for endocrine disrupting (ED) nature of solvents that are frequently used in the synthesis of perovskites. Information on such solvents is not readily available in the form of datasets, rather it is embedded in the literature, which forms an ever-expanding corpus of scientific articles. Exploiting this corpus to extract relevant information on solvents is a mammoth undertaking and analyzing their ED nature is even more challenging. Except for a few solvents, little is known if they possess ED characteristics because of the resources required for in-vivo experiments. We address this challenge of expensive experiments by utilizing a deep-learning based model. In this work, using Natural Language Processing (NLP), we have identified 35 different organic solvents from a database of more than 30,000 paragraphs that are relevant to chemical synthesis of perovskites. Out of them, we have suggested 11 solvents as potential ED chemicals using a recently developed deep learning model. To further inform the quality of the classification, we perform an uncertainty quantification associated with the classification. This work serves as a guide in screening out the potential ED solvents, particularly when sufficient data is not available on them, thus paving the way for safer alternatives in perovskite synthesis.
|
Deepesh Giri; Arpan Mukherjee; Krishna Rajan
|
Materials Science; Carbon-based Materials; Materials Processing; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2022-08-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f6bdd442ddf555d1b90a2c/original/uncertainty-informed-screening-for-safer-solvents-used-in-the-synthesis-of-perovskite-based-solar-cells-via-machine-learning.pdf
|
60c7557dbdbb899a20a3a828
|
10.26434/chemrxiv.14120447.v1
|
Development of Range-Corrected Deep Learning Potentials for Fast, Accurate Quantum Mechanical/molecular Mechanical Simulations of Chemical Reactions in Solution
|
We develop a new Deep Potential - Range Correction (DPRc) machine learning potential for combined quantum mechanical/molecular mechanical (QM/MM) simulations of chemical reactions in the condensed phase. The new range correction enables short-ranged QM/MM interactions to be tuned for higher accuracy, and the correction smoothly vanishes within a specified cutoff. We further develop an active learning procedure for robust neural network training. We test the DPRc model and training procedure against a series of 6 non-enzymatic phosphoryl transfer reactions in solution that are important in mechanistic studies of RNA-cleaving enzymes. Specifically, we apply DPRc corrections to a base QM model and test its ability to reproduce free energy profiles generated from a target QM model. We perform comparisons using the MNDO/d and DFTB2 semiempirical models because they produce free energy profiles which differ significantly from each other, thereby providing us a rigorous stress test for the DPRc model and training procedure. The comparisons show that accurate reproduction of the free energy profiles requires correction of the QM/MM interactions out to 6 Å. We further find that the model's initial training benefits from generating data from temperature replica exchange simulations and including high-temperature configurations into the fitting procedure so the resulting models are trained to properly avoid high-energy regions. A single DPRc model was trained to reproduce 4 different reactions and yielded good agreement with the free energy profiles made from the target QM/MM simulations. The DPRc model was further demonstrated to be transferable to 2D free energy surfaces and 1D free energy profiles that were not explicitly considered in the training. Examination of the computational performance of the DPRc model showed that it was fairly slow when run on CPUs, but was sped up almost 100-fold when using an NVIDIA V100 GPUs, resulting in almost negligible overhead. The new DPRc model and training procedure provide a potentially powerful new tool for the creation of next-generation QM/MM potentials for a wide spectrum of free energy applications ranging from drug discovery to enzyme design.<br />
|
Jinzhe Zeng; Timothy J Giese; Şölen Ekesan; Darrin M. York
|
Computational Chemistry and Modeling; Machine Learning
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7557dbdbb899a20a3a828/original/development-of-range-corrected-deep-learning-potentials-for-fast-accurate-quantum-mechanical-molecular-mechanical-simulations-of-chemical-reactions-in-solution.pdf
|
621506b22ad2fd5c14d2f79b
|
10.26434/chemrxiv-2022-9t3vx
|
The Magnetic and Electronic Structural Properties of the S3 State of Nature’s Water Oxidising Complex: A Combined Study in ELDOR-Detected Nuclear Magnetic Resonance Spectral Simulation and Broken Symmetry Density Functional Theory
|
ELDOR-detected Nuclear Magnetic Resonance (EDNMR) spectral simulations combined with broken symmetry density functional theory (BS-DFT) calculations are used to obtain and to assign the 55Mn hyperfine coupling constants (hfcs) for modified forms of the water oxidising complex in the penultimate S3 state of the water oxidation cycle. The study shows that an open cubane form of the core Mn4CaO6 cluster is the dominant S = 3 species in all cases studied experimentally with no need to invoke a closed cubane intermediate possessing a distorted pentacoordinate Mn4 ion. EDNMR simulations found that both the experimental bandwidth and multi-nuclear transitions may alter relative EDNMR peak intensities, potentially leading to incorrect assignment of hfcs. The implications of these findings for the water oxidation mechanism are discussed.
|
Ciarán J. Rogers; Olivia Hardwick; Thomas A. Corry; Felix Rummel; David Collison; Alice M. Bowen; Patrick J. O'Malley
|
Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Theory - Computational; Biophysical Chemistry; Structure
|
CC BY 4.0
|
CHEMRXIV
|
2022-05-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621506b22ad2fd5c14d2f79b/original/the-magnetic-and-electronic-structural-properties-of-the-s3-state-of-nature-s-water-oxidising-complex-a-combined-study-in-eldor-detected-nuclear-magnetic-resonance-spectral-simulation-and-broken-symmetry-density-functional-theory.pdf
|
636a2a16afea7f26939ae247
|
10.26434/chemrxiv-2022-qlch2
|
Lithiation-Functionalisation of Triazoles Bearing Electron-Withdrawing N-Substituents: Challenges and Solutions
|
The regioselective lithiation of 1,2,3-triazoles provides an opportunity to introduce additional functionality, however this simple functionalisation strategy using triazoles bearing electron-withdrawing N-substituents has not been investigated until now. Herein, we demonstrate that the lithiated triazole intermediates can readily decompose, even at −78 °C. In addition, lithiation-deuteration studies reveal lithiation can take place competitively on both the triazole and the electron-withdrawn aryl ring. Careful control of reaction conditions is therefore required to i) minimise decomposition pathways; and ii) facilitate regioselective functionalisation of the triazole.
|
Frances Bugden; Guy Clarkson; Mark Greenhalgh
|
Organic Chemistry; Organometallic Chemistry; Organic Synthesis and Reactions
|
CC BY 4.0
|
CHEMRXIV
|
2022-11-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636a2a16afea7f26939ae247/original/lithiation-functionalisation-of-triazoles-bearing-electron-withdrawing-n-substituents-challenges-and-solutions.pdf
|
62bd1a80d66f682df6b74394
|
10.26434/chemrxiv-2022-cfrfk
|
Heparan Sulfate Glycomimetics via Iterative Assembly of “Clickable” Disaccharides
|
Heparan sulfate (HS) glycosaminoglycans are widely expressed on the mammalian cell surfaces and extracellular matrices and play important roles in variety of cell functions. Studies on the structure-activity relationships of HS have long been hampered by the challenges in obtaining chemically defined HS structures with unique sulfation patterns. Here, we report a new approach to HS glycomimetics based on iterative assembly of clickable disaccharide building blocks that mimic the disaccharide repeating units of native HS. Variably sulfated clickable disaccharides were facilely assembled into a library of mass spec-sequencible HS-mimetic oligomers with defined sulfation patterns by solution-phase and solid-phase iterative syntheses. Microarray and surface plasmon resonance (SPR) binding assays corroborated with the molecular dynamic (MD) simulation and confirmed that these HS-mimetic oligomers bind protein fibroblast growth factor 2 (FGF-2) in a sulfation-dependent manner consistent with that of the native HS. This work established a general approach to HS glycomimetics that can potentially serve as alternatives to native HS in both fundamental research and disease models.
|
Cangjie Yang; Yu Deng; Yang Wang; Chaoshuang Xia; Putthipong Booneimsri; Chanthakarn Lertmaneedang; Akul Y Mehta; Kelly J Baker; Seung Hwang; James P Flynn; Muqing Cao; Chao Liu; Alec C Zhu; Richard D Cummings; Cheng Lin; Udayan Mohanty; Jia Niu
|
Biological and Medicinal Chemistry; Polymer Science; Biopolymers; Organic Polymers; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-06-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bd1a80d66f682df6b74394/original/heparan-sulfate-glycomimetics-via-iterative-assembly-of-clickable-disaccharides.pdf
|
66fbb79b51558a15efae5171
|
10.26434/chemrxiv-2024-c2l4j
|
Legion: A Platform for Gaussian Wavepacket Nonadiabatic
Dynamics
|
Nonadiabatic molecular dynamics is crucial in investigating the time evolution of excited
states in molecular systems. Among the various methods for performing such dynamics, those
employing frozen Gaussian wavepacket propagation, particularly the multiple spawning approach,
offer a favorable balance between computational cost and reliability. It propagates on-the-fly
trajectories used to build and propagate the nuclear wavepacket. Despite its potential, there is a lack of
efficient, flexible, and easily accessible Gaussian wavepacket propagation software. To address this,
we present Legion, a software that facilitates the development and application of classical-trajectory-
guided quantum wavepacket methods. The version presented here already contains a highly flexible
and fully functional ab initio multiple spawning implementation, with different strategies to improve
efficiency. Legion is written in Python for data management and Numpy/Fortran for numerical
operations. It is created under the umbrella of the Newton-X platform and inherits all of its electronic
structure interfaces beyond other direct interfaces. It also contains new approximations that allow it to
circumvent the computation of the nonadiabatic coupling, extending the electronic structure methods
that can be used for multiple spawning dynamics. We test, validate, and demonstrate Legion’s
functionalities through multiple spawning dynamics of fulvene (CASSCF and CASPT2) and DMABN
(TDDFT).
|
Rafael Souza Mattos; Saikat Mukherjee; Mario Barbatti
|
Physical Chemistry; Photochemistry (Physical Chem.); Quantum Mechanics
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-10-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fbb79b51558a15efae5171/original/legion-a-platform-for-gaussian-wavepacket-nonadiabatic-dynamics.pdf
|
66e0dc9451558a15efa15a39
|
10.26434/chemrxiv-2024-ds733
|
Balancing Act: Environmental, Social, and Economic Impacts of PFAS Removal from Water
|
Per- and polyfluoroalkyl substances (PFAS) are emerging water contaminants with significant environmental and health impacts, posing challenges in water treatment due to their degradation resistance. This study reviews 10 papers on the sustainability of technologies for PFAS removal, revealing a critical literature gap as regulations emerge. Our review shows sustainability varies across technologies and contexts. Specifically, single-use ion exchange (IX) demonstrates cost-effectiveness and environmental favorability for long-chain PFAS removal from groundwater and aqueous film-forming foam impacted water, while granular activated carbon (GAC) appears costlier due to rapid breakthroughs. These limited findings underscore the need for more comprehensive research to validate results across contexts and understand the full sustainability profile of PFAS treatment technologies, including removal and destruction. Current literature often overlooks key considerations like the ultimate fate of PFAS. To address these gaps, we propose a framework for future sustainability studies, enabling clearer technology evaluations under specific conditions. While IX shows broad applicability, treatment choice should consider water type, system boundary, functional unit, PFAS concentration, and ultimate fate of PFAS for a more holistic view of sustainability.
|
Md. Moshiur Rahman Tushar; Zaki Alam Pushan; Nirupam Aich; Lewis Rowles
|
Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science; Hydrology and Water Chemistry; Water Purification
|
CC BY 4.0
|
CHEMRXIV
|
2024-09-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e0dc9451558a15efa15a39/original/balancing-act-environmental-social-and-economic-impacts-of-pfas-removal-from-water.pdf
|
67126dc812ff75c3a1cc63fb
|
10.26434/chemrxiv-2024-rq2ls
|
How molar ratio between two anions affects physicochemical properties and biological activity of double salt ionic liquids (DSILs)?
|
The strategy of mixing ionic liquids opens up new possibilities for obtaining liquid chemical systems (i.e., double salt ionic liquids, DSILs) with well-defined, beneficial properties, which is particularly important for the design of new biologically active substances. Here, we describe the application of the DSIL strategy for obtaining new systems containing a common amphiphilic cation with a hexadecyl substituent and 2 anions derived from synthetic auxins at the different molar ratio – MCPA and dicamba, both suitable for use as novel herbicides with enhanced efficiency. Detailed analysis of the NMR spectra indicates the presence of new interactions in the structure of DSILs, which affect the chemical environment of the ions and are strictly dependent on the molar ratio of the parent ionic liquids. Moreover, a non-additive effect of combining two surface-inactive anions on the surface activity of DSILs was discovered. DSILs with molar ratios from 8:2 to 2:8 had better surface activity compared to their starting components containing only one anion. Moreover, in greenhouse experiments DSIL containing molar fraction of dicamba equal to 0.2 showed significantly better efficiency than the other tested systems. This enhancement can be explained by the occurrence of a synergistic effect between both utilized anions. However, insertion into DSIL greater content of the dicamba anion nullified this beneficial effect. The initial ecotoxicity studies also pointed out potential risks associated with the increased toxicity of the new DSIL systems to non-target organisms, which warrants further research on the effects of mixing ionic liquids on environmental loading.
|
Tomasz Rzemieniecki; Damian Krystian Kaczmarek; Witold Stachowiak; Katarzyna Marcinkowska; Michał Niemczak
|
Organic Chemistry; Analytical Chemistry; Agriculture and Food Chemistry; Organic Synthesis and Reactions; Environmental Analysis; Spectroscopy (Anal. Chem.)
|
CC BY 4.0
|
CHEMRXIV
|
2024-10-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67126dc812ff75c3a1cc63fb/original/how-molar-ratio-between-two-anions-affects-physicochemical-properties-and-biological-activity-of-double-salt-ionic-liquids-dsi-ls.pdf
|
677b54d881d2151a02059323
|
10.26434/chemrxiv-2025-xdzgq
|
Interface Morphogenesis with a Deformable Secondary Phase in Solid-State Lithium Batteries
|
The complex and uncontrolled morphological evolution of lithium metal at the interface with solid-state electrolytes limits performance of solid-state batteries, leading to inhomogeneous reactions and contact loss. Inspired by biological morphogenesis, we introduce a new interfacial self-regulation concept in which a deformable secondary phase dynamically aggregates at the interface in response to local electro-chemo-mechanical stimuli, serving to enhance contact. Stripping of a lithium electrode containing 5-20% redox-inactive sodium domains causes spontaneous sodium accumulation across the interface, with the sodium undergoing local plastic deformation as lithium is removed to attain intimate electrical contact without blocking transport channels. This process, characterized with operando X-ray tomography and electron microscopy, mitigates void formation and substantially improves battery cycling performance at the low stack pressures needed for practical applications. The counterintuitive strategy of adding inactive alkali metal to improve performance demonstrates that interfacial self-regulation is a promising pathway to efficient solid-state batteries.
|
Sun Geun Yoon; Bairav Vishnugopi; Douglas Nelson; Adrian Xiao Bin Yong; Yingjin Wang; Stephanie Sandoval; Talia Thomas; Kelsey Cavallaro; Pavel Shevchenko; Elif Pınar Alsaç; Congcheng Wang; Aditya Singla; Julia Greer; Elif Ertekin; Partha Mukherjee; Matthew McDowell
|
Materials Science; Energy; Energy Storage
|
CC BY NC 4.0
|
CHEMRXIV
|
2025-01-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677b54d881d2151a02059323/original/interface-morphogenesis-with-a-deformable-secondary-phase-in-solid-state-lithium-batteries.pdf
|
60c74b58bdbb8952ada3956e
|
10.26434/chemrxiv.12320567.v1
|
Mutations in Spike Protein of SARS-CoV-2 Modulate Receptor Binding, Membrane Fusion and Immunogenicity: An Insight into Viral Tropism and Pathogenesis of COVID-19
|
<p>SARS-CoV-2 uses RBD of Spike (S) protein to attach with human cell via ACE2
receptor, followed by protease priming at S1/S2 site resulted in host cell
entry and pathogenesis. In this context, we focused our aim in studying natural
mutations harboring in Spike protein of SARS-CoV-2. We have analyzed 420
COVID-19 cases. G476S and V483G mutation are observed which lies in the RBD
region where as the prevalent D614G mutation is observed in the vicinity of
S1/S2 site. Interestingly MD simulation supports strong favorable interaction
of ACE2 with RBD region containing V483A mutation as compared to G476S and
reference wild Wuhan S protein. Radius of gyration analysis also showed high degree of
compactness in V483A. The
landscape plot and Gibbs free energy also support our findings. Overall, our
study indicates that V483G in
the RBD region can enhance its binding with the human ACE2 receptor. Interestingly
D614G mutation in vicinity of S1/S2 region introduced a new cleavage site specific
for a serine protease elastase that is anticipated to broaden the virus host
cell tropism. Hence, both V483A and D614G mutations led to enhanced and broaden
the virus host cell entry and transmission of the disease. Further epitope
mapping analysis revealed G476S and D614G mutations as antigenic determinants
and thus these mutations are important while designing a therapeutics vaccine
or chimeric antibody. This
finding will help in further understanding the role of such arising mutations
in modulating immunogenicity, viral tropism and pathogenesis of the disease, which
in lieu will help in designing vaccine more precisely to mitigate pandemic COVID-19.
</p>
<p> </p>
|
Dr. Priyanka Saha; Ranabir Majumder; sourabrata chakraborty; Amit Kumar Srivastava; Mahitosh Mandal; Siddik Sarkar
|
Bioinformatics and Computational Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b58bdbb8952ada3956e/original/mutations-in-spike-protein-of-sars-co-v-2-modulate-receptor-binding-membrane-fusion-and-immunogenicity-an-insight-into-viral-tropism-and-pathogenesis-of-covid-19.pdf
|
6463e8a4a32ceeff2dc1d153
|
10.26434/chemrxiv-2023-8z8d7
|
PLAT Domain Protein 1 (PLAT1/PLAFP) Binds to the Arabidopsis thaliana Plasma Membrane and Inserts a Lipid
|
Robust agricultural yields depend on the plant's ability to fix carbon amid variable environmental conditions. Over seasonal and diurnal cycles, the plant must constantly adjust its metabolism according to available resources or external stressors. The metabolic changes that a plant undergoes in response to stress are well understood, but the long-distance signaling mechanisms that facilitate communication throughout the plant are less studied. The phloem is considered the predominant conduit for the bidirectional transport of these signals in the form of metabolites, nucleic acids, proteins, and lipids. Lipid trafficking through the phloem in particular attracted our attention due to its reliance on soluble lipid-binding proteins (LBP) that generate and solubilize otherwise membrane-associated lipids. The Phloem Lipid-Associated Family Protein (PLAFP) from Arabidopsis thaliana is generated in response to abiotic stress as is its lipid-ligand phosphatidic acid (PA). PLAFP is proposed to transport PA through the phloem in response to drought stress. To understand the interactions between PLAFP and PA, nearly 100 independent systems comprised of the protein and one PA, or a plasma membrane containing varying amounts of PA, were simulated using atomistic classical molecular dynamics methods. In these simulations, PLAFP is found to bind to plant plasma membrane models independent of the PA concentration. When bound to the membrane, PLAFP adopts a binding pose where W41 and R82 penetrate the membrane surface and anchor PLAFP. This triggers a separation of the two loop regions containing W41 and R82. Subsequent simulations indicate that PA insert into the β-sandwich of PLAFP, driven by interactions with multiple amino acids besides the W41 and R82 identified during the insertion process. Fine-tuning the protein-membrane and protein-PA interface by mutating a selection of these amino acids may facilitate engineering plant signaling processes by modulating the binding response.
|
Martin Kulke; Evan Kurtz; Duncan Boren; Dayna Olson; Amanda Koenig; Susanne Hoffmann-Benning; Josh Vermaas
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Biophysics; Plant Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6463e8a4a32ceeff2dc1d153/original/plat-domain-protein-1-plat1-plafp-binds-to-the-arabidopsis-thaliana-plasma-membrane-and-inserts-a-lipid.pdf
|
60c7457d9abda20765f8c59f
|
10.26434/chemrxiv.10032278.v1
|
Electrochemical CO2 Reduction on Nanostructured Metal Electrodes: Fact or Defect?
|
<div>
<p>Electrochemical CO<sub>2</sub>
reduction has received an increased amount of interest in the last decade as a promising
avenue for storing renewable electricity in chemical bonds. Despite
considerable progress on catalyst performance using nanostructured electrodes,
the sensitivity of the reaction to process conditions has led to debate on the origin
of the activity and high selectivity. Additionally, this raises questions on
the transferability of the performance and knowledge to other electrochemical
systems. At its core, the discrepancy is primarily a result of the highly
porous nature of nanostructured electrodes, which are vulnerable to both mass
transport effects and structural changes during the electrolysis. Both effects
are not straightforward to identify and difficult to decouple. Despite the
susceptibility of nanostructured electrodes to mass transfer limitations, we
highlight that nanostructured silver electrodes exhibit considerably higher
activity when normalized to the electrochemically active surface in contrast to
gold and copper electrodes. Alongside, we provide a discussion on how
active surface area and thickness of the catalytic layer itself can influence
the selectivity, stability, activity and mass transfer inside and outside of
the three dimensional catalyst layer. Key parameters and potential solutions
are highlighted to decouple mass transfer effects from the measured activity in
electrochemical cells utilizing CO<sub>2</sub> saturated aqueous solutions. </p>
</div>
<br />
|
Recep Kas; Kailun Yang; Divya Bohra; Ruud Kortlever; Thomas Burdyny; Wilson A. Smith
|
Electrocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-10-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7457d9abda20765f8c59f/original/electrochemical-co2-reduction-on-nanostructured-metal-electrodes-fact-or-defect.pdf
|
66a7c598c9c6a5c07a6b04c8
|
10.26434/chemrxiv-2024-294z8
|
Pinpointing the Onset of Water Harvesting in Reticular Frameworks from Structure
|
Covalent organic frameworks (COFs) have emerged as promising atmospheric water harvesters, offering a potential solution to the pressing global issue of water scarcity, which threatens millions of lives worldwide. This study presents a series of 2D COFs, including HCOF-3, HCOF-2, and a newly developed structure named COF-309, designed for optimized water harvesting performance with high working capacity at low relative humidity. To elucidate their water sorption behavior, we introduce a hydrophilicity index directly linked to intrinsic properties such as the strength and spatial density of adsorptive sites. This index is mathematically correlated with the step of water adsorption isotherms. Our correlation provides a predictive tool that extends to other microporous COFs and metal–organic frameworks, significantly enhancing the ability to predict their onset positions of water adsorption isotherms based on structural characteristics. This advancement holds the potential to guide the development of more efficient materials for atmospheric water harvesting.
|
Ha Nguyen; Andrea Darù; Saumil Chheda; Ali Alawadhi; S. Ephraim Neumann; Lifen Wang; Xuedong Bai; Majed Alawad; Christian Borgs; Jennifer Chayes; Joachim Sauer; Laura Gagliardi; Omar Yaghi
|
Theoretical and Computational Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Materials Chemistry; Crystallography – Organic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a7c598c9c6a5c07a6b04c8/original/pinpointing-the-onset-of-water-harvesting-in-reticular-frameworks-from-structure.pdf
|
60dad13366f2c4ad691434d8
|
10.26434/chemrxiv-2021-ssr8z
|
Exploring the Solution Formation of UiO Family Hf Metal-Organic Framework clusters with in situ X-Ray Pair Distribution Function Analysis
|
The structures of Zr and Hf metal-organic frameworks (MOFs) are very sensitive to small changes in synthetic conditions. One key difference affecting the structure of UiO MOF phases is the shape and nuclearity of Zr or Hf metal clusters acting as nodes in the framework; although these clusters are crucial, their evolution during MOF synthesis is not fully understood. In this paper, we explore the nature of Hf metal clusters which form in different reaction solutions, including in a mixture of DMF, formic acid and water. We show that the choice of solvent and reaction temperature in UiO MOF syntheses determines the cluster identity and hence the MOF structure. Using in situ X-ray pair distribution function measurements, we demonstrate that the evolution of different Hf cluster species can be tracked during UiO MOF synthesis, from solution stages to the full crystalline framework, and use our understanding to propose a formation mechanism for the hcp UiO-66(Hf) MOF, in which first the metal clusters aggregate from the M6 cluster (as in fcu UiO-66) to the hcp-characteristic M12 double cluster, and following this, the crystalline hcp framework forms. These insights pave the way towards rationally designing syntheses of as-yet unknown MOF structures, via tuning the synthesis conditions to select different cluster species.
|
Francesca C.N. Firth; Michael W. Gaultois; Yue Wu; Joshua Stratford; Dean S. Keeble; Clare P. Grey; Matthew J. Cliffe
|
Materials Science; Inorganic Chemistry; Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Materials Chemistry; Crystallography – Inorganic
|
CC BY 4.0
|
CHEMRXIV
|
2021-06-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60dad13366f2c4ad691434d8/original/exploring-the-solution-formation-of-ui-o-family-hf-metal-organic-framework-clusters-with-in-situ-x-ray-pair-distribution-function-analysis.pdf
|
67656cfa81d2151a02603f48
|
10.26434/chemrxiv-2024-dsh9t
|
RandomNets Improve Neural Network Regression Performance via Implicit Ensembling
|
Artificial feed-forward neural networks have long been recognized as powerful machine learning models and are widely used in QSAR and QSPR modeling of molecular properties. Inspired by Random Forest models and the robust techniques of sample and feature bagging, the RandomNets model was developed as an efficient, vectorized solution for ensemble creation, training, and inference. The model adds an extra dimension to the tensors passing through the neural network, combined with input feature masking and optional subsampling of the dataset during training. This vectorized approach improves efficiency and simplifies training and inference of the implicit ensemble. Training a 25-member implicit ensemble requires only twice the time of a comparable baseline network but significantly improves prediction performance, as measured by R² and MSE on test sets from 133 bioactivity datasets, with an average performance increase of around 25%. Compared to the conceptually similar input masking technique using dropout, the implicit ensemble demonstrates reduced sensitivity to hyperparameter choices, similar or improved performance, and a fourfold reduction in training time. Additionally, the implicit ensemble provides the standard deviation of individual predictions, which can help identify uncertain predictions.
|
Esben Jannik Bjerrum
|
Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-12-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67656cfa81d2151a02603f48/original/random-nets-improve-neural-network-regression-performance-via-implicit-ensembling.pdf
|
648dc7ccbe16ad5c5711a30a
|
10.26434/chemrxiv-2023-zhf3g
|
Mechanisms of Dissolution from Gibbsite Step Edges Elucidated by Ab Initio Molecular Dynamics with Enhanced Sampling
|
Many predictive models of geochemical processes (e.g., fate and transport of metals) and industrial utilization of minerals rely upon a detailed understanding of mineral dissolution. Yet atomistic details are rarely known due to the complex mineral/fluid interfacial environment. Here, ab initio molecular dynamics simulations with enhanced sampling has been used to explore the detailed process of the detachment of an aluminate monomer from two types of step edges at the gibbsite aqueous interface. Gibbsite is a primary source of Al in soils and mineral within the industrial processing of aluminum. Surface pit models in conjunction with changes to solution composition that mimic pH effects are employed to create realistic starting points for the simulation. The results indicate two potential pathways for detachment that are differentiated based upon the extent of water hydration. The energy profiles of the elementary bond-breaking events indicate the scission of the first or the second hydroxo bridge is the rate-limiting step for the monomer dissociation. The heights of the energy barriers depend upon the local morphology which influence the number of bridges (quasi-)simultaneously broken (1 or 2) or the Al-O coordination of the neighboring aluminum atoms (5 or 6) at the armchair edge.
|
Qing Guo; Maxime Pouvreau; Kevin Rosso; Aurora Clark
|
Theoretical and Computational Chemistry; Inorganic Chemistry; Minerals; Reaction (Inorg.); Computational Chemistry and Modeling; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-06-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648dc7ccbe16ad5c5711a30a/original/mechanisms-of-dissolution-from-gibbsite-step-edges-elucidated-by-ab-initio-molecular-dynamics-with-enhanced-sampling.pdf
|
60c743b5567dfef0e1ec4178
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10.26434/chemrxiv.8298776.v2
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Analytic First-Order Derivatives of Partially Contracted N-Electron Valence State Second-Order Perturbation Theory (PC-NEVPT2)
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A balanced treatment of dynamic and static electron correlation is important in computational chemistry, and multireference perturbation theory (MRPT) is able to do this at a reasonable computational cost. In this paper, analytic first-order derivatives, speci cally gradients and dipole moments, are developed for a particular MRPT method, state-specific partially contracted n-electron valence state second-order perturbation theory (PC-NEVPT2). Only one linear equation needs to be solved for the derivative calculation if the Z-vector method is employed, which facilitates the practical application of this approach. Comparison of the calculated results with experimental geometrical parameters of O<sub>3</sub> indicates excellent agreement, although the calculated results for O<sub>3</sub><sup>-</sup> are slightly outside the experimental error bars. The 0-0 transition energies of various methylpyrimidines and trans-polyacetylene are calculated by performing geometry optimizations and seminumerical second-order geometrical derivative calculations. In particular, the deviations of 0-0 transition energies of trans-polyacetylene from experimental values are consistently less than 0.1 eV with PC-NEVPT2, indicating the reliability of the method. These results demonstrate the importance of adding dynamic electron correlation on top of methods dominated by static electron correlation and of developing analytic derivatives for highly accurate methods.
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Yoshio Nishimoto
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Theory - Computational; Quantum Mechanics
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CC BY NC ND 4.0
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CHEMRXIV
|
2019-08-01
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743b5567dfef0e1ec4178/original/analytic-first-order-derivatives-of-partially-contracted-n-electron-valence-state-second-order-perturbation-theory-pc-nevpt2.pdf
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611be56758eb564dbf924a87
|
10.26434/chemrxiv-2021-0qqwv
|
Transfer C-H Borylation of Alkenes under Rh(I)-Catalysis: In-sight into the Mechanism, Selectivity-Control & Synthetic Capacity
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Transfer C-H borylation of alkenes bears the potential to unlock a range of attractive transformations for modular synthe-sis and late-stage derivatization of complex molecules. However, its scarce precedence associated with a limited mechanistic understanding hinders the development of practical synthetic protocols. Here we report a Rh(I)-catalyzed transfer C-H borylation reaction that is founded on an unprecedented yet crucial elementary step of the
beta-boryl elimination engaging the Rh(I)-(beta-borylalkyl) intermediate. A thorough mechanistic investigation involving a series of catalytic and stoichiometric experiments and complementary computational studies revealed that this step proceeds with a considerably low free energy barrier, further elucidated the full catalytic cycle, and provided insight into the features con-trolling the activity and the selectivity. Driven by this mechanistic understanding, we devised a protocol that is compatible with a plethora of functional groups, including often problematic motifs, and applicable not only to terminal but also inter-nal alkenes and varied electronic and steric properties. The method proved also to be effective in complex settings of the late-stage borylation of derivatives of macrocyclic mycoestrogen Zearalenol, bioactive Brompheniramine, Chlorpromazine, and CD3254, and the synthesis of the boronic acid bio¬isostere of the drug Ozagrel. Besides the valuable new method, these mechanistic investigations set the stage for the development of other hydrogen-for-functional group exchange reactions undergoing a similar pathway.
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Pawel Dydio; Lukas Veth; Hanusch Grab; Sebastian Martinez; Cyril Antheaume
|
Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Homogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-08-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611be56758eb564dbf924a87/original/transfer-c-h-borylation-of-alkenes-under-rh-i-catalysis-in-sight-into-the-mechanism-selectivity-control-synthetic-capacity.pdf
|
669812ce01103d79c5475b44
|
10.26434/chemrxiv-2024-rm0rf
|
Exfoliation of a Metal-Organic Framework Enabled by Post-Synthetic Cleavage of a Dipyridyl Dianthracene Ligand
|
The synthetic tunability and porosity of two-dimensional (2D) metal-organic frameworks (MOFs) renders them a promising class of materials for ultrathin and nanoscale applications. Conductive 2D MOFs are of particular interest for applications in nanoelectronics, chemo-sensing, and memory storage. However, the lack of covalency along the stacking axis typically leads to poor crystallinity in 2D MOFs, limiting structural analysis and precluding exfoliation. One strategy to improve crystal growth is to increase order along the stacking direction. Here, we demonstrate the synthesis of mechanically exfoliatable macroscopic crystals of a 2D zinc MOF by selective dimensional reduction of a 3D zinc MOF bearing a dianthracene (diAn) ligand along the stacking axis. The diAn ligand, a thermally cleavable analogue of 4,4’ bipyridine, is synthesized by the direct functionalization of dianthraldehyde in a novel “dianthracene-first” approach. This work presents a new strategy for the growth of macroscopic crystals of 2D materials while introducing the functionalization of dianthraldehyde as a means to access new stimuli-responsive ligands.
|
Madison Logelin; Eric Schreiber; Brandon Mercado; Amymarie Bartholomew
|
Inorganic Chemistry; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669812ce01103d79c5475b44/original/exfoliation-of-a-metal-organic-framework-enabled-by-post-synthetic-cleavage-of-a-dipyridyl-dianthracene-ligand.pdf
|
6527876a45aaa5fdbbd31cff
|
10.26434/chemrxiv-2023-ss0w5
|
Diverse Metastable Diarylacetonitrile Radicals Generated by Polymer Mechanochemistry
|
Fluorescent radicals have attracted great attention as luminescent materials, mostly on account of their potential to achieve higher luminescence efficiency than closed-shell molecules. However, analyzing fluorescent radicals at ambient conditions remains a challenging task, because radicals are usually unstable in air. In addition, to the best of our knowledge, research aimed at controlling fluorescence wavelengths through substituent changes has not yet been accomplished. Here, we report diverse metastable diarylacetonitrile (DAAN) radicals, which contain different substituents, generated by polymeric mechanochemical reactions. The DAAN radicals, generated by ball-milling powdered polystyrene together with DAAN derivatives, were dispersed within the polystyrene matrix, where they retained their radical state, which allowed measuring solid-state fluorescence spectra. These measurements revealed that a wide range of fluorescence wavelengths from green to red (λem,max = 517–635 nm) can be achieved only by changing the substituents on the aromatic rings in these DAAN radicals. This phenomenon has not been observed for the well-studied triarylmethyl radicals. The fluorescence wavelength of these DAAN radicals can be precisely estimated by time-dependent density-functional theory (TD-DFT) calculations. The amount of DAAN radicals generated upon ball-milling is discussed in conjunction with DFT calculations and experimental results. Our results suggest that the orbital interactions with polymeric mechanoradicals, the bond-dissociation enthalpy, and the steric protection of the radical center are of paramount importance for the generation of DAAN radicals. The results of this study can be expected to provide useful guidelines for the development of advanced fluorescent radicals.
|
Takumi Yamamoto; Daisuke Aoki; Koichiro Mikami; Hideyuki Otsuka
|
Theoretical and Computational Chemistry; Polymer Science; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-10-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6527876a45aaa5fdbbd31cff/original/diverse-metastable-diarylacetonitrile-radicals-generated-by-polymer-mechanochemistry.pdf
|
60c758aabdbb89d828a3ade9
|
10.26434/chemrxiv.14388557.v1
|
Linking Mechanistic Analysis of Catalytic Reactivity Cliffs to Ligand Classification
|
Statistical analysis of reaction data with molecular descriptors can enable chemists to identify reactivity cliffs that result from a mechanistic dependence on a specific structural feature. In this study, we develop a broadly applicable and quantitative classification workflow that identifies reactivity cliffs in eleven Ni- and Pd-catalyzed cross-coupling datasets employing monodentate phosphine ligands. A unique ligand steric descriptor, %<i>V</i><sub>bur</sub> (<i>min</i>), is found to divide these datasets into active and inactive regions at a similar threshold value. Organometallic studies demonstrate that this threshold corresponds to the binary outcome of bisligated versus monoligated metal and that %<i>V</i><sub>bur</sub> (<i>min</i>) is a physically meaningful and predictive representation of ligand structure in catalysis. Taken together, we expect that this strategy will be of broad value in mechanistic investigation of structure-reactivity relationships, while providing a means to rationally partition datasets for data-driven modeling.
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Samuel Newman-Stonebraker; Sleight Smith; Julia Borowski; Ellyn Peters; Tobias Gensch; Heather Johnson; Matthew Sigman; Abigail Doyle
|
Machine Learning; Homogeneous Catalysis; Catalysis; Kinetics and Mechanism - Organometallic Reactions; Ligands (Organomet.); Transition Metal Complexes (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758aabdbb89d828a3ade9/original/linking-mechanistic-analysis-of-catalytic-reactivity-cliffs-to-ligand-classification.pdf
|
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